Query 001276
Match_columns 1109
No_of_seqs 795 out of 5659
Neff 7.7
Searched_HMMs 46136
Date Thu Mar 28 20:32:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001276.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001276hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1421 Predicted signaling-as 100.0 8E-155 2E-159 1297.2 75.7 917 19-1101 35-953 (955)
2 PRK10139 serine endoprotease; 100.0 6.8E-53 1.5E-57 496.1 47.6 378 36-456 40-447 (455)
3 TIGR02037 degP_htrA_DO peripla 100.0 1.3E-52 2.8E-57 495.9 47.3 384 37-456 2-421 (428)
4 PRK10942 serine endoprotease; 100.0 1.1E-50 2.3E-55 479.8 48.0 378 36-456 38-465 (473)
5 PRK10139 serine endoprotease; 100.0 3.1E-50 6.7E-55 473.6 46.1 390 619-1076 43-455 (455)
6 TIGR02037 degP_htrA_DO peripla 100.0 6.2E-50 1.3E-54 473.1 44.7 395 621-1074 6-427 (428)
7 KOG1421 Predicted signaling-as 100.0 7.1E-50 1.5E-54 450.8 37.6 442 621-1107 57-504 (955)
8 PRK10942 serine endoprotease; 100.0 7.3E-49 1.6E-53 464.1 45.5 360 649-1075 110-472 (473)
9 TIGR02038 protease_degS peripl 100.0 3.3E-44 7.1E-49 411.4 37.3 300 32-367 41-349 (351)
10 PRK10898 serine endoprotease; 100.0 1.4E-43 3E-48 405.7 38.4 301 32-368 41-351 (353)
11 TIGR02038 protease_degS peripl 100.0 4E-39 8.6E-44 369.4 36.0 299 619-974 48-349 (351)
12 PRK10898 serine endoprotease; 100.0 1.7E-38 3.7E-43 363.7 33.9 300 620-975 49-351 (353)
13 COG0265 DegQ Trypsin-like seri 100.0 2E-33 4.4E-38 324.1 33.1 295 36-367 33-341 (347)
14 COG0265 DegQ Trypsin-like seri 100.0 1.2E-28 2.6E-33 284.4 29.7 294 620-973 37-340 (347)
15 KOG1320 Serine protease [Postt 99.9 1.4E-22 2.9E-27 231.7 23.5 316 34-365 126-467 (473)
16 KOG1320 Serine protease [Postt 99.8 3.2E-18 6.9E-23 196.0 22.3 309 621-972 133-467 (473)
17 KOG3209 WW domain-containing p 99.7 1.1E-15 2.3E-20 175.5 27.8 178 257-457 349-566 (984)
18 PRK10779 zinc metallopeptidase 99.7 3.2E-16 7E-21 186.4 19.4 157 903-1078 129-289 (449)
19 TIGR00054 RIP metalloprotease 99.6 6.8E-14 1.5E-18 164.9 17.9 144 900-1079 128-272 (420)
20 PRK10779 zinc metallopeptidase 99.5 7.1E-14 1.5E-18 166.4 17.3 143 302-456 130-279 (449)
21 PF12812 PDZ_1: PDZ-like domai 99.5 3.3E-14 7.1E-19 125.6 7.8 76 369-444 1-77 (78)
22 PF13365 Trypsin_2: Trypsin-li 99.5 1.9E-13 4.1E-18 132.5 12.5 110 70-216 1-120 (120)
23 TIGR00054 RIP metalloprotease 99.4 3.3E-12 7.1E-17 150.7 15.4 131 297-456 128-261 (420)
24 PF13180 PDZ_2: PDZ domain; PD 99.2 7.3E-11 1.6E-15 106.7 11.0 68 296-364 13-82 (82)
25 PF12812 PDZ_1: PDZ-like domai 99.2 1.3E-10 2.7E-15 102.9 8.6 76 977-1056 2-78 (78)
26 PF13180 PDZ_2: PDZ domain; PD 99.1 6.1E-10 1.3E-14 100.7 11.2 69 1008-1077 14-82 (82)
27 PF13365 Trypsin_2: Trypsin-li 99.0 1.3E-09 2.9E-14 105.4 10.7 55 652-710 1-65 (120)
28 cd00987 PDZ_serine_protease PD 98.9 7.3E-09 1.6E-13 95.2 11.7 87 261-361 1-89 (90)
29 cd00987 PDZ_serine_protease PD 98.9 8E-09 1.7E-13 94.9 11.2 88 985-1074 2-89 (90)
30 cd00986 PDZ_LON_protease PDZ d 98.8 2.5E-08 5.4E-13 89.4 10.9 70 297-367 8-78 (79)
31 cd00991 PDZ_archaeal_metallopr 98.8 2.9E-08 6.2E-13 89.1 10.7 68 1008-1076 10-77 (79)
