Query 041421
Match_columns 315
No_of_seqs 360 out of 2814
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 06:51:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041421.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041421hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10139 serine endoprotease; 100.0 3.2E-36 7E-41 291.2 23.8 208 98-314 41-253 (455)
2 PRK10942 serine endoprotease; 100.0 1.7E-34 3.6E-39 280.5 23.1 209 98-314 39-274 (473)
3 TIGR02038 protease_degS peripl 100.0 4.4E-34 9.5E-39 268.6 24.1 196 94-314 42-241 (351)
4 PRK10898 serine endoprotease; 100.0 4.6E-34 1E-38 268.4 23.4 195 95-314 43-242 (353)
5 TIGR02037 degP_htrA_DO peripla 100.0 2.7E-33 5.9E-38 270.3 23.5 210 99-314 3-220 (428)
6 COG0265 DegQ Trypsin-like seri 99.9 8E-26 1.7E-30 212.8 19.7 201 97-314 33-235 (347)
7 PRK13562 acetolactate synthase 99.9 2.6E-25 5.7E-30 162.8 5.2 63 1-63 16-82 (84)
8 PRK08178 acetolactate synthase 99.9 7.3E-25 1.6E-29 164.4 3.3 67 1-68 22-89 (96)
9 PRK06737 acetolactate synthase 99.9 7.4E-24 1.6E-28 153.7 5.0 60 1-60 16-76 (76)
10 COG0440 IlvH Acetolactate synt 99.9 3E-23 6.5E-28 169.9 6.8 102 1-116 18-120 (163)
11 TIGR00119 acolac_sm acetolacta 99.8 1.3E-20 2.8E-25 156.3 7.8 101 1-115 15-116 (157)
12 PRK11152 ilvM acetolactate syn 99.8 3.9E-21 8.5E-26 139.7 4.1 58 1-59 17-75 (76)
13 PRK11895 ilvH acetolactate syn 99.8 1.4E-20 3E-25 156.6 7.6 101 1-115 16-117 (161)
14 KOG2663 Acetolactate synthase, 99.8 1.2E-21 2.6E-26 168.7 -0.5 76 1-76 91-167 (309)
15 PF13710 ACT_5: ACT domain; PD 99.8 1.2E-20 2.5E-25 133.3 3.4 57 1-57 6-63 (63)
16 KOG1320 Serine protease [Postt 99.8 5.8E-19 1.3E-23 167.8 12.9 202 95-314 126-345 (473)
17 CHL00100 ilvH acetohydroxyacid 99.8 1.3E-19 2.8E-24 152.5 6.5 101 1-115 16-117 (174)
18 PF13365 Trypsin_2: Trypsin-li 99.7 2.3E-17 5E-22 130.7 11.5 109 153-291 1-120 (120)
19 PF00089 Trypsin: Trypsin; In 99.5 3.9E-13 8.3E-18 117.0 16.8 162 151-313 25-217 (220)
20 KOG1421 Predicted signaling-as 99.4 1.2E-12 2.5E-17 127.1 12.9 191 98-314 53-253 (955)
21 cd00190 Tryp_SPc Trypsin-like 99.4 6.4E-12 1.4E-16 110.1 16.4 143 152-295 26-207 (232)
22 smart00020 Tryp_SPc Trypsin-li 99.3 6.5E-11 1.4E-15 103.9 15.5 144 151-295 26-207 (229)
23 KOG1320 Serine protease [Postt 98.9 3E-09 6.5E-14 101.9 8.2 186 102-313 55-247 (473)
24 COG3591 V8-like Glu-specific e 98.7 1.2E-07 2.6E-12 84.2 11.8 131 153-295 66-223 (251)
25 KOG3627 Trypsin [Amino acid tr 98.6 1.2E-06 2.6E-11 78.6 15.4 142 152-295 39-227 (256)
26 PF00863 Peptidase_C4: Peptida 98.6 3.5E-06 7.7E-11 74.3 15.6 143 154-310 35-185 (235)
27 PF05579 Peptidase_S32: Equine 97.9 5.7E-05 1.2E-09 67.0 8.6 115 151-295 112-228 (297)
28 PF03761 DUF316: Domain of unk 97.6 0.0024 5.1E-08 58.3 14.3 108 196-312 159-271 (282)
29 PF05580 Peptidase_S55: SpoIVB 97.4 0.0044 9.6E-08 53.7 13.2 161 148-313 17-216 (218)
30 cd04878 ACT_AHAS N-terminal AC 97.4 0.0002 4.4E-09 50.5 4.3 58 1-58 14-72 (72)
31 PF13291 ACT_4: ACT domain; PD 97.4 0.00023 5E-09 52.2 4.6 59 1-59 20-80 (80)
32 COG5640 Secreted trypsin-like 97.4 0.0005 1.1E-08 63.5 7.5 26 270-295 223-251 (413)
33 KOG1421 Predicted signaling-as 97.4 0.0028 6.1E-08 63.0 12.9 139 152-293 551-696 (955)
34 PF10459 Peptidase_S46: Peptid 97.4 0.0007 1.5E-08 69.0 8.8 21 152-172 48-68 (698)
35 cd04879 ACT_3PGDH-like ACT_3PG 97.3 0.00019 4.1E-09 50.5 2.4 58 1-60 13-71 (71)
36 PRK06349 homoserine dehydrogen 97.2 0.00024 5.2E-09 68.9 3.4 57 1-57 362-419 (426)
37 COG3978 Acetolactate synthase 97.1 0.00034 7.4E-09 50.4 2.5 61 2-63 18-79 (86)
38 PF01842 ACT: ACT domain; Int 97.0 0.00032 7E-09 48.9 1.5 53 1-53 14-66 (66)
39 cd04888 ACT_PheB-BS C-terminal 96.9 0.0016 3.6E-08 46.8 4.8 60 1-60 14-75 (76)
40 PF00548 Peptidase_C3: 3C cyst 96.8 0.017 3.7E-07 49.0 10.8 135 152-295 26-170 (172)
41 cd04874 ACT_Af1403 N-terminal 96.8 0.002 4.3E-08 45.5 4.3 58 1-59 14-71 (72)
42 cd04881 ACT_HSDH-Hom ACT_HSDH_ 96.7 0.0013 2.9E-08 47.2 2.8 58 1-58 14-73 (79)
43 cd04901 ACT_3PGDH C-terminal A 96.4 0.0009 1.9E-08 47.3 0.4 57 1-60 13-69 (69)
44 cd04903 ACT_LSD C-terminal ACT 96.4 0.0024 5.2E-08 44.8 2.5 57 1-59 13-70 (71)
45 cd04887 ACT_MalLac-Enz ACT_Mal 96.3 0.0051 1.1E-07 44.1 3.6 57 1-57 13-70 (74)
46 PRK08577 hypothetical protein; 96.2 0.0065 1.4E-07 49.5 4.4 61 1-61 70-133 (136)
47 PF10459 Peptidase_S46: Peptid 96.2 0.0035 7.6E-08 64.1 3.3 31 265-295 623-653 (698)
48 cd04877 ACT_TyrR N-terminal AC 96.2 0.0068 1.5E-07 43.7 3.9 58 1-61 14-71 (74)
49 cd04876 ACT_RelA-SpoT ACT dom 96.2 0.0091 2E-07 40.8 4.4 57 2-58 13-70 (71)
50 cd04902 ACT_3PGDH-xct C-termin 96.2 0.0025 5.5E-08 45.3 1.5 59 1-61 13-72 (73)
51 TIGR02860 spore_IV_B stage IV 96.1 0.093 2E-06 50.2 12.0 42 269-313 354-396 (402)
52 PF00949 Peptidase_S7: Peptida 96.1 0.011 2.3E-07 47.8 4.8 30 266-295 88-117 (132)
53 PRK04435 hypothetical protein; 96.0 0.011 2.3E-07 48.9 4.9 61 1-61 83-145 (147)
54 PF08192 Peptidase_S64: Peptid 96.0 0.042 9.2E-07 55.0 9.4 113 196-314 541-683 (695)
55 cd04908 ACT_Bt0572_1 N-termina 95.3 0.016 3.4E-07 40.8 2.7 22 1-22 15-36 (66)
56 PF00944 Peptidase_S3: Alphavi 95.3 0.028 6E-07 45.0 4.2 27 269-295 100-126 (158)
57 PF02122 Peptidase_S39: Peptid 94.9 0.075 1.6E-06 46.2 6.2 133 163-310 43-182 (203)
58 PF09342 DUF1986: Domain of un 94.8 0.3 6.5E-06 43.4 9.7 85 151-236 28-131 (267)
59 cd04905 ACT_CM-PDT C-terminal 94.8 0.031 6.6E-07 40.9 3.1 53 1-53 15-71 (80)
60 cd04883 ACT_AcuB C-terminal AC 94.5 0.039 8.5E-07 39.1 3.0 49 1-51 15-64 (72)
61 cd04880 ACT_AAAH-PDT-like ACT 94.4 0.065 1.4E-06 38.5 4.0 55 1-55 13-71 (75)
62 cd04869 ACT_GcvR_2 ACT domains 94.3 0.025 5.4E-07 41.2 1.6 52 1-52 13-70 (81)
63 PF00947 Pico_P2A: Picornaviru 93.9 0.28 6.2E-06 39.0 6.9 34 261-295 76-109 (127)
64 PF05416 Peptidase_C37: Southa 93.4 0.23 5.1E-06 47.2 6.7 140 149-300 377-531 (535)
65 cd04886 ACT_ThrD-II-like C-ter 93.2 0.093 2E-06 36.6 3.1 51 1-51 12-67 (73)
66 cd02116 ACT ACT domains are co 93.1 0.091 2E-06 33.8 2.7 47 1-48 12-59 (60)
67 cd04889 ACT_PDH-BS-like C-term 93.0 0.051 1.1E-06 36.6 1.4 36 1-36 12-47 (56)
68 PF03510 Peptidase_C24: 2C end 92.7 1.1 2.3E-05 34.7 8.3 101 155-283 3-105 (105)
69 PRK11092 bifunctional (p)ppGpp 92.1 0.18 3.8E-06 52.1 4.4 60 1-60 640-700 (702)
70 cd04870 ACT_PSP_1 CT domains f 91.8 0.072 1.6E-06 38.4 0.9 51 2-53 14-65 (75)
71 cd04884 ACT_CBS C-terminal ACT 91.7 0.22 4.8E-06 35.4 3.4 54 1-54 13-69 (72)
72 cd04904 ACT_AAAH ACT domain of 91.5 0.36 7.9E-06 34.7 4.3 57 1-57 14-72 (74)
73 PF02395 Peptidase_S6: Immunog 91.4 0.99 2.2E-05 47.0 9.0 61 152-217 66-130 (769)
74 PRK00194 hypothetical protein; 91.1 0.071 1.5E-06 39.8 0.3 57 1-58 17-75 (90)
75 PF02907 Peptidase_S29: Hepati 91.1 0.25 5.4E-06 39.7 3.3 129 153-312 14-146 (148)
76 cd04872 ACT_1ZPV ACT domain pr 90.7 0.077 1.7E-06 39.5 0.2 55 1-56 15-71 (88)
77 cd04875 ACT_F4HF-DF N-terminal 90.6 0.19 4E-06 36.0 2.1 52 1-52 13-67 (74)
78 PF13740 ACT_6: ACT domain; PD 90.0 0.24 5.3E-06 35.8 2.3 49 2-51 17-65 (76)
79 cd04900 ACT_UUR-like_1 ACT dom 90.0 0.35 7.7E-06 34.5 3.1 50 1-50 15-71 (73)
80 cd04873 ACT_UUR-ACR-like ACT d 90.0 0.39 8.4E-06 33.4 3.3 48 1-49 14-67 (70)
81 cd04909 ACT_PDH-BS C-terminal 90.0 0.2 4.3E-06 35.2 1.7 49 1-50 15-64 (69)
82 PRK10872 relA (p)ppGpp synthet 89.2 0.42 9.1E-06 49.5 4.0 60 1-60 680-741 (743)
83 PRK11589 gcvR glycine cleavage 89.1 0.16 3.5E-06 43.8 0.8 56 2-57 110-171 (190)
84 COG4492 PheB ACT domain-contai 89.1 0.65 1.4E-05 37.2 4.1 60 2-61 87-148 (150)
85 cd04925 ACT_ACR_2 ACT domain-c 87.5 0.51 1.1E-05 33.9 2.5 51 1-52 14-72 (74)
86 cd04882 ACT_Bt0572_2 C-termina 87.3 0.37 8E-06 33.0 1.7 46 1-50 13-59 (65)
87 cd04899 ACT_ACR-UUR-like_2 C-t 87.1 0.86 1.9E-05 31.8 3.5 50 1-51 14-69 (70)
88 cd04935 ACT_AKiii-DAPDC_1 ACT 86.6 0.87 1.9E-05 32.9 3.4 48 2-54 19-71 (75)
89 cd04926 ACT_ACR_4 C-terminal 85.7 0.9 1.9E-05 32.4 3.0 34 1-35 15-48 (72)
90 cd04893 ACT_GcvR_1 ACT domains 84.7 0.55 1.2E-05 34.0 1.5 50 2-52 16-65 (77)
91 cd04930 ACT_TH ACT domain of t 83.9 1.8 3.8E-05 34.2 4.1 57 1-57 55-113 (115)
92 cd04934 ACT_AK-Hom3_1 CT domai 83.5 1.1 2.4E-05 32.1 2.7 48 2-54 19-69 (73)
93 cd04871 ACT_PSP_2 ACT domains 82.7 0.25 5.4E-06 36.6 -1.1 53 1-53 14-74 (84)
94 cd04912 ACT_AKiii-LysC-EC-like 82.5 1.9 4.1E-05 30.9 3.6 44 2-50 19-67 (75)
95 COG2150 Predicted regulator of 82.3 0.93 2E-05 37.6 2.0 56 2-59 110-166 (167)
96 cd04931 ACT_PAH ACT domain of 81.9 1.7 3.6E-05 32.7 3.1 52 1-52 28-82 (90)
97 cd04927 ACT_ACR-like_2 Second 81.8 1.8 3.8E-05 31.3 3.2 51 1-51 14-70 (76)
98 cd04929 ACT_TPH ACT domain of 80.4 2.5 5.4E-05 30.5 3.5 50 1-50 14-65 (74)
99 COG0317 SpoT Guanosine polypho 80.3 2.4 5.3E-05 43.5 4.6 59 1-59 641-700 (701)
100 cd04932 ACT_AKiii-LysC-EC_1 AC 76.8 2.6 5.7E-05 30.4 2.8 48 2-54 19-71 (75)
101 cd04928 ACT_TyrKc Uncharacteri 76.5 2.6 5.7E-05 29.9 2.6 35 1-35 15-49 (68)
102 cd04913 ACT_AKii-LysC-BS-like_ 76.0 2.3 5.1E-05 29.5 2.3 47 2-50 17-63 (75)
103 PF01732 DUF31: Putative pepti 75.9 1.6 3.6E-05 41.5 1.9 24 271-294 351-374 (374)
104 PF04455 Saccharop_dh_N: LOR/S 75.7 9.3 0.0002 29.5 5.6 43 12-54 31-74 (103)
105 cd04890 ACT_AK-like_1 ACT doma 74.3 2.4 5.2E-05 28.8 1.9 42 2-48 18-61 (62)
106 PF04350 PilO: Pilus assembly 71.6 4.5 9.7E-05 32.6 3.2 61 3-63 58-122 (144)
107 PF10741 T2SM_b: Type II secre 70.9 10 0.00023 29.3 5.1 63 2-64 20-86 (110)
108 COG2716 GcvR Glycine cleavage 70.8 0.78 1.7E-05 38.5 -1.4 57 1-57 106-168 (176)
109 cd04885 ACT_ThrD-I Tandem C-te 69.1 7.9 0.00017 27.0 3.7 48 2-50 13-61 (68)
110 PRK11899 prephenate dehydratas 66.2 7.1 0.00015 35.8 3.7 56 2-57 209-268 (279)
111 PRK13581 D-3-phosphoglycerate 66.2 3.6 7.7E-05 41.2 1.9 57 2-60 467-524 (526)
112 PRK13011 formyltetrahydrofolat 64.4 5 0.00011 36.9 2.3 52 2-53 22-75 (286)
113 cd04933 ACT_AK1-AT_1 ACT domai 62.8 7.2 0.00016 28.4 2.5 44 2-50 19-70 (78)
114 PRK15385 magnesium transport p 61.4 27 0.00058 30.9 6.2 53 7-59 164-220 (225)
115 cd04895 ACT_ACR_1 ACT domain-c 61.2 10 0.00022 27.2 3.0 49 1-49 15-69 (72)
116 cd04891 ACT_AK-LysC-DapG-like_ 60.6 8.7 0.00019 25.1 2.5 45 2-48 16-60 (61)
117 PF09902 DUF2129: Uncharacteri 58.3 17 0.00037 26.0 3.6 27 33-59 34-60 (71)
118 cd04911 ACT_AKiii-YclM-BS_1 AC 56.9 9 0.0002 27.8 2.1 46 4-54 21-69 (76)
119 PRK14428 acylphosphatase; Prov 53.8 28 0.00061 26.5 4.5 35 29-63 47-81 (97)
120 cd01735 LSm12_N LSm12 belongs 52.7 60 0.0013 22.5 5.5 34 174-207 6-39 (61)
121 COG4747 ACT domain-containing 51.3 18 0.00038 28.7 3.0 53 4-59 20-76 (142)
122 PRK11898 prephenate dehydratas 50.8 16 0.00035 33.4 3.3 54 2-55 212-269 (283)
123 cd04897 ACT_ACR_3 ACT domain-c 50.4 20 0.00043 25.9 3.0 52 1-52 15-72 (75)
124 TIGR01270 Trp_5_monoox tryptop 49.8 16 0.00034 35.8 3.1 58 1-58 45-105 (464)
125 PF03927 NapD: NapD protein; 49.0 26 0.00057 25.5 3.5 32 28-59 39-71 (79)
126 PRK14449 acylphosphatase; Prov 48.9 37 0.00079 25.3 4.4 33 29-61 42-74 (90)
127 PRK14435 acylphosphatase; Prov 48.8 24 0.00052 26.4 3.4 36 28-63 40-75 (90)
128 TIGR00655 PurU formyltetrahydr 48.8 15 0.00033 33.6 2.7 49 2-50 15-66 (280)
129 PF12381 Peptidase_C3G: Tungro 48.6 13 0.00027 32.6 2.0 48 262-311 167-218 (231)
130 cd04919 ACT_AK-Hom3_2 ACT doma 48.4 13 0.00029 25.2 1.9 43 3-50 20-62 (66)
131 cd00600 Sm_like The eukaryotic 48.3 57 0.0012 21.9 5.1 32 175-206 7-38 (63)
132 cd04910 ACT_AK-Ectoine_1 ACT d 48.2 24 0.00053 25.2 3.1 45 3-52 20-64 (71)
133 TIGR01327 PGDH D-3-phosphoglyc 47.9 11 0.00025 37.6 2.0 57 2-60 466-523 (525)
134 PF00571 CBS: CBS domain CBS d 47.5 15 0.00033 23.9 2.0 21 275-295 29-49 (57)
135 PRK14423 acylphosphatase; Prov 47.5 39 0.00085 25.3 4.4 35 29-63 44-78 (92)
136 PRK14444 acylphosphatase; Prov 47.0 39 0.00083 25.3 4.3 34 29-62 43-76 (92)
137 cd01720 Sm_D2 The eukaryotic S 46.9 46 0.001 24.7 4.6 37 170-206 10-46 (87)
138 PRK14429 acylphosphatase; Prov 46.7 43 0.00094 24.9 4.5 35 29-63 41-75 (90)
139 PRK14421 acylphosphatase; Prov 46.1 35 0.00075 26.1 3.9 35 29-63 43-77 (99)
140 PRK14451 acylphosphatase; Prov 46.0 38 0.00082 25.2 4.1 35 29-63 42-76 (89)
141 cd04936 ACT_AKii-LysC-BS-like_ 46.0 19 0.0004 23.9 2.3 42 3-51 19-60 (63)
142 PRK14425 acylphosphatase; Prov 45.5 46 0.00099 25.1 4.5 35 29-63 45-79 (94)
143 cd04892 ACT_AK-like_2 ACT doma 44.7 18 0.0004 23.8 2.1 44 3-51 19-62 (65)
144 COG3062 NapD Uncharacterized p 44.1 58 0.0013 24.5 4.7 36 23-59 38-74 (94)
145 PRK06027 purU formyltetrahydro 43.8 12 0.00025 34.5 1.2 52 2-53 21-75 (286)
146 PRK02886 hypothetical protein; 43.6 37 0.00081 25.3 3.6 27 33-59 38-64 (87)
147 PRK14445 acylphosphatase; Prov 43.4 35 0.00077 25.4 3.6 35 29-63 43-77 (91)
148 PRK14430 acylphosphatase; Prov 43.0 49 0.0011 24.8 4.3 35 29-63 43-77 (92)
149 PRK14433 acylphosphatase; Prov 42.9 42 0.00092 24.8 3.9 34 29-62 40-73 (87)
150 cd01731 archaeal_Sm1 The archa 42.9 70 0.0015 22.3 4.9 32 175-206 11-42 (68)
151 COG0298 HypC Hydrogenase matur 42.8 65 0.0014 23.6 4.6 47 187-235 5-52 (82)
152 PRK02302 hypothetical protein; 42.1 40 0.00088 25.2 3.6 27 33-59 40-66 (89)
153 cd01722 Sm_F The eukaryotic Sm 41.7 60 0.0013 22.7 4.4 32 175-206 12-43 (68)
154 PRK00737 small nuclear ribonuc 41.7 73 0.0016 22.6 4.9 32 175-206 15-46 (72)
155 cd01726 LSm6 The eukaryotic Sm 41.2 70 0.0015 22.2 4.6 32 175-206 11-42 (67)
156 cd06168 LSm9 The eukaryotic Sm 40.9 75 0.0016 22.9 4.8 32 175-206 11-42 (75)
157 PRK14436 acylphosphatase; Prov 40.7 57 0.0012 24.4 4.4 34 29-62 43-76 (91)
158 PF08669 GCV_T_C: Glycine clea 40.6 45 0.00098 24.6 3.9 32 276-307 34-67 (95)
159 PRK14440 acylphosphatase; Prov 40.2 50 0.0011 24.6 4.0 34 29-62 42-75 (90)
160 cd01717 Sm_B The eukaryotic Sm 39.7 72 0.0016 23.0 4.7 32 175-206 11-42 (79)
161 PRK10622 pheA bifunctional cho 39.6 34 0.00074 32.8 3.7 56 2-57 312-371 (386)
162 cd01730 LSm3 The eukaryotic Sm 38.9 64 0.0014 23.5 4.3 31 175-205 12-42 (82)
163 PRK14442 acylphosphatase; Prov 38.9 58 0.0013 24.3 4.2 35 29-63 43-77 (91)
164 PRK14420 acylphosphatase; Prov 38.2 53 0.0011 24.4 3.8 34 29-62 41-74 (91)
165 PRK11589 gcvR glycine cleavage 38.2 18 0.0004 31.1 1.5 51 2-53 23-73 (190)
166 cd04906 ACT_ThrD-I_1 First of 37.7 41 0.00088 24.5 3.1 48 2-51 16-65 (85)
167 PF13113 DUF3970: Protein of u 37.6 37 0.00081 23.3 2.5 22 32-53 4-25 (60)
168 PRK09977 putative Mg(2+) trans 37.1 64 0.0014 28.4 4.7 53 5-58 160-213 (215)
169 PRK14448 acylphosphatase; Prov 37.0 53 0.0011 24.5 3.7 35 29-63 41-75 (90)
170 PRK14438 acylphosphatase; Prov 36.9 65 0.0014 24.0 4.2 34 29-62 42-75 (91)
171 cd01729 LSm7 The eukaryotic Sm 36.7 92 0.002 22.7 4.8 31 175-205 13-43 (81)
172 PRK14427 acylphosphatase; Prov 35.9 69 0.0015 24.1 4.2 32 29-60 45-76 (94)
173 PF01732 DUF31: Putative pepti 35.7 27 0.00058 33.3 2.3 23 150-172 35-67 (374)
174 cd04914 ACT_AKi-DapG-BS_1 ACT 35.6 26 0.00057 24.3 1.7 30 2-36 17-46 (67)
175 cd04896 ACT_ACR-like_3 ACT dom 35.5 31 0.00068 24.9 2.1 51 1-51 14-71 (75)
176 COG0077 PheA Prephenate dehydr 35.4 49 0.0011 30.3 3.8 56 2-57 209-268 (279)
177 cd01732 LSm5 The eukaryotic Sm 34.8 92 0.002 22.4 4.5 31 175-205 14-44 (76)
178 PRK14450 acylphosphatase; Prov 34.6 78 0.0017 23.5 4.3 35 27-61 40-74 (91)
179 PRK14437 acylphosphatase; Prov 34.6 70 0.0015 24.8 4.1 35 29-63 62-96 (109)
180 TIGR01268 Phe4hydrox_tetr phen 34.4 51 0.0011 32.1 4.0 52 1-52 30-84 (436)
181 PRK14446 acylphosphatase; Prov 34.3 76 0.0016 23.6 4.1 35 29-63 41-75 (88)
182 PF14827 Cache_3: Sensory doma 34.0 29 0.00063 26.8 1.9 17 279-295 94-110 (116)
183 cd01719 Sm_G The eukaryotic Sm 33.9 1.1E+02 0.0025 21.6 4.8 31 175-205 11-41 (72)
184 cd01728 LSm1 The eukaryotic Sm 33.9 1.1E+02 0.0024 21.9 4.7 31 175-205 13-43 (74)
185 PRK14422 acylphosphatase; Prov 33.9 75 0.0016 23.8 4.1 32 29-60 45-76 (93)
186 PRK14441 acylphosphatase; Prov 33.3 85 0.0018 23.5 4.3 33 29-61 44-76 (93)
187 PRK14447 acylphosphatase; Prov 32.7 94 0.002 23.4 4.5 38 25-62 40-77 (95)
188 smart00651 Sm snRNP Sm protein 32.3 1.3E+02 0.0028 20.5 4.8 32 175-206 9-40 (67)
189 PF08753 NikR_C: NikR C termin 32.2 78 0.0017 22.8 3.8 36 24-59 39-74 (78)
190 PRK05092 PII uridylyl-transfer 32.2 36 0.00077 36.7 2.8 52 1-52 746-804 (931)
191 PRK14424 acylphosphatase; Prov 31.8 65 0.0014 24.3 3.4 34 29-62 46-79 (94)
192 PF09383 NIL: NIL domain; Int 31.2 1.9E+02 0.0041 20.3 5.7 29 24-52 42-70 (76)
193 PRK05092 PII uridylyl-transfer 31.0 40 0.00086 36.4 2.9 53 1-53 857-915 (931)
194 PRK14439 acylphosphatase; Prov 30.7 88 0.0019 26.2 4.2 32 29-60 114-146 (163)
195 cd01721 Sm_D3 The eukaryotic S 30.4 1.4E+02 0.003 21.0 4.8 32 175-206 11-42 (70)
196 PRK14426 acylphosphatase; Prov 29.6 1.1E+02 0.0023 22.9 4.3 23 29-51 43-65 (92)
197 PRK03381 PII uridylyl-transfer 29.2 42 0.00092 35.3 2.7 50 2-52 614-666 (774)
198 TIGR00300 conserved hypothetic 29.1 1.1E+02 0.0023 29.5 5.0 40 12-51 31-71 (407)
199 COG1958 LSM1 Small nuclear rib 28.7 1.3E+02 0.0028 21.6 4.5 33 175-207 18-50 (79)
200 cd01727 LSm8 The eukaryotic Sm 28.3 1.5E+02 0.0032 21.0 4.7 32 175-206 10-41 (74)
201 cd04922 ACT_AKi-HSDH-ThrA_2 AC 27.2 51 0.0011 22.0 2.0 44 2-50 19-62 (66)
202 PF01423 LSM: LSM domain ; In 27.2 1.5E+02 0.0033 20.2 4.5 33 175-207 9-41 (67)
203 PF02601 Exonuc_VII_L: Exonucl 27.2 65 0.0014 29.8 3.3 38 148-185 277-314 (319)
204 cd04868 ACT_AK-like ACT domain 26.7 52 0.0011 20.9 2.0 41 2-47 18-58 (60)
205 cd04924 ACT_AK-Arch_2 ACT doma 26.6 51 0.0011 22.0 2.0 44 3-51 20-63 (66)
206 COG1254 AcyP Acylphosphatases 26.3 1.5E+02 0.0033 22.2 4.6 32 29-60 43-74 (92)
207 cd04916 ACT_AKiii-YclM-BS_2 AC 26.0 59 0.0013 21.7 2.2 43 3-50 20-62 (66)
208 PF00708 Acylphosphatase: Acyl 25.8 79 0.0017 23.3 3.0 34 29-62 43-76 (91)
209 cd04918 ACT_AK1-AT_2 ACT domai 25.7 50 0.0011 22.6 1.7 43 3-50 19-61 (65)
210 PRK14443 acylphosphatase; Prov 25.7 1.6E+02 0.0036 22.1 4.7 34 28-61 42-76 (93)
211 PRK06635 aspartate kinase; Rev 25.6 69 0.0015 30.7 3.3 49 1-51 277-325 (404)
212 PRK10553 assembly protein for 24.8 1.8E+02 0.0038 21.6 4.6 34 26-59 40-74 (87)
213 PLN02317 arogenate dehydratase 24.6 98 0.0021 29.7 4.0 56 2-57 298-371 (382)
214 cd04627 CBS_pair_14 The CBS do 24.3 42 0.0009 25.5 1.3 21 275-295 98-118 (123)
215 PRK14432 acylphosphatase; Prov 24.1 1.2E+02 0.0026 22.7 3.6 23 29-51 41-64 (93)
216 COG1707 ACT domain-containing 23.9 90 0.002 26.3 3.1 60 2-62 17-77 (218)
217 PRK14452 acylphosphatase; Prov 23.6 1E+02 0.0022 23.8 3.3 35 29-63 59-93 (107)
218 PF12594 DUF3764: Protein of u 23.5 1.4E+02 0.003 22.3 3.7 40 10-49 30-69 (86)
219 PF03462 PCRF: PCRF domain; I 22.6 1.3E+02 0.0029 23.4 3.8 30 8-37 76-106 (115)
220 PF01455 HupF_HypC: HupF/HypC 22.6 2.8E+02 0.0061 19.5 5.4 43 187-232 5-47 (68)
221 PF10049 DUF2283: Protein of u 22.4 53 0.0012 21.5 1.3 12 283-294 36-47 (50)
222 PRK05007 PII uridylyl-transfer 22.4 78 0.0017 33.9 3.2 52 1-52 715-772 (884)
223 KOG2972 Uncharacterized conser 22.1 17 0.00036 32.5 -1.5 56 1-59 216-271 (276)
224 cd04603 CBS_pair_KefB_assoc Th 21.8 58 0.0013 24.2 1.6 21 275-295 86-106 (111)
225 PRK08818 prephenate dehydrogen 21.4 44 0.00095 31.9 1.0 40 1-40 310-349 (370)
226 PF14438 SM-ATX: Ataxin 2 SM d 21.3 2.5E+02 0.0055 19.8 4.8 29 175-203 13-44 (77)
227 PF10369 ALS_ss_C: Small subun 21.2 2.1E+02 0.0044 20.4 4.3 30 29-59 37-66 (75)
228 PRK07431 aspartate kinase; Pro 21.0 75 0.0016 32.2 2.6 36 2-37 286-321 (587)
229 PF02566 OsmC: OsmC-like prote 21.0 2E+02 0.0043 21.0 4.4 45 7-51 27-84 (100)
230 cd04937 ACT_AKi-DapG-BS_2 ACT 20.3 73 0.0016 21.6 1.7 43 2-51 19-61 (64)
231 cd04620 CBS_pair_7 The CBS dom 20.3 62 0.0013 24.0 1.5 21 275-295 90-110 (115)
No 1
>PRK10139 serine endoprotease; Provisional
Probab=100.00 E-value=3.2e-36 Score=291.19 Aligned_cols=208 Identities=38% Similarity=0.616 Sum_probs=170.5
Q ss_pred HHHHHHHhcCCceEEEEEEeeecCCCCCCCCCCCCCCcCCcccccc--ccccccceeEEEEEEeC-CcEEEEcccccCCC
Q 041421 98 EMIRVFKENIPSVVLIGNLGIRDGNGEGRGGDQSPHTHSRYFAEDQ--SETQFLQASGAGFLWDQ-DGHIVTNHHVICDA 174 (315)
Q Consensus 98 ~~~~~v~~~~~sVV~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~GSGfiI~~-~g~VlT~aHvv~~~ 174 (315)
.++++++++.||||.|.+...... . ..++..+++||+... .+.+...+.||||+|++ +||||||+|||.++
T Consensus 41 ~~~~~~~~~~pavV~i~~~~~~~~-~-----~~~~~~~~~~f~~~~~~~~~~~~~~~GSG~ii~~~~g~IlTn~HVv~~a 114 (455)
T PRK10139 41 SLAPMLEKVLPAVVSVRVEGTASQ-G-----QKIPEEFKKFFGDDLPDQPAQPFEGLGSGVIIDAAKGYVLTNNHVINQA 114 (455)
T ss_pred cHHHHHHHhCCcEEEEEEEEeecc-c-----ccCchhHHHhccccCCccccccccceEEEEEEECCCCEEEeChHHhCCC
Confidence 689999999999999998754331 0 112233445554321 11223457899999985 79999999999999
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCeEEEEeeCCCCCCceEEeEEeeecccc
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQKICAIGHPLGLPFTCTTGVISALGREI 254 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~v~~iG~p~g~~~~~~~g~v~~~~~~~ 254 (315)
+.+.|++.|++.++|++++.|+.+||||||++. ...+++++|+++..+++|++|+++|||++...+++.|+|++..+..
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~~-~~~l~~~~lg~s~~~~~G~~V~aiG~P~g~~~tvt~GivS~~~r~~ 193 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQN-PSKLTQIAIADSDKLRVGDFAVAVGNPFGLGQTATSGIISALGRSG 193 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEecC-CCCCceeEecCccccCCCCEEEEEecCCCCCCceEEEEEccccccc
Confidence 999999999999999999999999999999985 3458899999888999999999999999999999999999987753
Q ss_pred cCCCCceeecEEEEccCCCCCCccchhccCCCeEEEEEeee--cCCCcceEEEEEcchhhhc
Q 041421 255 PAGTGRLIRGVIQIDASINLGNSGGPLLDSSGSLIGVNTFI--TSGAFTGIGFATPIDTAVL 314 (315)
Q Consensus 255 ~~~~~~~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~--~~~~~~~~~~aiP~~~i~~ 314 (315)
... ..+.+++++|+++++|||||||+|.+|+||||+++. ..+...|+|||||++.++.
T Consensus 194 ~~~--~~~~~~iqtda~in~GnSGGpl~n~~G~vIGi~~~~~~~~~~~~gigfaIP~~~~~~ 253 (455)
T PRK10139 194 LNL--EGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSVGIGFAIPSNMART 253 (455)
T ss_pred cCC--CCcceEEEECCccCCCCCcceEECCCCeEEEEEEEEEcCCCCccceEEEEEhHHHHH
Confidence 211 123568999999999999999999999999999997 3445678999999998875
No 2
>PRK10942 serine endoprotease; Provisional
Probab=100.00 E-value=1.7e-34 Score=280.48 Aligned_cols=209 Identities=38% Similarity=0.588 Sum_probs=169.0
Q ss_pred HHHHHHHhcCCceEEEEEEeeecCCCCCCCCCCCCCCcCCcccccc------------------------ccccccceeE
Q 041421 98 EMIRVFKENIPSVVLIGNLGIRDGNGEGRGGDQSPHTHSRYFAEDQ------------------------SETQFLQASG 153 (315)
Q Consensus 98 ~~~~~v~~~~~sVV~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------------~~~~~~~~~G 153 (315)
++.++++++.||||.|++...... . ...++..++.||+... .+++...+.|
T Consensus 39 ~~~~~~~~~~pavv~i~~~~~~~~-~----~~~~~~~~~~ff~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G 113 (473)
T PRK10942 39 SLAPMLEKVMPSVVSINVEGSTTV-N----TPRMPRQFQQFFGDNSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALG 113 (473)
T ss_pred cHHHHHHHhCCceEEEEEEEeccc-c----CCCCChhHHHhhcccccccccccccccccccccccccccccccccccceE
Confidence 599999999999999998764431 0 1112223444443210 0122346789
Q ss_pred EEEEEeC-CcEEEEcccccCCCCeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCeEEEE
Q 041421 154 AGFLWDQ-DGHIVTNHHVICDASKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQKICAI 232 (315)
Q Consensus 154 SGfiI~~-~g~VlT~aHvv~~~~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~v~~i 232 (315)
|||+|++ +||||||+||+.+.+.+.|++.|++.++|++++.|+.+||||||++. ...+++++|+++..+++|++|+++
T Consensus 114 SG~ii~~~~G~IlTn~HVv~~a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki~~-~~~l~~~~lg~s~~l~~G~~V~ai 192 (473)
T PRK10942 114 SGVIIDADKGYVVTNNHVVDNATKIKVQLSDGRKFDAKVVGKDPRSDIALIQLQN-PKNLTAIKMADSDALRVGDYTVAI 192 (473)
T ss_pred EEEEEECCCCEEEeChhhcCCCCEEEEEECCCCEEEEEEEEecCCCCEEEEEecC-CCCCceeEecCccccCCCCEEEEE
Confidence 9999996 59999999999999999999999999999999999999999999975 345889999988899999999999
Q ss_pred eeCCCCCCceEEeEEeeecccccCCCCceeecEEEEccCCCCCCccchhccCCCeEEEEEeee--cCCCcceEEEEEcch
Q 041421 233 GHPLGLPFTCTTGVISALGREIPAGTGRLIRGVIQIDASINLGNSGGPLLDSSGSLIGVNTFI--TSGAFTGIGFATPID 310 (315)
Q Consensus 233 G~p~g~~~~~~~g~v~~~~~~~~~~~~~~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~--~~~~~~~~~~aiP~~ 310 (315)
|+|++...+++.|+|+...+.... ...+.+++++|+++++|+|||||+|.+|+||||+++. .++.+.+++||||++
T Consensus 193 G~P~g~~~tvt~GiVs~~~r~~~~--~~~~~~~iqtda~i~~GnSGGpL~n~~GeviGI~t~~~~~~g~~~g~gfaIP~~ 270 (473)
T PRK10942 193 GNPYGLGETVTSGIVSALGRSGLN--VENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSN 270 (473)
T ss_pred cCCCCCCcceeEEEEEEeecccCC--cccccceEEeccccCCCCCcCccCCCCCeEEEEEEEEEcCCCCcccEEEEEEHH
Confidence 999999889999999998764221 1223578999999999999999999999999999987 345557899999999
Q ss_pred hhhc
Q 041421 311 TAVL 314 (315)
Q Consensus 311 ~i~~ 314 (315)
.++.
T Consensus 271 ~~~~ 274 (473)
T PRK10942 271 MVKN 274 (473)
T ss_pred HHHH
Confidence 8874
No 3
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=100.00 E-value=4.4e-34 Score=268.63 Aligned_cols=196 Identities=38% Similarity=0.532 Sum_probs=163.5
Q ss_pred cchhHHHHHHHhcCCceEEEEEEeeecCCCCCCCCCCCCCCcCCccccccccccccceeEEEEEEeCCcEEEEcccccCC
Q 041421 94 MDELEMIRVFKENIPSVVLIGNLGIRDGNGEGRGGDQSPHTHSRYFAEDQSETQFLQASGAGFLWDQDGHIVTNHHVICD 173 (315)
Q Consensus 94 ~~~~~~~~~v~~~~~sVV~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GSGfiI~~~g~VlT~aHvv~~ 173 (315)
..+..+.++++++.||||+|.+..... +.+ ......+.||||+|+++|+||||+||+.+
T Consensus 42 ~~~~~~~~~~~~~~psVV~I~~~~~~~----------------~~~-----~~~~~~~~GSG~vi~~~G~IlTn~HVV~~ 100 (351)
T TIGR02038 42 TVEISFNKAVRRAAPAVVNIYNRSISQ----------------NSL-----NQLSIQGLGSGVIMSKEGYILTNYHVIKK 100 (351)
T ss_pred ccchhHHHHHHhcCCcEEEEEeEeccc----------------ccc-----ccccccceEEEEEEeCCeEEEecccEeCC
Confidence 445578999999999999999865332 100 01223568999999999999999999999
Q ss_pred CCeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCeEEEEeeCCCCCCceEEeEEeeeccc
Q 041421 174 ASKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQKICAIGHPLGLPFTCTTGVISALGRE 253 (315)
Q Consensus 174 ~~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~v~~iG~p~g~~~~~~~g~v~~~~~~ 253 (315)
++.+.|.+.||+.++|+++++|+.+||||||++.. .+++++++++..+++|++|+++|||++...+++.|+++...+.
T Consensus 101 ~~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~~~--~~~~~~l~~s~~~~~G~~V~aiG~P~~~~~s~t~GiIs~~~r~ 178 (351)
T TIGR02038 101 ADQIVVALQDGRKFEAELVGSDPLTDLAVLKIEGD--NLPTIPVNLDRPPHVGDVVLAIGNPYNLGQTITQGIISATGRN 178 (351)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEecCC--CCceEeccCcCccCCCCEEEEEeCCCCCCCcEEEEEEEeccCc
Confidence 99999999999999999999999999999999864 3788899877889999999999999998889999999998775
Q ss_pred ccCCCCceeecEEEEccCCCCCCccchhccCCCeEEEEEeee-c---CCCcceEEEEEcchhhhc
Q 041421 254 IPAGTGRLIRGVIQIDASINLGNSGGPLLDSSGSLIGVNTFI-T---SGAFTGIGFATPIDTAVL 314 (315)
Q Consensus 254 ~~~~~~~~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~-~---~~~~~~~~~aiP~~~i~~ 314 (315)
.... ....+++++|+.+++|||||||+|.+|+||||+++. . .+...+++||||++.++.
T Consensus 179 ~~~~--~~~~~~iqtda~i~~GnSGGpl~n~~G~vIGI~~~~~~~~~~~~~~g~~faIP~~~~~~ 241 (351)
T TIGR02038 179 GLSS--VGRQNFIQTDAAINAGNSGGALINTNGELVGINTASFQKGGDEGGEGINFAIPIKLAHK 241 (351)
T ss_pred ccCC--CCcceEEEECCccCCCCCcceEECCCCeEEEEEeeeecccCCCCccceEEEecHHHHHH
Confidence 4321 123578999999999999999999999999999876 1 122357999999998875
No 4
>PRK10898 serine endoprotease; Provisional
Probab=100.00 E-value=4.6e-34 Score=268.37 Aligned_cols=195 Identities=38% Similarity=0.513 Sum_probs=162.0
Q ss_pred chhHHHHHHHhcCCceEEEEEEeeecCCCCCCCCCCCCCCcCCccccccccccccceeEEEEEEeCCcEEEEcccccCCC
Q 041421 95 DELEMIRVFKENIPSVVLIGNLGIRDGNGEGRGGDQSPHTHSRYFAEDQSETQFLQASGAGFLWDQDGHIVTNHHVICDA 174 (315)
Q Consensus 95 ~~~~~~~~v~~~~~sVV~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GSGfiI~~~g~VlT~aHvv~~~ 174 (315)
....+.++++++.||||.|.+....+ .+. +.....+.||||+|+++|+||||+||+.++
T Consensus 43 ~~~~~~~~~~~~~psvV~v~~~~~~~-----------------~~~----~~~~~~~~GSGfvi~~~G~IlTn~HVv~~a 101 (353)
T PRK10898 43 TPASYNQAVRRAAPAVVNVYNRSLNS-----------------TSH----NQLEIRTLGSGVIMDQRGYILTNKHVINDA 101 (353)
T ss_pred ccchHHHHHHHhCCcEEEEEeEeccc-----------------cCc----ccccccceeeEEEEeCCeEEEecccEeCCC
Confidence 34578899999999999999865432 000 011234689999999889999999999999
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCeEEEEeeCCCCCCceEEeEEeeecccc
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQKICAIGHPLGLPFTCTTGVISALGREI 254 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~v~~iG~p~g~~~~~~~g~v~~~~~~~ 254 (315)
+.+.|.+.||+.++|+++++|+.+||||||++.. .+++++|+++..+++|++|+++|||++...+++.|+++...+..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~~~--~l~~~~l~~~~~~~~G~~V~aiG~P~g~~~~~t~Giis~~~r~~ 179 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKINAT--NLPVIPINPKRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIG 179 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEcCC--CCCeeeccCcCcCCCCCEEEEEeCCCCcCCCcceeEEEeccccc
Confidence 9999999999999999999999999999999863 47889998777889999999999999988889999999887753
Q ss_pred cCCCCceeecEEEEccCCCCCCccchhccCCCeEEEEEeee-cCC----CcceEEEEEcchhhhc
Q 041421 255 PAGTGRLIRGVIQIDASINLGNSGGPLLDSSGSLIGVNTFI-TSG----AFTGIGFATPIDTAVL 314 (315)
Q Consensus 255 ~~~~~~~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~-~~~----~~~~~~~aiP~~~i~~ 314 (315)
.... ...+++++|+++++|||||||+|.+|+||||+++. ... ...+++||||++.++.
T Consensus 180 ~~~~--~~~~~iqtda~i~~GnSGGPl~n~~G~vvGI~~~~~~~~~~~~~~~g~~faIP~~~~~~ 242 (353)
T PRK10898 180 LSPT--GRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPTQLATK 242 (353)
T ss_pred cCCc--cccceEEeccccCCCCCcceEECCCCeEEEEEEEEecccCCCCcccceEEEEchHHHHH
Confidence 3211 12468999999999999999999999999999976 211 1257999999999764
No 5
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=100.00 E-value=2.7e-33 Score=270.35 Aligned_cols=210 Identities=40% Similarity=0.586 Sum_probs=168.3
Q ss_pred HHHHHHhcCCceEEEEEEeeecCCCCCCCCCCCCCCcCCcccccc------ccccccceeEEEEEEeCCcEEEEcccccC
Q 041421 99 MIRVFKENIPSVVLIGNLGIRDGNGEGRGGDQSPHTHSRYFAEDQ------SETQFLQASGAGFLWDQDGHIVTNHHVIC 172 (315)
Q Consensus 99 ~~~~v~~~~~sVV~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~GSGfiI~~~g~VlT~aHvv~ 172 (315)
++++++++.||||.|.+......... ....+..+.+||+... ...+...+.||||+|+++|+||||+||+.
T Consensus 3 ~~~~~~~~~p~vv~i~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GSGfii~~~G~IlTn~Hvv~ 79 (428)
T TIGR02037 3 FAPLVEKVAPAVVNISVEGTVKRRNR---PPALPPFFRQFFGDDMPNFPRQQRERKVRGLGSGVIISADGYILTNNHVVD 79 (428)
T ss_pred HHHHHHHhCCceEEEEEEEEecccCC---CcccchhHHHhhcccccCcccccccccccceeeEEEECCCCEEEEcHHHcC
Confidence 67899999999999998764431100 0001112233443211 12234568999999998899999999999
Q ss_pred CCCeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCeEEEEeeCCCCCCceEEeEEeeecc
Q 041421 173 DASKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQKICAIGHPLGLPFTCTTGVISALGR 252 (315)
Q Consensus 173 ~~~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~v~~iG~p~g~~~~~~~g~v~~~~~ 252 (315)
++..+.|++.+++.++|+++..|+.+|||||+++.+ ..+++++|+++..+++|++|+++|||++...+++.|+++...+
T Consensus 80 ~~~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~~~-~~~~~~~l~~~~~~~~G~~v~aiG~p~g~~~~~t~G~vs~~~~ 158 (428)
T TIGR02037 80 GADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAK-KNLPVIKLGDSDKLRVGDWVLAIGNPFGLGQTVTSGIVSALGR 158 (428)
T ss_pred CCCeEEEEeCCCCEEEEEEEEecCCCCEEEEEecCC-CCceEEEccCCCCCCCCCEEEEEECCCcCCCcEEEEEEEeccc
Confidence 999999999999999999999999999999999863 4689999988888999999999999999989999999998876
Q ss_pred cccCCCCceeecEEEEccCCCCCCccchhccCCCeEEEEEeee--cCCCcceEEEEEcchhhhc
Q 041421 253 EIPAGTGRLIRGVIQIDASINLGNSGGPLLDSSGSLIGVNTFI--TSGAFTGIGFATPIDTAVL 314 (315)
Q Consensus 253 ~~~~~~~~~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~--~~~~~~~~~~aiP~~~i~~ 314 (315)
... ....+..++++++++.+|+|||||+|.+|+||||+++. ..+...+++||||++.++.
T Consensus 159 ~~~--~~~~~~~~i~tda~i~~GnSGGpl~n~~G~viGI~~~~~~~~g~~~g~~faiP~~~~~~ 220 (428)
T TIGR02037 159 SGL--GIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAIYSPSGGNVGIGFAIPSNMAKN 220 (428)
T ss_pred Ccc--CCCCccceEEECCCCCCCCCCCceECCCCeEEEEEeEEEcCCCCccceEEEEEhHHHHH
Confidence 532 11233568999999999999999999999999999887 3345578999999998875
No 6
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=8e-26 Score=212.85 Aligned_cols=201 Identities=40% Similarity=0.617 Sum_probs=165.9
Q ss_pred hHHHHHHHhcCCceEEEEEEeeecCCCCCCCCCCCCCCcCCccccccccccccceeEEEEEEeCCcEEEEcccccCCCCe
Q 041421 97 LEMIRVFKENIPSVVLIGNLGIRDGNGEGRGGDQSPHTHSRYFAEDQSETQFLQASGAGFLWDQDGHIVTNHHVICDASK 176 (315)
Q Consensus 97 ~~~~~~v~~~~~sVV~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GSGfiI~~~g~VlT~aHvv~~~~~ 176 (315)
..+..+++++.|+||.|........ ..+| ..........+.||||+++++|+|+||.|++.++..
T Consensus 33 ~~~~~~~~~~~~~vV~~~~~~~~~~--------------~~~~-~~~~~~~~~~~~gSg~i~~~~g~ivTn~hVi~~a~~ 97 (347)
T COG0265 33 LSFATAVEKVAPAVVSIATGLTAKL--------------RSFF-PSDPPLRSAEGLGSGFIISSDGYIVTNNHVIAGAEE 97 (347)
T ss_pred cCHHHHHHhcCCcEEEEEeeeeecc--------------hhcc-cCCcccccccccccEEEEcCCeEEEecceecCCcce
Confidence 5788999999999999999765440 1122 111100111478999999988999999999999999
Q ss_pred EEEEeCCCcEEEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCeEEEEeeCCCCCCceEEeEEeeecccccC
Q 041421 177 VKVSFSDQSTFYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQKICAIGHPLGLPFTCTTGVISALGREIPA 256 (315)
Q Consensus 177 ~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~v~~iG~p~g~~~~~~~g~v~~~~~~~~~ 256 (315)
+.+.+.||+.++++++..|+..|+|++|++.... ++.+.++++..++.|+++.++|+|++...+++.|+++...+. ..
T Consensus 98 i~v~l~dg~~~~a~~vg~d~~~dlavlki~~~~~-~~~~~~~~s~~l~vg~~v~aiGnp~g~~~tvt~Givs~~~r~-~v 175 (347)
T COG0265 98 ITVTLADGREVPAKLVGKDPISDLAVLKIDGAGG-LPVIALGDSDKLRVGDVVVAIGNPFGLGQTVTSGIVSALGRT-GV 175 (347)
T ss_pred EEEEeCCCCEEEEEEEecCCccCEEEEEeccCCC-CceeeccCCCCcccCCEEEEecCCCCcccceeccEEeccccc-cc
Confidence 9999999999999999999999999999987443 778899989999999999999999998899999999999886 21
Q ss_pred CCCceeecEEEEccCCCCCCccchhccCCCeEEEEEeee--cCCCcceEEEEEcchhhhc
Q 041421 257 GTGRLIRGVIQIDASINLGNSGGPLLDSSGSLIGVNTFI--TSGAFTGIGFATPIDTAVL 314 (315)
Q Consensus 257 ~~~~~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~--~~~~~~~~~~aiP~~~i~~ 314 (315)
.......+++++|+.+++|+||||++|.+|+++||++.. ..+...+++||||++.++.
T Consensus 176 ~~~~~~~~~IqtdAain~gnsGgpl~n~~g~~iGint~~~~~~~~~~gigfaiP~~~~~~ 235 (347)
T COG0265 176 GSAGGYVNFIQTDAAINPGNSGGPLVNIDGEVVGINTAIIAPSGGSSGIGFAIPVNLVAP 235 (347)
T ss_pred cCcccccchhhcccccCCCCCCCceEcCCCcEEEEEEEEecCCCCcceeEEEecHHHHHH
Confidence 111225678999999999999999999999999999999 3333567999999998764
No 7
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=99.91 E-value=2.6e-25 Score=162.79 Aligned_cols=63 Identities=27% Similarity=0.449 Sum_probs=58.3
Q ss_pred CceeeeeccccCceEeeeeec-cCCCCeeEEEEEEE-CChHHHHHHHHHHhhccceEEEe--eccCC
Q 041421 1 MNQIAGVFARRKYNIESLAAI-GLDKDRALFTIVVS-GTDRELQQVVEQLQKLVNVLNVS--TKQSS 63 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~-~~~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v~--~~~~~ 63 (315)
|+||+|||+||||||+||+|+ ++++++|||||+++ ||++.++||+|||+||+||++|. ++++.
T Consensus 16 L~Rit~lFsRRg~NI~SLtvg~Te~~~iSRmtivv~~~d~~~ieqI~kQL~KlidVikV~~~~~~~~ 82 (84)
T PRK13562 16 LNRITSAFVRLQYNIDTLHVTHSEQPGISNMEIQVDIQDDTSLHILIKKLKQQINVLTVECYDLVDN 82 (84)
T ss_pred HHHHHHHHhccCcCeeeEEecccCCCCceEEEEEEeCCCHHHHHHHHHHHhCCccEEEEEEeecccc
Confidence 689999999999999999995 45699999999998 99999999999999999999999 66654
No 8
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=99.90 E-value=7.3e-25 Score=164.45 Aligned_cols=67 Identities=33% Similarity=0.571 Sum_probs=61.0
Q ss_pred CceeeeeccccCceEeeeeec-cCCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEeeccCCCCccc
Q 041421 1 MNQIAGVFARRKYNIESLAAI-GLDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSSSSSSL 68 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~~~~~~ 68 (315)
|+||+|||+||||||+||+|+ ++++++|||||++. +++.++||+|||+||+||++|.++++++++..
T Consensus 22 L~RIaglFsRRgyNIeSLtvg~te~~~iSRmtivv~-~~~~i~Qi~kQL~KLidVikV~~l~~~~~v~~ 89 (96)
T PRK08178 22 MSHVCGLFARRAFNVEGILCLPIQDGDKSRIWLLVN-DDQRLEQMISQIEKLEDVLKVRRNQSDPTMFN 89 (96)
T ss_pred HHHHHHHHhcCCcCeeeEEEeecCCCCceEEEEEEc-CchHHHHHHHHHhCCcCEEEEEECCCchhHHH
Confidence 689999999999999999995 55699999999998 67899999999999999999999999876533
No 9
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=99.89 E-value=7.4e-24 Score=153.67 Aligned_cols=60 Identities=35% Similarity=0.467 Sum_probs=56.7
Q ss_pred CceeeeeccccCceEeeeeec-cCCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEeec
Q 041421 1 MNQIAGVFARRKYNIESLAAI-GLDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTK 60 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~ 60 (315)
|+||++||+||||||+||+|+ ++++++|||||++.|+++.++||+|||+||+||++|.++
T Consensus 16 L~Ri~~lf~rRgfNI~Sl~vg~te~~~~sriti~~~~~~~~i~qi~kQL~KLidV~~V~~~ 76 (76)
T PRK06737 16 LLRISGIFARRGYYISSLNLNERDTSGVSEMKLTAVCTENEATLLVSQLKKLINVLQVNKL 76 (76)
T ss_pred HHHHHHHHhccCcceEEEEecccCCCCeeEEEEEEECCHHHHHHHHHHHhCCcCEEEEEeC
Confidence 689999999999999999995 556999999999999999999999999999999999875
No 10
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=99.88 E-value=3e-23 Score=169.89 Aligned_cols=102 Identities=33% Similarity=0.425 Sum_probs=87.6
Q ss_pred CceeeeeccccCceEeeeeec-cCCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEeeccCCCCcccCcccccccCCC
Q 041421 1 MNQIAGVFARRKYNIESLAAI-GLDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSSSSSSLEPFFLPFSGVD 79 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~~~~~~e~~l~~v~~~~ 79 (315)
|+|++|||+||||||+||+|+ ++++++|||||++.||+..+|||+|||+||+||++|.+++.+.+++||.+|+|+....
T Consensus 18 LsRv~glfsrRG~NIeSltv~~tE~~~~SRiTivv~g~~~~~EQi~kQL~kLidV~kV~d~~~~~~veRel~LiKv~~~~ 97 (163)
T COG0440 18 LSRVTGLFSRRGYNIESLTVGPTETPGLSRITIVVSGDEQVLEQIIKQLNKLIDVLKVLDLTSEPHVERELALIKVSAEG 97 (163)
T ss_pred eehhhHHHHhcCcccceEEEEecCCCCceEEEEEEcCCcchHHHHHHHHHhhccceeEEEcCCcchhheeeEEEEEecCc
Confidence 789999999999999999994 5568999999999999999999999999999999999999999999999999985322
Q ss_pred CCCccccccCCcCccchhHHHHHHHhcCCceEEEEEE
Q 041421 80 STTDSVVTQPCKHQMDELEMIRVFKENIPSVVLIGNL 116 (315)
Q Consensus 80 ~~~~~v~~~p~~~~~~~~~~~~~v~~~~~sVV~I~~~ 116 (315)
. ....+..+++-..-+||-|...
T Consensus 98 ~--------------~R~ei~~~~~ifr~~vvDvs~~ 120 (163)
T COG0440 98 S--------------ERGEIARITEIFRASVVDVSPE 120 (163)
T ss_pred c--------------chHHHHHHHHHhCceEEecCcc
Confidence 1 1334566777777788777654
No 11
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=99.83 E-value=1.3e-20 Score=156.27 Aligned_cols=101 Identities=35% Similarity=0.444 Sum_probs=87.5
Q ss_pred CceeeeeccccCceEeeeeeccC-CCCeeEEEEEEECChHHHHHHHHHHhhccceEEEeeccCCCCcccCcccccccCCC
Q 041421 1 MNQIAGVFARRKYNIESLAAIGL-DKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSSSSSSLEPFFLPFSGVD 79 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~~~~~~e~~l~~v~~~~ 79 (315)
|+||+++|+||||||+||++.++ +++++||||++.++++.++||+|||+||+||++|.++++++++.||.+|+|+...+
T Consensus 15 L~rI~~lf~rrg~NI~Sl~v~~t~~~~~sriti~V~~d~~~i~qi~kQl~Kli~V~~V~~~~~~~~v~rEl~LiKv~~~~ 94 (157)
T TIGR00119 15 LSRVAGLFTRRGFNIESLTVGPTEDPDLSRMTIVVVGDDKVLEQITKQLNKLVDVIKVSDLTESAIVERELCLVKVSAPG 94 (157)
T ss_pred HHHHHHHHHhCCceEEEEEEeecCCCCEEEEEEEEECCHHHHHHHHHHHhcCccEEEEEecCCCcceeeEEEEEEEECCc
Confidence 68999999999999999999655 48999999999999999999999999999999999999999999999999986411
Q ss_pred CCCccccccCCcCccchhHHHHHHHhcCCceEEEEE
Q 041421 80 STTDSVVTQPCKHQMDELEMIRVFKENIPSVVLIGN 115 (315)
Q Consensus 80 ~~~~~v~~~p~~~~~~~~~~~~~v~~~~~sVV~I~~ 115 (315)
.....+.++++.....||-+..
T Consensus 95 --------------~~r~~i~~i~~~f~a~ivdv~~ 116 (157)
T TIGR00119 95 --------------EGRDEIIRLTNIFRGRIVDVSP 116 (157)
T ss_pred --------------cCHHHHHHHHHHhCCEEEEecC
Confidence 2345666777777777777654
No 12
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=99.82 E-value=3.9e-21 Score=139.70 Aligned_cols=58 Identities=22% Similarity=0.401 Sum_probs=53.8
Q ss_pred CceeeeeccccCceEeeeeec-cCCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEee
Q 041421 1 MNQIAGVFARRKYNIESLAAI-GLDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
|+||+|||+||||||+||+|+ ++++++|||||++. +++.++||+|||+||+||++|..
T Consensus 17 L~Ri~~lf~rRGfnI~sl~v~~t~~~~~sriti~v~-~~~~i~ql~kQL~KL~dV~~V~~ 75 (76)
T PRK11152 17 LERVLRVVRHRGFQVCSMNMTQNTDAQNINIELTVA-SERPIDLLSSQLNKLVDVAHVEI 75 (76)
T ss_pred HHHHHHHHhcCCeeeeeEEeeecCCCCEEEEEEEEC-CCchHHHHHHHHhcCcCeEEEEE
Confidence 689999999999999999995 45799999999995 99999999999999999999974
No 13
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=99.82 E-value=1.4e-20 Score=156.62 Aligned_cols=101 Identities=29% Similarity=0.418 Sum_probs=87.4
Q ss_pred CceeeeeccccCceEeeeeeccC-CCCeeEEEEEEECChHHHHHHHHHHhhccceEEEeeccCCCCcccCcccccccCCC
Q 041421 1 MNQIAGVFARRKYNIESLAAIGL-DKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSSSSSSLEPFFLPFSGVD 79 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~~~~~~e~~l~~v~~~~ 79 (315)
|+||+++|+||||||+||++.++ +++++||||++++|++.++||+|||+||+||++|.++++++++.||.+|+|+....
T Consensus 16 L~rI~~lf~rrg~NI~Sl~v~~te~~~~sriti~V~~~~~~i~qi~kQl~KLidV~~V~~~~~~~~v~rEl~LiKv~~~~ 95 (161)
T PRK11895 16 LSRVAGLFSRRGYNIESLTVGPTEDPGLSRMTIVTSGDEQVIEQITKQLNKLIDVLKVVDLTEEAHVERELALVKVRASG 95 (161)
T ss_pred HHHHHHHHHhCCCcEEEEEeeecCCCCEEEEEEEEECCHHHHHHHHHHHhccccEEEEEecCCcchhheEEEEEEEECCc
Confidence 68999999999999999999655 48999999999999999999999999999999999999999999999999986411
Q ss_pred CCCccccccCCcCccchhHHHHHHHhcCCceEEEEE
Q 041421 80 STTDSVVTQPCKHQMDELEMIRVFKENIPSVVLIGN 115 (315)
Q Consensus 80 ~~~~~v~~~p~~~~~~~~~~~~~v~~~~~sVV~I~~ 115 (315)
.....+.++++....-||-+..
T Consensus 96 --------------~~r~~i~~i~~~f~a~ivdv~~ 117 (161)
T PRK11895 96 --------------ENRAEILRLADIFRAKIVDVTP 117 (161)
T ss_pred --------------ccHHHHHHHHHHhCCEEEEecC
Confidence 1244666777777777777654
No 14
>KOG2663 consensus Acetolactate synthase, small subunit [Amino acid transport and metabolism]
Probab=99.82 E-value=1.2e-21 Score=168.70 Aligned_cols=76 Identities=33% Similarity=0.430 Sum_probs=73.4
Q ss_pred CceeeeeccccCceEeeeee-ccCCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEeeccCCCCcccCccccccc
Q 041421 1 MNQIAGVFARRKYNIESLAA-IGLDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSSSSSSLEPFFLPFS 76 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~~~~~~e~~l~~v~ 76 (315)
|+||+|+|+|||||||||.| .+++++++|||||+.|.|+.++|.++||+||++|++|.|++.++.++||.||+|+.
T Consensus 91 lsRisGvlAaRGfNIdSLvVc~tevk~LsrmTIVl~Gtd~VveQa~rQiedlVnV~aVlDyt~e~~VeRELmlakvs 167 (309)
T KOG2663|consen 91 LSRISGVLAARGFNIDSLVVCLTEVKALSRMTIVLQGTDGVVEQARRQIEDLVNVYAVLDYTNEPIVERELMLAKVS 167 (309)
T ss_pred HHHHHHHHHhccCCchheeeechhhhhhhhceEEEeccHHHHHHHHHHHHHhhhhheeeecCCChHHHHHHHHHHHH
Confidence 68999999999999999998 56779999999999999999999999999999999999999999999999999986
No 15
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=99.81 E-value=1.2e-20 Score=133.27 Aligned_cols=57 Identities=53% Similarity=0.781 Sum_probs=51.5
Q ss_pred CceeeeeccccCceEeeeeec-cCCCCeeEEEEEEECChHHHHHHHHHHhhccceEEE
Q 041421 1 MNQIAGVFARRKYNIESLAAI-GLDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNV 57 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v 57 (315)
|+||++||+||||||+||+++ +++++++||||++.++++.++||++||+||+||++|
T Consensus 6 L~Ri~~vf~rRg~nI~sl~v~~~~~~~~~riti~v~~~~~~i~~l~~Ql~KlidV~~V 63 (63)
T PF13710_consen 6 LNRITGVFRRRGFNIESLSVGPTEDPGISRITIVVSGDDREIEQLVKQLEKLIDVVKV 63 (63)
T ss_dssp HHHHHHHHHTTT-EECEEEEEE-SSTTEEEEEEEEES-CCHHHHHHHHHHCSTTEEEE
T ss_pred HHHHHHHHhcCCeEEeeEEeeecCCCCEEEEEEEEeeCchhHHHHHHHHhccCCeEeC
Confidence 689999999999999999995 457999999999999999999999999999999987
No 16
>KOG1320 consensus Serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.79 E-value=5.8e-19 Score=167.83 Aligned_cols=202 Identities=36% Similarity=0.453 Sum_probs=160.6
Q ss_pred chhHHHHHHHhcCCceEEEEEEeeecCCCCCCCCCCCCCCcCCccccccccccccceeEEEEEEeCCcEEEEcccccCCC
Q 041421 95 DELEMIRVFKENIPSVVLIGNLGIRDGNGEGRGGDQSPHTHSRYFAEDQSETQFLQASGAGFLWDQDGHIVTNHHVICDA 174 (315)
Q Consensus 95 ~~~~~~~~v~~~~~sVV~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GSGfiI~~~g~VlT~aHvv~~~ 174 (315)
....++.+.++...|||.|....-.. + . .+|.. ...+...||||+++.+|.++||+||+...
T Consensus 126 ~~~~v~~~~~~cd~Avv~Ie~~~f~~-------~------~-~~~e~----~~ip~l~~S~~Vv~gd~i~VTnghV~~~~ 187 (473)
T KOG1320|consen 126 YKAFVAAVFEECDLAVVYIESEEFWK-------G------M-NPFEL----GDIPSLNGSGFVVGGDGIIVTNGHVVRVE 187 (473)
T ss_pred hhhhHHHhhhcccceEEEEeeccccC-------C------C-ccccc----CCCcccCccEEEEcCCcEEEEeeEEEEEE
Confidence 45677889999999999999743111 0 0 01111 22356689999999999999999999643
Q ss_pred C-----------eEEEEeCCC--cEEEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCeEEEEeeCCCCCCc
Q 041421 175 S-----------KVKVSFSDQ--STFYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQKICAIGHPLGLPFT 241 (315)
Q Consensus 175 ~-----------~~~V~~~~g--~~~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~v~~iG~p~g~~~~ 241 (315)
. .+.+.++++ ...++.+...|+..|+|+++++.+..-.++++++-+..+..|+++..+|.|++...+
T Consensus 188 ~~~y~~~~~~l~~vqi~aa~~~~~s~ep~i~g~d~~~gvA~l~ik~~~~i~~~i~~~~~~~~~~G~~~~a~~~~f~~~nt 267 (473)
T KOG1320|consen 188 PRIYAHSSTVLLRVQIDAAIGPGNSGEPVIVGVDKVAGVAFLKIKTPENILYVIPLGVSSHFRTGVEVSAIGNGFGLLNT 267 (473)
T ss_pred eccccCCCcceeeEEEEEeecCCccCCCeEEccccccceEEEEEecCCcccceeecceeeeecccceeeccccCceeeee
Confidence 2 366777665 788899999999999999999765434788888888899999999999999999999
Q ss_pred eEEeEEeeecccccCCCC---ceeecEEEEccCCCCCCccchhccCCCeEEEEEeee--cCCCcceEEEEEcchhhhc
Q 041421 242 CTTGVISALGREIPAGTG---RLIRGVIQIDASINLGNSGGPLLDSSGSLIGVNTFI--TSGAFTGIGFATPIDTAVL 314 (315)
Q Consensus 242 ~~~g~v~~~~~~~~~~~~---~~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~--~~~~~~~~~~aiP~~~i~~ 314 (315)
.+.|.++...|....-.. ....+++++++.+++|+|||||+|.+|++||+++.. ..+-..+++|++|.+.++.
T Consensus 268 ~t~g~vs~~~R~~~~lg~~~g~~i~~~~qtd~ai~~~nsg~~ll~~DG~~IgVn~~~~~ri~~~~~iSf~~p~d~vl~ 345 (473)
T KOG1320|consen 268 LTQGMVSGQLRKSFKLGLETGVLISKINQTDAAINPGNSGGPLLNLDGEVIGVNTRKVTRIGFSHGISFKIPIDTVLV 345 (473)
T ss_pred eeecccccccccccccCcccceeeeeecccchhhhcccCCCcEEEecCcEeeeeeeeeEEeeccccceeccCchHhhh
Confidence 999999988887654222 456789999999999999999999999999999888 2233457899999998763
No 17
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=99.79 E-value=1.3e-19 Score=152.53 Aligned_cols=101 Identities=33% Similarity=0.440 Sum_probs=86.3
Q ss_pred CceeeeeccccCceEeeeeec-cCCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEeeccCCCCcccCcccccccCCC
Q 041421 1 MNQIAGVFARRKYNIESLAAI-GLDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSSSSSSLEPFFLPFSGVD 79 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~~~~~~e~~l~~v~~~~ 79 (315)
|+||+++|+||||||+||+++ +++++++||||++.++++.++||.+||+||+||++|.++++.+++.||.+|.|+...+
T Consensus 16 L~RIt~lFsrRg~NIesLsv~~t~~~~~sr~TIvv~~~~~~ieqL~kQL~KLidVl~V~~~~~~~~v~rEl~LiKv~~~~ 95 (174)
T CHL00100 16 LTRIAGLFARRGFNIESLAVGPAEQKGISRITMVVPGDDRTIEQLTKQLYKLVNILKVQDITNIPCVERELMLIKINVNS 95 (174)
T ss_pred HHHHHHHHHhCCCCeeEEEeeEcCCCCccEEEEEEECCHHHHHHHHHHHHHHhHhhEEEecCCccceeeEEEEEEEecCC
Confidence 689999999999999999994 4569999999999999888999999999999999999999999999999999985311
Q ss_pred CCCccccccCCcCccchhHHHHHHHhcCCceEEEEE
Q 041421 80 STTDSVVTQPCKHQMDELEMIRVFKENIPSVVLIGN 115 (315)
Q Consensus 80 ~~~~~v~~~p~~~~~~~~~~~~~v~~~~~sVV~I~~ 115 (315)
.....+.++++..+..||-+..
T Consensus 96 --------------~~r~ei~~~~~~f~a~ivdv~~ 117 (174)
T CHL00100 96 --------------QTRPEILEIAQIFRAKVVDLSE 117 (174)
T ss_pred --------------cCHHHHHHHHHHhCCEEEEecC
Confidence 1244566777777777776654
No 18
>PF13365 Trypsin_2: Trypsin-like peptidase domain; PDB: 1Y8T_A 2Z9I_A 3QO6_A 1L1J_A 1QY6_A 2O8L_A 3OTP_E 2ZLE_I 1KY9_A 3CS0_A ....
Probab=99.74 E-value=2.3e-17 Score=130.68 Aligned_cols=109 Identities=38% Similarity=0.559 Sum_probs=73.8
Q ss_pred EEEEEEeCCcEEEEcccccC--------CCCeEEEEeCCCcEEE--EEEEEeCCC-CCeEEEEecCCCCCccceEecCCC
Q 041421 153 GAGFLWDQDGHIVTNHHVIC--------DASKVKVSFSDQSTFY--AKVVGHDQD-KDLAVLHIDAPNHELRPIHVGVSA 221 (315)
Q Consensus 153 GSGfiI~~~g~VlT~aHvv~--------~~~~~~V~~~~g~~~~--a~vv~~d~~-~DiAll~v~~~~~~~~~l~l~~~~ 221 (315)
||||+|+++|+||||+||+. ....+.+...++.... +++++.++. +|+|||+++
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~All~v~--------------- 65 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVEDWNDGKQPDNSSVEVVFPDGRRVPPVAEVVYFDPDDYDLALLKVD--------------- 65 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTCCTT--G-TCSEEEEEETTSCEEETEEEEEEEETT-TTEEEEEES---------------
T ss_pred CEEEEEcCCceEEEchhheecccccccCCCCEEEEEecCCCEEeeeEEEEEECCccccEEEEEEe---------------
Confidence 79999998889999999998 4567888888888888 999999999 999999997
Q ss_pred CCCCCCeEEEEeeCCCCCCceEEeEEeeecccccCCCCceeecEEEEccCCCCCCccchhccCCCeEEEE
Q 041421 222 DLHVGQKICAIGHPLGLPFTCTTGVISALGREIPAGTGRLIRGVIQIDASINLGNSGGPLLDSSGSLIGV 291 (315)
Q Consensus 222 ~~~~G~~v~~iG~p~g~~~~~~~g~v~~~~~~~~~~~~~~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI 291 (315)
.....+... .............. .... ...+ +++.+.+|+|||||||.+|+||||
T Consensus 66 ------~~~~~~~~~-----~~~~~~~~~~~~~~--~~~~-~~~~-~~~~~~~G~SGgpv~~~~G~vvGi 120 (120)
T PF13365_consen 66 ------PWTGVGGGV-----RVPGSTSGVSPTST--NDNR-MLYI-TDADTRPGSSGGPVFDSDGRVVGI 120 (120)
T ss_dssp ------CEEEEEEEE-----EEEEEEEEEEEEEE--EETE-EEEE-ESSS-STTTTTSEEEETTSEEEEE
T ss_pred ------cccceeeee-----EeeeeccccccccC--cccc-eeEe-eecccCCCcEeHhEECCCCEEEeC
Confidence 000000000 00000000000000 0000 1114 799999999999999999999997
No 19
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=99.54 E-value=3.9e-13 Score=117.05 Aligned_cols=162 Identities=23% Similarity=0.340 Sum_probs=106.5
Q ss_pred eeEEEEEEeCCcEEEEcccccCCCCeEEEEeC-------CC--cEEEEEEEEeC----C---CCCeEEEEecCC---CCC
Q 041421 151 ASGAGFLWDQDGHIVTNHHVICDASKVKVSFS-------DQ--STFYAKVVGHD----Q---DKDLAVLHIDAP---NHE 211 (315)
Q Consensus 151 ~~GSGfiI~~~g~VlT~aHvv~~~~~~~V~~~-------~g--~~~~a~vv~~d----~---~~DiAll~v~~~---~~~ 211 (315)
..|+|++|+++ +|||+|||+.....+.+.+. ++ ..+..+-+..+ + .+|+|||+++.+ ...
T Consensus 25 ~~C~G~li~~~-~vLTaahC~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~h~~~~~~~~~~DiAll~L~~~~~~~~~ 103 (220)
T PF00089_consen 25 FFCTGTLISPR-WVLTAAHCVDGASDIKVRLGTYSIRNSDGSEQTIKVSKIIIHPKYDPSTYDNDIALLKLDRPITFGDN 103 (220)
T ss_dssp EEEEEEEEETT-EEEEEGGGHTSGGSEEEEESESBTTSTTTTSEEEEEEEEEEETTSBTTTTTTSEEEEEESSSSEHBSS
T ss_pred eeEeEEecccc-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 37999999986 99999999998556666543 22 23444443332 2 479999999986 346
Q ss_pred ccceEecCC-CCCCCCCeEEEEeeCCCCC----CceEEeEEeeecccc-cC-CCCceeecEEEEcc----CCCCCCccch
Q 041421 212 LRPIHVGVS-ADLHVGQKICAIGHPLGLP----FTCTTGVISALGREI-PA-GTGRLIRGVIQIDA----SINLGNSGGP 280 (315)
Q Consensus 212 ~~~l~l~~~-~~~~~G~~v~~iG~p~g~~----~~~~~g~v~~~~~~~-~~-~~~~~~~~~i~~~~----~i~~G~SGGP 280 (315)
+.++.+... ..+..|+.+.++||+.... ..+....+....... .. .........++... ..|.|+||||
T Consensus 104 ~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~c~~~~~~~~~~~g~sG~p 183 (220)
T PF00089_consen 104 IQPICLPSAGSDPNVGTSCIVVGWGRTSDNGYSSNLQSVTVPVVSRKTCRSSYNDNLTPNMICAGSSGSGDACQGDSGGP 183 (220)
T ss_dssp BEESBBTSTTHTTTTTSEEEEEESSBSSTTSBTSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEETTSSSBGGTTTTTSE
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 778888642 3357899999999987532 234444444433221 10 11112245667665 7899999999
Q ss_pred hccCCCeEEEEEeee-cCCCcceEEEEEcchhhh
Q 041421 281 LLDSSGSLIGVNTFI-TSGAFTGIGFATPIDTAV 313 (315)
Q Consensus 281 lvd~~G~vvGI~s~~-~~~~~~~~~~aiP~~~i~ 313 (315)
|+..++.|+||++.. ..+.....++..++...+
T Consensus 184 l~~~~~~lvGI~s~~~~c~~~~~~~v~~~v~~~~ 217 (220)
T PF00089_consen 184 LICNNNYLVGIVSFGENCGSPNYPGVYTRVSSYL 217 (220)
T ss_dssp EEETTEEEEEEEEEESSSSBTTSEEEEEEGGGGH
T ss_pred cccceeeecceeeecCCCCCCCcCEEEEEHHHhh
Confidence 998666799999998 222222357778877654
No 20
>KOG1421 consensus Predicted signaling-associated protein (contains a PDZ domain) [General function prediction only]
Probab=99.44 E-value=1.2e-12 Score=127.11 Aligned_cols=191 Identities=24% Similarity=0.311 Sum_probs=146.9
Q ss_pred HHHHHHHhcCCceEEEEEEeeecCCCCCCCCCCCCCCcCCccccccccccccceeEEEEEEeC-CcEEEEcccccC-CCC
Q 041421 98 EMIRVFKENIPSVVLIGNLGIRDGNGEGRGGDQSPHTHSRYFAEDQSETQFLQASGAGFLWDQ-DGHIVTNHHVIC-DAS 175 (315)
Q Consensus 98 ~~~~~v~~~~~sVV~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GSGfiI~~-~g~VlT~aHvv~-~~~ 175 (315)
.|...+.++-+|||.|....... ++.. . ...+.||||++++ .|++|||+|+++ ++-
T Consensus 53 ~w~~~ia~VvksvVsI~~S~v~~-----------------fdte-s----ag~~~atgfvvd~~~gyiLtnrhvv~pgP~ 110 (955)
T KOG1421|consen 53 DWRNTIANVVKSVVSIRFSAVRA-----------------FDTE-S----AGESEATGFVVDKKLGYILTNRHVVAPGPF 110 (955)
T ss_pred hhhhhhhhhcccEEEEEehheee-----------------cccc-c----ccccceeEEEEecccceEEEeccccCCCCc
Confidence 88889999999999999876443 1111 1 1345799999995 589999999997 455
Q ss_pred eEEEEeCCCcEEEEEEEEeCCCCCeEEEEecCCC---CCccceEecCCCCCCCCCeEEEEeeCCCCCCceEEeEEeeecc
Q 041421 176 KVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDAPN---HELRPIHVGVSADLHVGQKICAIGHPLGLPFTCTTGVISALGR 252 (315)
Q Consensus 176 ~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~~~---~~~~~l~l~~~~~~~~G~~v~~iG~p~g~~~~~~~g~v~~~~~ 252 (315)
...+.+.+....+.-.++.||.+|+.+++.+... ..+..++++ .+-.+.|.++.++|+..+...++..|.++++.+
T Consensus 111 va~avf~n~ee~ei~pvyrDpVhdfGf~r~dps~ir~s~vt~i~la-p~~akvgseirvvgNDagEklsIlagflSrldr 189 (955)
T KOG1421|consen 111 VASAVFDNHEEIEIYPVYRDPVHDFGFFRYDPSTIRFSIVTEICLA-PELAKVGSEIRVVGNDAGEKLSILAGFLSRLDR 189 (955)
T ss_pred eeEEEecccccCCcccccCCchhhcceeecChhhcceeeeeccccC-ccccccCCceEEecCCccceEEeehhhhhhccC
Confidence 6778888777777788999999999999998642 234556664 456789999999999888777888888888887
Q ss_pred cccCCCCcee----ecEEEEccCCCCCCccchhccCCCeEEEEEeee-cCCCcceEEEEEcchhhhc
Q 041421 253 EIPAGTGRLI----RGVIQIDASINLGNSGGPLLDSSGSLIGVNTFI-TSGAFTGIGFATPIDTAVL 314 (315)
Q Consensus 253 ~~~~~~~~~~----~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~-~~~~~~~~~~aiP~~~i~~ 314 (315)
......+..+ ..++|.......|.||+|++|-+|..|.++..+ ..+ +.+|++|++.++.
T Consensus 190 ~apdyg~~~yndfnTfy~QaasstsggssgspVv~i~gyAVAl~agg~~ss---as~ffLpLdrV~R 253 (955)
T KOG1421|consen 190 NAPDYGEDTYNDFNTFYIQAASSTSGGSSGSPVVDIPGYAVALNAGGSISS---ASDFFLPLDRVVR 253 (955)
T ss_pred CCccccccccccccceeeeehhcCCCCCCCCceecccceEEeeecCCcccc---cccceeeccchhh
Confidence 6553222221 246677888889999999999999999999887 333 3589999998753
No 21
>cd00190 Tryp_SPc Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Probab=99.43 E-value=6.4e-12 Score=110.09 Aligned_cols=143 Identities=21% Similarity=0.305 Sum_probs=91.3
Q ss_pred eEEEEEEeCCcEEEEcccccCCC--CeEEEEeCC---------CcEEEEEEEEeCC-------CCCeEEEEecCCC---C
Q 041421 152 SGAGFLWDQDGHIVTNHHVICDA--SKVKVSFSD---------QSTFYAKVVGHDQ-------DKDLAVLHIDAPN---H 210 (315)
Q Consensus 152 ~GSGfiI~~~g~VlT~aHvv~~~--~~~~V~~~~---------g~~~~a~vv~~d~-------~~DiAll~v~~~~---~ 210 (315)
.++|++|+++ +|||+|||+.+. ....+.+.. ...+..+-+..++ .+|||||+++.+. .
T Consensus 26 ~C~GtlIs~~-~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~DiAll~L~~~~~~~~ 104 (232)
T cd00190 26 FCGGSLISPR-WVLTAAHCVYSSAPSNYTVRLGSHDLSSNEGGGQVIKVKKVIVHPNYNPSTYDNDIALLKLKRPVTLSD 104 (232)
T ss_pred EEEEEEeeCC-EEEECHHhcCCCCCccEEEEeCcccccCCCCceEEEEEEEEEECCCCCCCCCcCCEEEEEECCcccCCC
Confidence 7999999986 999999999865 456666532 1223344444443 5799999998752 2
Q ss_pred CccceEecCCC-CCCCCCeEEEEeeCCCCCC-----ceEEeEEeeecccccC-C-C--CceeecEEEE-----ccCCCCC
Q 041421 211 ELRPIHVGVSA-DLHVGQKICAIGHPLGLPF-----TCTTGVISALGREIPA-G-T--GRLIRGVIQI-----DASINLG 275 (315)
Q Consensus 211 ~~~~l~l~~~~-~~~~G~~v~~iG~p~g~~~-----~~~~g~v~~~~~~~~~-~-~--~~~~~~~i~~-----~~~i~~G 275 (315)
.+.|+.|.... ....|+.+.+.||...... ......+......... . . .......++. ....|+|
T Consensus 105 ~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~g 184 (232)
T cd00190 105 NVRPICLPSSGYNLPAGTTCTVSGWGRTSEGGPLPDVLQEVNVPIVSNAECKRAYSYGGTITDNMLCAGGLEGGKDACQG 184 (232)
T ss_pred cccceECCCccccCCCCCEEEEEeCCcCCCCCCCCceeeEEEeeeECHHHhhhhccCcccCCCceEeeCCCCCCCccccC
Confidence 46888886443 5778999999998764321 2223333322221110 0 0 0111233443 3457899
Q ss_pred CccchhccCC---CeEEEEEeee
Q 041421 276 NSGGPLLDSS---GSLIGVNTFI 295 (315)
Q Consensus 276 ~SGGPlvd~~---G~vvGI~s~~ 295 (315)
+|||||+... +.++||+++.
T Consensus 185 dsGgpl~~~~~~~~~lvGI~s~g 207 (232)
T cd00190 185 DSGGPLVCNDNGRGVLVGIVSWG 207 (232)
T ss_pred CCCCcEEEEeCCEEEEEEEEehh
Confidence 9999999753 7899999997
No 22
>smart00020 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
Probab=99.32 E-value=6.5e-11 Score=103.92 Aligned_cols=144 Identities=20% Similarity=0.314 Sum_probs=91.3
Q ss_pred eeEEEEEEeCCcEEEEcccccCCC--CeEEEEeCCC--------cEEEEEEEEeC-------CCCCeEEEEecCC---CC
Q 041421 151 ASGAGFLWDQDGHIVTNHHVICDA--SKVKVSFSDQ--------STFYAKVVGHD-------QDKDLAVLHIDAP---NH 210 (315)
Q Consensus 151 ~~GSGfiI~~~g~VlT~aHvv~~~--~~~~V~~~~g--------~~~~a~vv~~d-------~~~DiAll~v~~~---~~ 210 (315)
..++|++|+++ +|||+|||+... ....|.+... ..+...-+..+ ..+|+|||+++.+ ..
T Consensus 26 ~~C~GtlIs~~-~VLTaahC~~~~~~~~~~v~~g~~~~~~~~~~~~~~v~~~~~~p~~~~~~~~~DiAll~L~~~i~~~~ 104 (229)
T smart00020 26 HFCGGSLISPR-WVLTAAHCVYGSDPSNIRVRLGSHDLSSGEEGQVIKVSKVIIHPNYNPSTYDNDIALLKLKSPVTLSD 104 (229)
T ss_pred cEEEEEEecCC-EEEECHHHcCCCCCcceEEEeCcccCCCCCCceEEeeEEEEECCCCCCCCCcCCEEEEEECcccCCCC
Confidence 37999999976 999999999875 3677777432 22334434433 3579999999875 22
Q ss_pred CccceEecCC-CCCCCCCeEEEEeeCCCCC------CceEEeEEeeecccccC---CCC-ceeecEEEE-----ccCCCC
Q 041421 211 ELRPIHVGVS-ADLHVGQKICAIGHPLGLP------FTCTTGVISALGREIPA---GTG-RLIRGVIQI-----DASINL 274 (315)
Q Consensus 211 ~~~~l~l~~~-~~~~~G~~v~~iG~p~g~~------~~~~~g~v~~~~~~~~~---~~~-~~~~~~i~~-----~~~i~~ 274 (315)
.+.|+.|... ..+..++.+.+.||+.... .......+......... ... ......++. ....|+
T Consensus 105 ~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~ 184 (229)
T smart00020 105 NVRPICLPSSNYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNVPIVSNATCRRAYSGGGAITDNMLCAGGLEGGKDACQ 184 (229)
T ss_pred ceeeccCCCcccccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEEEEeCHHHhhhhhccccccCCCcEeecCCCCCCcccC
Confidence 4678888643 2567899999999886542 12222333322221110 000 011223333 355799
Q ss_pred CCccchhccCCC--eEEEEEeee
Q 041421 275 GNSGGPLLDSSG--SLIGVNTFI 295 (315)
Q Consensus 275 G~SGGPlvd~~G--~vvGI~s~~ 295 (315)
|+|||||+...+ .++||+++.
T Consensus 185 gdsG~pl~~~~~~~~l~Gi~s~g 207 (229)
T smart00020 185 GDSGGPLVCNDGRWVLVGIVSWG 207 (229)
T ss_pred CCCCCeeEEECCCEEEEEEEEEC
Confidence 999999996443 899999997
No 23
>KOG1320 consensus Serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=98.92 E-value=3e-09 Score=101.90 Aligned_cols=186 Identities=23% Similarity=0.311 Sum_probs=131.0
Q ss_pred HHHhcCCceEEEEEEeeecCCCCCCCCCCCCCCcCCccccccccccccceeEEEEEEeCCcEEEEcccccC---CCCeEE
Q 041421 102 VFKENIPSVVLIGNLGIRDGNGEGRGGDQSPHTHSRYFAEDQSETQFLQASGAGFLWDQDGHIVTNHHVIC---DASKVK 178 (315)
Q Consensus 102 ~v~~~~~sVV~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GSGfiI~~~g~VlT~aHvv~---~~~~~~ 178 (315)
.++.+..|++.+.+..... .....|... + +....|+||.+... .++|++|+++ +.....
T Consensus 55 ~~~~~~~s~~~v~~~~~~~------------~~~~pw~~~----~-q~~~~~s~f~i~~~-~lltn~~~v~~~~~~~~v~ 116 (473)
T KOG1320|consen 55 VVDLALQSVVKVFSVSTEP------------SSVLPWQRT----R-QFSSGGSGFAIYGK-KLLTNAHVVAPNNDHKFVT 116 (473)
T ss_pred CccccccceeEEEeecccc------------cccCcceee----e-hhcccccchhhccc-ceeecCccccccccccccc
Confidence 4566777888888875543 122222222 2 34557999999854 8999999998 445555
Q ss_pred EEe-CCCcEEEEEEEEeCCCCCeEEEEecCCCC--CccceEecCCCCCCCCCeEEEEeeCCCCCCceEEeEEeeeccccc
Q 041421 179 VSF-SDQSTFYAKVVGHDQDKDLAVLHIDAPNH--ELRPIHVGVSADLHVGQKICAIGHPLGLPFTCTTGVISALGREIP 255 (315)
Q Consensus 179 V~~-~~g~~~~a~vv~~d~~~DiAll~v~~~~~--~~~~l~l~~~~~~~~G~~v~~iG~p~g~~~~~~~g~v~~~~~~~~ 255 (315)
+.- +.-+.+.+++...-...|+|++.++.... ...|+.+. .-+...+.++++| +....++.|.|.......+
T Consensus 117 v~~~gs~~k~~~~v~~~~~~cd~Avv~Ie~~~f~~~~~~~e~~--~ip~l~~S~~Vv~---gd~i~VTnghV~~~~~~~y 191 (473)
T KOG1320|consen 117 VKKHGSPRKYKAFVAAVFEECDLAVVYIESEEFWKGMNPFELG--DIPSLNGSGFVVG---GDGIIVTNGHVVRVEPRIY 191 (473)
T ss_pred cccCCCchhhhhhHHHhhhcccceEEEEeeccccCCCcccccC--CCcccCccEEEEc---CCcEEEEeeEEEEEEeccc
Confidence 542 22345778888888899999999986432 23344443 3445677899998 6677899999998877666
Q ss_pred CCCCceeecEEEEccCCCCCCccchhccCCCeEEEEEeee-cCCCcceEEEEEcchhhh
Q 041421 256 AGTGRLIRGVIQIDASINLGNSGGPLLDSSGSLIGVNTFI-TSGAFTGIGFATPIDTAV 313 (315)
Q Consensus 256 ~~~~~~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~-~~~~~~~~~~aiP~~~i~ 313 (315)
. .+......++++++..+|+||+|.+...+++.|+++.. .... .+++.||.-.+.
T Consensus 192 ~-~~~~~l~~vqi~aa~~~~~s~ep~i~g~d~~~gvA~l~ik~~~--~i~~~i~~~~~~ 247 (473)
T KOG1320|consen 192 A-HSSTVLLRVQIDAAIGPGNSGEPVIVGVDKVAGVAFLKIKTPE--NILYVIPLGVSS 247 (473)
T ss_pred c-CCCcceeeEEEEEeecCCccCCCeEEccccccceEEEEEecCC--cccceeecceee
Confidence 3 33333456899999999999999997678999999998 2222 478888876554
No 24
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=98.74 E-value=1.2e-07 Score=84.21 Aligned_cols=131 Identities=21% Similarity=0.248 Sum_probs=79.8
Q ss_pred EEEEEEeCCcEEEEcccccCCCC----eEEEEe----CCCc-EEE---EEEEEeCC---CCCeEEEEecCCCC-------
Q 041421 153 GAGFLWDQDGHIVTNHHVICDAS----KVKVSF----SDQS-TFY---AKVVGHDQ---DKDLAVLHIDAPNH------- 210 (315)
Q Consensus 153 GSGfiI~~~g~VlT~aHvv~~~~----~~~V~~----~~g~-~~~---a~vv~~d~---~~DiAll~v~~~~~------- 210 (315)
+++|+|+++ .+|||+||+.... .+.+.. +++. .+. .+...+.. ..|.+...+.....
T Consensus 66 ~~~~lI~pn-tvLTa~Hc~~s~~~G~~~~~~~p~g~~~~~~~~~~~~~~~~~~~~g~~~~~d~~~~~v~~~~~~~g~~~~ 144 (251)
T COG3591 66 TAATLIGPN-TVLTAGHCIYSPDYGEDDIAAAPPGVNSDGGPFYGITKIEIRVYPGELYKEDGASYDVGEAALESGINIG 144 (251)
T ss_pred eeEEEEcCc-eEEEeeeEEecCCCChhhhhhcCCcccCCCCCCCceeeEEEEecCCceeccCCceeeccHHHhccCCCcc
Confidence 466999986 9999999995433 122211 1221 111 11111222 44666655543111
Q ss_pred -CccceEecCCCCCCCCCeEEEEeeCCCCCCceEE----eEEeeecccccCCCCceeecEEEEccCCCCCCccchhccCC
Q 041421 211 -ELRPIHVGVSADLHVGQKICAIGHPLGLPFTCTT----GVISALGREIPAGTGRLIRGVIQIDASINLGNSGGPLLDSS 285 (315)
Q Consensus 211 -~~~~l~l~~~~~~~~G~~v~~iG~p~g~~~~~~~----g~v~~~~~~~~~~~~~~~~~~i~~~~~i~~G~SGGPlvd~~ 285 (315)
......+......+.++.+.++|||.+.....+. +.+.... ...+..++.+++|+||+|+++.+
T Consensus 145 ~~~~~~~~~~~~~~~~~d~i~v~GYP~dk~~~~~~~e~t~~v~~~~-----------~~~l~y~~dT~pG~SGSpv~~~~ 213 (251)
T COG3591 145 DVVNYLKRNTASEAKANDRITVIGYPGDKPNIGTMWESTGKVNSIK-----------GNKLFYDADTLPGSSGSPVLISK 213 (251)
T ss_pred ccccccccccccccccCceeEEEeccCCCCcceeEeeecceeEEEe-----------cceEEEEecccCCCCCCceEecC
Confidence 1222233334567889999999999876533222 3333221 23577888999999999999988
Q ss_pred CeEEEEEeee
Q 041421 286 GSLIGVNTFI 295 (315)
Q Consensus 286 G~vvGI~s~~ 295 (315)
.+++|+...+
T Consensus 214 ~~vigv~~~g 223 (251)
T COG3591 214 DEVIGVHYNG 223 (251)
T ss_pred ceEEEEEecC
Confidence 8999999998
No 25
>KOG3627 consensus Trypsin [Amino acid transport and metabolism]
Probab=98.64 E-value=1.2e-06 Score=78.64 Aligned_cols=142 Identities=21% Similarity=0.275 Sum_probs=84.1
Q ss_pred eEEEEEEeCCcEEEEcccccCCCC--eEEEEeCC---------C---cEEEE-EEEEeCC-------C-CCeEEEEecCC
Q 041421 152 SGAGFLWDQDGHIVTNHHVICDAS--KVKVSFSD---------Q---STFYA-KVVGHDQ-------D-KDLAVLHIDAP 208 (315)
Q Consensus 152 ~GSGfiI~~~g~VlT~aHvv~~~~--~~~V~~~~---------g---~~~~a-~vv~~d~-------~-~DiAll~v~~~ 208 (315)
.+.|.+|+++ |+||+|||+.+.. ...|.++. + ..... +++ .++ . +|||||+++.+
T Consensus 39 ~Cggsli~~~-~vltaaHC~~~~~~~~~~V~~G~~~~~~~~~~~~~~~~~~v~~~i-~H~~y~~~~~~~nDiall~l~~~ 116 (256)
T KOG3627|consen 39 LCGGSLISPR-WVLTAAHCVKGASASLYTVRLGEHDINLSVSEGEEQLVGDVEKII-VHPNYNPRTLENNDIALLRLSEP 116 (256)
T ss_pred eeeeEEeeCC-EEEEChhhCCCCCCcceEEEECccccccccccCchhhhceeeEEE-ECCCCCCCCCCCCCEEEEEECCC
Confidence 5677788765 9999999998865 66666531 1 11111 222 222 3 79999999874
Q ss_pred ---CCCccceEecCCCC---CCCCCeEEEEeeCCCC------CCceEEeEEeeecccccC-C-CC--ceeecEEEEc---
Q 041421 209 ---NHELRPIHVGVSAD---LHVGQKICAIGHPLGL------PFTCTTGVISALGREIPA-G-TG--RLIRGVIQID--- 269 (315)
Q Consensus 209 ---~~~~~~l~l~~~~~---~~~G~~v~~iG~p~g~------~~~~~~g~v~~~~~~~~~-~-~~--~~~~~~i~~~--- 269 (315)
...+.|+.|+.... ...+..+.+.||+... ...+....+..+...... . .. ......++..
T Consensus 117 v~~~~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~~~L~~~~v~i~~~~~C~~~~~~~~~~~~~~~Ca~~~~ 196 (256)
T KOG3627|consen 117 VTFSSHIQPICLPSSADPYFPPGGTTCLVSGWGRTESGGGPLPDTLQEVDVPIISNSECRRAYGGLGTITDTMLCAGGPE 196 (256)
T ss_pred cccCCcccccCCCCCcccCCCCCCCEEEEEeCCCcCCCCCCCCceeEEEEEeEcChhHhcccccCccccCCCEEeeCccC
Confidence 23577777753332 3445888889975421 122332333333221111 1 10 0112346654
Q ss_pred --cCCCCCCccchhccCC---CeEEEEEeee
Q 041421 270 --ASINLGNSGGPLLDSS---GSLIGVNTFI 295 (315)
Q Consensus 270 --~~i~~G~SGGPlvd~~---G~vvGI~s~~ 295 (315)
...|.|||||||+-.. ..++||++++
T Consensus 197 ~~~~~C~GDSGGPLv~~~~~~~~~~GivS~G 227 (256)
T KOG3627|consen 197 GGKDACQGDSGGPLVCEDNGRWVLVGIVSWG 227 (256)
T ss_pred CCCccccCCCCCeEEEeeCCcEEEEEEEEec
Confidence 2469999999999653 6999999998
No 26
>PF00863 Peptidase_C4: Peptidase family C4 This family belongs to family C4 of the peptidase classification.; InterPro: IPR001730 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. Nuclear inclusion A (NIA) proteases from potyviruses are cysteine peptidases belong to the MEROPS peptidase family C4 (NIa protease family, clan PA(C)) [, ]. Potyviruses include plant viruses in which the single-stranded RNA encodes a polyprotein with NIA protease activity, where proteolytic cleavage is specific for Gln+Gly sites. The NIA protease acts on the polyprotein, releasing itself by Gln+Gly cleavage at both the N- and C-termini. It further processes the polyprotein by cleavage at five similar sites in the C-terminal half of the sequence. In addition to its C-terminal protease activity, the NIA protease contains an N-terminal domain that has been implicated in the transcription process []. This peptidase is present in the nuclear inclusion protein of potyviruses.; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 3MMG_B 1Q31_B 1LVB_A 1LVM_A.
Probab=98.56 E-value=3.5e-06 Score=74.30 Aligned_cols=143 Identities=16% Similarity=0.307 Sum_probs=73.9
Q ss_pred EEEEEeCCcEEEEcccccCC-CCeEEEEeCCCcEEEEE-----EEEeCCCCCeEEEEecCCCCCccceEec-CCCCCCCC
Q 041421 154 AGFLWDQDGHIVTNHHVICD-ASKVKVSFSDQSTFYAK-----VVGHDQDKDLAVLHIDAPNHELRPIHVG-VSADLHVG 226 (315)
Q Consensus 154 SGfiI~~~g~VlT~aHvv~~-~~~~~V~~~~g~~~~a~-----vv~~d~~~DiAll~v~~~~~~~~~l~l~-~~~~~~~G 226 (315)
-|+... + +|+|++|.+.. ...+++....|. +... -+..-+..||.+++++. + ++|.+-. ....++.+
T Consensus 35 ~gigyG-~-~iItn~HLf~~nng~L~i~s~hG~-f~v~nt~~lkv~~i~~~DiviirmPk-D--fpPf~~kl~FR~P~~~ 108 (235)
T PF00863_consen 35 YGIGYG-S-YIITNAHLFKRNNGELTIKSQHGE-FTVPNTTQLKVHPIEGRDIVIIRMPK-D--FPPFPQKLKFRAPKEG 108 (235)
T ss_dssp EEEEET-T-EEEEEGGGGSSTTCEEEEEETTEE-EEECEGGGSEEEE-TCSSEEEEE--T-T--S----S---B----TT
T ss_pred EEEeEC-C-EEEEChhhhccCCCeEEEEeCceE-EEcCCccccceEEeCCccEEEEeCCc-c--cCCcchhhhccCCCCC
Confidence 466675 3 99999999954 456788776663 3221 23444689999999975 3 4443311 23567899
Q ss_pred CeEEEEeeCCCCCCceEEeEEeeecccccCCCCceeecEEEEccCCCCCCccchhccC-CCeEEEEEeeecCCCcceEEE
Q 041421 227 QKICAIGHPLGLPFTCTTGVISALGREIPAGTGRLIRGVIQIDASINLGNSGGPLLDS-SGSLIGVNTFITSGAFTGIGF 305 (315)
Q Consensus 227 ~~v~~iG~p~g~~~~~~~g~v~~~~~~~~~~~~~~~~~~i~~~~~i~~G~SGGPlvd~-~G~vvGI~s~~~~~~~~~~~~ 305 (315)
+.|+++|.-+...... ..++.......... ..++..-.+...|+-|+||++. +|.+|||++....... .+|
T Consensus 109 e~v~mVg~~fq~k~~~--s~vSesS~i~p~~~----~~fWkHwIsTk~G~CG~PlVs~~Dg~IVGiHsl~~~~~~--~N~ 180 (235)
T PF00863_consen 109 ERVCMVGSNFQEKSIS--STVSESSWIYPEEN----SHFWKHWISTKDGDCGLPLVSTKDGKIVGIHSLTSNTSS--RNY 180 (235)
T ss_dssp -EEEEEEEECSSCCCE--EEEEEEEEEEEETT----TTEEEE-C---TT-TT-EEEETTT--EEEEEEEEETTTS--SEE
T ss_pred CEEEEEEEEEEcCCee--EEECCceEEeecCC----CCeeEEEecCCCCccCCcEEEcCCCcEEEEEcCccCCCC--eEE
Confidence 9999999755433211 12222111000011 2345666666789999999986 9999999999844333 356
Q ss_pred EEcch
Q 041421 306 ATPID 310 (315)
Q Consensus 306 aiP~~ 310 (315)
..|+.
T Consensus 181 F~~f~ 185 (235)
T PF00863_consen 181 FTPFP 185 (235)
T ss_dssp EEE--
T ss_pred EEcCC
Confidence 66553
No 27
>PF05579 Peptidase_S32: Equine arteritis virus serine endopeptidase S32; InterPro: IPR008760 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S32 (clan PA(S)). The type example is equine arteritis virus serine endopeptidase (equine arteritis virus), which is involved in processing of nidovirus polyproteins [].; GO: 0004252 serine-type endopeptidase activity, 0016032 viral reproduction, 0019082 viral protein processing; PDB: 3FAN_A 3FAO_A 1MBM_A.
Probab=97.91 E-value=5.7e-05 Score=66.98 Aligned_cols=115 Identities=23% Similarity=0.329 Sum_probs=61.8
Q ss_pred eeEEEEEEeCCc--EEEEcccccCCCCeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCe
Q 041421 151 ASGAGFLWDQDG--HIVTNHHVICDASKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQK 228 (315)
Q Consensus 151 ~~GSGfiI~~~g--~VlT~aHvv~~~~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~ 228 (315)
+.|||-+.+.+| .++|+.||+. .+...|...+ .. +...++..-|+|.-.++.-....|.+++++. ..|.-
T Consensus 112 s~Gsggvft~~~~~vvvTAtHVlg-~~~a~v~~~g-~~---~~~tF~~~GDfA~~~~~~~~G~~P~~k~a~~---~~GrA 183 (297)
T PF05579_consen 112 SVGSGGVFTIGGNTVVVTATHVLG-GNTARVSGVG-TR---RMLTFKKNGDFAEADITNWPGAAPKYKFAQN---YTGRA 183 (297)
T ss_dssp SEEEEEEEECTTEEEEEEEHHHCB-TTEEEEEETT-EE---EEEEEEEETTEEEEEETTS-S---B--B-TT----SEEE
T ss_pred cccccceEEECCeEEEEEEEEEcC-CCeEEEEecc-eE---EEEEEeccCcEEEEECCCCCCCCCceeecCC---cccce
Confidence 355555555333 7999999998 5666665543 22 3455667789999999543334566666421 11221
Q ss_pred EEEEeeCCCCCCceEEeEEeeecccccCCCCceeecEEEEccCCCCCCccchhccCCCeEEEEEeee
Q 041421 229 ICAIGHPLGLPFTCTTGVISALGREIPAGTGRLIRGVIQIDASINLGNSGGPLLDSSGSLIGVNTFI 295 (315)
Q Consensus 229 v~~iG~p~g~~~~~~~g~v~~~~~~~~~~~~~~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~ 295 (315)
-+.. ..-+..|.+... ..++. ..+||||+|++..+|.+|||++.+
T Consensus 184 yW~t------~tGvE~G~ig~~-------------~~~~f---T~~GDSGSPVVt~dg~liGVHTGS 228 (297)
T PF05579_consen 184 YWLT------STGVEPGFIGGG-------------GAVCF---TGPGDSGSPVVTEDGDLIGVHTGS 228 (297)
T ss_dssp EEEE------TTEEEEEEEETT-------------EEEES---S-GGCTT-EEEETTC-EEEEEEEE
T ss_pred EEEc------ccCcccceecCc-------------eEEEE---cCCCCCCCccCcCCCCEEEEEecC
Confidence 1111 111233333211 11222 346999999999999999999998
No 28
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=97.56 E-value=0.0024 Score=58.34 Aligned_cols=108 Identities=15% Similarity=0.163 Sum_probs=63.8
Q ss_pred CCCCeEEEEecCC-CCCccceEecCCC-CCCCCCeEEEEeeCCCCCCceEEeEEeeecccccCCCCceeecEEEEccCCC
Q 041421 196 QDKDLAVLHIDAP-NHELRPIHVGVSA-DLHVGQKICAIGHPLGLPFTCTTGVISALGREIPAGTGRLIRGVIQIDASIN 273 (315)
Q Consensus 196 ~~~DiAll~v~~~-~~~~~~l~l~~~~-~~~~G~~v~~iG~p~g~~~~~~~g~v~~~~~~~~~~~~~~~~~~i~~~~~i~ 273 (315)
..++++|++++.+ .....|+.|+++. ....|+.+.+.|+... ..+....+....... ....+......+
T Consensus 159 ~~~~~mIlEl~~~~~~~~~~~Cl~~~~~~~~~~~~~~~yg~~~~--~~~~~~~~~i~~~~~-------~~~~~~~~~~~~ 229 (282)
T PF03761_consen 159 RPYSPMILELEEDFSKNVSPPCLADSSTNWEKGDEVDVYGFNST--GKLKHRKLKITNCTK-------CAYSICTKQYSC 229 (282)
T ss_pred cccceEEEEEcccccccCCCEEeCCCccccccCceEEEeecCCC--CeEEEEEEEEEEeec-------cceeEecccccC
Confidence 4579999999875 2567888887543 3567899999987211 112222222111100 123455566778
Q ss_pred CCCccchhccC-CC--eEEEEEeeecCCCcceEEEEEcchhh
Q 041421 274 LGNSGGPLLDS-SG--SLIGVNTFITSGAFTGIGFATPIDTA 312 (315)
Q Consensus 274 ~G~SGGPlvd~-~G--~vvGI~s~~~~~~~~~~~~aiP~~~i 312 (315)
.|++||||+.. +| .||||.+...........+.+.+...
T Consensus 230 ~~d~Gg~lv~~~~gr~tlIGv~~~~~~~~~~~~~~f~~v~~~ 271 (282)
T PF03761_consen 230 KGDRGGPLVKNINGRWTLIGVGASGNYECNKNNSYFFNVSWY 271 (282)
T ss_pred CCCccCeEEEEECCCEEEEEEEccCCCcccccccEEEEHHHh
Confidence 99999999843 55 58999887621111113455555544
No 29
>PF05580 Peptidase_S55: SpoIVB peptidase S55; InterPro: IPR008763 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S55 (SpoIVB peptidase family, clan PA(S)). The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis [, ].
Probab=97.43 E-value=0.0044 Score=53.72 Aligned_cols=161 Identities=17% Similarity=0.219 Sum_probs=87.6
Q ss_pred ccceeEEEEEEeC-CcEEEEcccccCCCCe-EEEEeCCCcEEEEEEEEeCC----------------C---------CCe
Q 041421 148 FLQASGAGFLWDQ-DGHIVTNHHVICDASK-VKVSFSDQSTFYAKVVGHDQ----------------D---------KDL 200 (315)
Q Consensus 148 ~~~~~GSGfiI~~-~g~VlT~aHvv~~~~~-~~V~~~~g~~~~a~vv~~d~----------------~---------~Di 200 (315)
...+.||=.++++ ++..--=.|.+.+.+. -.+.+.+|..+++++....+ . .+.
T Consensus 17 ~~aGiGTlTf~dp~~~~fgALGH~I~D~dt~~~~~i~~G~I~~a~I~~I~kg~~G~PGe~~G~~~~~~~~~G~I~~Nt~~ 96 (218)
T PF05580_consen 17 STAGIGTLTFYDPETGTFGALGHGISDVDTGQLIPIKNGEIYEASITSIKKGKKGQPGEKIGVFDNESNILGTIEKNTQF 96 (218)
T ss_pred CCcCeEEEEEEECCCCcEEecCCeEEcCCCCceeEecCCEEEEEEEEEEecCCCcCCceEEEEECCCCceEEEEEecccc
Confidence 3466788888986 3566666899887664 34556777777777765432 1 111
Q ss_pred EEE-EecCC----CCCccceEecCCCCCCCCCeEEEEeeCCCCCCceEEeEEeeecccccCCCCce--e----ecEEEEc
Q 041421 201 AVL-HIDAP----NHELRPIHVGVSADLHVGQKICAIGHPLGLPFTCTTGVISALGREIPAGTGRL--I----RGVIQID 269 (315)
Q Consensus 201 All-~v~~~----~~~~~~l~l~~~~~~~~G~~v~~iG~p~g~~~~~~~g~v~~~~~~~~~~~~~~--~----~~~i~~~ 269 (315)
-++ ++... .....+++++...++++|..-+..-..........- .|..+.+... ..... + ..++...
T Consensus 97 GI~G~~~~~~~~~~~~~~~~pva~~~evk~G~A~i~Tv~~G~~ie~f~i-eI~~v~~~~~-~~~k~~vi~vtd~~Ll~~T 174 (218)
T PF05580_consen 97 GIYGTLDQDDISNPSYNEPIPVAPKQEVKPGPAYILTVIDGTKIEEFDI-EIEKVLPQSS-PSGKGMVIKVTDPRLLEKT 174 (218)
T ss_pred ceeEEeccccccccccCceeEEEEHHHceEccEEEEEEEcCCeEEEeEE-EEEEEccCCC-CCCCcEEEEECCcchhhhh
Confidence 111 11111 123456667666778888643221111111111111 1222222111 01110 0 1223334
Q ss_pred cCCCCCCccchhccCCCeEEEEEeee-cCCCcceEEEEEcchhhh
Q 041421 270 ASINLGNSGGPLLDSSGSLIGVNTFI-TSGAFTGIGFATPIDTAV 313 (315)
Q Consensus 270 ~~i~~G~SGGPlvd~~G~vvGI~s~~-~~~~~~~~~~aiP~~~i~ 313 (315)
..+.+|+||+|++ .+|++||=++.. .++. ..||.+|++..+
T Consensus 175 GGIvqGMSGSPI~-qdGKLiGAVthvf~~dp--~~Gygi~ie~ML 216 (218)
T PF05580_consen 175 GGIVQGMSGSPII-QDGKLIGAVTHVFVNDP--TKGYGIFIEWML 216 (218)
T ss_pred CCEEecccCCCEE-ECCEEEEEEEEEEecCC--CceeeecHHHHh
Confidence 4577899999999 799999998888 4443 378999998764
No 30
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=97.43 E-value=0.0002 Score=50.54 Aligned_cols=58 Identities=52% Similarity=0.739 Sum_probs=47.5
Q ss_pred CceeeeeccccCceEeeeeeccC-CCCeeEEEEEEECChHHHHHHHHHHhhccceEEEe
Q 041421 1 MNQIAGVFARRKYNIESLAAIGL-DKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVS 58 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~ 58 (315)
|.+|+.+|++.++||+++..... ..+..++.+.+...++.+++++++|+++-+|.+|.
T Consensus 14 l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~v~~v~ 72 (72)
T cd04878 14 LNRISGLFARRGFNIESLTVGPTEDPGISRITIVVEGDDDVIEQIVKQLNKLVDVLKVS 72 (72)
T ss_pred HHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEEECCHHHHHHHHHHHhCCccEEEeC
Confidence 35678899999999999997544 46777888877743488999999999999999884
No 31
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=97.42 E-value=0.00023 Score=52.24 Aligned_cols=59 Identities=25% Similarity=0.377 Sum_probs=50.0
Q ss_pred CceeeeeccccCceEeeeeeccC-CCCeeEEEEEEE-CChHHHHHHHHHHhhccceEEEee
Q 041421 1 MNQIAGVFARRKYNIESLAAIGL-DKDRALFTIVVS-GTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~-~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
|+.|+.+++..+.||.++++... +.+..++++.++ .+-+.+++++++|+++-+|.+|..
T Consensus 20 L~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~R 80 (80)
T PF13291_consen 20 LADITSVISENGVNIRSINARTNKDDGTARITLTVEVKDLEHLNQIIRKLRQIPGVISVER 80 (80)
T ss_dssp HHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEEE
T ss_pred HHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEEC
Confidence 45688899999999999998555 377888777777 688899999999999999999963
No 32
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=97.41 E-value=0.0005 Score=63.53 Aligned_cols=26 Identities=31% Similarity=0.565 Sum_probs=21.3
Q ss_pred cCCCCCCccchhccC--CCe-EEEEEeee
Q 041421 270 ASINLGNSGGPLLDS--SGS-LIGVNTFI 295 (315)
Q Consensus 270 ~~i~~G~SGGPlvd~--~G~-vvGI~s~~ 295 (315)
...|+|+||||+|-. +|+ -+||++|+
T Consensus 223 ~daCqGDSGGPi~~~g~~G~vQ~GVvSwG 251 (413)
T COG5640 223 KDACQGDSGGPIFHKGEEGRVQRGVVSWG 251 (413)
T ss_pred cccccCCCCCceEEeCCCccEEEeEEEec
Confidence 467999999999954 454 68999999
No 33
>KOG1421 consensus Predicted signaling-associated protein (contains a PDZ domain) [General function prediction only]
Probab=97.40 E-value=0.0028 Score=63.03 Aligned_cols=139 Identities=17% Similarity=0.172 Sum_probs=95.1
Q ss_pred eEEEEEEe-CCcEEEEcccccC-CCCeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCeE
Q 041421 152 SGAGFLWD-QDGHIVTNHHVIC-DASKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQKI 229 (315)
Q Consensus 152 ~GSGfiI~-~~g~VlT~aHvv~-~~~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~v 229 (315)
.|||.+++ ..|++++.+.++. ++.+..|...|.-..+|.+.+.++...+|.+|.+... ...++|. ...+..|+++
T Consensus 551 kgt~~i~d~~~g~~vvsr~~vp~d~~d~~vt~~dS~~i~a~~~fL~~t~n~a~~kydp~~--~~~~kl~-~~~v~~gD~~ 627 (955)
T KOG1421|consen 551 KGTALIMDTSKGLGVVSRSVVPSDAKDQRVTEADSDGIPANVSFLHPTENVASFKYDPAL--EVQLKLT-DTTVLRGDEC 627 (955)
T ss_pred cCceEEEEccCCceeEecccCCchhhceEEeecccccccceeeEecCccceeEeccChhH--hhhhccc-eeeEecCCce
Confidence 69999998 3589999999995 5677888888888899999999999999999998532 3456664 4667899999
Q ss_pred EEEeeCCCCCCceEEeEEeeecccccC-----CCCceeecEEEEccCCCCCCccchhccCCCeEEEEEe
Q 041421 230 CAIGHPLGLPFTCTTGVISALGREIPA-----GTGRLIRGVIQIDASINLGNSGGPLLDSSGSLIGVNT 293 (315)
Q Consensus 230 ~~iG~p~g~~~~~~~g~v~~~~~~~~~-----~~~~~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s 293 (315)
...|+............++........ .-...-.+.|.+++.+.-+.--|-+.|.+|+|+|+--
T Consensus 628 ~f~g~~~~~r~ltaktsv~dvs~~~~ps~~~pr~r~~n~e~Is~~~nlsT~c~sg~ltdddg~vvalwl 696 (955)
T KOG1421|consen 628 TFEGFTEDLRALTAKTSVTDVSVVIIPSSVMPRFRATNLEVISFMDNLSTSCLSGRLTDDDGEVVALWL 696 (955)
T ss_pred eEecccccchhhcccceeeeeEEEEecCCCCcceeecceEEEEEeccccccccceEEECCCCeEEEEEe
Confidence 999988654332222222222111100 0001113566666655444445578888999999843
No 34
>PF10459 Peptidase_S46: Peptidase S46; InterPro: IPR019500 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents S46 peptidases, where dipeptidyl-peptidase 7 (DPP-7) is the best-characterised member of this family. It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains.
Probab=97.37 E-value=0.0007 Score=69.04 Aligned_cols=21 Identities=33% Similarity=0.487 Sum_probs=19.4
Q ss_pred eEEEEEEeCCcEEEEcccccC
Q 041421 152 SGAGFLWDQDGHIVTNHHVIC 172 (315)
Q Consensus 152 ~GSGfiI~~~g~VlT~aHvv~ 172 (315)
-|||.|||++|+||||.||..
T Consensus 48 GCSgsfVS~~GLvlTNHHC~~ 68 (698)
T PF10459_consen 48 GCSGSFVSPDGLVLTNHHCGY 68 (698)
T ss_pred ceeEEEEcCCceEEecchhhh
Confidence 599999999999999999963
No 35
>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=97.26 E-value=0.00019 Score=50.49 Aligned_cols=58 Identities=16% Similarity=0.270 Sum_probs=48.2
Q ss_pred CceeeeeccccCceEeeeeeccCC-CCeeEEEEEEECChHHHHHHHHHHhhccceEEEeec
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD-KDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTK 60 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~ 60 (315)
|++|+.+|+.+++||.++.+.... .+...+++.+... .+++++++|+++.+|.+|..+
T Consensus 13 l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v~~~--~~~~l~~~l~~~~~V~~v~~~ 71 (71)
T cd04879 13 IGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVDSP--VPEEVLEELKALPGIIRVRLI 71 (71)
T ss_pred HHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEcCCC--CCHHHHHHHHcCCCeEEEEEC
Confidence 467889999999999999984443 5788888888543 588999999999999999763
No 36
>PRK06349 homoserine dehydrogenase; Provisional
Probab=97.22 E-value=0.00024 Score=68.94 Aligned_cols=57 Identities=26% Similarity=0.408 Sum_probs=49.8
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEE-CChHHHHHHHHHHhhccceEEE
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS-GTDRELQQVVEQLQKLVNVLNV 57 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v 57 (315)
|++|+++|.++++||+|+.....+.+..+++|+++ .++..++++++||+||.+|.+.
T Consensus 362 La~I~~~f~~~~vsI~si~q~~~~~~~~~ivivT~~~~e~~l~~~i~~L~~l~~V~~~ 419 (426)
T PRK06349 362 LAKIAAIFAENGISIESILQKGAGGEGAEIVIVTHETSEAALRAALAAIEALDVVLGI 419 (426)
T ss_pred HHHHHHHHhhcCccEEEEEeccCCCCceeEEEEEEeCCHHHHHHHHHHHhcCcccccc
Confidence 46899999999999999997544457889999999 8899999999999999999664
No 37
>COG3978 Acetolactate synthase (isozyme II), small (regulatory) subunit [Function unknown]
Probab=97.12 E-value=0.00034 Score=50.37 Aligned_cols=61 Identities=25% Similarity=0.397 Sum_probs=49.7
Q ss_pred ceeeeeccccCceEeeeeecc-CCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 2 NQIAGVFARRKYNIESLAAIG-LDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
-||-++-.+|||-+-+++..+ .+.+.-.+.++|. .+..++-+..||+||.||..|+....+
T Consensus 18 eRVLrvtrhRGF~vcamnmt~~~da~~~nie~tV~-s~R~~~lL~~QLeKl~Dv~~V~i~~~~ 79 (86)
T COG3978 18 ERVLRVTRHRGFRVCAMNMTAAVDAGNANIELTVD-SDRSVDLLTSQLEKLYDVAHVEITQSE 79 (86)
T ss_pred HHHHHHhhhcCeEEEEeecccccccccceEEEEEc-CCCChHHHHHHHHHHccceeEEEeehh
Confidence 467778899999999999732 3566777888887 567899999999999999999876544
No 38
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=97.00 E-value=0.00032 Score=48.91 Aligned_cols=53 Identities=19% Similarity=0.376 Sum_probs=43.0
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhccc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKLVN 53 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~ 53 (315)
|.+|+.+|+++|+||.++...+...+...+.++...+....+++++.|+++.+
T Consensus 14 l~~v~~~la~~~inI~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 66 (66)
T PF01842_consen 14 LADVTEILADHGINIDSISQSSDKDGVGIVFIVIVVDEEDLEKLLEELEALPG 66 (66)
T ss_dssp HHHHHHHHHHTTEEEEEEEEEEESSTTEEEEEEEEEEGHGHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHcCCCHHHeEEEecCCCceEEEEEEECCCCCHHHHHHHHHcccC
Confidence 46789999999999999998544443566666777889999999999999754
No 39
>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=96.93 E-value=0.0016 Score=46.85 Aligned_cols=60 Identities=18% Similarity=0.245 Sum_probs=46.3
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEE-CChH-HHHHHHHHHhhccceEEEeec
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS-GTDR-ELQQVVEQLQKLVNVLNVSTK 60 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~ql~k~~~v~~v~~~ 60 (315)
|++|+.++++.+.||++++......+..++.+++. .+.+ .+++|+++|.++-+|.+|..+
T Consensus 14 l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~~ 75 (76)
T cd04888 14 LSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTSTMNGDIDELLEELREIDGVEKVELV 75 (76)
T ss_pred HHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEEe
Confidence 45778889999999999986322345666666665 3444 899999999999999999754
No 40
>PF00548 Peptidase_C3: 3C cysteine protease (picornain 3C); InterPro: IPR000199 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This signature defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies C3A and C3B. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [], the type example for clan PA. Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral C3 cysteine protease. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. ; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 3SJO_E 2H6M_A 1QA7_C 1HAV_B 2HAL_A 2H9H_A 3QZQ_B 3QZR_A 3R0F_B 3SJ9_A ....
Probab=96.82 E-value=0.017 Score=48.96 Aligned_cols=135 Identities=16% Similarity=0.191 Sum_probs=76.1
Q ss_pred eEEEEEEeCCcEEEEcccccCCCCeEEEEeCCCcEEEE--EEEEeCC---CCCeEEEEecCCCCCccceE--ecCCCCCC
Q 041421 152 SGAGFLWDQDGHIVTNHHVICDASKVKVSFSDQSTFYA--KVVGHDQ---DKDLAVLHIDAPNHELRPIH--VGVSADLH 224 (315)
Q Consensus 152 ~GSGfiI~~~g~VlT~aHvv~~~~~~~V~~~~g~~~~a--~vv~~d~---~~DiAll~v~~~~~~~~~l~--l~~~~~~~ 224 (315)
.++++.|.++ ++|-..| -.....+ .+ +|..++. .+...+. ..|+++++++... .++-+. +.+ ....
T Consensus 26 t~l~~gi~~~-~~lvp~H-~~~~~~i--~i-~g~~~~~~d~~~lv~~~~~~~Dl~~v~l~~~~-kfrDIrk~~~~-~~~~ 98 (172)
T PF00548_consen 26 TMLALGIYDR-YFLVPTH-EEPEDTI--YI-DGVEYKVDDSVVLVDRDGVDTDLTLVKLPRNP-KFRDIRKFFPE-SIPE 98 (172)
T ss_dssp EEEEEEEEBT-EEEEEGG-GGGCSEE--EE-TTEEEEEEEEEEEEETTSSEEEEEEEEEESSS--B--GGGGSBS-SGGT
T ss_pred EEecceEeee-EEEEECc-CCCcEEE--EE-CCEEEEeeeeEEEecCCCcceeEEEEEccCCc-ccCchhhhhcc-cccc
Confidence 6888889865 9999999 2223333 33 3444432 2223443 4699999997642 222111 111 1112
Q ss_pred CCCeEEEEeeCCCCCCceEEeEEeeecccccCCCCceeecEEEEccCCCCCCccchhccC---CCeEEEEEeee
Q 041421 225 VGQKICAIGHPLGLPFTCTTGVISALGREIPAGTGRLIRGVIQIDASINLGNSGGPLLDS---SGSLIGVNTFI 295 (315)
Q Consensus 225 ~G~~v~~iG~p~g~~~~~~~g~v~~~~~~~~~~~~~~~~~~i~~~~~i~~G~SGGPlvd~---~G~vvGI~s~~ 295 (315)
..+...++=.+.........+.++..+.- . .++......+..+++..+|+-||||+.. .++++||+.++
T Consensus 99 ~~~~~l~v~~~~~~~~~~~v~~v~~~~~i-~-~~g~~~~~~~~Y~~~t~~G~CG~~l~~~~~~~~~i~GiHvaG 170 (172)
T PF00548_consen 99 YPECVLLVNSTKFPRMIVEVGFVTNFGFI-N-LSGTTTPRSLKYKAPTKPGMCGSPLVSRIGGQGKIIGIHVAG 170 (172)
T ss_dssp EEEEEEEEESSSSTCEEEEEEEEEEEEEE-E-ETTEEEEEEEEEESEEETTGTTEEEEESCGGTTEEEEEEEEE
T ss_pred CCCcEEEEECCCCccEEEEEEEEeecCcc-c-cCCCEeeEEEEEccCCCCCccCCeEEEeeccCccEEEEEecc
Confidence 33444444322222223333444433332 2 3345556778888888899999999952 67999999986
No 41
>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=96.81 E-value=0.002 Score=45.46 Aligned_cols=58 Identities=22% Similarity=0.319 Sum_probs=48.2
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEee
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
|++|+.+|++.++||.++.....+.+..++++.+.+. +.++.++++|++.-+|..|.-
T Consensus 14 l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~~-~~~~~~~~~L~~~~~v~~v~~ 71 (72)
T cd04874 14 LRDLTGVIAEHGGNITYTQQFIEREGKARIYMELEGV-GDIEELVEELRSLPIVREVEI 71 (72)
T ss_pred HHHHHHHHHhCCCCEEEEEEeccCCCeEEEEEEEecc-ccHHHHHHHHhCCCCeEEEEe
Confidence 4578889999999999998744346778888888876 788899999999999998863
No 42
>cd04881 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains. The ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) encoded by the hom gene of Bacillus subtilis and other related sequences. HSDH reduces aspartate semi-aldehyde to the amino acid homoserine, one that is required for the biosynthesis of Met, Thr, and Ile from Asp. Neither the enzyme nor the aspartate pathway is found in the animal kingdom. This mostly bacterial HSDH group has a C-terminal ACT domain and is believed to be involved in enzyme regulation. A C-terminal deletion in the Corynebacterium glutamicum HSDH abolished allosteric inhibition by L-threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.71 E-value=0.0013 Score=47.16 Aligned_cols=58 Identities=24% Similarity=0.371 Sum_probs=46.6
Q ss_pred CceeeeeccccCceEeeeeeccCC-CCeeEEEEEEE-CChHHHHHHHHHHhhccceEEEe
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD-KDRALFTIVVS-GTDRELQQVVEQLQKLVNVLNVS 58 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v~ 58 (315)
|++|+.+|++.+.||+++...... .+..++.+++. .+.+.+++++++|+++.+|.++.
T Consensus 14 l~~i~~~l~~~~i~I~~~~~~~~~~~~~~~~~i~~~~~~~~~l~~~i~~L~~~~~V~~~~ 73 (79)
T cd04881 14 LAKITGILAEHGISIESVIQKEADGGETAPVVIVTHETSEAALNAALAEIEALDAVQGVP 73 (79)
T ss_pred HHHHHHHHHHcCCCeEEEEEcccCCCCceeEEEEEccCCHHHHHHHHHHHHcCccccCCc
Confidence 457788999999999999874332 37778888766 67888999999999999887653
No 43
>cd04901 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-
Probab=96.44 E-value=0.0009 Score=47.27 Aligned_cols=57 Identities=16% Similarity=0.215 Sum_probs=45.0
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEeec
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTK 60 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~ 60 (315)
|++|+.++++.++||.++..... .+...+.+.++.. .+++++++|.++.+|++|..+
T Consensus 13 l~~i~~~l~~~~~nI~~~~~~~~-~~~a~~~~~~~~~--~l~~li~~l~~~~~V~~v~~~ 69 (69)
T cd04901 13 LGQINTILAEHNINIAAQYLQTR-GEIGYVVIDIDSE--VSEELLEALRAIPGTIRVRLL 69 (69)
T ss_pred HHHHHHHHHHcCCCHHHHhccCC-CCEEEEEEEcCCC--CCHHHHHHHHcCCCeEEEEEC
Confidence 46788899999999999986333 3666666666544 888999999999999999753
No 44
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.42 E-value=0.0024 Score=44.80 Aligned_cols=57 Identities=25% Similarity=0.351 Sum_probs=46.7
Q ss_pred CceeeeeccccCceEeeeeecc-CCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEee
Q 041421 1 MNQIAGVFARRKYNIESLAAIG-LDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
|.+|+.+|++.+.||.++.+.. ...+...+.|.+... .+++++++|+++-.|.+|..
T Consensus 13 l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~i~v~~~--~~~~~i~~l~~~~~v~~v~~ 70 (71)
T cd04903 13 IAKVTSVLADHEINIAFMRVSRKEKGDQALMVIEVDQP--IDEEVIEEIKKIPNIHQVIL 70 (71)
T ss_pred HHHHHHHHHHcCcCeeeeEEEeccCCCeEEEEEEeCCC--CCHHHHHHHHcCCCceEEEE
Confidence 3567889999999999998744 346777888877755 78899999999999999875
No 45
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.28 E-value=0.0051 Score=44.06 Aligned_cols=57 Identities=12% Similarity=0.247 Sum_probs=47.7
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEE-CChHHHHHHHHHHhhccceEEE
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS-GTDRELQQVVEQLQKLVNVLNV 57 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v 57 (315)
|++|+.+++..|.||.++.......+...+.++++ .+.+.++++++.|+++-+|.--
T Consensus 13 L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~~~~~l~~i~~~L~~i~gV~~~ 70 (74)
T cd04887 13 LGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAPSEEHAETIVAAVRALPEVKVL 70 (74)
T ss_pred HHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcCCHHHHHHHHHHHhcCCCeEEE
Confidence 46788999999999999997444567888888887 6888899999999999998653
No 46
>PRK08577 hypothetical protein; Provisional
Probab=96.22 E-value=0.0065 Score=49.45 Aligned_cols=61 Identities=28% Similarity=0.408 Sum_probs=48.1
Q ss_pred CceeeeeccccCceEeeeeeccCC-CCeeEEEEEEE--CChHHHHHHHHHHhhccceEEEeecc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD-KDRALFTIVVS--GTDRELQQVVEQLQKLVNVLNVSTKQ 61 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~-~~~~~~~~~~~--~~~~~~~~~~~ql~k~~~v~~v~~~~ 61 (315)
|+.|+.+|+..++||.++.+.... .+..++++++. ..+..+++++++|+++-+|.+|....
T Consensus 70 La~I~~~l~~~~inI~~i~~~~~~~~~~~~i~l~vev~~~~~~l~~l~~~L~~l~~V~~V~~~~ 133 (136)
T PRK08577 70 LAKITGLLAEHGVDILATECEELKRGELAECVIIVDLSKSDIDLEELEEELKKLEEVKEVEIRQ 133 (136)
T ss_pred HHHHHHHHHHCCCCEEEEEEEEecCCCEEEEEEEEEeCCchhhHHHHHHHHHcCCCEEEEEEEE
Confidence 356788999999999999874433 56777777666 33468999999999999999998643
No 47
>PF10459 Peptidase_S46: Peptidase S46; InterPro: IPR019500 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents S46 peptidases, where dipeptidyl-peptidase 7 (DPP-7) is the best-characterised member of this family. It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains.
Probab=96.21 E-value=0.0035 Score=64.07 Aligned_cols=31 Identities=32% Similarity=0.462 Sum_probs=28.1
Q ss_pred EEEEccCCCCCCccchhccCCCeEEEEEeee
Q 041421 265 VIQIDASINLGNSGGPLLDSSGSLIGVNTFI 295 (315)
Q Consensus 265 ~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~ 295 (315)
.+.++..+..||||+|++|.+|+|||++|-+
T Consensus 623 ~FlstnDitGGNSGSPvlN~~GeLVGl~FDg 653 (698)
T PF10459_consen 623 NFLSTNDITGGNSGSPVLNAKGELVGLAFDG 653 (698)
T ss_pred EEEeccCcCCCCCCCccCCCCceEEEEeecC
Confidence 4677788899999999999999999999977
No 48
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=96.18 E-value=0.0068 Score=43.70 Aligned_cols=58 Identities=10% Similarity=0.206 Sum_probs=45.6
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEeecc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQ 61 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~ 61 (315)
|+.|+.+++..++||.++.+... +.-++++.+. +-+.+++++++|.++..|.+|....
T Consensus 14 l~dI~~~i~~~~~nI~~~~~~~~--~~i~l~i~v~-~~~~L~~li~~L~~i~gV~~V~R~~ 71 (74)
T cd04877 14 TQEVLDLLVEHNIDLRGIEIDPK--GRIYLNFPTI-EFEKLQTLMPEIRRIDGVEDVKTVP 71 (74)
T ss_pred HHHHHHHHHHCCCceEEEEEecC--CeEEEEeEec-CHHHHHHHHHHHhCCCCceEEEEee
Confidence 35678899999999999998433 4444555544 6777999999999999999998753
No 49
>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=96.17 E-value=0.0091 Score=40.82 Aligned_cols=57 Identities=23% Similarity=0.314 Sum_probs=46.1
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEE-CChHHHHHHHHHHhhccceEEEe
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS-GTDRELQQVVEQLQKLVNVLNVS 58 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v~ 58 (315)
+++..+|...++||.++.......+...+.+.+. .+...++.++++|.++..|.+|.
T Consensus 13 ~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~v~ 70 (71)
T cd04876 13 ADITTVIAEEKINILSVNTRTDDDGLATIRLTLEVRDLEHLARIMRKLRQIPGVIDVR 70 (71)
T ss_pred HHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEEEECCHHHHHHHHHHHhCCCCcEEEE
Confidence 4667889999999999987443456677777766 56788999999999999998875
No 50
>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=96.16 E-value=0.0025 Score=45.35 Aligned_cols=59 Identities=17% Similarity=0.269 Sum_probs=46.1
Q ss_pred CceeeeeccccCceEeeeeeccC-CCCeeEEEEEEECChHHHHHHHHHHhhccceEEEeecc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGL-DKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQ 61 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~ 61 (315)
|++|+.+|+++|.||.++.+... ..+...+.+.++++. ...+.+.|.++.+|++|..+.
T Consensus 13 l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~~~~--~~~~~~~l~~~~~v~~v~~~~ 72 (73)
T cd04902 13 IGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDEPV--PDEVLEELRALPGILSAKVVE 72 (73)
T ss_pred HHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeCCCC--CHHHHHHHHcCCCccEEEEEe
Confidence 46788999999999999987433 467777888777633 458888899999998887753
No 51
>TIGR02860 spore_IV_B stage IV sporulation protein B. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else.
Probab=96.08 E-value=0.093 Score=50.22 Aligned_cols=42 Identities=26% Similarity=0.495 Sum_probs=31.9
Q ss_pred ccCCCCCCccchhccCCCeEEEEEeee-cCCCcceEEEEEcchhhh
Q 041421 269 DASINLGNSGGPLLDSSGSLIGVNTFI-TSGAFTGIGFATPIDTAV 313 (315)
Q Consensus 269 ~~~i~~G~SGGPlvd~~G~vvGI~s~~-~~~~~~~~~~aiP~~~i~ 313 (315)
.+.+.+|+||+|++ .+|++||=++-. .++.. .||.|-++...
T Consensus 354 tgGivqGMSGSPi~-q~gkliGAvtHVfvndpt--~GYGi~ie~Ml 396 (402)
T TIGR02860 354 TGGIVQGMSGSPII-QNGKVIGAVTHVFVNDPT--SGYGVYIEWML 396 (402)
T ss_pred hCCEEecccCCCEE-ECCEEEEEEEEEEecCCC--cceeehHHHHH
Confidence 44667899999999 799999987777 44444 57888776643
No 52
>PF00949 Peptidase_S7: Peptidase S7, Flavivirus NS3 serine protease ; InterPro: IPR001850 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature identifies serine peptidases belong to MEROPS peptidase family S7 (flavivirin family, clan PA(S)). The protein fold of the peptidase domain for members of this family resembles that of chymotrypsin, the type example for clan PA. Flaviviruses produce a polyprotein from the ssRNA genome. The N terminus of the NS3 protein (approx. 180 aa) is required for the processing of the polyprotein. NS3 also has conserved homology with NTP-binding proteins and DEAD family of RNA helicase [, , ].; GO: 0003723 RNA binding, 0003724 RNA helicase activity, 0005524 ATP binding; PDB: 2IJO_B 3E90_D 2GGV_B 2FP7_B 2WV9_A 3U1I_B 3U1J_B 2WZQ_A 2WHX_A 3L6P_A ....
Probab=96.07 E-value=0.011 Score=47.78 Aligned_cols=30 Identities=27% Similarity=0.498 Sum_probs=22.3
Q ss_pred EEEccCCCCCCccchhccCCCeEEEEEeee
Q 041421 266 IQIDASINLGNSGGPLLDSSGSLIGVNTFI 295 (315)
Q Consensus 266 i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~ 295 (315)
...+..+.+|.||+|+||.+|+++||....
T Consensus 88 ~~~~~d~~~GsSGSpi~n~~g~ivGlYg~g 117 (132)
T PF00949_consen 88 GAIDLDFPKGSSGSPIFNQNGEIVGLYGNG 117 (132)
T ss_dssp EEE---S-TTGTT-EEEETTSCEEEEEEEE
T ss_pred EeeecccCCCCCCCceEcCCCcEEEEEccc
Confidence 344455778999999999999999999988
No 53
>PRK04435 hypothetical protein; Provisional
Probab=96.05 E-value=0.011 Score=48.92 Aligned_cols=61 Identities=21% Similarity=0.257 Sum_probs=48.0
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEE--CChHHHHHHHHHHhhccceEEEeecc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS--GTDRELQQVVEQLQKLVNVLNVSTKQ 61 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~ql~k~~~v~~v~~~~ 61 (315)
|++|..++++.+.||.+++.....++...++++++ ..+..+++|+.+|+++-.|.+|+-+.
T Consensus 83 Ls~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs~~~~~L~~Li~~L~~i~gV~~V~i~~ 145 (147)
T PRK04435 83 LSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTSSMEGDIDELLEKLRNLDGVEKVELIG 145 (147)
T ss_pred HHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeCChHHHHHHHHHHHHcCCCcEEEEEEe
Confidence 45678889999999999986333356777777666 33448999999999999999998754
No 54
>PF08192 Peptidase_S64: Peptidase family S64; InterPro: IPR012985 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1 [] and belongs to MEROPS petidase family S64 (clan PA). The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced. The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment. This family is predicted to be distantly related to the trypsin family (MEROPS peptidase family S1) and to have a typical trypsin-like catalytic triad [].
Probab=95.97 E-value=0.042 Score=54.96 Aligned_cols=113 Identities=19% Similarity=0.301 Sum_probs=69.2
Q ss_pred CCCCeEEEEecCCC-------C------CccceEecC------CCCCCCCCeEEEEeeCCCCCCceEEeEEeeecccccC
Q 041421 196 QDKDLAVLHIDAPN-------H------ELRPIHVGV------SADLHVGQKICAIGHPLGLPFTCTTGVISALGREIPA 256 (315)
Q Consensus 196 ~~~DiAll~v~~~~-------~------~~~~l~l~~------~~~~~~G~~v~~iG~p~g~~~~~~~g~v~~~~~~~~~ 256 (315)
.-.|+||++++..- . .-+.+.+.+ -....+|.+|+-+|...+ .+.|.+.+.. ..++
T Consensus 541 ~LsD~AIIkV~~~~~~~N~LGddi~f~~~dP~l~f~NlyV~~~~~~~~~G~~VfK~GrTTg----yT~G~lNg~k-lvyw 615 (695)
T PF08192_consen 541 RLSDWAIIKVNKERKCQNYLGDDIQFNEPDPTLMFQNLYVREVVSNLVPGMEVFKVGRTTG----YTTGILNGIK-LVYW 615 (695)
T ss_pred cccceEEEEeCCCceecCCCCccccccCCCccccccccchhhhhhccCCCCeEEEecccCC----ccceEecceE-EEEe
Confidence 34699999997521 0 112233321 134567999999997655 3556666553 2233
Q ss_pred CCCcee-ecEEEEc----cCCCCCCccchhccCCC------eEEEEEeeecCCCcceEEEEEcchhhhc
Q 041421 257 GTGRLI-RGVIQID----ASINLGNSGGPLLDSSG------SLIGVNTFITSGAFTGIGFATPIDTAVL 314 (315)
Q Consensus 257 ~~~~~~-~~~i~~~----~~i~~G~SGGPlvd~~G------~vvGI~s~~~~~~~~~~~~aiP~~~i~~ 314 (315)
.++... .+++... .-...||||+=|++.-+ .|+||.++- +|....+|...|+.+|.+
T Consensus 616 ~dG~i~s~efvV~s~~~~~Fa~~GDSGS~VLtk~~d~~~gLgvvGMlhsy-dge~kqfglftPi~~il~ 683 (695)
T PF08192_consen 616 ADGKIQSSEFVVSSDNNPAFASGGDSGSWVLTKLEDNNKGLGVVGMLHSY-DGEQKQFGLFTPINEILD 683 (695)
T ss_pred cCCCeEEEEEEEecCCCccccCCCCcccEEEecccccccCceeeEEeeec-CCccceeeccCcHHHHHH
Confidence 333332 2333333 23457999999998633 399999886 444556899999998864
No 55
>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=95.28 E-value=0.016 Score=40.75 Aligned_cols=22 Identities=14% Similarity=0.339 Sum_probs=19.2
Q ss_pred CceeeeeccccCceEeeeeecc
Q 041421 1 MNQIAGVFARRKYNIESLAAIG 22 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~ 22 (315)
|++|+.+|+++|+||+|+.+..
T Consensus 15 La~v~~~l~~~~inI~~i~~~~ 36 (66)
T cd04908 15 LAAVTEILSEAGINIRALSIAD 36 (66)
T ss_pred HHHHHHHHHHCCCCEEEEEEEe
Confidence 5788999999999999999733
No 56
>PF00944 Peptidase_S3: Alphavirus core protein ; InterPro: IPR000930 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. Togavirin, also known as Sindbis virus core endopeptidase, is a serine protease resident at the N terminus of the p130 polyprotein of togaviruses []. The endopeptidase signature identifies the peptidase as belonging to the MEROPS peptidase family S3 (togavirin family, clan PA(S)). The polyprotein also includes structural proteins for the nucleocapsid core and for the glycoprotein spikes []. Togavirin is only active while part of the polyprotein, cleavage at a Trp-Ser bond resulting in total lack of activity []. Mutagenesis studies have identified the location of the His-Asp-Ser catalytic triad, and X-ray studies have revealed the protein fold to be similar to that of chymotrypsin [, ].; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 2YEW_D 1EP5_A 3J0C_F 1EP6_C 1WYK_D 1DYL_A 1VCQ_B 1VCP_B 1LD4_D 1KXA_A ....
Probab=95.27 E-value=0.028 Score=44.99 Aligned_cols=27 Identities=26% Similarity=0.396 Sum_probs=23.8
Q ss_pred ccCCCCCCccchhccCCCeEEEEEeee
Q 041421 269 DASINLGNSGGPLLDSSGSLIGVNTFI 295 (315)
Q Consensus 269 ~~~i~~G~SGGPlvd~~G~vvGI~s~~ 295 (315)
.+.-.+|+||-|++|..|+||||+..+
T Consensus 100 ~g~g~~GDSGRpi~DNsGrVVaIVLGG 126 (158)
T PF00944_consen 100 TGVGKPGDSGRPIFDNSGRVVAIVLGG 126 (158)
T ss_dssp TTS-STTSTTEEEESTTSBEEEEEEEE
T ss_pred cCCCCCCCCCCccCcCCCCEEEEEecC
Confidence 455678999999999999999999998
No 57
>PF02122 Peptidase_S39: Peptidase S39; InterPro: IPR000382 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. ORF2 of Potato leafroll virus (PLrV) encodes a polyprotein which is translated following a -1 frameshift. The polyprotein has a putative linear arrangement of membrane achor-VPg-peptidase-polmerase domains. The serine peptidase domain which is found in this group of sequences belongs to MEROPS peptidase family S39 (clan PA(S)). It is likely that the peptidase domain is involved in the cleavage of the polyprotein []. The nucleotide sequence for the RNA of PLrV has been determined [, ]. The sequence contains six large open reading frames (ORFs). The 5' coding region encodes two polypeptides of 28K and 70K, which overlap in different reading frames; it is suggested that the third ORF in the 5' block is translated by frameshift readthrough near the end of the 70K protein, yielding a 118K polypeptide []. Segments of the predicted amino acid sequences of these ORFs resemble those of known viral RNA polymerases, ATP-binding proteins and viral genome-linked proteins. The nucleotide sequence of the genomic RNA of Beet western yellows virus (BWYV) has been determined []. The sequence contains six long ORFs. A cluster of three of these ORFs, including the coat protein cistron, display extensive amino acid sequence similarity to corresponding ORFs of a second luteovirus: Barley yellow dwarf virus [].; GO: 0004252 serine-type endopeptidase activity, 0022415 viral reproductive process, 0016021 integral to membrane; PDB: 1ZYO_A.
Probab=94.86 E-value=0.075 Score=46.20 Aligned_cols=133 Identities=17% Similarity=0.188 Sum_probs=47.7
Q ss_pred EEEEcccccCCCCeEEEEeCCCcEEE---EEEEEeCCCCCeEEEEecCC---CCCccceEecCCCCCCCCCeEEEEeeCC
Q 041421 163 HIVTNHHVICDASKVKVSFSDQSTFY---AKVVGHDQDKDLAVLHIDAP---NHELRPIHVGVSADLHVGQKICAIGHPL 236 (315)
Q Consensus 163 ~VlT~aHvv~~~~~~~V~~~~g~~~~---a~vv~~d~~~DiAll~v~~~---~~~~~~l~l~~~~~~~~G~~v~~iG~p~ 236 (315)
.++|++||.......... .+|+..+ -+.+..+...|++||+.... ...++.+.+.....+. -|-
T Consensus 43 ~L~ta~Hv~~~~~~~~~~-k~g~kipl~~f~~~~~~~~~D~~il~~P~n~~s~Lg~k~~~~~~~~~~~-------~g~-- 112 (203)
T PF02122_consen 43 ALLTARHVWSRPSKVTSL-KTGEKIPLAEFTDLLESRIADFVILRGPPNWESKLGVKAAQLSQNSQLA-------KGP-- 112 (203)
T ss_dssp EEEE-HHHHTSSS---EE-ETTEEEE--S-EEEEE-TTT-EEEEE--HHHHHHHT-----B----SEE-------EEE--
T ss_pred ceecccccCCCccceeEc-CCCCcccchhChhhhCCCccCEEEEecCcCHHHHhCcccccccchhhhC-------CCC--
Confidence 799999999886554333 3344443 24455678899999999732 1134444442222111 110
Q ss_pred CCCCceEEeEEeeecccccCCCCceeecEEEEccCCCCCCccchhccCCCeEEEEEeee-cCCCcceEEEEEcch
Q 041421 237 GLPFTCTTGVISALGREIPAGTGRLIRGVIQIDASINLGNSGGPLLDSSGSLIGVNTFI-TSGAFTGIGFATPID 310 (315)
Q Consensus 237 g~~~~~~~g~v~~~~~~~~~~~~~~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~-~~~~~~~~~~aiP~~ 310 (315)
-..+....+........+.... ......-+...+|.||.|+++.+ +++|++... ..+..++..+--|+.
T Consensus 113 ~~~y~~~~~~~~~~sa~i~g~~----~~~~~vls~T~~G~SGtp~y~g~-~vvGvH~G~~~~~~~~n~n~~spip 182 (203)
T PF02122_consen 113 VSFYGFSSGEWPCSSAKIPGTE----GKFASVLSNTSPGWSGTPYYSGK-NVVGVHTGSPSGSNRENNNRMSPIP 182 (203)
T ss_dssp SSTTSEEEEEEEEEE-S----S----TTEEEE-----TT-TT-EEE-SS--EEEEEEEE----------------
T ss_pred eeeeeecCCCceeccCcccccc----CcCCceEcCCCCCCCCCCeEECC-CceEeecCccccccccccccccccc
Confidence 0011112211111111111111 22345556677899999999877 899999985 222333455555544
No 58
>PF09342 DUF1986: Domain of unknown function (DUF1986); InterPro: IPR015420 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found in serine endopeptidases belonging to MEROPS peptidase family S1A (clan PA). It is found in unusual mosaic proteins, which are encoded by the Drosophila nudel gene (see P98159 from SWISSPROT). Nudel is involved in defining embryonic dorsoventral polarity. Three proteases; ndl, gd and snk process easter to create active easter. Active easter defines cell identities along the dorsal-ventral continuum by activating the spz ligand for the Tl receptor in the ventral region of the embryo. Nudel, pipe and windbeutel together trigger the protease cascade within the extraembryonic perivitelline compartment which induces dorsoventral polarity of the Drosophila embryo [].
Probab=94.77 E-value=0.3 Score=43.35 Aligned_cols=85 Identities=16% Similarity=0.293 Sum_probs=59.0
Q ss_pred eeEEEEEEeCCcEEEEcccccCCC----CeEEEEeCCCcEEE------EEEEEeC-----CCCCeEEEEecCCC---CCc
Q 041421 151 ASGAGFLWDQDGHIVTNHHVICDA----SKVKVSFSDQSTFY------AKVVGHD-----QDKDLAVLHIDAPN---HEL 212 (315)
Q Consensus 151 ~~GSGfiI~~~g~VlT~aHvv~~~----~~~~V~~~~g~~~~------a~vv~~d-----~~~DiAll~v~~~~---~~~ 212 (315)
-.+||++|+++ |+|++-.|+.+. ..+.+.++.++.+. -++...| +..+++||.++.+. ..+
T Consensus 28 ~~CsgvLlD~~-WlLvsssCl~~I~L~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~~~V~~S~v~LLHL~~~~~fTr~V 106 (267)
T PF09342_consen 28 YWCSGVLLDPH-WLLVSSSCLRGISLSHHYVSALLGGGKTYLSVDGPHEQISRVDCFKDVPESNVLLLHLEQPANFTRYV 106 (267)
T ss_pred EEEEEEEeccc-eEEEeccccCCcccccceEEEEecCcceecccCCChheEEEeeeeeeccccceeeeeecCcccceeee
Confidence 37999999986 999999999864 34677777766442 1233333 68899999998863 245
Q ss_pred cceEecC-CCCCCCCCeEEEEeeCC
Q 041421 213 RPIHVGV-SADLHVGQKICAIGHPL 236 (315)
Q Consensus 213 ~~l~l~~-~~~~~~G~~v~~iG~p~ 236 (315)
.|+-+.+ .......+.++++|.-.
T Consensus 107 lP~flp~~~~~~~~~~~CVAVg~d~ 131 (267)
T PF09342_consen 107 LPTFLPETSNENESDDECVAVGHDD 131 (267)
T ss_pred cccccccccCCCCCCCceEEEEccc
Confidence 6666653 23445566888998554
No 59
>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=94.77 E-value=0.031 Score=40.87 Aligned_cols=53 Identities=25% Similarity=0.412 Sum_probs=38.7
Q ss_pred CceeeeeccccCceEeeeeeccCC--CCeeEEEEEEECC--hHHHHHHHHHHhhccc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD--KDRALFTIVVSGT--DRELQQVVEQLQKLVN 53 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~--~~~~~~~~~~~~~--~~~~~~~~~ql~k~~~ 53 (315)
|.+|..+|+++|+||.||...+.. .....+-+-+++. ++.++++++.|++..+
T Consensus 15 L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~~~~~~~~~~~l~~l~~~~~ 71 (80)
T cd04905 15 LYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEGHIEDPNVAEALEELKRLTE 71 (80)
T ss_pred HHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEECCCCCHHHHHHHHHHHHhCC
Confidence 567889999999999999875443 3333444455564 7889999999998554
No 60
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=94.45 E-value=0.039 Score=39.06 Aligned_cols=49 Identities=22% Similarity=0.417 Sum_probs=36.1
Q ss_pred CceeeeeccccCceEeeeeeccC-CCCeeEEEEEEECChHHHHHHHHHHhhc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGL-DKDRALFTIVVSGTDRELQQVVEQLQKL 51 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ql~k~ 51 (315)
|.+++.+|+++|+||+++..... ..+...+.|.+.+++. +++++.|.+.
T Consensus 15 l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~--~~~~~~L~~~ 64 (72)
T cd04883 15 LADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNP--RPIIEDLRRA 64 (72)
T ss_pred HHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCH--HHHHHHHHHC
Confidence 45788899999999999986333 4677788888876443 3777777653
No 61
>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=94.35 E-value=0.065 Score=38.49 Aligned_cols=55 Identities=18% Similarity=0.302 Sum_probs=41.9
Q ss_pred CceeeeeccccCceEeeeeeccCC--CCeeEEEEEEEC--ChHHHHHHHHHHhhccceE
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD--KDRALFTIVVSG--TDRELQQVVEQLQKLVNVL 55 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~--~~~~~~~~~~~~--~~~~~~~~~~ql~k~~~v~ 55 (315)
|++|-..|+++|.||.+|.-.+.. +.-.++.|-+.+ ++..++++++.|++...-+
T Consensus 13 L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~~~~~~~ 71 (75)
T cd04880 13 LAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFEGHIDDPDVKEALEELKRVTEDV 71 (75)
T ss_pred HHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHHhCCee
Confidence 456778999999999999764443 444566677777 5888999999999865543
No 62
>cd04869 ACT_GcvR_2 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR in
Probab=94.28 E-value=0.025 Score=41.22 Aligned_cols=52 Identities=19% Similarity=0.278 Sum_probs=36.0
Q ss_pred CceeeeeccccCceEeeeeeccC-----CCCeeEEEEEEECCh-HHHHHHHHHHhhcc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGL-----DKDRALFTIVVSGTD-RELQQVVEQLQKLV 52 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~-----~~~~~~~~~~~~~~~-~~~~~~~~ql~k~~ 52 (315)
++||+.+|+++|.||.++...+. ..+.-.|++.+...+ ..+.++.+.|+++-
T Consensus 13 v~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~p~~~~~~~l~~~l~~l~ 70 (81)
T cd04869 13 VHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLALPAGTDLDALREELEELC 70 (81)
T ss_pred HHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEecCCCCCHHHHHHHHHHHH
Confidence 46899999999999999987322 224555666666443 35777777777654
No 63
>PF00947 Pico_P2A: Picornavirus core protein 2A; InterPro: IPR000081 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This domain defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies 3CA and 3CB. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [], the type example for clan PA. Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease []. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0016032 viral reproduction; PDB: 2HRV_B 1Z8R_A.
Probab=93.86 E-value=0.28 Score=39.00 Aligned_cols=34 Identities=24% Similarity=0.295 Sum_probs=26.7
Q ss_pred eeecEEEEccCCCCCCccchhccCCCeEEEEEeee
Q 041421 261 LIRGVIQIDASINLGNSGGPLLDSSGSLIGVNTFI 295 (315)
Q Consensus 261 ~~~~~i~~~~~i~~G~SGGPlvd~~G~vvGI~s~~ 295 (315)
..++++...++..||+-||+|+-..| |+||++++
T Consensus 76 ~Q~~~l~g~Gp~~PGdCGg~L~C~HG-ViGi~Tag 109 (127)
T PF00947_consen 76 YQYNLLIGEGPAEPGDCGGILRCKHG-VIGIVTAG 109 (127)
T ss_dssp EEECEEEEE-SSSTT-TCSEEEETTC-EEEEEEEE
T ss_pred eecCceeecccCCCCCCCceeEeCCC-eEEEEEeC
Confidence 34567777889999999999995555 99999998
No 64
>PF05416 Peptidase_C37: Southampton virus-type processing peptidase; InterPro: IPR001665 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C37, (clan PA(C)). The type example is calicivirin from Southampton virus, an endopeptidase that cleaves the polyprotein at sites N-terminal to itself, liberating the polyprotein helicase. Southampton virus is a positive-stranded ssRNA virus belonging to the Caliciviruses, which are viruses that cause gastroenteritis. The calicivirus genome contains two open reading frames, ORF1 and ORF2. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity []. The regions of the polyprotein in which these activities lie are similar to proteins produced by the picornaviruses []. ORF2 encodes a structural, capsid protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely the Norwalk-like viruses or small round structured viruses (SRSVs), and those classed as non-SRSVs.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 2FYQ_A 2FYR_A 1WQS_D 4ASH_A 2IPH_B.
Probab=93.43 E-value=0.23 Score=47.20 Aligned_cols=140 Identities=19% Similarity=0.283 Sum_probs=69.4
Q ss_pred cceeEEEEEEeCCcEEEEcccccCCC-CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecCCC-CCccceEecCCCCCCCC
Q 041421 149 LQASGAGFLWDQDGHIVTNHHVICDA-SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDAPN-HELRPIHVGVSADLHVG 226 (315)
Q Consensus 149 ~~~~GSGfiI~~~g~VlT~aHvv~~~-~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~~~-~~~~~l~l~~~~~~~~G 226 (315)
.-++|-||.++++ .++|+-||+... ..+ | | .+..-+.++..-+++-++++.+- .++.-+-|. .-.+.|
T Consensus 377 ~fGsGWGfWVS~~-lfITttHViP~g~~E~---F--G--v~i~~i~vh~sGeF~~~rFpk~iRPDvtgmiLE--eGapEG 446 (535)
T PF05416_consen 377 KFGSGWGFWVSPT-LFITTTHVIPPGAKEA---F--G--VPISQIQVHKSGEFCRFRFPKPIRPDVTGMILE--EGAPEG 446 (535)
T ss_dssp EETTEEEEESSSS-EEEEEGGGS-STTSEE---T--T--EECGGEEEEEETTEEEEEESS-SSTTS---EE---SS--TT
T ss_pred ecCCceeeeecce-EEEEeeeecCCcchhh---h--C--CChhHeEEeeccceEEEecCCCCCCCccceeec--cCCCCc
Confidence 4568999999986 999999999532 211 0 1 11122334445677778887642 235555552 233456
Q ss_pred CeEEEE-eeCCCC--CCceEEeEEeeecccccCCCCceeecEEEE-------ccCCCCCCccchhccCCCe---EEEEEe
Q 041421 227 QKICAI-GHPLGL--PFTCTTGVISALGREIPAGTGRLIRGVIQI-------DASINLGNSGGPLLDSSGS---LIGVNT 293 (315)
Q Consensus 227 ~~v~~i-G~p~g~--~~~~~~g~v~~~~~~~~~~~~~~~~~~i~~-------~~~i~~G~SGGPlvd~~G~---vvGI~s 293 (315)
.-+.++ =.+.|. +..+..|....+.-.-....++ ..++.+ |-...|||-|+|-+-..|+ |+|++.
T Consensus 447 tV~siLiKR~sGEllpLAvRMgt~AsmkIqgr~v~GQ--~GMLLTGaNAK~mDLGT~PGDCGcPYvyKrgNd~VV~GVH~ 524 (535)
T PF05416_consen 447 TVCSILIKRPSGELLPLAVRMGTHASMKIQGRTVHGQ--MGMLLTGANAKGMDLGTIPGDCGCPYVYKRGNDWVVIGVHA 524 (535)
T ss_dssp -EEEEEEE-TTSBEEEEEEEEEEEEEEEETTEEEEEE--EEEETTSTT-SSTTTS--TTGTT-EEEEEETTEEEEEEEEE
T ss_pred eEEEEEEEcCCccchhhhhhhccceeEEEcceeecce--eeeeeecCCccccccCCCCCCCCCceeeecCCcEEEEEEEe
Confidence 555443 344442 2234445444332110000011 223333 2345689999999987664 899999
Q ss_pred eecCCCc
Q 041421 294 FITSGAF 300 (315)
Q Consensus 294 ~~~~~~~ 300 (315)
+...+++
T Consensus 525 AAtr~GN 531 (535)
T PF05416_consen 525 AATRSGN 531 (535)
T ss_dssp EE-SSSS
T ss_pred hhccCCC
Confidence 9844444
No 65
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=93.22 E-value=0.093 Score=36.60 Aligned_cols=51 Identities=10% Similarity=0.176 Sum_probs=38.5
Q ss_pred CceeeeeccccCceEeeeeeccC----CCCeeEEEEEEEC-ChHHHHHHHHHHhhc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGL----DKDRALFTIVVSG-TDRELQQVVEQLQKL 51 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~----~~~~~~~~~~~~~-~~~~~~~~~~ql~k~ 51 (315)
|.+|+.+++..|.||.++..... ..+...+.+.+.. +.+.++++++.|.+.
T Consensus 12 L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~~~~~l~~l~~~l~~~ 67 (73)
T cd04886 12 LAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETRGAEHIEEIIAALREA 67 (73)
T ss_pred HHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeCCHHHHHHHHHHHHHc
Confidence 46788899999999999986332 2566777777764 447789999999874
No 66
>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=93.14 E-value=0.091 Score=33.76 Aligned_cols=47 Identities=30% Similarity=0.421 Sum_probs=34.8
Q ss_pred CceeeeeccccCceEeeeeeccC-CCCeeEEEEEEECChHHHHHHHHHH
Q 041421 1 MNQIAGVFARRKYNIESLAAIGL-DKDRALFTIVVSGTDRELQQVVEQL 48 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ql 48 (315)
|.+|.+.|+++++||.++..... .....++++.+...+ .+++++++|
T Consensus 12 l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l 59 (60)
T cd02116 12 LAKVLSVLAEAGINITSIEQRTSGDGGEADIFIVVDGDG-DLEKLLEAL 59 (60)
T ss_pred HHHHHHHHHHCCCcEEEEEeEEcCCCCeEEEEEEEechH-HHHHHHHHh
Confidence 35678899999999999987332 355677888887654 677777665
No 67
>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=93.03 E-value=0.051 Score=36.59 Aligned_cols=36 Identities=11% Similarity=0.320 Sum_probs=26.4
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEEC
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSG 36 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~ 36 (315)
|.|++.+|+++|+||+++.+...+.+...+.+.++.
T Consensus 12 l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~v~~ 47 (56)
T cd04889 12 LAEVTEILAEAGINIKAISIAETRGEFGILRLIFSD 47 (56)
T ss_pred HHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEEECC
Confidence 468899999999999999984443455555555553
No 68
>PF03510 Peptidase_C24: 2C endopeptidase (C24) cysteine protease family; InterPro: IPR000317 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. The two signatures that defines this group of calivirus polyproteins identify a cysteine peptidase signature that belongs to MEROPS peptidase family C24 (clan PA(C)). Caliciviruses are positive-stranded ssRNA viruses that cause gastroenteritis. The calicivirus genome contains two open reading frames, ORF1 and ORF2. ORF2 encodes a structural protein []; while ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity. The regions of the polyprotein in which these activities lie are similar to proteins produced by the picornaviruses. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely those classified as small round structured viruses (SRSVs) and those classed as non-SRSVs. Calicivirus proteases from the non-SRSV group, which are members of the PA protease clan, constitute family C24 of the cysteine proteases (proteases from SRSVs belong to the C37 family). As mentioned above, the protease activity resides within a polyprotein. The enzyme cleaves the polyprotein at sites N-terminal to itself, liberating the polyprotein helicase.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=92.72 E-value=1.1 Score=34.66 Aligned_cols=101 Identities=26% Similarity=0.387 Sum_probs=55.2
Q ss_pred EEEEeCCcEEEEcccccCCCCeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCeEEEEee
Q 041421 155 GFLWDQDGHIVTNHHVICDASKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQKICAIGH 234 (315)
Q Consensus 155 GfiI~~~g~VlT~aHvv~~~~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~v~~iG~ 234 (315)
++=|. +|.++|+.||.+.++.+ +|..+ +++. ..-|+|+++.+... .+.+++++ |.+++ |
T Consensus 3 avHIG-nG~~vt~tHva~~~~~v-----~g~~f--~~~~--~~ge~~~v~~~~~~--~p~~~ig~------g~Pv~---~ 61 (105)
T PF03510_consen 3 AVHIG-NGRYVTVTHVAKSSDSV-----DGQPF--KIVK--TDGELCWVQSPLVH--LPAAQIGT------GKPVY---D 61 (105)
T ss_pred eEEeC-CCEEEEEEEEeccCceE-----cCcCc--EEEE--eccCEEEEECCCCC--CCeeEecc------CCCEE---e
Confidence 55565 58999999999877655 22222 3333 34599999997533 55666643 44554 4
Q ss_pred CCCCCCceE--EeEEeeecccccCCCCceeecEEEEccCCCCCCccchhcc
Q 041421 235 PLGLPFTCT--TGVISALGREIPAGTGRLIRGVIQIDASINLGNSGGPLLD 283 (315)
Q Consensus 235 p~g~~~~~~--~g~v~~~~~~~~~~~~~~~~~~i~~~~~i~~G~SGGPlvd 283 (315)
+++...... .+.... ..+....-...+.....+||-|-|.||
T Consensus 62 ~~~~~~~t~~~~~~~~t-------~~~~v~G~~~~~~~~T~~GDCGlPY~d 105 (105)
T PF03510_consen 62 TWGLHPVTTWSEGTYNT-------PTGTVNGWHVKITNPTKKGDCGLPYFD 105 (105)
T ss_pred cCCCccEEEeccceEEc-------CCcEEEEEEEeCCCCccCCccCCcccC
Confidence 444332211 111111 111111112233347788999999886
No 69
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=92.08 E-value=0.18 Score=52.06 Aligned_cols=60 Identities=15% Similarity=0.220 Sum_probs=50.4
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEE-CChHHHHHHHHHHhhccceEEEeec
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS-GTDRELQQVVEQLQKLVNVLNVSTK 60 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v~~~ 60 (315)
|+.|+.+++.-+.||.+++....+.+...+.|.++ .+-+.+++|+++|.++-+|++|...
T Consensus 640 L~dI~~~i~~~~~nI~~v~~~~~~~~~~~~~~~ieV~~~~~L~~i~~~Lr~i~~V~~V~R~ 700 (702)
T PRK11092 640 LANLTAAINTTGSNIQSLNTEEKDGRVYSAFIRLTARDRVHLANIMRKIRVMPDVIKVTRN 700 (702)
T ss_pred HHHHHHHHHHCCCCeEEEEEEEcCCCEEEEEEEEEECCHHHHHHHHHHHhCCCCcceEEEc
Confidence 46788899999999999997444456777777776 6788999999999999999999874
No 70
>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=91.80 E-value=0.072 Score=38.40 Aligned_cols=51 Identities=16% Similarity=0.199 Sum_probs=36.6
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChH-HHHHHHHHHhhccc
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDR-ELQQVVEQLQKLVN 53 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ql~k~~~ 53 (315)
++|+.+|+.+|.||..++. ..-.+.-.|.+.+...+. .++++.+.|+++-+
T Consensus 14 ~~vt~~la~~~~nI~dl~~-~~~~~~f~~~~~v~~p~~~~~~~l~~~l~~l~~ 65 (75)
T cd04870 14 SALTEVLAAHGVRILDVGQ-AVIHGRLSLGILVQIPDSADSEALLKDLLFKAH 65 (75)
T ss_pred HHHHHHHHHCCCCEEeccc-EEEcCeeEEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence 5788999999999999974 222344556666665443 68888888887654
No 71
>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=91.72 E-value=0.22 Score=35.36 Aligned_cols=54 Identities=13% Similarity=0.097 Sum_probs=35.6
Q ss_pred CceeeeeccccCceEeeeeeccC--CCCeeEEEEEEE-CChHHHHHHHHHHhhccce
Q 041421 1 MNQIAGVFARRKYNIESLAAIGL--DKDRALFTIVVS-GTDRELQQVVEQLQKLVNV 54 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~--~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v 54 (315)
|.+++.++++.|.||.|+..... +.+...+.+.+. ..+..++.|++.|++...|
T Consensus 13 L~~l~~~i~~~g~nI~~i~~~~~~~~~~~~~~~v~v~~e~~~~~~~i~~~L~~~~~~ 69 (72)
T cd04884 13 LKPVVDTLREFNARIISILTAFEDAPDGMRRVFIRVTPMDRSKENELIEELKAKFTV 69 (72)
T ss_pred HHHHHHHHHHCCCeEEEEEeccccCCCCccEEEEEEEEecchHHHHHHHHHhCcccE
Confidence 45678899999999999986333 344444444333 2233488888888776444
No 72
>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=91.49 E-value=0.36 Score=34.68 Aligned_cols=57 Identities=14% Similarity=0.226 Sum_probs=42.2
Q ss_pred CceeeeeccccCceEeeeeeccCC--CCeeEEEEEEECChHHHHHHHHHHhhccceEEE
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD--KDRALFTIVVSGTDRELQQVVEQLQKLVNVLNV 57 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v 57 (315)
|.+|-..|+++|+|+..|--.+.. +.-..+-|-++|+++.+++++++|.+...-+++
T Consensus 14 L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~Ffvd~~~~~~~~~~~l~~L~~~~~~~~~ 72 (74)
T cd04904 14 LARALKLFEEFGVNLTHIESRPSRRNGSEYEFFVDCEVDRGDLDQLISSLRRVVADVNI 72 (74)
T ss_pred HHHHHHHHHHCCCcEEEEECCCCCCCCceEEEEEEEEcChHHHHHHHHHHHHhcCeEEE
Confidence 345667899999999999865543 444556667778888899999999986554443
No 73
>PF02395 Peptidase_S6: Immunoglobulin A1 protease Serine protease Prosite pattern; InterPro: IPR000710 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S6 (clan PA(S)). The type sample being the IgA1-specific serine endopeptidase from Neisseria gonorrhoeae []. These cleave prolyl bonds in the hinge regions of immunoglobulin A heavy chains. Similar specificity is shown by the unrelated family of M26 metalloendopeptidases.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 3SZE_A 3H09_B 3SYJ_A 1WXR_A 3AK5_B.
Probab=91.42 E-value=0.99 Score=46.99 Aligned_cols=61 Identities=25% Similarity=0.354 Sum_probs=35.0
Q ss_pred eEEEEEEeCCcEEEEcccccCCCCeEEEEeCC--CcEEEEEEEEeC--CCCCeEEEEecCCCCCccceEe
Q 041421 152 SGAGFLWDQDGHIVTNHHVICDASKVKVSFSD--QSTFYAKVVGHD--QDKDLAVLHIDAPNHELRPIHV 217 (315)
Q Consensus 152 ~GSGfiI~~~g~VlT~aHvv~~~~~~~V~~~~--g~~~~a~vv~~d--~~~DiAll~v~~~~~~~~~l~l 217 (315)
.|...+|++. ||+|.+|...+... |.|.. ...| +++..+ +..|+.+-|+..--.++.|+..
T Consensus 66 ~G~aTLigpq-YiVSV~HN~~gy~~--v~FG~~g~~~Y--~iV~RNn~~~~Df~~pRLnK~VTEvaP~~~ 130 (769)
T PF02395_consen 66 KGVATLIGPQ-YIVSVKHNGKGYNS--VSFGNEGQNTY--KIVDRNNYPSGDFHMPRLNKFVTEVAPAEM 130 (769)
T ss_dssp TSS-EEEETT-EEEBETTG-TSCCE--ECESCSSTCEE--EEEEEEBETTSTEBEEEESS---SS----B
T ss_pred CceEEEecCC-eEEEEEccCCCcCc--eeecccCCceE--EEEEccCCCCcccceeecCceEEEEecccc
Confidence 3779999986 99999999855544 44443 3445 344333 3469999999764334455554
No 74
>PRK00194 hypothetical protein; Validated
Probab=91.09 E-value=0.071 Score=39.79 Aligned_cols=57 Identities=18% Similarity=0.246 Sum_probs=38.3
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEECC--hHHHHHHHHHHhhccceEEEe
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGT--DRELQQVVEQLQKLVNVLNVS 58 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~ql~k~~~v~~v~ 58 (315)
+++|+++|+.+|.||..++... ..+.-.+.+++... +..++.+.+.|+++.+.+.+.
T Consensus 17 va~vt~~la~~g~nI~~~~~~~-~~~~~~~~~~v~~~~~~~~~~~l~~~l~~l~~~~~~~ 75 (90)
T PRK00194 17 IAGVSTVLAELNVNILDISQTI-MDGYFTMIMLVDISESKKDFAELKEELEELGKELGVK 75 (90)
T ss_pred HHHHHHHHHHcCCCEEehhhHh-hCCeeEEEEEEEecCCCCCHHHHHHHHHHHHHHcCCE
Confidence 4678999999999999998632 34444454455533 234677877777777665543
No 75
>PF02907 Peptidase_S29: Hepatitis C virus NS3 protease; InterPro: IPR004109 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature identifies the Hepatitis C virus NS3 protein as a serine protease which belongs to MEROPS peptidase family S29 (hepacivirin family, clan PA(S)), which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. The NS2 proteinase (IPR002518 from INTERPRO), a zinc-dependent enzyme, performs a single proteolytic cut to release the N terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4. It has been suggested that the NS3 serine protease of hepatitus C is involved in cell transformation and that the ability to transform requires an active enzyme [].; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0019087 transformation of host cell by virus; PDB: 2QV1_B 3LOX_C 2OBQ_C 2OC1_C 2OC0_A 3LON_A 3KNX_A 2O8M_A 2OBO_A 2OC8_A ....
Probab=91.09 E-value=0.25 Score=39.70 Aligned_cols=129 Identities=22% Similarity=0.216 Sum_probs=64.1
Q ss_pred EEEEEEeCCcEEEEcccccCCCCeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCeEEEE
Q 041421 153 GAGFLWDQDGHIVTNHHVICDASKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQKICAI 232 (315)
Q Consensus 153 GSGfiI~~~g~VlT~aHvv~~~~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~v~~i 232 (315)
--|+.|+ |..-|.+|--... ++--..| +..-.+.+...|+..-..+.....+.|-.-+. +.++++
T Consensus 14 fmgt~vn--GV~wT~~HGagsr---tlAgp~G---pv~q~~~s~~~Dlv~~p~P~Ga~SL~pCtCg~-------~dlylV 78 (148)
T PF02907_consen 14 FMGTCVN--GVMWTVYHGAGSR---TLAGPKG---PVNQMYTSVDDDLVGWPAPPGARSLTPCTCGS-------SDLYLV 78 (148)
T ss_dssp EEEEEET--TEEEEEHHHHTTS---EEEBTTS---EB-ESEEETTTTEEEEE-STTB--BBB-SSSS-------SEEEEE
T ss_pred eehhEEc--cEEEEEEecCCcc---cccCCCC---cceEeEEcCCCCCcccccccccccCCccccCC-------ccEEEE
Confidence 3577885 7888999975321 1111112 23445667788998887765333344333221 245555
Q ss_pred eeCCCCCCceEEeEEeeecccccCCCCceeecEEEE--ccCCCCCCccchhccCCCeEEEEEeee--cCCCcceEEEEEc
Q 041421 233 GHPLGLPFTCTTGVISALGREIPAGTGRLIRGVIQI--DASINLGNSGGPLLDSSGSLIGVNTFI--TSGAFTGIGFATP 308 (315)
Q Consensus 233 G~p~g~~~~~~~g~v~~~~~~~~~~~~~~~~~~i~~--~~~i~~G~SGGPlvd~~G~vvGI~s~~--~~~~~~~~~~aiP 308 (315)
=+-. .+-.+ ..+. +. +-.+.. ..+...|.||||++-.+|.+|||..+. ..+.-..+-|. |
T Consensus 79 tr~~----~v~p~----rr~g------d~-~~~L~sp~pis~lkGSSGgPiLC~~GH~vG~f~aa~~trgvak~i~f~-P 142 (148)
T PF02907_consen 79 TRDA----DVIPV----RRRG------DS-RASLLSPRPISDLKGSSGGPILCPSGHAVGMFRAAVCTRGVAKAIDFI-P 142 (148)
T ss_dssp -TTS-----EEEE----EEES------TT-EEEEEEEEEHHHHTT-TT-EEEETTSEEEEEEEEEEEETTEEEEEEEE-E
T ss_pred eccC----cEeee----EEcC------CC-ceEecCCceeEEEecCCCCcccCCCCCEEEEEEEEEEcCCceeeEEEE-e
Confidence 3111 11111 1110 00 000111 112246999999998899999998887 44444455664 7
Q ss_pred chhh
Q 041421 309 IDTA 312 (315)
Q Consensus 309 ~~~i 312 (315)
.+.+
T Consensus 143 ~e~l 146 (148)
T PF02907_consen 143 VETL 146 (148)
T ss_dssp HHHH
T ss_pred eeec
Confidence 6644
No 76
>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=90.72 E-value=0.077 Score=39.50 Aligned_cols=55 Identities=15% Similarity=0.190 Sum_probs=38.9
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEECCh--HHHHHHHHHHhhccceEE
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTD--RELQQVVEQLQKLVNVLN 56 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~ql~k~~~v~~ 56 (315)
+++|+++|+++|.||..+.... ..+.-.|.+++.... ..++++.+.|+++-+-..
T Consensus 15 va~vt~~la~~g~nI~~~~~~~-~~~~f~~~~~v~~~~~~~~~~~L~~~l~~l~~~~~ 71 (88)
T cd04872 15 VAGVSTKLAELNVNILDISQTI-MDGYFTMIMIVDISESNLDFAELQEELEELGKELG 71 (88)
T ss_pred HHHHHHHHHHcCCCEEechhHh-hCCccEEEEEEEeCCCCCCHHHHHHHHHHHHHHcC
Confidence 3678999999999999998633 344445555555443 458888888888775543
No 77
>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=90.63 E-value=0.19 Score=36.00 Aligned_cols=52 Identities=12% Similarity=0.125 Sum_probs=35.2
Q ss_pred CceeeeeccccCceEeeeeecc-CCCCeeEEEEEEECCh--HHHHHHHHHHhhcc
Q 041421 1 MNQIAGVFARRKYNIESLAAIG-LDKDRALFTIVVSGTD--RELQQVVEQLQKLV 52 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~-~~~~~~~~~~~~~~~~--~~~~~~~~ql~k~~ 52 (315)
+++|+..|+.+|+||..+.... .....-.|.+.+..+. ..++++.+.|+++-
T Consensus 13 v~~it~~l~~~g~nI~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~l~~~l~~l~ 67 (74)
T cd04875 13 VAAVSGFLAEHGGNIVESDQFVDPDSGRFFMRVEFELEGFDLSREALEAAFAPVA 67 (74)
T ss_pred HHHHHHHHHHcCCCEEeeeeeecCCCCeEEEEEEEEeCCCCCCHHHHHHHHHHHH
Confidence 3578999999999999998632 2344444545555443 35788888777754
No 78
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=90.03 E-value=0.24 Score=35.77 Aligned_cols=49 Identities=27% Similarity=0.373 Sum_probs=38.2
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhc
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKL 51 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~ 51 (315)
++|++.+++.|.||..+...... +.-.+++.++++++.++++.+.|+++
T Consensus 17 ~~v~~~l~~~g~ni~d~~~~~~~-~~f~~~~~v~~~~~~~~~l~~~L~~l 65 (76)
T PF13740_consen 17 AAVTGVLAEHGCNIEDSRQAVLG-GRFTLIMLVSIPEDSLERLESALEEL 65 (76)
T ss_dssp HHHHHHHHCTT-EEEEEEEEEET-TEEEEEEEEEESHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCcEEEEEEEEEc-CeEEEEEEEEeCcccHHHHHHHHHHH
Confidence 46788999999999999863333 44557788888888999999999987
No 79
>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=89.99 E-value=0.35 Score=34.51 Aligned_cols=50 Identities=26% Similarity=0.273 Sum_probs=33.4
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEE-C------ChHHHHHHHHHHhh
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS-G------TDRELQQVVEQLQK 50 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~-~------~~~~~~~~~~ql~k 50 (315)
|.+|+++|++.|+||.+-.+.+...+..--++.+. . +++..+++.+.|.+
T Consensus 15 l~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~~~~~~~~~~~~~~~~l~~~L~~ 71 (73)
T cd04900 15 FARIAGALDQLGLNILDARIFTTRDGYALDTFVVLDPDGEPIGERERLARIREALED 71 (73)
T ss_pred HHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEECCCCCCCChHHHHHHHHHHHHh
Confidence 46899999999999999887555434333333332 1 34566777777765
No 80
>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=89.98 E-value=0.39 Score=33.36 Aligned_cols=48 Identities=25% Similarity=0.321 Sum_probs=32.3
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEECCh------HHHHHHHHHHh
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTD------RELQQVVEQLQ 49 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~ql~ 49 (315)
|.+|+++|+..++||.++.+.+.+. ....++.+.+.+ +..+++.+-|.
T Consensus 14 l~~i~~~l~~~~~~I~~~~~~~~~~-~~~~~~~v~~~~~~~~~~~~~~~l~~~l~ 67 (70)
T cd04873 14 LADITRVLADLGLNIHDARISTTGE-RALDVFYVTDSDGRPLDPERIARLEEALE 67 (70)
T ss_pred HHHHHHHHHHCCCeEEEEEEeecCC-EEEEEEEEECCCCCcCCHHHHHHHHHHHH
Confidence 4578899999999999999744433 556666666444 45555555443
No 81
>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=89.97 E-value=0.2 Score=35.16 Aligned_cols=49 Identities=8% Similarity=0.241 Sum_probs=32.6
Q ss_pred CceeeeeccccCceEeeeeeccCC-CCeeEEEEEEECChHHHHHHHHHHhh
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD-KDRALFTIVVSGTDRELQQVVEQLQK 50 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ql~k 50 (315)
|.+++.+|++.|+||+++...... .....+.++++.+ +..+++.+-|++
T Consensus 15 L~~l~~~l~~~~i~i~~~~~~~~~~~~~~~~~i~v~~~-~~~~~~~~~L~~ 64 (69)
T cd04909 15 IAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQ-EDRERAKEILKE 64 (69)
T ss_pred HHHHHHHHHHcCCCceeeEeEEeecCCcEEEEEEECCH-HHHHHHHHHHHH
Confidence 457889999999999999863321 1234455666633 356677776665
No 82
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=89.17 E-value=0.42 Score=49.47 Aligned_cols=60 Identities=17% Similarity=0.261 Sum_probs=50.5
Q ss_pred CceeeeeccccCceEeeeeeccCC-CCeeEEEEEEE-CChHHHHHHHHHHhhccceEEEeec
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD-KDRALFTIVVS-GTDRELQQVVEQLQKLVNVLNVSTK 60 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v~~~ 60 (315)
|+.|+.+++.-+.||.++++.+.. .+...|+++++ .+-+.+++++++|.++-+|++|...
T Consensus 680 L~dIt~~is~~~~nI~~v~~~~~~~~~~~~~~~~ieV~~~~~L~~l~~~L~~i~~V~~v~R~ 741 (743)
T PRK10872 680 LRDITTILANEKVNVLGVASRSDTKQQLATIDMTIEIYNLQVLGRVLGKLNQVPDVIDARRL 741 (743)
T ss_pred HHHHHHHHHHCCCCeEEEEeEEcCCCCEEEEEEEEEECCHHHHHHHHHHHhcCCCcCeEEec
Confidence 456788899999999999974433 57788888777 6888999999999999999999874
No 83
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=89.07 E-value=0.16 Score=43.76 Aligned_cols=56 Identities=14% Similarity=0.249 Sum_probs=38.7
Q ss_pred ceeeeeccccCceEeeeeec--c---CCCCeeEEEEEEE-CChHHHHHHHHHHhhccceEEE
Q 041421 2 NQIAGVFARRKYNIESLAAI--G---LDKDRALFTIVVS-GTDRELQQVVEQLQKLVNVLNV 57 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~--~---~~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v 57 (315)
.+||.+|+.||+||++|+.. + ..+..-+|.+.+. ..+..++++...|+++-+=+.|
T Consensus 110 ~~vT~~la~~~iNI~~L~T~~~~a~~~~~~lf~~~~~v~lP~~~~~~~L~~~l~~l~~eL~v 171 (190)
T PRK11589 110 ERFTALFDSHHMNIAELVSRTQPAEGERPAQLHIQITAHSPASQDAANIEQAFKALCTELNA 171 (190)
T ss_pred HHHHHHHHHcCCChhheEEeeecCCCCCcccEEEEEEEEcCCCCCHHHHHHHHHHHHHHhCc
Confidence 47899999999999999863 2 2345666777666 3444577777777776554433
No 84
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=89.06 E-value=0.65 Score=37.21 Aligned_cols=60 Identities=20% Similarity=0.335 Sum_probs=44.8
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEE--CChHHHHHHHHHHhhccceEEEeecc
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS--GTDRELQQVVEQLQKLVNVLNVSTKQ 61 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~ql~k~~~v~~v~~~~ 61 (315)
+++-...+|++.||-+|+=.-.-++...+||.+. +-+..++.|+..|.|+..|.+|+-..
T Consensus 87 S~vLd~iA~~~~nvLTI~Q~ipl~g~Anvtlsi~~ssm~~~V~~ii~kl~k~e~V~kVeivg 148 (150)
T COG4492 87 SDVLDVIAREEINVLTIHQTIPLQGRANVTLSIDTSSMEKDVDKIIEKLRKVEGVEKVEIVG 148 (150)
T ss_pred HHHHHHHHHhCCcEEEEecccccCceeeEEEEEEchhhhhhHHHHHHHHhcccceeEEEEee
Confidence 3444567899999999984222355566666555 66888999999999999999998653
No 85
>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=87.55 E-value=0.51 Score=33.89 Aligned_cols=51 Identities=20% Similarity=0.290 Sum_probs=36.1
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEE----C----ChHHHHHHHHHHhhcc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS----G----TDRELQQVVEQLQKLV 52 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~----~----~~~~~~~~~~ql~k~~ 52 (315)
|++|++.|++.|.||.+-.+.+. .+..-.++.|. + +++..++|.+.|.+.+
T Consensus 14 l~~i~~~l~~~~lnI~~A~i~t~-~~~~~d~f~V~d~~~~~~~~~~~~~~~i~~~L~~~l 72 (74)
T cd04925 14 LSEVFAVLADLHCNVVEARAWTH-NGRLACVIYVRDEETGAPIDDPIRLASIEDRLDNVL 72 (74)
T ss_pred HHHHHHHHHHCCCcEEEEEEEEE-CCEEEEEEEEEcCcCCCCCCCHHHHHHHHHHHHHHh
Confidence 46799999999999999887544 44444444443 1 3466788888887743
No 86
>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=87.33 E-value=0.37 Score=33.00 Aligned_cols=46 Identities=22% Similarity=0.354 Sum_probs=31.5
Q ss_pred CceeeeeccccCceEeeeeeccCC-CCeeEEEEEEECChHHHHHHHHHHhh
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD-KDRALFTIVVSGTDRELQQVVEQLQK 50 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ql~k 50 (315)
|.+++++|++.|+||.++...... .+..++.+.++. .+++.+-|++
T Consensus 13 L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve~----~~~~~~~L~~ 59 (65)
T cd04882 13 LHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTED----IEKAIEVLQE 59 (65)
T ss_pred HHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeCC----HHHHHHHHHH
Confidence 457889999999999999863333 466777777764 4444444443
No 87
>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=87.08 E-value=0.86 Score=31.77 Aligned_cols=50 Identities=20% Similarity=0.210 Sum_probs=34.0
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEEC------ChHHHHHHHHHHhhc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSG------TDRELQQVVEQLQKL 51 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~ql~k~ 51 (315)
|++|+++|+..++||.++.+.+.. +..-.++.+.. +++..++|.+.|.+.
T Consensus 14 l~~i~~~l~~~~~~I~~~~~~~~~-~~~~~~f~i~~~~~~~~~~~~~~~i~~~l~~~ 69 (70)
T cd04899 14 LADVTRVLAELGLNIHSAKIATLG-ERAEDVFYVTDADGQPLDPERQEALRAALGEA 69 (70)
T ss_pred HHHHHHHHHHCCCeEEEEEEEecC-CEEEEEEEEECCCCCcCCHHHHHHHHHHHHhh
Confidence 467889999999999999984433 35555555542 345666677776653
No 88
>cd04935 ACT_AKiii-DAPDC_1 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. This CD includes the first of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=86.65 E-value=0.87 Score=32.87 Aligned_cols=48 Identities=10% Similarity=0.267 Sum_probs=37.2
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECCh-----HHHHHHHHHHhhccce
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTD-----RELQQVVEQLQKLVNV 54 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~ql~k~~~v 54 (315)
.||.+.|+|.+.|++-++- .+ ..+++++..++ +.++++++.|+++-+|
T Consensus 19 ~~IF~~La~~~I~vDmI~~-s~----~~isftv~~~~~~~~~~~~~~l~~el~~~~~v 71 (75)
T cd04935 19 ADVFAPFKKHGVSVDLVST-SE----TNVTVSLDPDPNGLDPDVLDALLDDLNQICRV 71 (75)
T ss_pred HHHHHHHHHcCCcEEEEEe-CC----CEEEEEEeCcccccchHHHHHHHHHHHhceEE
Confidence 4667789999999999974 11 67888888554 3899999999995544
No 89
>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=85.72 E-value=0.9 Score=32.36 Aligned_cols=34 Identities=15% Similarity=0.211 Sum_probs=25.1
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEE
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS 35 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~ 35 (315)
|.+|+++|++.++||.|..+.+. .+....++.+.
T Consensus 15 l~~i~~~l~~~~lnI~sa~i~t~-~~~~~d~f~v~ 48 (72)
T cd04926 15 LSDVTRVFRENGLTVTRAEISTQ-GDMAVNVFYVT 48 (72)
T ss_pred HHHHHHHHHHCCcEEEEEEEecC-CCeEEEEEEEE
Confidence 46789999999999999987444 34555566554
No 90
>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=84.71 E-value=0.55 Score=34.01 Aligned_cols=50 Identities=16% Similarity=0.149 Sum_probs=31.4
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhcc
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKLV 52 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~ 52 (315)
++|+++++.+|.||..+..-. ..+.--|.+.++.+....+++.+.|+++.
T Consensus 16 a~vs~~la~~g~nI~d~~q~~-~~~~F~m~~~~~~~~~~~~~l~~~l~~~~ 65 (77)
T cd04893 16 NELTRAVSESGCNILDSRMAI-LGTEFALTMLVEGSWDAIAKLEAALPGLA 65 (77)
T ss_pred HHHHHHHHHcCCCEEEceeeE-EcCEEEEEEEEEeccccHHHHHHHHHHHH
Confidence 578999999999999998633 33333344444434344566665555543
No 91
>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=83.91 E-value=1.8 Score=34.17 Aligned_cols=57 Identities=14% Similarity=0.184 Sum_probs=41.5
Q ss_pred CceeeeeccccCceEeeeeeccCC--CCeeEEEEEEECChHHHHHHHHHHhhccceEEE
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD--KDRALFTIVVSGTDRELQQVVEQLQKLVNVLNV 57 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v 57 (315)
|.+|-..|+.+|+|+.+|--.+.. ..-..+-|-++|+.+.+++++++|.+...-++|
T Consensus 55 L~~iL~~Fa~~gINLt~IESRP~~~~~~eY~FfIdieg~~~~~~~aL~~L~~~~~~~kv 113 (115)
T cd04930 55 LSRILKVFETFEAKIHHLESRPSRKEGGDLEVLVRCEVHRSDLLQLISSLRQVAEDVRL 113 (115)
T ss_pred HHHHHHHHHHCCCCEEEEECCcCCCCCceEEEEEEEEeCHHHHHHHHHHHHHhcCeeEe
Confidence 345667899999999999865543 334455566778888899999999886664443
No 92
>cd04934 ACT_AK-Hom3_1 CT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydro
Probab=83.49 E-value=1.1 Score=32.14 Aligned_cols=48 Identities=17% Similarity=0.324 Sum_probs=36.4
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECCh--H-HHHHHHHHHhhccce
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTD--R-ELQQVVEQLQKLVNV 54 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~--~-~~~~~~~ql~k~~~v 54 (315)
.+|-.+|+|.|.|++-++. ++ ..+++++..++ + .++.|++.|+|+-+|
T Consensus 19 ~~If~~la~~~I~vd~I~~-s~----~~isftv~~~~~~~~~l~~l~~el~~~~~v 69 (73)
T cd04934 19 ARIFAILDKYRLSVDLIST-SE----VHVSMALHMENAEDTNLDAAVKDLQKLGTV 69 (73)
T ss_pred HHHHHHHHHcCCcEEEEEe-CC----CEEEEEEehhhcChHHHHHHHHHHHHheEE
Confidence 4667789999999999974 11 66888888543 3 888999999995444
No 93
>cd04871 ACT_PSP_2 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_2 CD includes the second of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains
Probab=82.69 E-value=0.25 Score=36.60 Aligned_cols=53 Identities=23% Similarity=0.396 Sum_probs=38.4
Q ss_pred CceeeeeccccCceEeeeeec-cC-------CCCeeEEEEEEECChHHHHHHHHHHhhccc
Q 041421 1 MNQIAGVFARRKYNIESLAAI-GL-------DKDRALFTIVVSGTDRELQQVVEQLQKLVN 53 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~-~~-------~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~ 53 (315)
++||+.+++.+|.||+.|+-- +. .+...-|.+.+.+.+..++.+.++|.++-.
T Consensus 14 ia~Vs~~lA~~~~NI~~I~~l~~~~~~~~~~~~~~~~~e~~v~~~~~~~~~lr~~L~~la~ 74 (84)
T cd04871 14 LAAVTRVVADQGLNIDRIRRLSGRVPLEEQDDSPKACVEFSVRGQPADLEALRAALLELAS 74 (84)
T ss_pred HHHHHHHHHHcCCCHHHHHHhhccccccccCCCCcEEEEEEEeCCCCCHHHHHHHHHHHhc
Confidence 468899999999999999752 11 123445777777777778888888876644
No 94
>cd04912 ACT_AKiii-LysC-EC-like_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC) and plants, (Zea mays Ask1, Ask2, and Arabidopsis thaliana AK1). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Like the A. thaliana AK1 (AK1-AT), the E. coli AKIII (LysC) has two bound feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The lysine-sensitive plant isoenzyme is synergistically inhibited by S-adenosylmethionine. A homolog of this group appears to be the Saccharomyces cerevisiae AK (Hom3) which clusters with this group as well. Members of this CD
Probab=82.45 E-value=1.9 Score=30.88 Aligned_cols=44 Identities=14% Similarity=0.320 Sum_probs=34.9
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECCh-----HHHHHHHHHHhh
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTD-----RELQQVVEQLQK 50 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~ql~k 50 (315)
.||...|++.++|++.++. . ..++++++..++ +.+..+.+.|+|
T Consensus 19 ~~if~~L~~~~I~v~~i~~--s---~~~is~~v~~~~~~~~~~~~~~~~~~l~~ 67 (75)
T cd04912 19 AKVFEIFAKHGLSVDLIST--S---EVSVSLTLDPTKNLSDQLLLDALVKDLSQ 67 (75)
T ss_pred HHHHHHHHHcCCeEEEEEc--C---CcEEEEEEEchhhccchHHHHHHHHHHHh
Confidence 4566778999999999973 1 167888888554 589999999999
No 95
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=82.32 E-value=0.93 Score=37.58 Aligned_cols=56 Identities=20% Similarity=0.279 Sum_probs=44.2
Q ss_pred ceeeeeccccCceEeeeeec-cCCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEee
Q 041421 2 NQIAGVFARRKYNIESLAAI-GLDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
+-|+++.+.||++|.-+-+. ++-.+-+++||+++ ......++.||.|+--|.+|+-
T Consensus 110 A~V~~~iak~gi~Irqi~~~dpe~~~e~~l~IVte--~~iP~~li~el~~i~gVk~i~I 166 (167)
T COG2150 110 AGVASLIAKRGISIRQIISEDPELQEEPKLTIVTE--RPIPGDLIDELKKIDGVKKISI 166 (167)
T ss_pred HHHHHHHHHcCceEEEEecCCcccCCCceEEEEEe--ccCCHHHHHHHhcccCceeEEe
Confidence 45788999999999999863 33477899999976 3455678899999999988763
No 96
>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=81.86 E-value=1.7 Score=32.71 Aligned_cols=52 Identities=15% Similarity=0.310 Sum_probs=37.0
Q ss_pred CceeeeeccccCceEeeeeeccCC--CCeeEEEEEEECC-hHHHHHHHHHHhhcc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD--KDRALFTIVVSGT-DRELQQVVEQLQKLV 52 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~--~~~~~~~~~~~~~-~~~~~~~~~ql~k~~ 52 (315)
|.++-..|+++|+||.+|.-.+.. ..-..+-|-++|. ++.++++++.|.+-+
T Consensus 28 L~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~FfVDieg~~~~~~~~~l~~L~~~~ 82 (90)
T cd04931 28 LAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFINLDKKSAPALDPIIKSLRNDI 82 (90)
T ss_pred HHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEEcCCCHHHHHHHHHHHHHh
Confidence 345667899999999999875543 3334555666675 778888888888733
No 97
>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=81.79 E-value=1.8 Score=31.28 Aligned_cols=51 Identities=14% Similarity=0.255 Sum_probs=33.1
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEE-C-----ChHHHHHHHHHHhhc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS-G-----TDRELQQVVEQLQKL 51 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~-~-----~~~~~~~~~~ql~k~ 51 (315)
|++|++.|++.|+||.+-.+.+...+..-=++.|. . +++..+++.+.|.+.
T Consensus 14 fa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d~~~~~~~~~~~~~l~~~L~~~ 70 (76)
T cd04927 14 LHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITDARELLHTKKRREETYDYLRAV 70 (76)
T ss_pred HHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeCCCCCCCCHHHHHHHHHHHHHH
Confidence 46889999999999999888654444333333333 2 224566677776653
No 98
>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=80.36 E-value=2.5 Score=30.47 Aligned_cols=50 Identities=12% Similarity=0.193 Sum_probs=37.6
Q ss_pred CceeeeeccccCceEeeeeeccCC--CCeeEEEEEEECChHHHHHHHHHHhh
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD--KDRALFTIVVSGTDRELQQVVEQLQK 50 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ql~k 50 (315)
|.++-..|.++|+|+..|.-.+.. +.-..+-|-++|+.+.++++++.|.+
T Consensus 14 L~~iL~~f~~~~inl~~IeSRP~~~~~~~y~F~id~e~~~~~i~~~l~~l~~ 65 (74)
T cd04929 14 LAKALKLFQELGINVVHIESRKSKRRSSEFEIFVDCECDQRRLDELVQLLKR 65 (74)
T ss_pred HHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEEcCHHHHHHHHHHHHH
Confidence 345667899999999999875543 44455667777888888888888876
No 99
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=80.26 E-value=2.4 Score=43.50 Aligned_cols=59 Identities=19% Similarity=0.303 Sum_probs=47.6
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEE-CChHHHHHHHHHHhhccceEEEee
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS-GTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
|+-|+.++++-+.||.+++....+.++.-|.|.+. .+-..+.+|+.||..+-+|++|..
T Consensus 641 L~~i~~~i~~~~~ni~~v~~~~~~~~~~~~~~~i~v~n~~~L~~i~~~l~~~~~V~~v~R 700 (701)
T COG0317 641 LRDVSQVLANEKINVLGVNTRSDKDQFATMQFTIEVKNLNHLGRVLARLKQLPDVISVRR 700 (701)
T ss_pred HHHHHHHHHhCCCceEEeeccccCCceEEEEEEEEECcHHHHHHHHHHHhcCCCeEEEEe
Confidence 34567788999999999997444667766666555 588889999999999999999875
No 100
>cd04932 ACT_AKiii-LysC-EC_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The E. coli AKIII (LysC) binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=76.84 E-value=2.6 Score=30.35 Aligned_cols=48 Identities=13% Similarity=0.390 Sum_probs=34.5
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChH----HHH-HHHHHHhhccce
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDR----ELQ-QVVEQLQKLVNV 54 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~----~~~-~~~~ql~k~~~v 54 (315)
.+|..+|++.++||+-|+- .+ ..+++++..++. .+. .|.+.|+|+-+|
T Consensus 19 ~~IF~~La~~~I~VDmI~~--s~---~~iSftv~~~d~~~~~~~~~~l~~~l~~~~~v 71 (75)
T cd04932 19 AKVFGILAKHNISVDLITT--SE---ISVALTLDNTGSTSDQLLTQALLKELSQICDV 71 (75)
T ss_pred HHHHHHHHHcCCcEEEEee--cC---CEEEEEEeccccchhHHHHHHHHHHHHhccEE
Confidence 4566789999999999974 11 568888886653 354 688888885544
No 101
>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=76.51 E-value=2.6 Score=29.88 Aligned_cols=35 Identities=26% Similarity=0.321 Sum_probs=27.1
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEE
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS 35 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~ 35 (315)
+++++|.|++.|+||.+-.+-+...+..--++.|.
T Consensus 15 Fa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~ 49 (68)
T cd04928 15 LSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVT 49 (68)
T ss_pred HHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEe
Confidence 36889999999999999888666667665555554
No 102
>cd04913 ACT_AKii-LysC-BS-like_1 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins. This CD includes the N-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive aspartokinase isoenzymes. The B. subtilis 168 AKII is induced by methionine and repressed and inhibited by lysine. Although Corynebacterium glutamicum is known to contain a single aspartokinase, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In corynebacteria and other various Gram-positive bacteria, the DAP-lysine pathway is fee
Probab=76.00 E-value=2.3 Score=29.49 Aligned_cols=47 Identities=17% Similarity=0.285 Sum_probs=28.0
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhh
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQK 50 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k 50 (315)
.|+...+++.|.||+.++-.....+..++++++. ++..++.++.|++
T Consensus 17 ~~i~~~L~~~~I~i~~i~~~~~~~~~~~is~~v~--~~d~~~~~~~l~~ 63 (75)
T cd04913 17 AKIFGALAEANINVDMIVQNVSRDGTTDISFTVP--KSDLKKALAVLEK 63 (75)
T ss_pred HHHHHHHHHcCCeEEEEEeCCCCCCcEEEEEEec--HHHHHHHHHHHHH
Confidence 4567788999999998874322232345666665 3334444444444
No 103
>PF01732 DUF31: Putative peptidase (DUF31); InterPro: IPR022382 This domain has no known function. It is found in various hypothetical proteins and putative lipoproteins from mycoplasmas.
Probab=75.88 E-value=1.6 Score=41.53 Aligned_cols=24 Identities=25% Similarity=0.426 Sum_probs=21.3
Q ss_pred CCCCCCccchhccCCCeEEEEEee
Q 041421 271 SINLGNSGGPLLDSSGSLIGVNTF 294 (315)
Q Consensus 271 ~i~~G~SGGPlvd~~G~vvGI~s~ 294 (315)
.+..|.||+.++|.+|++|||.++
T Consensus 351 ~l~gGaSGS~V~n~~~~lvGIy~g 374 (374)
T PF01732_consen 351 SLGGGASGSMVINQNNELVGIYFG 374 (374)
T ss_pred CCCCCCCcCeEECCCCCEEEEeCC
Confidence 566899999999999999999763
No 104
>PF04455 Saccharop_dh_N: LOR/SDH bifunctional enzyme conserved region ; InterPro: IPR007545 Lysine-oxoglutarate reductase/Saccharopine dehydrogenase (LOR/SDH) is a bifunctional enzyme. This conserved region is commonly found immediately N-terminal to saccharopine dehydrogenase conserved region (IPR005097 from INTERPRO) in eukaryotes [, ].; PDB: 3C2Q_B 3MGJ_A.
Probab=75.71 E-value=9.3 Score=29.46 Aligned_cols=43 Identities=19% Similarity=0.322 Sum_probs=31.8
Q ss_pred CceEeeeeeccCCCCeeEEEEEEE-CChHHHHHHHHHHhhccce
Q 041421 12 KYNIESLAAIGLDKDRALFTIVVS-GTDRELQQVVEQLQKLVNV 54 (315)
Q Consensus 12 ~~ni~s~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v 54 (315)
.|.|..+.++....+.|.-.+.|. .|++.+++|+.+|..|-.+
T Consensus 31 ~F~i~~~~vG~~~~d~S~a~l~V~a~d~~~L~~Il~~L~~lga~ 74 (103)
T PF04455_consen 31 DFEILEFDVGKSKDDTSYARLQVSAPDEEHLDEILDELHQLGAV 74 (103)
T ss_dssp EEEEEEEE--SSTTS-EEEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred CEEEEEEEeCCCCCCceeEEEEEecCCHHHHHHHHHHHHHHcCC
Confidence 478899998777777777666666 4677899999999998766
No 105
>cd04890 ACT_AK-like_1 ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes the first of two ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids, lysine, threonine, methionine, and isoleucine. This CD, includes the first ACT domain of the Escherichia coli (EC) isoenzyme, AKIII (LysC) and the Arabidopsis isoenzyme, asparate kinase 1, both enzymes monofunctional and involved in lysine synthesis, as well as the the first ACT domain of Bacillus subtilis (BS) isoenzyme, AKIII (YclM), and of the Saccharomyces cerevisiae AK (Hom3). Also included are the first ACT domains of the Methylomicrobium alcaliphilum AK, the first enzyme of the ectoine biosynthetic pathway. Members of this CD bel
Probab=74.25 E-value=2.4 Score=28.81 Aligned_cols=42 Identities=10% Similarity=0.320 Sum_probs=31.2
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECCh--HHHHHHHHHH
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTD--RELQQVVEQL 48 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~ql 48 (315)
.+|-.+|.+.+.|++-++- .+ -.+++++..++ +.++.+++.|
T Consensus 18 ~~if~~l~~~~i~v~~i~t--~~---~~is~~v~~~~~~~~~~~l~~~l 61 (62)
T cd04890 18 RKIFEILEKHGISVDLIPT--SE---NSVTLYLDDSLLPKKLKRLLAEL 61 (62)
T ss_pred HHHHHHHHHcCCeEEEEec--CC---CEEEEEEehhhhhHHHHHHHHhh
Confidence 3566788999999999973 11 56888888666 6777777765
No 106
>PF04350 PilO: Pilus assembly protein, PilO; PDB: 2RJZ_B.
Probab=71.55 E-value=4.5 Score=32.59 Aligned_cols=61 Identities=15% Similarity=0.194 Sum_probs=44.8
Q ss_pred eeeeeccccCceEeeeeeccC--CCCeeE--EEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 3 QIAGVFARRKYNIESLAAIGL--DKDRAL--FTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 3 ri~~~f~rr~~ni~s~~~~~~--~~~~~~--~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
.|..+-.+.|..+.+++...+ .+.+.+ ++|.+.|+=..+-+.+++|+++..++.|.+++=.
T Consensus 58 ~l~~~A~~~gv~l~~~~p~~~~~~~~~~~~pv~i~l~G~Y~~l~~Fl~~l~~l~riv~i~~~~l~ 122 (144)
T PF04350_consen 58 DLNRLAKKSGVKLTSFEPGEEEKKEFYIEIPVTISLEGSYHQLLNFLNDLENLPRIVNIENLSLS 122 (144)
T ss_dssp HHHHHHHHTT-EEEEEEE---EE-SSEEEEEEEEEEEEEHHHHHHHHHHHHTSSS-EEEEEEEEE
T ss_pred HHHHHHHHCCCeEEEeecCcccccCceEEEEEEEEEEeeHHHHHHHHHHHHcCCCeEEEeeeEEE
Confidence 344555678999999997432 355655 7778889999999999999999999999887644
No 107
>PF10741 T2SM_b: Type II secretion system (T2SS), protein M subtype b; InterPro: IPR007690 General secretion pathway (GSP) protein M is a membrane protein involved in the export of proteins in bacteria. It consists of a short cytosolic N-terminal domain, a transmembrane domain, and a C-terminal periplasmic domain. The precise function of this protein is unknown, though in Vibrio cholerae, the EpsM protein interacts with the EpsL protein, and also forms homodimers [],; GO: 0006858 extracellular transport
Probab=70.88 E-value=10 Score=29.25 Aligned_cols=63 Identities=14% Similarity=0.101 Sum_probs=50.1
Q ss_pred ceeeeeccccCceEeeeeecc--CCCCeeE--EEEEEECChHHHHHHHHHHhhccceEEEeeccCCC
Q 041421 2 NQIAGVFARRKYNIESLAAIG--LDKDRAL--FTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSSS 64 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~--~~~~~~~--~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~~ 64 (315)
+|+..+..+.|-+|.|..+.+ .+..+.+ +.+.+.|+-+.+.+++..||..-..+-|++++-..
T Consensus 20 ~~l~~~v~~aG~~v~s~q~~p~~~~~~~~~i~v~~~~~g~~~~L~~~L~~LE~~~P~l~Vd~L~i~~ 86 (110)
T PF10741_consen 20 QRLRALVAAAGGQVSSSQVLPPRPDGNFRRISVRVSLEGDIEALQAFLYALESGRPFLFVDDLSIQP 86 (110)
T ss_pred HHHHHHHHHcCCEEEEEEecCCCCCCcceEEEEEEEEEeCHHHHHHHHHHHhcCCCeEEEeEEEEEe
Confidence 356667788899999999843 3345654 66677799999999999999999999998877663
No 108
>COG2716 GcvR Glycine cleavage system regulatory protein [Amino acid transport and metabolism]
Probab=70.81 E-value=0.78 Score=38.49 Aligned_cols=57 Identities=18% Similarity=0.261 Sum_probs=37.3
Q ss_pred CceeeeeccccCceEeeeeeccC-----CCCeeEEEEEEE-CChHHHHHHHHHHhhccceEEE
Q 041421 1 MNQIAGVFARRKYNIESLAAIGL-----DKDRALFTIVVS-GTDRELQQVVEQLQKLVNVLNV 57 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~-----~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v 57 (315)
+++++.+|.++|+||++|++.+. ....-.+.|.+. .-.-.+.++..+++.|-|=+.|
T Consensus 106 v~~~T~lf~~~~inie~L~~~~~~a~~s~~~lfha~it~~lPa~~~i~~l~~~f~al~~~L~v 168 (176)
T COG2716 106 VEEFTALFDGHGINIENLVSRTYPAPGSSAPLFHAQITARLPANLSISALRDAFEALCDELNV 168 (176)
T ss_pred HHHHHHHHHhcCCchhhceeeeeecCCCCccceehhhhccCCCcCcHHHHHHHHHHHHHhhcc
Confidence 36789999999999999997332 222223333333 3345577888888877665444
No 109
>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=69.12 E-value=7.9 Score=26.96 Aligned_cols=48 Identities=15% Similarity=0.203 Sum_probs=34.7
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEE-CChHHHHHHHHHHhh
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS-GTDRELQQVVEQLQK 50 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ql~k 50 (315)
.++..+++. +-||-.+.-.-...+..++.+.++ .+.+.++++.++|++
T Consensus 13 ~~~~~~i~~-~~nI~~~~~~~~~~~~~~v~v~ie~~~~~~~~~i~~~L~~ 61 (68)
T cd04885 13 KKFLELLGP-PRNITEFHYRNQGGDEARVLVGIQVPDREDLAELKERLEA 61 (68)
T ss_pred HHHHHHhCC-CCcEEEEEEEcCCCCceEEEEEEEeCCHHHHHHHHHHHHH
Confidence 455667788 999999975322355667777777 456789999999976
No 110
>PRK11899 prephenate dehydratase; Provisional
Probab=66.18 E-value=7.1 Score=35.76 Aligned_cols=56 Identities=20% Similarity=0.293 Sum_probs=40.9
Q ss_pred ceeeeeccccCceEeeeeeccCC--CCeeEEEEEEEC--ChHHHHHHHHHHhhccceEEE
Q 041421 2 NQIAGVFARRKYNIESLAAIGLD--KDRALFTIVVSG--TDRELQQVVEQLQKLVNVLNV 57 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~--~~~~~~~~~~~~--~~~~~~~~~~ql~k~~~v~~v 57 (315)
.++-+.|++||+|+.+|--.+.. +.-..+-|-++| +++.+++.+++|+++-.-++|
T Consensus 209 ~~vL~~Fa~~gINLtkIeSRP~~~~~~~Y~F~id~eg~~~d~~v~~aL~~l~~~~~~~kv 268 (279)
T PRK11899 209 YKALGGFATNGVNMTKLESYMVGGSFTATQFYADIEGHPEDRNVALALEELRFFSEEVRI 268 (279)
T ss_pred HHHHHHHHHcCCCeeeEEeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHHhcCcEEE
Confidence 45567899999999999875543 455566677776 467788999999886654444
No 111
>PRK13581 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=66.15 E-value=3.6 Score=41.21 Aligned_cols=57 Identities=21% Similarity=0.300 Sum_probs=41.9
Q ss_pred ceeeeeccccCceEeeeeeccCC-CCeeEEEEEEECChHHHHHHHHHHhhccceEEEeec
Q 041421 2 NQIAGVFARRKYNIESLAAIGLD-KDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTK 60 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~ 60 (315)
.+|+.+|.+.++||.++.+.... .+..-| +++-|+..-+.++++|.++.+|.+|..+
T Consensus 467 ~~v~~~L~~~~iNIa~m~~~r~~~g~~al~--~i~~D~~v~~~~l~~i~~~~~i~~~~~i 524 (526)
T PRK13581 467 GKVGTLLGEAGINIAGMQLGRREAGGEALM--VLSVDDPVPEEVLEELRALPGILSAKAV 524 (526)
T ss_pred HHHHHHHhhcCCCchhcEeccCCCCCeEEE--EEECCCCCCHHHHHHHhcCCCcceEEEE
Confidence 46788899999999999984433 333334 4445556668888889999999888765
No 112
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=64.41 E-value=5 Score=36.89 Aligned_cols=52 Identities=10% Similarity=0.149 Sum_probs=34.8
Q ss_pred ceeeeeccccCceEeeeeecc-CCCCeeEEEEEEE-CChHHHHHHHHHHhhccc
Q 041421 2 NQIAGVFARRKYNIESLAAIG-LDKDRALFTIVVS-GTDRELQQVVEQLQKLVN 53 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~-~~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~ 53 (315)
++||++|+.+|.||+.++..+ ...+.-.|.+.+. .....++++...|+++-+
T Consensus 22 a~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~~p~~~~~~~L~~~L~~l~~ 75 (286)
T PRK13011 22 AAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFHSEEGLDEDALRAGFAPIAA 75 (286)
T ss_pred HHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEecCCCCCHHHHHHHHHHHHH
Confidence 578999999999999999732 3355555666654 223346666666666544
No 113
>cd04933 ACT_AK1-AT_1 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the first of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine. This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. Like the Escherichia coli AKIII (LysC), Arabidopsis AK1 binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. A loop in common is involved in the binding of both Lys and S-adenosylmethionine providing an explanation for the synergistic inhibition by these effectors. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=62.75 E-value=7.2 Score=28.40 Aligned_cols=44 Identities=20% Similarity=0.409 Sum_probs=30.9
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChH--------HHHHHHHHHhh
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDR--------ELQQVVEQLQK 50 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~ql~k 50 (315)
.+|...|++.|+|++-|+- .+ ..+++++..++. .++++.+.|+|
T Consensus 19 a~IF~~La~~~InVDmI~q--s~---~sISftV~~sd~~~~~~~~~~l~~~~~~~~~ 70 (78)
T cd04933 19 AKVFSIFETLGISVDVVAT--SE---VSISLTLDPSKLWSRELIQQELDHVVEELEK 70 (78)
T ss_pred HHHHHHHHHcCCcEEEEEe--cC---CEEEEEEEhhhhhhhhhHHHHHHHHHHHHHH
Confidence 4566789999999999974 11 668888885553 45566666665
No 114
>PRK15385 magnesium transport protein MgtC; Provisional
Probab=61.38 E-value=27 Score=30.92 Aligned_cols=53 Identities=6% Similarity=0.112 Sum_probs=39.0
Q ss_pred eccccCceEeeeeeccC-CCCeeEEEE--EEEC-ChHHHHHHHHHHhhccceEEEee
Q 041421 7 VFARRKYNIESLAAIGL-DKDRALFTI--VVSG-TDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 7 ~f~rr~~ni~s~~~~~~-~~~~~~~~~--~~~~-~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
.+...+|.+.++.+... +++...|+. ...+ ++..+++++.+|.....|.+|.=
T Consensus 164 ~l~~~~~~~~~l~~~~~~~~~~~ei~a~l~~~~~~~~~le~iv~~L~~~pgV~~v~W 220 (225)
T PRK15385 164 IVKEAAICLQGLGSVPAQEQGYKEIRAELVGHADYRKTRELIISRIGDNDNITAIHW 220 (225)
T ss_pred HHHhCCCceEEeEeeecCCCCeEEEEEEEEecCCchhhHHHHHHHHhCCCCeEEEEE
Confidence 45677999999997433 344444444 4443 58889999999999999999864
No 115
>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=61.20 E-value=10 Score=27.16 Aligned_cols=49 Identities=12% Similarity=0.031 Sum_probs=33.2
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeE-EEEEEE-C----ChHHHHHHHHHHh
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRAL-FTIVVS-G----TDRELQQVVEQLQ 49 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~-~~~~~~-~----~~~~~~~~~~ql~ 49 (315)
|.+|+..|++-|.+|.+-.+.+..+.+-- +-+.-. | |++.++.|.++|.
T Consensus 15 L~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d~~g~kl~d~~~~~~l~~~L~ 69 (72)
T cd04895 15 LLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTDQLGNKLTDDSLIAYIEKSLG 69 (72)
T ss_pred HHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEECCCCCCCCCHHHHHHHHHHhc
Confidence 56899999999999999998665544433 333222 2 3566777777764
No 116
>cd04891 ACT_AK-LysC-DapG-like_1 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII and related proteins. This CD includes the N-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, as well as, the first and third, of four, ACT domains present in cyanobacteria AK. Also included are the N-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase isoenzyme AKI found in Bacilli (Bacillus subtilis strain 168), Clostridia, and Actinobacteria bacterial species. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=60.58 E-value=8.7 Score=25.14 Aligned_cols=45 Identities=13% Similarity=0.195 Sum_probs=28.0
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHH
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQL 48 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql 48 (315)
.|+...|.+.+.||+.++.....++...+++++. ++..++.++.|
T Consensus 16 ~~i~~~L~~~~i~i~~i~~~~~~~~~~~is~~v~--~~~~~~~~~~l 60 (61)
T cd04891 16 AKIFSALAEAGINVDMIVQSVSRGGTTDISFTVP--KSDLEKALAIL 60 (61)
T ss_pred HHHHHHHHHcCCcEEEEEEcCCCCCcEEEEEEEe--HHHHHHHHHHh
Confidence 4667788999999999986333333345666665 34444444433
No 117
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=58.29 E-value=17 Score=26.02 Aligned_cols=27 Identities=26% Similarity=0.452 Sum_probs=23.9
Q ss_pred EEECChHHHHHHHHHHhhccceEEEee
Q 041421 33 VVSGTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 33 ~~~~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
++--|++.+++++++|+||-.|.+|+.
T Consensus 34 vlYvn~~~~e~~~~kl~~l~fVk~Ve~ 60 (71)
T PF09902_consen 34 VLYVNEEDVEEIIEKLKKLKFVKKVEP 60 (71)
T ss_pred EEEECHHHHHHHHHHHhcCCCeeEEec
Confidence 344799999999999999999999975
No 118
>cd04911 ACT_AKiii-YclM-BS_1 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Bacillus subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from Bacillus subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=56.94 E-value=9 Score=27.80 Aligned_cols=46 Identities=9% Similarity=0.276 Sum_probs=34.2
Q ss_pred eeeeccccCceEeeeeeccCCCCeeEEEEEEECC---hHHHHHHHHHHhhccce
Q 041421 4 IAGVFARRKYNIESLAAIGLDKDRALFTIVVSGT---DRELQQVVEQLQKLVNV 54 (315)
Q Consensus 4 i~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ql~k~~~v 54 (315)
+-.+|.+.|.++|-+.- ++..|+|++..+ ++.+++|++.|.+..+.
T Consensus 21 ~L~I~E~~~is~Eh~PS-----GID~~Siii~~~~~~~~~~~~i~~~i~~~~~p 69 (76)
T cd04911 21 LLSILEDNGISYEHMPS-----GIDDISIIIRDNQLTDEKEQKILAEIKEELHP 69 (76)
T ss_pred HHHHHHHcCCCEeeecC-----CCccEEEEEEccccchhhHHHHHHHHHHhcCC
Confidence 34567777888887763 555699999977 66888999999886544
No 119
>PRK14428 acylphosphatase; Provisional
Probab=53.78 E-value=28 Score=26.46 Aligned_cols=35 Identities=23% Similarity=0.168 Sum_probs=27.4
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
++.|.++|+++.++++++.|.+-..--+|+.++.+
T Consensus 47 sVei~~qG~~~~i~~fi~~l~~gP~~a~V~~v~~~ 81 (97)
T PRK14428 47 SVELEAQGSSDAVQALVEQLAIGPRWSEVSHVAVH 81 (97)
T ss_pred EEEEEEEcCHHHHHHHHHHHhhCCCccEEEEEEEE
Confidence 58999999999999999999876555555554444
No 120
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=52.73 E-value=60 Score=22.49 Aligned_cols=34 Identities=18% Similarity=0.230 Sum_probs=28.4
Q ss_pred CCeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecC
Q 041421 174 ASKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDA 207 (315)
Q Consensus 174 ~~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~ 207 (315)
...+.+.+..|..++++++++|....+.+|+.+.
T Consensus 6 Gs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 6 GSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred ccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 3456677778899999999999999999998654
No 121
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=51.32 E-value=18 Score=28.65 Aligned_cols=53 Identities=21% Similarity=0.190 Sum_probs=34.8
Q ss_pred eeeeccccCceEeeeee-ccCCCCeeEEEEEEECChHHHHHHHHHHh---hccceEEEee
Q 041421 4 IAGVFARRKYNIESLAA-IGLDKDRALFTIVVSGTDRELQQVVEQLQ---KLVNVLNVST 59 (315)
Q Consensus 4 i~~~f~rr~~ni~s~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ql~---k~~~v~~v~~ 59 (315)
++..+...|+||..++. .+.+.++-||. | .+.+...+..+.-. |+-||+.|+-
T Consensus 20 ~~~~L~eagINiRA~tiAdt~dFGIiRmv--V-~~~d~A~~~Lee~gF~Vr~~dVlaVEm 76 (142)
T COG4747 20 VANKLKEAGINIRAFTIADTGDFGIIRMV--V-DRPDEAHSVLEEAGFTVRETDVLAVEM 76 (142)
T ss_pred HHHHHHHcCCceEEEEeccccCcceEEEE--c-CChHHHHHHHHHCCcEEEeeeEEEEEe
Confidence 34556788999999998 45678888884 3 35566666655432 4455655543
No 122
>PRK11898 prephenate dehydratase; Provisional
Probab=50.79 E-value=16 Score=33.44 Aligned_cols=54 Identities=20% Similarity=0.248 Sum_probs=37.4
Q ss_pred ceeeeeccccCceEeeeeeccCC--CCeeEEEEEEECC--hHHHHHHHHHHhhccceE
Q 041421 2 NQIAGVFARRKYNIESLAAIGLD--KDRALFTIVVSGT--DRELQQVVEQLQKLVNVL 55 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~--~~~~~~~~~~~~~--~~~~~~~~~ql~k~~~v~ 55 (315)
.++-..|+++|+|+-+|--.+.. +.-..+-|-++|+ ++.++++++.|++...-+
T Consensus 212 ~~~L~~F~~~~INLt~IeSRP~~~~~~~y~F~vd~eg~~~~~~~~~al~~L~~~~~~~ 269 (283)
T PRK11898 212 YKALSEFAWRGINLTRIESRPTKTGLGTYFFFIDVEGHIDDVLVAEALKELEALGEDV 269 (283)
T ss_pred HHHHHHHHHCCCCeeeEecccCCCCCccEEEEEEEEccCCCHHHHHHHHHHHHhcCcE
Confidence 45567899999999999875542 3334544555554 447999999999865533
No 123
>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=50.42 E-value=20 Score=25.90 Aligned_cols=52 Identities=17% Similarity=0.205 Sum_probs=35.9
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeE-EEEEEE-C----ChHHHHHHHHHHhhcc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRAL-FTIVVS-G----TDRELQQVVEQLQKLV 52 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~-~~~~~~-~----~~~~~~~~~~ql~k~~ 52 (315)
|.+|+..|++-||+|.+-.+.+..+...- +-|.-. | +++..+.|.+.|.+.+
T Consensus 15 L~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d~~g~kl~~~~~~~~l~~~L~~al 72 (75)
T cd04897 15 LFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRHKDGRTLSTEGERQRVIKCLEAAI 72 (75)
T ss_pred HHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEcCCCCccCCHHHHHHHHHHHHHHH
Confidence 56788999999999999998665444332 333221 3 5667788888887654
No 124
>TIGR01270 Trp_5_monoox tryptophan 5-monooxygenase, tetrameric. This model describes tryptophan 5-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tyrosine 3-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria.
Probab=49.78 E-value=16 Score=35.83 Aligned_cols=58 Identities=21% Similarity=0.238 Sum_probs=44.3
Q ss_pred CceeeeeccccCceEeeeeeccCCCC--e-eEEEEEEECChHHHHHHHHHHhhccceEEEe
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKD--R-ALFTIVVSGTDRELQQVVEQLQKLVNVLNVS 58 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~--~-~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~ 58 (315)
|.++-.+|.++|+|+..|--.+.... - ..+-|-++++...+.++++.|.+..+.++|.
T Consensus 45 L~~vL~vFa~~gINLThIESRPsk~~~~e~Y~FfVD~Eg~~~~l~~aL~~Lk~~~~~~~~~ 105 (464)
T TIGR01270 45 LSKAIAIFQDRHINILHLESRDSKDGTSKTMDVLVDVELFHYGLQEAMDLLKSGLDVHEVS 105 (464)
T ss_pred HHHHHHHHHHCCCCEEEEECCcCCCCCCccEEEEEEEEcCHHHHHHHHHHHHHhcccceec
Confidence 44566789999999999986554322 2 3455667788889999999999988876665
No 125
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=48.96 E-value=26 Score=25.46 Aligned_cols=32 Identities=16% Similarity=0.314 Sum_probs=27.6
Q ss_pred eEEEEEEE-CChHHHHHHHHHHhhccceEEEee
Q 041421 28 ALFTIVVS-GTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 28 ~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
.||.++++ .+.+.+.+.+++|+.|..|+.+.-
T Consensus 39 GKiVVtiE~~~~~~~~~~~~~i~~l~GVlsa~l 71 (79)
T PF03927_consen 39 GKIVVTIEAESSEEEVDLIDAINALPGVLSASL 71 (79)
T ss_dssp TEEEEEEEESSHHHHHHHHHHHCCSTTEEEEEE
T ss_pred CeEEEEEEeCChHHHHHHHHHHHcCCCceEEEE
Confidence 78999999 456789999999999999999864
No 126
>PRK14449 acylphosphatase; Provisional
Probab=48.90 E-value=37 Score=25.30 Aligned_cols=33 Identities=9% Similarity=0.279 Sum_probs=26.7
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeecc
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQ 61 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~ 61 (315)
++.|.++|+++.++++++.|.+=..--+|++++
T Consensus 42 ~Vei~~~G~~~~v~~f~~~l~~~~~~a~V~~i~ 74 (90)
T PRK14449 42 SVEVVAEGDEENIKELINFIKTGLRWARVDNVE 74 (90)
T ss_pred eEEEEEEeCHHHHHHHHHHHhhCCCceEEEEEE
Confidence 689999999999999999999755555555544
No 127
>PRK14435 acylphosphatase; Provisional
Probab=48.82 E-value=24 Score=26.35 Aligned_cols=36 Identities=14% Similarity=0.161 Sum_probs=28.1
Q ss_pred eEEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 28 ALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 28 ~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
-++.|.+.|+++.++++++.|.+-..--+|+.++.+
T Consensus 40 G~Vei~~~G~~~~i~~f~~~l~~gp~~a~V~~v~~~ 75 (90)
T PRK14435 40 GSVFIHAEGDENALRRFLNEVAKGPPAAVVTNVSVE 75 (90)
T ss_pred CCEEEEEEECHHHHHHHHHHHhhCCCCcEEEEEEEE
Confidence 358899999999999999999886555555555444
No 128
>TIGR00655 PurU formyltetrahydrofolate deformylase. This model describes formyltetrahydrofolate deformylases. The enzyme is a homohexamer. Sequences from a related enzyme formyl tetrahydrofolate-specific enzyme, phosphoribosylglycinamide formyltransferase, serve as an outgroup for phylogenetic analysis. Putative members of this family, scoring below the trusted cutoff, include a sequence from Rhodobacter capsulatus that lacks an otherwise conserved C-terminal region.
Probab=48.82 E-value=15 Score=33.62 Aligned_cols=49 Identities=14% Similarity=0.126 Sum_probs=30.2
Q ss_pred ceeeeeccccCceEeeeeec-cCCCCeeEEEEEEECCh--HHHHHHHHHHhh
Q 041421 2 NQIAGVFARRKYNIESLAAI-GLDKDRALFTIVVSGTD--RELQQVVEQLQK 50 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~-~~~~~~~~~~~~~~~~~--~~~~~~~~ql~k 50 (315)
++||++++++|.||..++-- ..+.+.--|.+.++.++ ...+++...|+.
T Consensus 15 A~Vt~~La~~g~NI~d~sq~~~~~~~~F~mr~~v~~~~~~~~~~~l~~~l~~ 66 (280)
T TIGR00655 15 AAISTFIAKHGANIISNDQHTDPETGRFFMRVEFQLEGFRLEESSLLAAFKS 66 (280)
T ss_pred HHHHHHHHHCCCCEEeeeEEEcCCCCeEEEEEEEEeCCCCCCHHHHHHHHHH
Confidence 57899999999999999852 22334444555555332 234555544444
No 129
>PF12381 Peptidase_C3G: Tungro spherical virus-type peptidase; InterPro: IPR024387 This entry represents a rice tungro spherical waikavirus-type peptidase that belongs to MEROPS peptidase family C3G. It is a picornain 3C-type protease, and is responsible for the self-cleavage of the positive single-stranded polyproteins of a number of plant viral genomes. The location of the protease activity of the polyprotein is at the C-terminal end, adjacent and N-terminal to the putative RNA polymerase [, ].
Probab=48.58 E-value=13 Score=32.60 Aligned_cols=48 Identities=19% Similarity=0.421 Sum_probs=34.8
Q ss_pred eecEEEEccCCCCCCccchhccC----CCeEEEEEeeecCCCcceEEEEEcchh
Q 041421 262 IRGVIQIDASINLGNSGGPLLDS----SGSLIGVNTFITSGAFTGIGFATPIDT 311 (315)
Q Consensus 262 ~~~~i~~~~~i~~G~SGGPlvd~----~G~vvGI~s~~~~~~~~~~~~aiP~~~ 311 (315)
.+.-++...+..+|+-|||++=. ..+++||+.++.. +.+.|||-++.+
T Consensus 167 ir~gleY~~~t~~GdCGs~i~~~~t~~~RKIvGiHVAG~~--~~~~gYAe~itQ 218 (231)
T PF12381_consen 167 IRQGLEYQMPTMNGDCGSPIVRNNTQMVRKIVGIHVAGSA--NHAMGYAESITQ 218 (231)
T ss_pred eeeeeeEECCCcCCCccceeeEcchhhhhhhheeeecccc--cccceehhhhhH
Confidence 34556667788899999999832 3589999998832 245789877653
No 130
>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=48.41 E-value=13 Score=25.17 Aligned_cols=43 Identities=12% Similarity=0.219 Sum_probs=28.3
Q ss_pred eeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhh
Q 041421 3 QIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQK 50 (315)
Q Consensus 3 ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k 50 (315)
|+...+.+.+.|++.++-...+ .++.+++..+ ..++.++.|.|
T Consensus 20 ~if~~L~~~~I~v~~i~q~~s~---~~isf~v~~~--~~~~a~~~lh~ 62 (66)
T cd04919 20 RMFTTLADHRINIEMISQGASE---INISCVIDEK--DAVKALNIIHT 62 (66)
T ss_pred HHHHHHHHCCCCEEEEEecCcc---ceEEEEEeHH--HHHHHHHHHHH
Confidence 5566789999999999753322 6677777743 34555666655
No 131
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=48.29 E-value=57 Score=21.92 Aligned_cols=32 Identities=19% Similarity=0.330 Sum_probs=27.8
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEec
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHID 206 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~ 206 (315)
..+.|.+.+|+.+.+.+..+|...++.|-...
T Consensus 7 ~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~ 38 (63)
T cd00600 7 KTVRVELKDGRVLEGVLVAFDKYMNLVLDDVE 38 (63)
T ss_pred CEEEEEECCCcEEEEEEEEECCCCCEEECCEE
Confidence 46788999999999999999999888877664
No 132
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=48.18 E-value=24 Score=25.18 Aligned_cols=45 Identities=18% Similarity=0.288 Sum_probs=35.7
Q ss_pred eeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhcc
Q 041421 3 QIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKLV 52 (315)
Q Consensus 3 ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~ 52 (315)
+|..+++|.+.+|-+-.. +---+|+.+.++.+.++++.+.|+|..
T Consensus 20 ~i~~~l~~~~v~ii~K~~-----nANtit~yl~~~~k~~~r~~~~Le~~~ 64 (71)
T cd04910 20 EILELLQRFKVSIIAKDT-----NANTITHYLAGSLKTIKRLTEDLENRF 64 (71)
T ss_pred HHHHHHHHcCCeEEEEec-----CCCeEEEEEEcCHHHHHHHHHHHHHhC
Confidence 456678888888888743 334588889999999999999998854
No 133
>TIGR01327 PGDH D-3-phosphoglycerate dehydrogenase. This model represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli.
Probab=47.87 E-value=11 Score=37.59 Aligned_cols=57 Identities=16% Similarity=0.230 Sum_probs=40.5
Q ss_pred ceeeeeccccCceEeeeeeccCC-CCeeEEEEEEECChHHHHHHHHHHhhccceEEEeec
Q 041421 2 NQIAGVFARRKYNIESLAAIGLD-KDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTK 60 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~ 60 (315)
.+|+.++.+.++||-++.+.... .+..-|.|. -|+..-+.++++|.++.+|.+|..+
T Consensus 466 ~~v~~~L~~~~iNIa~m~~~R~~~g~~al~~i~--~D~~v~~~~l~~i~~~~~i~~v~~i 523 (525)
T TIGR01327 466 GKVGTLLGTAGINIASMQLGRKEKGGEALMLLS--LDQPVPDEVLEEIKAIPDILSVFVV 523 (525)
T ss_pred hHHHhHHhhcCCChHHcEeecCCCCCeEEEEEE--cCCCCCHHHHHHHhcCCCccEEEEE
Confidence 46788899999999999984433 333344444 4555567788888888888887764
No 134
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=47.52 E-value=15 Score=23.92 Aligned_cols=21 Identities=33% Similarity=0.547 Sum_probs=17.9
Q ss_pred CCccchhccCCCeEEEEEeee
Q 041421 275 GNSGGPLLDSSGSLIGVNTFI 295 (315)
Q Consensus 275 G~SGGPlvd~~G~vvGI~s~~ 295 (315)
+.+.-|++|.+|+++|+++..
T Consensus 29 ~~~~~~V~d~~~~~~G~is~~ 49 (57)
T PF00571_consen 29 GISRLPVVDEDGKLVGIISRS 49 (57)
T ss_dssp TSSEEEEESTTSBEEEEEEHH
T ss_pred CCcEEEEEecCCEEEEEEEHH
Confidence 567789999999999999864
No 135
>PRK14423 acylphosphatase; Provisional
Probab=47.47 E-value=39 Score=25.28 Aligned_cols=35 Identities=14% Similarity=0.098 Sum_probs=27.7
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
++.|.++|+++.++++++.|++-..-.+|++++.+
T Consensus 44 ~Vei~~~G~~~~i~~f~~~l~~gp~~a~V~~v~~~ 78 (92)
T PRK14423 44 RVEAVFEGPRDAVEAMVEWCHEGSPAAVVEDVEVE 78 (92)
T ss_pred eEEEEEEECHHHHHHHHHHHHhCCCceEEEEEEEE
Confidence 57889999999999999999886666666665543
No 136
>PRK14444 acylphosphatase; Provisional
Probab=46.96 E-value=39 Score=25.33 Aligned_cols=34 Identities=12% Similarity=0.070 Sum_probs=26.7
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQS 62 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~ 62 (315)
++.|.++|+++.++++++.|.+...--+|+.++.
T Consensus 43 ~Vei~~qG~~~~i~~f~~~l~~gp~~a~V~~i~~ 76 (92)
T PRK14444 43 RVEAVFEGSRPAVQKMISWCYSGPSHARVERVEV 76 (92)
T ss_pred cEEEEEEcCHHHHHHHHHHHHhCCCCcEEEEEEE
Confidence 4789999999999999999997765555555433
No 137
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=46.90 E-value=46 Score=24.74 Aligned_cols=37 Identities=8% Similarity=0.296 Sum_probs=30.5
Q ss_pred ccCCCCeEEEEeCCCcEEEEEEEEeCCCCCeEEEEec
Q 041421 170 VICDASKVKVSFSDQSTFYAKVVGHDQDKDLAVLHID 206 (315)
Q Consensus 170 vv~~~~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~ 206 (315)
++.....+.|.+.+++.+.+.+.++|....+.|=.+.
T Consensus 10 ~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~ 46 (87)
T cd01720 10 AVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVK 46 (87)
T ss_pred HHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceE
Confidence 3444568899999999999999999999998876653
No 138
>PRK14429 acylphosphatase; Provisional
Probab=46.69 E-value=43 Score=24.90 Aligned_cols=35 Identities=14% Similarity=0.157 Sum_probs=26.9
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
++.|.++|+++.++++++.|.+=..--+|++++.+
T Consensus 41 ~Vei~~qG~~~~i~~f~~~l~~gp~~a~V~~i~~~ 75 (90)
T PRK14429 41 SVEILAQGSDPAVDNLIAWCEVGVPCTEVLRVTVE 75 (90)
T ss_pred eEEEEEEeCHHHHHHHHHHHhhCCCceEEEEEEEE
Confidence 57899999999999999999875545555554443
No 139
>PRK14421 acylphosphatase; Provisional
Probab=46.08 E-value=35 Score=26.07 Aligned_cols=35 Identities=6% Similarity=0.169 Sum_probs=27.3
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
++.|.++|+++.++++++.|.+-..--+|+.++.+
T Consensus 43 ~Vei~~~G~~~~i~~f~~~l~~gP~~a~V~~v~~~ 77 (99)
T PRK14421 43 SVEALFAGPADAVAEMIARCRRGPSAARVDAVEDE 77 (99)
T ss_pred EEEEEEeCCHHHHHHHHHHHHhCCCCcEEEEEEEE
Confidence 78899999999999999999876555555554444
No 140
>PRK14451 acylphosphatase; Provisional
Probab=46.00 E-value=38 Score=25.22 Aligned_cols=35 Identities=17% Similarity=0.134 Sum_probs=28.1
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
++.|.++|+++.++++++.|.+-..--+|++++.+
T Consensus 42 ~Vei~~qG~~~~i~~f~~~l~~gp~~a~V~~v~~~ 76 (89)
T PRK14451 42 RVEVFACGKEDKLEEFYTWLQKGPLNARVDVCTRE 76 (89)
T ss_pred CEEEEEEECHHHHHHHHHHHhhCCCceEEEEEEEE
Confidence 58899999999999999999987665666655443
No 141
>cd04936 ACT_AKii-LysC-BS-like_2 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains. This CD includes the C-terminal of the two ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis strain 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive AK isoenzymes. The B. subtilis strain 168 AKII is induced by methionine and repressed and inhibited by lysine. Although C. glutamicum is known to contain a single AK, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In corynebacteria and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regu
Probab=45.96 E-value=19 Score=23.90 Aligned_cols=42 Identities=14% Similarity=0.298 Sum_probs=27.5
Q ss_pred eeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhc
Q 041421 3 QIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKL 51 (315)
Q Consensus 3 ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~ 51 (315)
|+.+.+++.+.|++.++. . + ..+++++.. +..+++.+-|+|.
T Consensus 19 ~i~~~L~~~~i~v~~i~~-s-~---~~is~~v~~--~d~~~~~~~l~~~ 60 (63)
T cd04936 19 KMFEALAEAGINIEMIST-S-E---IKISCLIDE--DDAEKAVRALHEA 60 (63)
T ss_pred HHHHHHHHCCCcEEEEEc-c-C---ceEEEEEeH--HHHHHHHHHHHHH
Confidence 455667899999999984 1 1 557777763 4445555555553
No 142
>PRK14425 acylphosphatase; Provisional
Probab=45.45 E-value=46 Score=25.06 Aligned_cols=35 Identities=17% Similarity=0.299 Sum_probs=28.1
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
++.|.++|+++.++++++.|.+-..--+|+.++.+
T Consensus 45 sVei~~qG~~~~le~f~~~l~~gp~~a~V~~i~~~ 79 (94)
T PRK14425 45 SVTALIAGPDSAISAMIERFRRGPPGASVSGVETE 79 (94)
T ss_pred eEEEEEEeCHHHHHHHHHHHhhCCCceEEEEEEEE
Confidence 68999999999999999999987665566555444
No 143
>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=44.66 E-value=18 Score=23.76 Aligned_cols=44 Identities=18% Similarity=0.263 Sum_probs=27.4
Q ss_pred eeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhc
Q 041421 3 QIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKL 51 (315)
Q Consensus 3 ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~ 51 (315)
++...|++.+.|++.++-.. .. ..+++++. ++..++..+.|+|.
T Consensus 19 ~i~~~l~~~~i~v~~i~~~~--~~-~~i~~~v~--~~~~~~~~~~l~~~ 62 (65)
T cd04892 19 RIFSALAEAGINIIMISQGS--SE-VNISFVVD--EDDADKAVKALHEE 62 (65)
T ss_pred HHHHHHHHCCCcEEEEEcCC--Cc-eeEEEEEe--HHHHHHHHHHHHHH
Confidence 34556789999999997422 12 44555554 45566667777664
No 144
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=44.11 E-value=58 Score=24.51 Aligned_cols=36 Identities=25% Similarity=0.424 Sum_probs=28.7
Q ss_pred CCCCeeEEEEEEECC-hHHHHHHHHHHhhccceEEEee
Q 041421 23 LDKDRALFTIVVSGT-DRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 23 ~~~~~~~~~~~~~~~-~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
+++. -++.+|++++ .+.+-+=++++++|..|+.|.-
T Consensus 38 ~d~~-GKlVVVie~~~~~~l~~tie~i~nl~gVlav~l 74 (94)
T COG3062 38 EDAE-GKLVVVIEAEDSETLLETIESIRNLPGVLAVSL 74 (94)
T ss_pred cCCC-ceEEEEEEcCchHHHHHHHHHHhcCCceeEEEE
Confidence 3444 7899999955 6668888899999999999864
No 145
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=43.81 E-value=12 Score=34.47 Aligned_cols=52 Identities=12% Similarity=0.134 Sum_probs=32.5
Q ss_pred ceeeeeccccCceEeeeeeccC-CCCeeEEEEEEEC--ChHHHHHHHHHHhhccc
Q 041421 2 NQIAGVFARRKYNIESLAAIGL-DKDRALFTIVVSG--TDRELQQVVEQLQKLVN 53 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~-~~~~~~~~~~~~~--~~~~~~~~~~ql~k~~~ 53 (315)
+.|+.+|+.+|.||+.++.... ..+.-.|.+.+.. ....++++...|+++-+
T Consensus 21 a~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~~~~~~~~~~L~~~L~~l~~ 75 (286)
T PRK06027 21 AAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEGDGLIFNLETLRADFAALAE 75 (286)
T ss_pred HHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence 4688999999999999997321 3334444444443 22336666666666553
No 146
>PRK02886 hypothetical protein; Provisional
Probab=43.60 E-value=37 Score=25.28 Aligned_cols=27 Identities=19% Similarity=0.256 Sum_probs=24.0
Q ss_pred EEECChHHHHHHHHHHhhccceEEEee
Q 041421 33 VVSGTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 33 ~~~~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
++--+++.+++++++|.+|-.|.+|+.
T Consensus 38 vlYvn~~~~e~~~~kl~~l~fVk~Ve~ 64 (87)
T PRK02886 38 VLYCDMEQVEDIMNKLSSLPFVKRVEP 64 (87)
T ss_pred EEEECHHHHHHHHHHHhcCCCeeEEcc
Confidence 444899999999999999999999965
No 147
>PRK14445 acylphosphatase; Provisional
Probab=43.35 E-value=35 Score=25.43 Aligned_cols=35 Identities=11% Similarity=0.174 Sum_probs=26.7
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
++.|.++|+++.++++++.|.+...--+|+++..+
T Consensus 43 ~Vei~~qG~~~~l~~f~~~l~~gP~~a~V~~i~~~ 77 (91)
T PRK14445 43 TVEIEAQGSSGMIDELIKQAERGPSRSSVTSIMVE 77 (91)
T ss_pred eEEEEEEECHHHHHHHHHHHHhCCCCcEEEEEEEE
Confidence 47899999999999999999986554445544433
No 148
>PRK14430 acylphosphatase; Provisional
Probab=42.97 E-value=49 Score=24.80 Aligned_cols=35 Identities=17% Similarity=0.210 Sum_probs=27.4
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
+..|.++|+++.+++++..|.+-..--+|++++.+
T Consensus 43 sVei~~qG~~~~i~~f~~~l~~gp~~a~V~~v~~~ 77 (92)
T PRK14430 43 TVEVMASGTVRQLEALRAWMEAGPPAAQVTKVEVG 77 (92)
T ss_pred cEEEEEEcCHHHHHHHHHHHHhCCCceEEEEEEEE
Confidence 47899999999999999999876555556555443
No 149
>PRK14433 acylphosphatase; Provisional
Probab=42.93 E-value=42 Score=24.84 Aligned_cols=34 Identities=15% Similarity=0.222 Sum_probs=25.8
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQS 62 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~ 62 (315)
++.|.++|+++.++++++.|.+-..--+|++++.
T Consensus 40 ~Vei~~~G~~~~i~~f~~~l~~gP~~a~V~~i~~ 73 (87)
T PRK14433 40 RVEVVAEGPKEALERLLHWLRRGPRHARVEAVDV 73 (87)
T ss_pred CEEEEEEECHHHHHHHHHHHhhCCCCcEEEEEEE
Confidence 5889999999999999999987655444444433
No 150
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=42.88 E-value=70 Score=22.27 Aligned_cols=32 Identities=16% Similarity=0.203 Sum_probs=28.6
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEec
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHID 206 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~ 206 (315)
..+.|.+.+|+.+.+.+..+|...++.|-...
T Consensus 11 ~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~ 42 (68)
T cd01731 11 KPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAE 42 (68)
T ss_pred CEEEEEECCCCEEEEEEEEECCcceEEEeeEE
Confidence 46889999999999999999999999888774
No 151
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=42.79 E-value=65 Score=23.58 Aligned_cols=47 Identities=17% Similarity=0.396 Sum_probs=31.6
Q ss_pred EEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCeEEE-EeeC
Q 041421 187 FYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQKICA-IGHP 235 (315)
Q Consensus 187 ~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~v~~-iG~p 235 (315)
+|++++..+...++|++.+-.-... --+.|- ..+++.|++|.+ +||-
T Consensus 5 iPgqI~~I~~~~~~A~Vd~gGvkre-V~l~Lv-~~~v~~GdyVLVHvGfA 52 (82)
T COG0298 5 IPGQIVEIDDNNHLAIVDVGGVKRE-VNLDLV-GEEVKVGDYVLVHVGFA 52 (82)
T ss_pred cccEEEEEeCCCceEEEEeccEeEE-EEeeee-cCccccCCEEEEEeeEE
Confidence 4778889998888999999652211 223332 237899999987 5654
No 152
>PRK02302 hypothetical protein; Provisional
Probab=42.07 E-value=40 Score=25.21 Aligned_cols=27 Identities=30% Similarity=0.343 Sum_probs=24.0
Q ss_pred EEECChHHHHHHHHHHhhccceEEEee
Q 041421 33 VVSGTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 33 ~~~~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
++--+++.+++++++|.+|-.|.+|+.
T Consensus 40 vlYvn~~~~e~~~~kl~~l~fVk~Ve~ 66 (89)
T PRK02302 40 VLYVNKEDVEQKLEELSKLKFVKKVRP 66 (89)
T ss_pred EEEECHHHHHHHHHHHhcCCCeeEEcc
Confidence 445899999999999999999999965
No 153
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=41.74 E-value=60 Score=22.68 Aligned_cols=32 Identities=16% Similarity=0.174 Sum_probs=27.7
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEec
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHID 206 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~ 206 (315)
..+.|.+.+|+.+.+++..+|...++.|=.+.
T Consensus 12 ~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~ 43 (68)
T cd01722 12 KPVIVKLKWGMEYKGTLVSVDSYMNLQLANTE 43 (68)
T ss_pred CEEEEEECCCcEEEEEEEEECCCEEEEEeeEE
Confidence 46889999999999999999999988886653
No 154
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=41.74 E-value=73 Score=22.55 Aligned_cols=32 Identities=22% Similarity=0.289 Sum_probs=28.3
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEec
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHID 206 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~ 206 (315)
..+.|.+.+|+.+.+.+..+|+..++.|-...
T Consensus 15 k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~ 46 (72)
T PRK00737 15 SPVLVRLKGGREFRGELQGYDIHMNLVLDNAE 46 (72)
T ss_pred CEEEEEECCCCEEEEEEEEEcccceeEEeeEE
Confidence 46889999999999999999999999887764
No 155
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=41.15 E-value=70 Score=22.24 Aligned_cols=32 Identities=13% Similarity=0.155 Sum_probs=27.9
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEec
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHID 206 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~ 206 (315)
..+.|.+.+|+.+.+++..+|+..++.|-.+.
T Consensus 11 ~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~ 42 (67)
T cd01726 11 RPVVVKLNSGVDYRGILACLDGYMNIALEQTE 42 (67)
T ss_pred CeEEEEECCCCEEEEEEEEEccceeeEEeeEE
Confidence 46889999999999999999999998886664
No 156
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=40.95 E-value=75 Score=22.85 Aligned_cols=32 Identities=13% Similarity=0.263 Sum_probs=27.6
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEec
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHID 206 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~ 206 (315)
..+.|.+.||+.+.+.+..+|...+|.|=...
T Consensus 11 ~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~ 42 (75)
T cd06168 11 RTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQ 42 (75)
T ss_pred CeEEEEEcCCeEEEEEEEEEcCCCcEEecCcE
Confidence 46889999999999999999999998876553
No 157
>PRK14436 acylphosphatase; Provisional
Probab=40.74 E-value=57 Score=24.36 Aligned_cols=34 Identities=9% Similarity=0.162 Sum_probs=26.8
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQS 62 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~ 62 (315)
++.|.++|+++.++++++-|.+-..--+|+.++.
T Consensus 43 ~Vei~~qG~~~~i~~f~~~l~~gp~~a~V~~v~~ 76 (91)
T PRK14436 43 SVEAVLEGDEERVEALIGWAHQGPPLARVTRVEV 76 (91)
T ss_pred cEEEEEEcCHHHHHHHHHHHhhCCCceEEEEEEE
Confidence 5789999999999999999987655555555543
No 158
>PF08669 GCV_T_C: Glycine cleavage T-protein C-terminal barrel domain; InterPro: IPR013977 This entry shows glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. ; PDB: 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 3GIR_A 1WOO_A 1WOS_A 1WOR_A ....
Probab=40.62 E-value=45 Score=24.64 Aligned_cols=32 Identities=25% Similarity=0.296 Sum_probs=22.8
Q ss_pred CccchhccCCCeEEEEEeee--cCCCcceEEEEE
Q 041421 276 NSGGPLLDSSGSLIGVNTFI--TSGAFTGIGFAT 307 (315)
Q Consensus 276 ~SGGPlvd~~G~vvGI~s~~--~~~~~~~~~~ai 307 (315)
..|.|+++.+|+.||.+++. .......+++|.
T Consensus 34 ~~g~~v~~~~g~~vG~vTS~~~sp~~~~~Iala~ 67 (95)
T PF08669_consen 34 RGGEPVYDEDGKPVGRVTSGAYSPTLGKNIALAY 67 (95)
T ss_dssp STTCEEEETTTEEEEEEEEEEEETTTTEEEEEEE
T ss_pred CCCCEEEECCCcEEeEEEEEeECCCCCceEEEEE
Confidence 45789997799999999988 223334566664
No 159
>PRK14440 acylphosphatase; Provisional
Probab=40.17 E-value=50 Score=24.61 Aligned_cols=34 Identities=15% Similarity=0.252 Sum_probs=26.5
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQS 62 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~ 62 (315)
++.|.++|+++.++++++.|.+-..-.+|+.++.
T Consensus 42 ~Vei~~~G~~~~v~~f~~~l~~gp~~a~V~~i~~ 75 (90)
T PRK14440 42 SVEVVAEGYEEALSKLLERIKQGPPAAEVEKVDF 75 (90)
T ss_pred CEEEEEEcCHHHHHHHHHHHhhCCCCcEEEEEEE
Confidence 6789999999999999999987655555555443
No 160
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=39.71 E-value=72 Score=22.98 Aligned_cols=32 Identities=16% Similarity=0.410 Sum_probs=27.6
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEec
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHID 206 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~ 206 (315)
..+.|.+.||+.+.+.+..+|...++.|=...
T Consensus 11 ~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~ 42 (79)
T cd01717 11 YRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCE 42 (79)
T ss_pred CEEEEEECCCcEEEEEEEEEcCccCEEcCCEE
Confidence 46788999999999999999999988876553
No 161
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=39.55 E-value=34 Score=32.85 Aligned_cols=56 Identities=16% Similarity=0.242 Sum_probs=40.0
Q ss_pred ceeeeeccccCceEeeeeeccCC--CCeeEEEEEEECC--hHHHHHHHHHHhhccceEEE
Q 041421 2 NQIAGVFARRKYNIESLAAIGLD--KDRALFTIVVSGT--DRELQQVVEQLQKLVNVLNV 57 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~--~~~~~~~~~~~~~--~~~~~~~~~ql~k~~~v~~v 57 (315)
.++=+.|+.||+|+.+|--.+.. +.-..+-|-++|+ +..+++.+++|++.-.-+++
T Consensus 312 ~~~L~~Fa~~giNLtkIeSRP~~~~~~~Y~Ffid~eg~~~d~~~~~aL~~l~~~~~~~kv 371 (386)
T PRK10622 312 VEALLVLRNHNLIMTKLESRPIHGNPWEEMFYLDVQANLRSAEMQKALKELGEITRSLKV 371 (386)
T ss_pred HHHHHHHHHcCCCeeEEEeeecCCCCceEEEEEEEeCCCCCHHHHHHHHHHHHhcCcEEE
Confidence 34556799999999999875543 4555666777764 56789999999886554443
No 162
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=38.95 E-value=64 Score=23.50 Aligned_cols=31 Identities=13% Similarity=0.244 Sum_probs=26.9
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEe
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHI 205 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v 205 (315)
..+.|.+.+|+.+.+.+.++|...+|.|=..
T Consensus 12 k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~ 42 (82)
T cd01730 12 ERVYVKLRGDRELRGRLHAYDQHLNMILGDV 42 (82)
T ss_pred CEEEEEECCCCEEEEEEEEEccceEEeccce
Confidence 4688999999999999999999998887544
No 163
>PRK14442 acylphosphatase; Provisional
Probab=38.93 E-value=58 Score=24.29 Aligned_cols=35 Identities=14% Similarity=0.115 Sum_probs=27.2
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
++.|.++|+++.++++++.|.+...--+|+.++.+
T Consensus 43 ~Vei~~qG~~~~i~~f~~~l~~gp~~a~V~~v~~~ 77 (91)
T PRK14442 43 RVEVVWEGEEDRAKALERWLGRGPRHAEVSAVEVE 77 (91)
T ss_pred CEEEEEEcCHHHHHHHHHHHhhCCCCeEEEEEEEE
Confidence 58899999999999999999986555555554433
No 164
>PRK14420 acylphosphatase; Provisional
Probab=38.17 E-value=53 Score=24.41 Aligned_cols=34 Identities=18% Similarity=0.229 Sum_probs=25.4
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQS 62 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~ 62 (315)
++.|.++|+++.++++++.|.+=..--+|+.++.
T Consensus 41 ~Vei~~qG~~~~i~~f~~~l~~~p~~a~V~~i~~ 74 (91)
T PRK14420 41 TVEIEAEGPEEALQLFLDAIEKGSPFSKVTDVHI 74 (91)
T ss_pred cEEEEEEECHHHHHHHHHHHHhCCCCCEEEEEEE
Confidence 5789999999999999999986544434444433
No 165
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=38.16 E-value=18 Score=31.06 Aligned_cols=51 Identities=18% Similarity=0.164 Sum_probs=37.6
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhccc
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKLVN 53 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~ 53 (315)
++|+.+++..|.||...+. +.-.+.--|++.+.+....++++...|.++.+
T Consensus 23 a~vs~~l~~~g~NI~ds~~-t~lgg~Fa~i~lvs~~~~~~~~le~~L~~l~~ 73 (190)
T PRK11589 23 NTITRHVSSCGCNIEDSRL-AMLGEEFTFIMLLSGSWNAITLIESTLPLKGA 73 (190)
T ss_pred HHHHHHHHHcCCCeeehhh-HhhCCceEEEEEEeCChhHHHHHHHHHHhhhh
Confidence 4678899999999999986 33233344555668888888888888877763
No 166
>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=37.65 E-value=41 Score=24.52 Aligned_cols=48 Identities=21% Similarity=0.234 Sum_probs=31.7
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEEC-C-hHHHHHHHHHHhhc
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSG-T-DRELQQVVEQLQKL 51 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~ql~k~ 51 (315)
.++..+++ +-||..+.-.-...+..++.++++. + .+.++++++.|++.
T Consensus 16 ~~ll~~l~--~anI~~~~y~~~~~~~~~v~i~ie~~~~~~~~~~i~~~L~~~ 65 (85)
T cd04906 16 KKFCELIG--PRNITEFNYRYADEKDAHIFVGVSVANGAEELAELLEDLKSA 65 (85)
T ss_pred HHHHHHhC--CCceeEEEEEccCCCeeEEEEEEEeCCcHHHHHHHHHHHHHC
Confidence 45556677 6688866542222356677777773 4 58899999988873
No 167
>PF13113 DUF3970: Protein of unknown function (DUF3970)
Probab=37.59 E-value=37 Score=23.26 Aligned_cols=22 Identities=27% Similarity=0.593 Sum_probs=18.7
Q ss_pred EEEECChHHHHHHHHHHhhccc
Q 041421 32 IVVSGTDRELQQVVEQLQKLVN 53 (315)
Q Consensus 32 ~~~~~~~~~~~~~~~ql~k~~~ 53 (315)
+-+.|.+++|++++++++++-.
T Consensus 4 VRl~G~~eEi~~fi~~~~~~~~ 25 (60)
T PF13113_consen 4 VRLSGTKEEIEEFIKSFEKLKG 25 (60)
T ss_pred EEecCCHHHHHHHHHhhhhcCC
Confidence 5567999999999999999554
No 168
>PRK09977 putative Mg(2+) transport ATPase; Provisional
Probab=37.14 E-value=64 Score=28.35 Aligned_cols=53 Identities=13% Similarity=0.229 Sum_probs=35.3
Q ss_pred eeeccccCceEeeeeeccCCCCeeEEEEEEE-CChHHHHHHHHHHhhccceEEEe
Q 041421 5 AGVFARRKYNIESLAAIGLDKDRALFTIVVS-GTDRELQQVVEQLQKLVNVLNVS 58 (315)
Q Consensus 5 ~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ql~k~~~v~~v~ 58 (315)
...|.++++.+.++.....+++ ..+++.+. ..+...+++.++|.++.+|.+|+
T Consensus 160 ~~~l~~~~i~i~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~L~~~~~V~~v~ 213 (215)
T PRK09977 160 LDWFKQQKIKTDLVSLQENEDH-EVVAIDITLHATTSIEDLYRLLKGIAGVKGVS 213 (215)
T ss_pred HHHHHHcCceEEEEEEEecCCC-cEEEEEEEECCCCCHHHHHHHHhcCCCceEEE
Confidence 3467788999999986322211 12333222 25677889999999999998885
No 169
>PRK14448 acylphosphatase; Provisional
Probab=37.04 E-value=53 Score=24.47 Aligned_cols=35 Identities=17% Similarity=0.150 Sum_probs=27.5
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
++.|.++|+++.++++++-|.+-..--+|+.++.+
T Consensus 41 ~Vei~~~G~~~~v~~f~~~l~~gp~~a~V~~v~~~ 75 (90)
T PRK14448 41 SVEVVAVGSDAQIAAFRDWLQHGPPTAVVCNVIEQ 75 (90)
T ss_pred CEEEEEEeCHHHHHHHHHHHHhCCCceEEEEEEEE
Confidence 57899999999999999999886655555555443
No 170
>PRK14438 acylphosphatase; Provisional
Probab=36.93 E-value=65 Score=24.00 Aligned_cols=34 Identities=9% Similarity=0.040 Sum_probs=25.8
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQS 62 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~ 62 (315)
++.|+++|+++.++++++.|.+-..--+|+.+..
T Consensus 42 ~Vei~~qG~~~~i~~f~~~l~~gp~~a~V~~v~~ 75 (91)
T PRK14438 42 SVQGCFEGEETDVAALIDWCHHGPSRARVSGVIV 75 (91)
T ss_pred EEEEEEEECHHHHHHHHHHHhhCCCCcEEEEEEE
Confidence 5779999999999999999987655444444433
No 171
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=36.70 E-value=92 Score=22.68 Aligned_cols=31 Identities=23% Similarity=0.269 Sum_probs=26.8
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEe
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHI 205 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v 205 (315)
..+.|.+.+|+.+.+.+..+|...++.|=..
T Consensus 13 k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~ 43 (81)
T cd01729 13 KKIRVKFQGGREVTGILKGYDQLLNLVLDDT 43 (81)
T ss_pred CeEEEEECCCcEEEEEEEEEcCcccEEecCE
Confidence 4678889999999999999999988887555
No 172
>PRK14427 acylphosphatase; Provisional
Probab=35.92 E-value=69 Score=24.07 Aligned_cols=32 Identities=16% Similarity=0.203 Sum_probs=23.9
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeec
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTK 60 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~ 60 (315)
++.|.++|+++.++++++.|.+-..--+|+.+
T Consensus 45 sVei~~qG~~~~i~~f~~~l~~~p~~a~V~~i 76 (94)
T PRK14427 45 SVALVAEGTGEQVEKLLDWLNSDRAPGRVERV 76 (94)
T ss_pred eEEEEEEECHHHHHHHHHHHhhCCCCcEEEEE
Confidence 57899999999999999999874333334433
No 173
>PF01732 DUF31: Putative peptidase (DUF31); InterPro: IPR022382 This domain has no known function. It is found in various hypothetical proteins and putative lipoproteins from mycoplasmas.
Probab=35.67 E-value=27 Score=33.26 Aligned_cols=23 Identities=39% Similarity=0.632 Sum_probs=18.3
Q ss_pred ceeEEEEEEe---C-Cc------EEEEcccccC
Q 041421 150 QASGAGFLWD---Q-DG------HIVTNHHVIC 172 (315)
Q Consensus 150 ~~~GSGfiI~---~-~g------~VlT~aHvv~ 172 (315)
...|||+|++ + ++ ++.||.||+.
T Consensus 35 ~~~GT~WIlDy~~~~~~~~p~k~y~ATNlHVa~ 67 (374)
T PF01732_consen 35 SVSGTGWILDYKKPEDNKYPTKWYFATNLHVAS 67 (374)
T ss_pred cCcceEEEEEEeccCCCCCCeEEEEEechhhhc
Confidence 3579999998 1 22 7999999987
No 174
>cd04914 ACT_AKi-DapG-BS_1 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI. This CD includes the N-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria, bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive aspartokinase isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The B. subtilis AKI is tetrameric consisting of two alpha and
Probab=35.55 E-value=26 Score=24.33 Aligned_cols=30 Identities=10% Similarity=0.205 Sum_probs=21.5
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEEC
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSG 36 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~ 36 (315)
.+|.+.+++++.||+-|+.. .+ .+++++..
T Consensus 17 a~if~~La~~~InvDmI~~~-~~----~isFtv~~ 46 (67)
T cd04914 17 QRVFKALANAGISVDLINVS-PE----EVIFTVDG 46 (67)
T ss_pred HHHHHHHHHcCCcEEEEEec-CC----CEEEEEch
Confidence 34667889999999999653 22 37777774
No 175
>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=35.48 E-value=31 Score=24.88 Aligned_cols=51 Identities=12% Similarity=0.076 Sum_probs=34.5
Q ss_pred CceeeeeccccCceEeeeeec--cCCCCe-eEEEEEEEC----ChHHHHHHHHHHhhc
Q 041421 1 MNQIAGVFARRKYNIESLAAI--GLDKDR-ALFTIVVSG----TDRELQQVVEQLQKL 51 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~--~~~~~~-~~~~~~~~~----~~~~~~~~~~ql~k~ 51 (315)
|.+|+..|.+-|++|.+-.+. +..+.. .-+-+...| |++..+.|.+.|.+.
T Consensus 14 L~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv~~~g~kl~d~~~~~~L~~~L~~~ 71 (75)
T cd04896 14 LYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIVQSDGKKIMDPKKQAALCARLREE 71 (75)
T ss_pred HHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEEeCCCCccCCHHHHHHHHHHHHHH
Confidence 568899999999999999886 554433 334443334 456667777777653
No 176
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=35.45 E-value=49 Score=30.28 Aligned_cols=56 Identities=25% Similarity=0.474 Sum_probs=40.0
Q ss_pred ceeeeeccccCceEeeeeeccCC--CCeeEEEEEEEC--ChHHHHHHHHHHhhccceEEE
Q 041421 2 NQIAGVFARRKYNIESLAAIGLD--KDRALFTIVVSG--TDRELQQVVEQLQKLVNVLNV 57 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~--~~~~~~~~~~~~--~~~~~~~~~~ql~k~~~v~~v 57 (315)
.++-+.|+.||+|+-.|--.+.. ..-..+-|-++| ++..+.+.++.|.++-..+++
T Consensus 209 ~~~L~~Fa~~gINlTkIESRP~k~~~~~Y~F~iD~eg~~~~~~v~~AL~el~~~t~~~ki 268 (279)
T COG0077 209 YKALGVFAKRGINLTKIESRPLKTGLGEYLFFIDIEGHIDDPLVKEALEELKEITEFVKI 268 (279)
T ss_pred HHHHHHHHHcCcceeeEeecccCCCCeeEEEEEEEecCcCcHhHHHHHHHHHhheeEEEE
Confidence 34557899999999999875543 455566666664 455688888888887766555
No 177
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=34.75 E-value=92 Score=22.42 Aligned_cols=31 Identities=13% Similarity=0.378 Sum_probs=27.1
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEe
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHI 205 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v 205 (315)
..+.|.+.+|+.+.+.+..+|...++.|=..
T Consensus 14 ~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da 44 (76)
T cd01732 14 SRIWIVMKSDKEFVGTLLGFDDYVNMVLEDV 44 (76)
T ss_pred CEEEEEECCCeEEEEEEEEeccceEEEEccE
Confidence 5688899999999999999999998887654
No 178
>PRK14450 acylphosphatase; Provisional
Probab=34.64 E-value=78 Score=23.54 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=26.1
Q ss_pred eeEEEEEEECChHHHHHHHHHHhhccceEEEeecc
Q 041421 27 RALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQ 61 (315)
Q Consensus 27 ~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~ 61 (315)
-+++.|.++|+++.++++++-|.+-..--+|++++
T Consensus 40 G~~Vei~~~G~~~~v~~f~~~l~~gp~~a~V~~v~ 74 (91)
T PRK14450 40 GNEVEVVAEGDKDSLLEFLDLLRSGPPRAEVKEVE 74 (91)
T ss_pred CCEEEEEEEeCHHHHHHHHHHHhhCCCCcEEEEEE
Confidence 34588899999999999999998754444444433
No 179
>PRK14437 acylphosphatase; Provisional
Probab=34.63 E-value=70 Score=24.84 Aligned_cols=35 Identities=17% Similarity=0.055 Sum_probs=27.7
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
++.|.++|+++.++++++.|.+-..--+|+.++.+
T Consensus 62 ~Vei~~qG~~~~ie~f~~~L~~gP~~a~V~~i~~~ 96 (109)
T PRK14437 62 DVELVACGERDSIMILTEWLWEGPPQAAVSNVNWE 96 (109)
T ss_pred CEEEEEEECHHHHHHHHHHHHhCCCceEEEEEEEE
Confidence 58999999999999999999976655555555433
No 180
>TIGR01268 Phe4hydrox_tetr phenylalanine-4-hydroxylase, tetrameric form. The member of this family from Drosophila has been described as having both phenylalanine-4-hydroxylase and tryptophan 5-monoxygenase activity (PubMed:1371286). However, a Drosophila member of the tryptophan 5-monoxygenase clade has subsequently been discovered.
Probab=34.36 E-value=51 Score=32.15 Aligned_cols=52 Identities=17% Similarity=0.302 Sum_probs=37.9
Q ss_pred CceeeeeccccCceEeeeeeccCC--CCeeEEEEEEECC-hHHHHHHHHHHhhcc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLD--KDRALFTIVVSGT-DRELQQVVEQLQKLV 52 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~--~~~~~~~~~~~~~-~~~~~~~~~ql~k~~ 52 (315)
|.+|-.+|+++|+|+..|--.+.. +.-..+-|-+++. +..++++++.|.+..
T Consensus 30 L~~vL~vFa~~gINLthIESRPsk~~~~eY~FFVD~eg~~~~~v~~aL~~Lk~~~ 84 (436)
T TIGR01268 30 LAETLKLFQAHDVNLTHIESRPSKTHPGEYEFFVEFDEASDRKLEGVIEHLRQKA 84 (436)
T ss_pred HHHHHHHHHHCCCCeeEEecccCCCCCccEEEEEEEecCccHHHHHHHHHHHHhc
Confidence 456677899999999999865543 3333455566665 578899999998877
No 181
>PRK14446 acylphosphatase; Provisional
Probab=34.33 E-value=76 Score=23.59 Aligned_cols=35 Identities=14% Similarity=0.148 Sum_probs=28.3
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
+..|.++|+++.++++++-|.+...--+|+.++.+
T Consensus 41 sVei~~qG~~~~l~~f~~~l~~gP~~a~V~~v~~~ 75 (88)
T PRK14446 41 SVEVVAAGSAAALEALEAWLWQGPPAATVAAVTRT 75 (88)
T ss_pred CEEEEEEeCHHHHHHHHHHHhhCCCceEEEEEEEE
Confidence 57889999999999999999987666666665544
No 182
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=34.04 E-value=29 Score=26.85 Aligned_cols=17 Identities=41% Similarity=0.681 Sum_probs=13.0
Q ss_pred chhccCCCeEEEEEeee
Q 041421 279 GPLLDSSGSLIGVNTFI 295 (315)
Q Consensus 279 GPlvd~~G~vvGI~s~~ 295 (315)
.|++|.+|+++|++..+
T Consensus 94 ~PV~d~~g~viG~V~VG 110 (116)
T PF14827_consen 94 APVYDSDGKVIGVVSVG 110 (116)
T ss_dssp EEEE-TTS-EEEEEEEE
T ss_pred EeeECCCCcEEEEEEEE
Confidence 48998899999999875
No 183
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=33.87 E-value=1.1e+02 Score=21.61 Aligned_cols=31 Identities=13% Similarity=0.173 Sum_probs=26.7
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEe
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHI 205 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v 205 (315)
..+.|.+.+|+.+.+.+..+|....|.|=.+
T Consensus 11 k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~ 41 (72)
T cd01719 11 KKLSLKLNGNRKVSGILRGFDPFMNLVLDDA 41 (72)
T ss_pred CeEEEEECCCeEEEEEEEEEcccccEEeccE
Confidence 4678889999999999999999988887655
No 184
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=33.87 E-value=1.1e+02 Score=21.91 Aligned_cols=31 Identities=23% Similarity=0.220 Sum_probs=26.9
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEe
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHI 205 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v 205 (315)
..+.|.+.+|+.+.+.+..+|+...+.|=..
T Consensus 13 k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~ 43 (74)
T cd01728 13 KKVVVLLRDGRKLIGILRSFDQFANLVLQDT 43 (74)
T ss_pred CEEEEEEcCCeEEEEEEEEECCcccEEecce
Confidence 5688899999999999999999988887555
No 185
>PRK14422 acylphosphatase; Provisional
Probab=33.86 E-value=75 Score=23.81 Aligned_cols=32 Identities=13% Similarity=0.109 Sum_probs=24.1
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeec
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTK 60 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~ 60 (315)
++.|.++|+++.++++++.|.+=..--+|+.+
T Consensus 45 ~Vei~~~G~~~~i~~f~~~l~~gp~~a~V~~i 76 (93)
T PRK14422 45 RVQVVAEGPRAACEKLLQLLRGDDTPGRVDKV 76 (93)
T ss_pred CEEEEEEcCHHHHHHHHHHHHhCCCCcEEEEE
Confidence 47899999999999999999874333334433
No 186
>PRK14441 acylphosphatase; Provisional
Probab=33.30 E-value=85 Score=23.50 Aligned_cols=33 Identities=9% Similarity=-0.001 Sum_probs=25.0
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeecc
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQ 61 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~ 61 (315)
++.|.++|+++.++++++.|.+...--+|+.++
T Consensus 44 ~Vei~~qG~~~~i~~f~~~l~~gp~~a~V~~v~ 76 (93)
T PRK14441 44 RVEAEAEGERAAVGALVRWCHAGPPAARVDRVE 76 (93)
T ss_pred EEEEEEEECHHHHHHHHHHHhhCCCCcEEEEEE
Confidence 577999999999999999998765444444443
No 187
>PRK14447 acylphosphatase; Provisional
Probab=32.73 E-value=94 Score=23.35 Aligned_cols=38 Identities=16% Similarity=0.104 Sum_probs=27.8
Q ss_pred CCeeEEEEEEECChHHHHHHHHHHhhccceEEEeeccC
Q 041421 25 KDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQS 62 (315)
Q Consensus 25 ~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~ 62 (315)
++-+++.|+++|+++.++++++-|.+-..-.+|+.+..
T Consensus 40 ~dG~~Vei~~qG~~~~l~~f~~~l~~gp~~a~V~~v~~ 77 (95)
T PRK14447 40 SDGRTVEAVLEGPRDAVLKVIEWARVGPPGARVEDVEV 77 (95)
T ss_pred CCCCEEEEEEEeCHHHHHHHHHHHhhCCCCeEEEEEEE
Confidence 44446889999999999999999986544444444433
No 188
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=32.27 E-value=1.3e+02 Score=20.52 Aligned_cols=32 Identities=19% Similarity=0.358 Sum_probs=27.4
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEec
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHID 206 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~ 206 (315)
..+.|.+.+|+.+.+.+..+|...++.|=...
T Consensus 9 ~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~ 40 (67)
T smart00651 9 KRVLVELKNGREYRGTLKGFDQFMNLVLEDVE 40 (67)
T ss_pred cEEEEEECCCcEEEEEEEEECccccEEEccEE
Confidence 46788999999999999999999888876654
No 189
>PF08753 NikR_C: NikR C terminal nickel binding domain; InterPro: IPR014864 NikR is a transcription factor that regulates nickel uptake. It consists of two dimeric DNA binding domains separated by a tetrameric regulatory domain that binds nickel. This protein corresponds to the C-terminal regulatory domain which contains four nickel binding sites at the tetramer interface []. ; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 2WVB_B 2WVD_C 3QSI_B 3LGH_A 2CAD_A ....
Probab=32.24 E-value=78 Score=22.83 Aligned_cols=36 Identities=33% Similarity=0.501 Sum_probs=29.7
Q ss_pred CCCeeEEEEEEECChHHHHHHHHHHhhccceEEEee
Q 041421 24 DKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
+++.---+|++.|+-+.++++.++|.++-.|..+..
T Consensus 39 ~~~~ClEvivv~G~~~~I~~l~~~l~~~kGV~~~~l 74 (78)
T PF08753_consen 39 DHDNCLEVIVVRGPADRIKELAEKLRSLKGVKHVKL 74 (78)
T ss_dssp SSSEEEEEEEEEEEHHHHHHHHHHHHTSTTEEEEEE
T ss_pred cCCCeEEEEEEEcCHHHHHHHHHHHhccCCeeEEEE
Confidence 344444567888999999999999999999988865
No 190
>PRK05092 PII uridylyl-transferase; Provisional
Probab=32.22 E-value=36 Score=36.69 Aligned_cols=52 Identities=25% Similarity=0.320 Sum_probs=39.2
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEE---EC----ChHHHHHHHHHHhhcc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVV---SG----TDRELQQVVEQLQKLV 52 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~---~~----~~~~~~~~~~ql~k~~ 52 (315)
+++|+++|++.|+||.+-.+.+...+..-.++.| .| +++.++.|.+.|++..
T Consensus 746 fa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~~~g~~~~~~~~~~~l~~~L~~~l 804 (931)
T PRK05092 746 FSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQDAFGRDEDEPRRLARLAKAIEDAL 804 (931)
T ss_pred HHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHH
Confidence 3578999999999999998866666766666666 23 4567888888887754
No 191
>PRK14424 acylphosphatase; Provisional
Probab=31.80 E-value=65 Score=24.26 Aligned_cols=34 Identities=9% Similarity=0.146 Sum_probs=25.7
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQS 62 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~ 62 (315)
++.|+++|+++.++++++.|.+-..--+|..++.
T Consensus 46 ~Vei~~qG~~~~v~~f~~~l~~gp~~a~V~~v~~ 79 (94)
T PRK14424 46 TVEAMIQGPAAQIDRMLAWLRHGPPAARVTEVTF 79 (94)
T ss_pred CEEEEEEECHHHHHHHHHHHHhCCCCcEEEEEEE
Confidence 6889999999999999999987554444444433
No 192
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=31.20 E-value=1.9e+02 Score=20.29 Aligned_cols=29 Identities=14% Similarity=0.331 Sum_probs=24.4
Q ss_pred CCCeeEEEEEEECChHHHHHHHHHHhhcc
Q 041421 24 DKDRALFTIVVSGTDRELQQVVEQLQKLV 52 (315)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~ql~k~~ 52 (315)
+..+.+|++-+.|+++.+++.++.|+..-
T Consensus 42 ~~~~G~l~l~l~g~~~~~~~a~~~L~~~~ 70 (76)
T PF09383_consen 42 GTPFGILILELPGDDEEIEKAIAYLREQG 70 (76)
T ss_dssp TEEEEEEEEEEES-HHHHHHHHHHHHHTT
T ss_pred CeeEEEEEEEEECCHHHHHHHHHHHHHCC
Confidence 35678999999999999999999999864
No 193
>PRK05092 PII uridylyl-transferase; Provisional
Probab=31.00 E-value=40 Score=36.36 Aligned_cols=53 Identities=9% Similarity=0.129 Sum_probs=35.8
Q ss_pred CceeeeeccccCceEeeeeeccCCCCe-eEEEEEEE-----CChHHHHHHHHHHhhccc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDR-ALFTIVVS-----GTDRELQQVVEQLQKLVN 53 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~-~~~~~~~~-----~~~~~~~~~~~ql~k~~~ 53 (315)
|.+|++.|++.|+||.+..+.+..... .-+.|.-. .+++..++|.+.|.+.++
T Consensus 857 l~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d~~g~~i~~~~~~~~l~~~L~~~L~ 915 (931)
T PRK05092 857 LYDLTRALSDLNLNIASAHIATYGERAVDVFYVTDLFGLKITNEARQAAIRRALLAALA 915 (931)
T ss_pred HHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeCCCCCcCCCHHHHHHHHHHHHHHhc
Confidence 468999999999999999986553222 22333221 244567888888887664
No 194
>PRK14439 acylphosphatase; Provisional
Probab=30.67 E-value=88 Score=26.19 Aligned_cols=32 Identities=13% Similarity=0.225 Sum_probs=24.2
Q ss_pred EEEEEEECChHHHHHHHHHHhh-ccceEEEeec
Q 041421 29 LFTIVVSGTDRELQQVVEQLQK-LVNVLNVSTK 60 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k-~~~v~~v~~~ 60 (315)
++.|.++|+++.++++++.|.+ ...--+|+.+
T Consensus 114 sVEI~aQG~ee~Ie~Fi~~L~~~gPp~A~Ve~I 146 (163)
T PRK14439 114 SVEVVACGEEGQVEKLMQWLKSGGPRSARVERV 146 (163)
T ss_pred CEEEEEEcCHHHHHHHHHHHhhCCCCCeEEEEE
Confidence 5789999999999999999988 3333334443
No 195
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=30.40 E-value=1.4e+02 Score=20.96 Aligned_cols=32 Identities=9% Similarity=0.257 Sum_probs=28.5
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEec
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHID 206 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~ 206 (315)
..+.|.+.+|..+.+++..+|...++.|-.+.
T Consensus 11 ~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~ 42 (70)
T cd01721 11 HIVTVELKTGEVYRGKLIEAEDNMNCQLKDVT 42 (70)
T ss_pred CEEEEEECCCcEEEEEEEEEcCCceeEEEEEE
Confidence 46888999999999999999999999988774
No 196
>PRK14426 acylphosphatase; Provisional
Probab=29.58 E-value=1.1e+02 Score=22.89 Aligned_cols=23 Identities=17% Similarity=0.400 Sum_probs=20.9
Q ss_pred EEEEEEECChHHHHHHHHHHhhc
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKL 51 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~ 51 (315)
++.|.++|+++.++++++.|.+-
T Consensus 43 ~Vei~~~G~~~~i~~f~~~l~~g 65 (92)
T PRK14426 43 SVEVVACGEEEQVEKLMEWLKEG 65 (92)
T ss_pred cEEEEEEeCHHHHHHHHHHHhcC
Confidence 58899999999999999999875
No 197
>PRK03381 PII uridylyl-transferase; Provisional
Probab=29.21 E-value=42 Score=35.35 Aligned_cols=50 Identities=20% Similarity=0.284 Sum_probs=34.7
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECCh---HHHHHHHHHHhhcc
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTD---RELQQVVEQLQKLV 52 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~ql~k~~ 52 (315)
++|+|+|++.|+||.+-.+-+ ..+..-.++.|...+ ...+++.+.|++..
T Consensus 614 a~i~~vL~~~glnI~dA~i~t-~dg~~ld~F~V~~~~~~~~~~~~l~~~L~~~L 666 (774)
T PRK03381 614 SKAAGVLALHRLRVRSASVRS-HDGVAVLEFVVSPRFGSPPDAALLRQDLRRAL 666 (774)
T ss_pred HHHHHHHHHCCCeEEEeEEEe-cCCEEEEEEEEECCCCCcchHHHHHHHHHHHH
Confidence 589999999999999998755 555555555555321 23566777777654
No 198
>TIGR00300 conserved hypothetical protein TIGR00300. All members of the family come from genome projects. A partial length search brings in two plant lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzymes hitting the N-terminal region of the family.
Probab=29.13 E-value=1.1e+02 Score=29.45 Aligned_cols=40 Identities=18% Similarity=0.305 Sum_probs=28.5
Q ss_pred CceEeeeeeccCCCCeeEEEEEEE-CChHHHHHHHHHHhhc
Q 041421 12 KYNIESLAAIGLDKDRALFTIVVS-GTDRELQQVVEQLQKL 51 (315)
Q Consensus 12 ~~ni~s~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ql~k~ 51 (315)
.|.|+.+.++....+.|.-.|.|. .+++.+++|+.||.++
T Consensus 31 ~f~v~~f~vG~~k~d~S~a~~~V~a~~~~~l~~Il~~l~~~ 71 (407)
T TIGR00300 31 DFRVLEFNIGKRKNDPSYARILVSARDHQHLEEILTELIDL 71 (407)
T ss_pred ceEEEEEecCCccCCCccEEEEEecCCHHHHHHHHHHHHHc
Confidence 488999998655444444333344 4788899999999985
No 199
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=28.74 E-value=1.3e+02 Score=21.59 Aligned_cols=33 Identities=21% Similarity=0.402 Sum_probs=28.6
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecC
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDA 207 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~ 207 (315)
..+.|.+.+|+.+.+++.++|....+.|--+..
T Consensus 18 ~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e 50 (79)
T COG1958 18 KRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEE 50 (79)
T ss_pred CEEEEEECCCCEEEEEEEEEccceeEEEeceEE
Confidence 678899999999999999999999888876643
No 200
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=28.34 E-value=1.5e+02 Score=21.05 Aligned_cols=32 Identities=22% Similarity=0.232 Sum_probs=27.3
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEec
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHID 206 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~ 206 (315)
..+.|.+.+++.+.+.+.++|....+.|=...
T Consensus 10 ~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~ 41 (74)
T cd01727 10 KTVSVITVDGRVIVGTLKGFDQATNLILDDSH 41 (74)
T ss_pred CEEEEEECCCcEEEEEEEEEccccCEEccceE
Confidence 46788899999999999999999888876653
No 201
>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=27.19 E-value=51 Score=22.04 Aligned_cols=44 Identities=11% Similarity=0.223 Sum_probs=28.0
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhh
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQK 50 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k 50 (315)
.||...+++.++|++.++-...+ .++++++.. +..++.++.|.+
T Consensus 19 ~~i~~~l~~~~I~v~~i~~~~s~---~~is~~v~~--~~~~~~~~~lh~ 62 (66)
T cd04922 19 ATFFSALAKANVNIRAIAQGSSE---RNISAVIDE--DDATKALRAVHE 62 (66)
T ss_pred HHHHHHHHHCCCCEEEEEecCcc---cEEEEEEeH--HHHHHHHHHHHH
Confidence 35566688999999999742222 667777764 334555555554
No 202
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=27.17 E-value=1.5e+02 Score=20.15 Aligned_cols=33 Identities=21% Similarity=0.390 Sum_probs=28.9
Q ss_pred CeEEEEeCCCcEEEEEEEEeCCCCCeEEEEecC
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQDKDLAVLHIDA 207 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~~~DiAll~v~~ 207 (315)
..+.|.+.+|+.+.+.+..+|...++.|-.+..
T Consensus 9 ~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~ 41 (67)
T PF01423_consen 9 KRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTE 41 (67)
T ss_dssp SEEEEEETTSEEEEEEEEEEETTEEEEEEEEEE
T ss_pred cEEEEEEeCCEEEEEEEEEeechheEEeeeEEE
Confidence 568899999999999999999998888887754
No 203
>PF02601 Exonuc_VII_L: Exonuclease VII, large subunit; InterPro: IPR020579 Exonuclease VII 3.1.11.6 from EC is composed of two nonidentical subunits; one large subunit and 4 small ones []. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains the OB-fold domains (IPR004365 from INTERPRO) that bind to nucleic acids at the N terminus. This entry represents Exonuclease VII, large subunit, C-terminal. ; GO: 0008855 exodeoxyribonuclease VII activity
Probab=27.15 E-value=65 Score=29.79 Aligned_cols=38 Identities=18% Similarity=0.404 Sum_probs=32.4
Q ss_pred ccceeEEEEEEeCCcEEEEcccccCCCCeEEEEeCCCc
Q 041421 148 FLQASGAGFLWDQDGHIVTNHHVICDASKVKVSFSDQS 185 (315)
Q Consensus 148 ~~~~~GSGfiI~~~g~VlT~aHvv~~~~~~~V~~~~g~ 185 (315)
.....|-.++.+++|.++|+..-+...+.+.+.+.||.
T Consensus 277 ~~L~RGYaiv~~~~g~vI~s~~~l~~gd~i~i~l~DG~ 314 (319)
T PF02601_consen 277 KILKRGYAIVRDKDGKVITSVKQLKPGDEIEIRLADGS 314 (319)
T ss_pred HHHhCceEEEECCCCCEECCHHHCCCCCEEEEEEcceE
Confidence 34456778888778999999999999999999999985
No 204
>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=26.68 E-value=52 Score=20.87 Aligned_cols=41 Identities=15% Similarity=0.275 Sum_probs=25.2
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHH
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQ 47 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q 47 (315)
.|+...+.+.++||+.++.... + ..+++++.. +..+++.+-
T Consensus 18 ~~i~~~l~~~~i~i~~i~~~~~--~-~~~s~~v~~--~~~~~~~~~ 58 (60)
T cd04868 18 AKIFSALAEAGINVDMISQSES--E-VNISFTVDE--SDLEKAVKA 58 (60)
T ss_pred HHHHHHHHHCCCcEEEEEcCCC--c-EEEEEEEeH--HHHHHHHHH
Confidence 3556678889999999986322 2 346666663 345555443
No 205
>cd04924 ACT_AK-Arch_2 ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). Included in this CD is the second of two ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). The first or N-terminal ACT domain of these proteins cluster with the ThrA-like ACT 1 domains (ACT_AKi-HSDH-ThrA-like_1) which includes the threonine-sensitive archaeal Methanococcus jannaschii aspartokinase ACT 1 domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=26.58 E-value=51 Score=21.97 Aligned_cols=44 Identities=11% Similarity=0.157 Sum_probs=27.6
Q ss_pred eeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhc
Q 041421 3 QIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKL 51 (315)
Q Consensus 3 ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~ 51 (315)
++...+++.+.|++-++-...+ .++++++.. +..++..+.|++.
T Consensus 20 ~i~~~L~~~~I~v~~i~q~~s~---~~isf~i~~--~~~~~~~~~Lh~~ 63 (66)
T cd04924 20 RVFGALGKAGINVIMISQGSSE---YNISFVVAE--DDGWAAVKAVHDE 63 (66)
T ss_pred HHHHHHHHCCCCEEEEEecCcc---ceEEEEEeH--HHHHHHHHHHHHH
Confidence 4556678999999999752222 556677663 3355555555554
No 206
>COG1254 AcyP Acylphosphatases [Energy production and conversion]
Probab=26.33 E-value=1.5e+02 Score=22.23 Aligned_cols=32 Identities=25% Similarity=0.309 Sum_probs=25.4
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeec
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTK 60 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~ 60 (315)
++.|++.|+++.++++++-|.|=..-.+|+++
T Consensus 43 sVeiva~G~~~~v~~~~~~l~~g~~~a~V~~v 74 (92)
T COG1254 43 SVEIVAEGPDEAVEKFIEWLRKGPPAAKVERV 74 (92)
T ss_pred eEEEEEEcCHHHHHHHHHHHHhCCCceEEEEE
Confidence 78999999999999999999965544444444
No 207
>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=25.99 E-value=59 Score=21.71 Aligned_cols=43 Identities=14% Similarity=0.193 Sum_probs=27.0
Q ss_pred eeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhh
Q 041421 3 QIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQK 50 (315)
Q Consensus 3 ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k 50 (315)
|+...+++.+.|++.++-...+ ..+++++..+ ..++.++.|+|
T Consensus 20 ~i~~~L~~~~i~v~~i~~~~s~---~~isf~v~~~--d~~~~~~~lh~ 62 (66)
T cd04916 20 RATAALAKAGINIRMINQGSSE---ISIMIGVHNE--DADKAVKAIYE 62 (66)
T ss_pred HHHHHHHHCCCCEEEEEecCcc---cEEEEEEeHH--HHHHHHHHHHH
Confidence 4556678999999999853322 5567777643 34444555554
No 208
>PF00708 Acylphosphatase: Acylphosphatase; InterPro: IPR001792 Acylphosphatase (3.6.1.7 from EC) is an enzyme of approximately 98 amino acid residues that specifically catalyses the hydrolysis of the carboxyl-phosphate bond of acylphosphates [], its substrates including 1,3-diphosphoglycerate and carbamyl phosphate []. The enzyme has a mainly beta-sheet structure with 2 short alpha-helical segments. It is distributed in a tissue-specific manner in a wide variety of species, although its physiological role is as yet unknown []: it may, however, play a part in the regulation of the glycolytic pathway and pyrimidine biosynthesis []. There are two known isozymes. One seems to be specific to muscular tissues, the other, called 'organ-common type', is found in many different tissues. While bacterial and archebacterial hypothetical proteins that are highly similar to that enzyme and that probably possess the same activity. These proteins include: Escherichia coli putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (gene yccX). Bacillus subtilis putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (gene yflL). Archaeoglobus fulgidus putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (O29440 from SWISSPROT). An acylphosphatase-like domain is also found in some prokaryotic hydrogenase maturation HypF carbamoyltransferases [, ].; PDB: 1APS_A 1GXT_A 1GXU_A 2HLT_A 2FHM_A 2HLU_A 3BR8_A 1ULR_A 3TRG_A 2BJD_A ....
Probab=25.78 E-value=79 Score=23.29 Aligned_cols=34 Identities=18% Similarity=0.218 Sum_probs=26.5
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQS 62 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~ 62 (315)
++.|+++|+++.++++++-|.+-..-.+|.+++.
T Consensus 43 ~V~i~~~G~~~~l~~f~~~l~~g~p~a~V~~i~~ 76 (91)
T PF00708_consen 43 SVEIEAEGEEEQLEEFIKWLKKGPPPARVDEIEV 76 (91)
T ss_dssp EEEEEEEEEHHHHHHHHHHHHHSSTTSEEEEEEE
T ss_pred EEEEEEEeCHHHHHHHHHHHHhCCCCcEEEEEEE
Confidence 7899999999999999999998654344444433
No 209
>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=25.73 E-value=50 Score=22.59 Aligned_cols=43 Identities=19% Similarity=0.285 Sum_probs=26.8
Q ss_pred eeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhh
Q 041421 3 QIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQK 50 (315)
Q Consensus 3 ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k 50 (315)
|+...|++.++|+.-++-++.+ ..++++++ ++..++.++.|.+
T Consensus 19 ~i~~aL~~~~I~v~~i~~g~s~---~sis~~v~--~~~~~~av~~Lh~ 61 (65)
T cd04918 19 RAFHVLYTKGVNVQMISQGASK---VNISLIVN--DSEAEGCVQALHK 61 (65)
T ss_pred HHHHHHHHCCCCEEEEEecCcc---ceEEEEEe--HHHHHHHHHHHHH
Confidence 4555678899999888853332 24555555 4555666666655
No 210
>PRK14443 acylphosphatase; Provisional
Probab=25.68 E-value=1.6e+02 Score=22.06 Aligned_cols=34 Identities=9% Similarity=0.123 Sum_probs=25.8
Q ss_pred eEEEEEEECChHHHHHHHHHHhhccc-eEEEeecc
Q 041421 28 ALFTIVVSGTDRELQQVVEQLQKLVN-VLNVSTKQ 61 (315)
Q Consensus 28 ~~~~~~~~~~~~~~~~~~~ql~k~~~-v~~v~~~~ 61 (315)
.++.|.++|+++.++++++.|.+=.. --+|+.+.
T Consensus 42 G~Vei~~qG~~~~l~~f~~~l~~g~p~~a~V~~v~ 76 (93)
T PRK14443 42 GSVEIHAIAEEENLNKFIDAIKKGPSPGCRIEHVY 76 (93)
T ss_pred CEEEEEEECCHHHHHHHHHHHhcCCCCcEEEEEEE
Confidence 36889999999999999999988543 44444443
No 211
>PRK06635 aspartate kinase; Reviewed
Probab=25.64 E-value=69 Score=30.70 Aligned_cols=49 Identities=20% Similarity=0.336 Sum_probs=33.3
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKL 51 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~ 51 (315)
|.||...|.+.|+||+.++....+++...+++++.. +..++..+.|+++
T Consensus 277 l~~i~~~L~~~~I~i~~is~s~~~~~~~~is~~v~~--~~~~~a~~~L~~~ 325 (404)
T PRK06635 277 AAQIFGALAEANINVDMIVQNVSEDGKTDITFTVPR--DDLEKALELLEEV 325 (404)
T ss_pred HHHHHHHHHHcCCeEEEEEecCCCCCceeEEEEEcH--HHHHHHHHHHHHH
Confidence 356777899999999999864444556677777753 3345556666663
No 212
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=24.81 E-value=1.8e+02 Score=21.63 Aligned_cols=34 Identities=26% Similarity=0.379 Sum_probs=27.4
Q ss_pred CeeEEEEEEECC-hHHHHHHHHHHhhccceEEEee
Q 041421 26 DRALFTIVVSGT-DRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 26 ~~~~~~~~~~~~-~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
+--||.+|++++ .+.+-..+++|+.|..|+.+.-
T Consensus 40 ~~GKiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~l 74 (87)
T PRK10553 40 PSGQLIVVVEAEDSETLLQTIESVRNVEGVLAVSL 74 (87)
T ss_pred CCCeEEEEEEeCChHHHHHHHHHHHcCCCceEEEE
Confidence 346899999954 5667788999999999999864
No 213
>PLN02317 arogenate dehydratase
Probab=24.56 E-value=98 Score=29.70 Aligned_cols=56 Identities=23% Similarity=0.290 Sum_probs=37.1
Q ss_pred ceeeeeccccCceEeeeeeccCC--C--------------CeeEEEEEEECC--hHHHHHHHHHHhhccceEEE
Q 041421 2 NQIAGVFARRKYNIESLAAIGLD--K--------------DRALFTIVVSGT--DRELQQVVEQLQKLVNVLNV 57 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~--~--------------~~~~~~~~~~~~--~~~~~~~~~ql~k~~~v~~v 57 (315)
.++=..|+.|++|+..|.-.+.. + .-..+-|-+++. ++.+++.++.|++.-.-++|
T Consensus 298 ~k~L~~Fa~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~eY~FyVD~eg~~~d~~~~~aL~~L~~~~~~lrv 371 (382)
T PLN02317 298 FKALAVFALRDINLTKIESRPQRKRPLRVVDDSNSGTAKYFDYLFYVDFEASMADPRAQNALAHLQEFATFLRV 371 (382)
T ss_pred HHHHHHHHHCCCCEEEEEeeecCCCCccccccccccccccccEEEEEEEEcCcCCHHHHHHHHHHHHhcCeEEE
Confidence 34556899999999999764432 1 123444555555 67788899998886654443
No 214
>cd04627 CBS_pair_14 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=24.34 E-value=42 Score=25.52 Aligned_cols=21 Identities=33% Similarity=0.491 Sum_probs=16.8
Q ss_pred CCccchhccCCCeEEEEEeee
Q 041421 275 GNSGGPLLDSSGSLIGVNTFI 295 (315)
Q Consensus 275 G~SGGPlvd~~G~vvGI~s~~ 295 (315)
+.+.=|++|.+|+++|+++..
T Consensus 98 ~~~~lpVvd~~~~~vGiit~~ 118 (123)
T cd04627 98 GISSVAVVDNQGNLIGNISVT 118 (123)
T ss_pred CCceEEEECCCCcEEEEEeHH
Confidence 444569998889999999875
No 215
>PRK14432 acylphosphatase; Provisional
Probab=24.06 E-value=1.2e+02 Score=22.74 Aligned_cols=23 Identities=17% Similarity=0.198 Sum_probs=20.4
Q ss_pred EEEEEEE-CChHHHHHHHHHHhhc
Q 041421 29 LFTIVVS-GTDRELQQVVEQLQKL 51 (315)
Q Consensus 29 ~~~~~~~-~~~~~~~~~~~ql~k~ 51 (315)
++.|++. |+++.++++++.|.+=
T Consensus 41 ~Vei~~~~G~~~~v~~f~~~l~~g 64 (93)
T PRK14432 41 RVEIVAFFNTKEQMKKFEKLLKNG 64 (93)
T ss_pred CEEEEEEECCHHHHHHHHHHHHhC
Confidence 5789998 9999999999999874
No 216
>COG1707 ACT domain-containing protein [General function prediction only]
Probab=23.91 E-value=90 Score=26.32 Aligned_cols=60 Identities=20% Similarity=0.375 Sum_probs=44.8
Q ss_pred ceeeeeccccCceEeeeeeccCCC-CeeEEEEEEECChHHHHHHHHHHhhccceEEEeeccC
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDK-DRALFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQS 62 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~ 62 (315)
..++|+.+.+|-||.-..---+.+ ...++-+-++|- +..+.++..|...-.|++|+.+..
T Consensus 17 ~~ltgiiae~ggNIt~~q~~~~~~g~~~~iYmEiEgi-~d~e~l~~~lks~d~v~ev~i~~s 77 (218)
T COG1707 17 RDLTGIIAEEGGNITYAQQFLEKDGEKALIYMEIEGI-DDFEKLLERLKSFDYVIEVEIHRS 77 (218)
T ss_pred HHHHHHHHhcCCceEeeehhhhccCceEEEEEEeeCC-CCHHHHHHHhhccceEEEeeecch
Confidence 457899999999998776422333 367777777754 357889999999999999987544
No 217
>PRK14452 acylphosphatase; Provisional
Probab=23.57 E-value=1e+02 Score=23.82 Aligned_cols=35 Identities=11% Similarity=0.034 Sum_probs=26.8
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEeeccCC
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVSTKQSS 63 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~~~~~ 63 (315)
++.|.++|+++.++++.+-+++-..--+|+.++.+
T Consensus 59 sVeI~~qG~~~~ve~F~~~l~~gP~~A~V~~v~~~ 93 (107)
T PRK14452 59 SVEVQAEGPPLALSELRAWCERGPPGARVKRVDPS 93 (107)
T ss_pred CEEEEEEcCHHHHHHHHHHHhcCCCCcEEEEEEEE
Confidence 58899999999999998878776555555555444
No 218
>PF12594 DUF3764: Protein of unknown function (DUF3764); InterPro: IPR022240 This family of proteins is found in bacteria. Proteins in this family are typically between 89 and 101 amino acids in length.
Probab=23.50 E-value=1.4e+02 Score=22.27 Aligned_cols=40 Identities=15% Similarity=0.218 Sum_probs=32.6
Q ss_pred ccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHh
Q 041421 10 RRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQ 49 (315)
Q Consensus 10 rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~ 49 (315)
++-++|.+|=.+-..++-+|++++.++.+..++++..-=+
T Consensus 30 ~~e~gIk~lyrGvskdDp~kv~vI~Qa~egv~~~f~~~~~ 69 (86)
T PF12594_consen 30 HKEFGIKSLYRGVSKDDPQKVIVIHQAPEGVMQKFFEDNE 69 (86)
T ss_pred HHhcCCeEEEEecccCCCceEEEEEecCHHHHHHHHhCcH
Confidence 4568899998766668889999999999999999876544
No 219
>PF03462 PCRF: PCRF domain; InterPro: IPR005139 This domain is found in peptide chain release factors. Peptide chain release factors are important for protein synthesis since they direct the termination of translation in response to the peptide chain termination codons UAG and UAA. These are structurally distinct but both contain the PCRF domain [].; GO: 0016149 translation release factor activity, codon specific, 0006415 translational termination, 0005737 cytoplasm; PDB: 3D5A_X 3D5C_X 3MR8_V 3MS0_V 3F1G_X 3F1E_X 1ZBT_A 2IHR_1 2X9R_Y 2X9T_Y ....
Probab=22.63 E-value=1.3e+02 Score=23.36 Aligned_cols=30 Identities=23% Similarity=0.242 Sum_probs=23.7
Q ss_pred ccccCceEeeeeecc-CCCCeeEEEEEEECC
Q 041421 8 FARRKYNIESLAAIG-LDKDRALFTIVVSGT 37 (315)
Q Consensus 8 f~rr~~ni~s~~~~~-~~~~~~~~~~~~~~~ 37 (315)
+.||||+.+-+.... +.-++.+.|+.+.|.
T Consensus 76 a~~~gw~~~~l~~~~~~~~G~k~a~~~I~G~ 106 (115)
T PF03462_consen 76 AERRGWKVEVLDYSPGEEGGIKSATLEISGE 106 (115)
T ss_dssp HHHTT-EEEEEEEEE-SSSSEEEEEEEEEST
T ss_pred HHHcCCEEEEEecCCCCccceeEEEEEEEcC
Confidence 468999999998743 346999999999986
No 220
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=22.63 E-value=2.8e+02 Score=19.45 Aligned_cols=43 Identities=23% Similarity=0.384 Sum_probs=29.3
Q ss_pred EEEEEEEeCCCCCeEEEEecCCCCCccceEecCCCCCCCCCeEEEE
Q 041421 187 FYAKVVGHDQDKDLAVLHIDAPNHELRPIHVGVSADLHVGQKICAI 232 (315)
Q Consensus 187 ~~a~vv~~d~~~DiAll~v~~~~~~~~~l~l~~~~~~~~G~~v~~i 232 (315)
++++++..+.....|++.... ....+.+.--.++++|++|.+-
T Consensus 5 iP~~Vv~v~~~~~~A~v~~~G---~~~~V~~~lv~~v~~Gd~VLVH 47 (68)
T PF01455_consen 5 IPGRVVEVDEDGGMAVVDFGG---VRREVSLALVPDVKVGDYVLVH 47 (68)
T ss_dssp EEEEEEEEETTTTEEEEEETT---EEEEEEGTTCTSB-TT-EEEEE
T ss_pred ccEEEEEEeCCCCEEEEEcCC---cEEEEEEEEeCCCCCCCEEEEe
Confidence 578888888788999998864 2344444333458999999875
No 221
>PF10049 DUF2283: Protein of unknown function (DUF2283); InterPro: IPR019270 Members of this family of hypothetical proteins have no known function.
Probab=22.43 E-value=53 Score=21.49 Aligned_cols=12 Identities=25% Similarity=0.825 Sum_probs=7.6
Q ss_pred cCCCeEEEEEee
Q 041421 283 DSSGSLIGVNTF 294 (315)
Q Consensus 283 d~~G~vvGI~s~ 294 (315)
|.+|++|||-..
T Consensus 36 d~~G~ivGIEIl 47 (50)
T PF10049_consen 36 DEDGRIVGIEIL 47 (50)
T ss_pred CCCCCEEEEEEE
Confidence 456777777543
No 222
>PRK05007 PII uridylyl-transferase; Provisional
Probab=22.37 E-value=78 Score=33.95 Aligned_cols=52 Identities=13% Similarity=0.213 Sum_probs=36.2
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEE-C-----ChHHHHHHHHHHhhcc
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVS-G-----TDRELQQVVEQLQKLV 52 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~-~-----~~~~~~~~~~ql~k~~ 52 (315)
|++|++.|++.|+||.+-.+.+..++..-=++.|. . +++.+++|.+.|.+.+
T Consensus 715 fa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~d~~g~~~~~~~~~~I~~~L~~aL 772 (884)
T PRK05007 715 FAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLEPDGSPLSQDRHQVIRKALEQAL 772 (884)
T ss_pred HHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEECCCCCCCCHHHHHHHHHHHHHHH
Confidence 46899999999999999988666555544344442 1 2356677777777755
No 223
>KOG2972 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.07 E-value=17 Score=32.48 Aligned_cols=56 Identities=14% Similarity=0.175 Sum_probs=35.6
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhccceEEEee
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
|+.|+..|..+||+|.+.... =-..+.|-+-+. +.+.+.+++.-|+.+.||..|.+
T Consensus 216 l~qV~~~Lr~~G~~i~d~~le--~~P~~~vev~~~-~lEk~qkL~q~L~e~edV~~iy~ 271 (276)
T KOG2972|consen 216 LNQVAHKLRSKGFEIKDSGLE--FIPLEEVEVDVP-ALEKIQKLIQALYENEDVMFIYD 271 (276)
T ss_pred HHHHHHHhhcCCceeeccccc--cccCCccccCcc-chHHHHHHHHHHhhchhHHHHhh
Confidence 456778899999999966531 111222222222 36667777888888888877654
No 224
>cd04603 CBS_pair_KefB_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the KefB (Kef-type K+ transport systems) domain which is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists 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.
Probab=21.83 E-value=58 Score=24.23 Aligned_cols=21 Identities=19% Similarity=0.167 Sum_probs=16.1
Q ss_pred CCccchhccCCCeEEEEEeee
Q 041421 275 GNSGGPLLDSSGSLIGVNTFI 295 (315)
Q Consensus 275 G~SGGPlvd~~G~vvGI~s~~ 295 (315)
+.+--|++|.+|+++|+++..
T Consensus 86 ~~~~lpVvd~~~~~~Giit~~ 106 (111)
T cd04603 86 EPPVVAVVDKEGKLVGTIYER 106 (111)
T ss_pred CCCeEEEEcCCCeEEEEEEhH
Confidence 334458998889999999864
No 225
>PRK08818 prephenate dehydrogenase; Provisional
Probab=21.44 E-value=44 Score=31.94 Aligned_cols=40 Identities=15% Similarity=0.199 Sum_probs=27.3
Q ss_pred CceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHH
Q 041421 1 MNQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRE 40 (315)
Q Consensus 1 l~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~ 40 (315)
|.+|.++|+++|+||.+|......+....+-|-+.+.++.
T Consensus 310 L~~vl~~la~~~INit~Ies~~~r~~~y~f~i~~~~~~~~ 349 (370)
T PRK08818 310 LRTLLHVFEQHGVNLSSIHSSRTPAGELHFRIGFEPGSDR 349 (370)
T ss_pred HHHHHHHHHHcCcccceEEEecccCceEEEEEEEeccccH
Confidence 4578899999999999998733334433366666654443
No 226
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=21.26 E-value=2.5e+02 Score=19.80 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=20.9
Q ss_pred CeEEEEeCCCcEEEEEEEEeCC---CCCeEEE
Q 041421 175 SKVKVSFSDQSTFYAKVVGHDQ---DKDLAVL 203 (315)
Q Consensus 175 ~~~~V~~~~g~~~~a~vv~~d~---~~DiAll 203 (315)
..+.|++.+|..|++-+...++ +.+++|=
T Consensus 13 ~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk 44 (77)
T PF14438_consen 13 QTVEVTTKNGSVYEGIFHSASPESNEFDVVLK 44 (77)
T ss_dssp SEEEEEETTS-EEEEEEEEE-T---T--EEEE
T ss_pred CEEEEEECCCCEEEEEEEeCCCcccceeEEEE
Confidence 5688999999999999999988 6677663
No 227
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=21.19 E-value=2.1e+02 Score=20.42 Aligned_cols=30 Identities=17% Similarity=0.417 Sum_probs=25.0
Q ss_pred EEEEEEECChHHHHHHHHHHhhccceEEEee
Q 041421 29 LFTIVVSGTDRELQQVVEQLQKLVNVLNVST 59 (315)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~ql~k~~~v~~v~~ 59 (315)
.++|-+.|+.+.++.+++.|.+ ..++++..
T Consensus 37 ~~iie~tG~~~kid~fi~~l~~-~gi~Ei~R 66 (75)
T PF10369_consen 37 SIIIELTGTPEKIDAFIKLLKP-FGILEIAR 66 (75)
T ss_dssp EEEEEEEE-HHHHHHHHHHSTG-GGEEEEEE
T ss_pred EEEEEEcCCHHHHHHHHHHhhh-cCCEEEEc
Confidence 5888888999999999999999 77777654
No 228
>PRK07431 aspartate kinase; Provisional
Probab=20.98 E-value=75 Score=32.22 Aligned_cols=36 Identities=11% Similarity=0.099 Sum_probs=26.2
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECC
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGT 37 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~ 37 (315)
+||.+.|.+.|.||+.++-...+.+...+.+++..+
T Consensus 286 a~if~~l~~~~I~v~~i~qs~~~~~~~~isf~i~~~ 321 (587)
T PRK07431 286 AQLFEELAAQGVNVDLIIQSIHEGNSNDIAFTVAEN 321 (587)
T ss_pred HHHHHHHHHcCCcEEEEEeccCCCCCccEEEEEeHH
Confidence 567788999999999998544445556677777643
No 229
>PF02566 OsmC: OsmC-like protein; InterPro: IPR003718 Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. The transcription of the osmC gene of E. coli is regulated as a function of the phase of growth and is induced during the late exponential phase when the growth rate slows before entry into stationary phase. The transcription is initiated by two overlapping promoters, osmCp1 and osmCp2 []. An organic hydroperoxide detoxification protein (OHR) from Xanthomonas campestris pv. phaseoli is highly induced by organic hydroperoxides, weakly induced by H2O2, and not induced at all by a superoxide generator. Ohr may be a new type of organic hydroperoxide detoxification protein [, ].; GO: 0006950 response to stress; PDB: 2D7V_A 2BJO_A 1USP_A 2PN2_A 2QL8_A 1N2F_A 1UKK_A 1VLA_D 3CJE_A 2ONF_B ....
Probab=20.97 E-value=2e+02 Score=20.99 Aligned_cols=45 Identities=27% Similarity=0.372 Sum_probs=26.6
Q ss_pred eccccCceEeeeeec-c-C--CCC---eeEEE--EEEE--CCh--HHHHHHHHHHhhc
Q 041421 7 VFARRKYNIESLAAI-G-L--DKD---RALFT--IVVS--GTD--RELQQVVEQLQKL 51 (315)
Q Consensus 7 ~f~rr~~ni~s~~~~-~-~--~~~---~~~~~--~~~~--~~~--~~~~~~~~ql~k~ 51 (315)
.+.++|+.++++.+. . + .++ +.++. +.+. +++ +.++.+++..+|.
T Consensus 27 ~a~~~gi~~~~~~v~v~~~~~~~~~~~~~~i~~~~~v~~~~~~~~~~~~~~~~~a~~~ 84 (100)
T PF02566_consen 27 VAEKRGIDLEDLEVEVEGELDPEGPRRFESIHLRITVKSDGDDDEEELEELLERAEKR 84 (100)
T ss_dssp HHHHTT-EEEEEEEEEEEEEETTTCECEEEEEEEEEEEETTSHHHHHHHHHHHHHHHH
T ss_pred HHHHcCCCcceEEEEEEEEEeecCCccceEEEEEEEEEcCCCCcHHHHHHHHHHHHhh
Confidence 467899999999872 1 1 122 55544 4443 333 6677777766553
No 230
>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=20.28 E-value=73 Score=21.57 Aligned_cols=43 Identities=19% Similarity=0.375 Sum_probs=26.3
Q ss_pred ceeeeeccccCceEeeeeeccCCCCeeEEEEEEECChHHHHHHHHHHhhc
Q 041421 2 NQIAGVFARRKYNIESLAAIGLDKDRALFTIVVSGTDRELQQVVEQLQKL 51 (315)
Q Consensus 2 ~ri~~~f~rr~~ni~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~k~ 51 (315)
.|+...+.+.++|+..++- .-.++.+++. ++..++.++.|++-
T Consensus 19 ~~if~aL~~~~I~v~~~~~-----Se~~is~~v~--~~~~~~av~~Lh~~ 61 (64)
T cd04937 19 AKIVGALSKEGIEILQTAD-----SHTTISCLVS--EDDVKEAVNALHEA 61 (64)
T ss_pred HHHHHHHHHCCCCEEEEEc-----CccEEEEEEc--HHHHHHHHHHHHHH
Confidence 3555667889999976652 1224555554 55566677776664
No 231
>cd04620 CBS_pair_7 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=20.27 E-value=62 Score=24.02 Aligned_cols=21 Identities=38% Similarity=0.437 Sum_probs=16.6
Q ss_pred CCccchhccCCCeEEEEEeee
Q 041421 275 GNSGGPLLDSSGSLIGVNTFI 295 (315)
Q Consensus 275 G~SGGPlvd~~G~vvGI~s~~ 295 (315)
+...-|++|.+|+++|+++..
T Consensus 90 ~~~~~pVvd~~~~~~Gvit~~ 110 (115)
T cd04620 90 QIRHLPVLDDQGQLIGLVTAE 110 (115)
T ss_pred CCceEEEEcCCCCEEEEEEhH
Confidence 334568998889999999864
Done!