32 cd00991 PDZ_archaeal_metallopr 98.8 2.7E-08 5.8E-13 89.3 10.5 68 295-363 8-77 (79)
33 cd00986 PDZ_LON_protease PDZ d 98.7 9.8E-08 2.1E-12 85.6 10.6 69 1008-1078 8-76 (79)
34 cd00990 PDZ_glycyl_aminopeptid 98.7 1E-07 2.2E-12 85.6 10.3 66 297-365 12-78 (80)
35 cd00989 PDZ_metalloprotease PD 98.7 1.6E-07 3.4E-12 84.1 10.7 66 1009-1076 13-78 (79)
36 PF00089 Trypsin: Trypsin; In 98.7 5.3E-07 1.2E-11 96.7 16.0 176 47-238 13-219 (220)
37 TIGR01713 typeII_sec_gspC gene 98.6 3E-07 6.4E-12 101.1 14.1 99 233-364 159-259 (259)
38 cd00989 PDZ_metalloprotease PD 98.6 2.1E-07 4.5E-12 83.3 9.0 63 300-362 14-77 (79)
39 cd00988 PDZ_CTP_protease PDZ d 98.6 3.5E-07 7.5E-12 83.1 10.1 66 297-363 13-82 (85)
40 cd00988 PDZ_CTP_protease PDZ d 98.5 5.7E-07 1.2E-11 81.7 9.7 68 1008-1077 13-83 (85)
41 cd00990 PDZ_glycyl_aminopeptid 98.5 7.7E-07 1.7E-11 79.9 9.9 66 1009-1078 13-78 (80)
42 TIGR01713 typeII_sec_gspC gene 98.5 1.1E-06 2.5E-11 96.5 13.2 99 833-970 159-258 (259)
43 KOG3580 Tight junction protein 98.5 6.3E-07 1.4E-11 102.4 11.2 56 1008-1063 429-486 (1027)
44 KOG3209 WW domain-containing p 98.4 2.5E-06 5.5E-11 99.7 13.3 146 300-452 676-834 (984)
45 cd00190 Tryp_SPc Trypsin-like 98.3 8.3E-06 1.8E-10 88.1 15.4 162 46-221 12-208 (232)
46 cd00136 PDZ PDZ domain, also c 98.3 2.8E-06 6.1E-11 74.0 8.2 53 298-351 14-69 (70)
47 KOG3580 Tight junction protein 98.2 7.5E-06 1.6E-10 93.9 12.6 158 296-456 218-490 (1027)
48 cd00136 PDZ PDZ domain, also c 98.2 3.6E-06 7.8E-11 73.4 7.8 53 1009-1062 14-68 (70)
49 smart00020 Tryp_SPc Trypsin-li 98.2 4E-05 8.7E-10 82.9 16.4 153 66-221 24-208 (229)
50 PF00863 Peptidase_C4: Peptida 98.0 0.0001 2.2E-09 78.9 15.3 165 44-233 15-185 (235)
51 COG3591 V8-like Glu-specific e 98.0 2.8E-05 6.1E-10 83.7 11.0 178 47-242 38-249 (251)
52 PF14685 Tricorn_PDZ: Tricorn 98.0 4.6E-05 1E-09 69.1 9.7 64 297-360 11-86 (88)
53 smart00228 PDZ Domain present 98.0 3.6E-05 7.8E-10 69.5 8.7 58 297-355 26-85 (85)
54 PF00595 PDZ: PDZ domain (Also 97.9 2.9E-05 6.2E-10 69.9 7.8 54 297-352 25-81 (81)
55 TIGR00225 prc C-terminal pepti 97.9 2.7E-05 5.9E-10 89.8 9.0 67 300-366 64-133 (334)
56 PF00595 PDZ: PDZ domain (Also 97.9 3.5E-05 7.6E-10 69.3 7.5 53 1008-1062 25-79 (81)
57 cd00992 PDZ_signaling PDZ doma 97.9 4.4E-05 9.6E-10 68.6 8.0 53 1008-1062 26-80 (82)
58 KOG3834 Golgi reassembly stack 97.9 0.00018 3.8E-09 81.1 14.0 164 899-1081 14-183 (462)
59 TIGR02860 spore_IV_B stage IV 97.9 9.4E-05 2E-09 85.2 12.2 68 1008-1077 105-180 (402)
60 TIGR03279 cyano_FeS_chp putati 97.9 2.8E-05 6E-10 90.0 7.9 64 1012-1079 2-65 (433)
61 smart00228 PDZ Domain present 97.9 4.4E-05 9.5E-10 68.9 7.8 59 1008-1067 26-84 (85)
62 PLN00049 carboxyl-terminal pro 97.9 6.9E-05 1.5E-09 88.0 11.3 76 1009-1086 103-180 (389)
63 TIGR00225 prc C-terminal pepti 97.8 9.3E-05 2E-09 85.4 10.9 77 1009-1087 63-143 (334)
64 TIGR03279 cyano_FeS_chp putati 97.8 5.3E-05 1.1E-09 87.7 8.5 59 303-364 3-63 (433)
65 TIGR02860 spore_IV_B stage IV 97.8 0.0001 2.3E-09 84.8 10.2 68 296-363 104-179 (402)
66 PLN00049 carboxyl-terminal pro 97.7 9.9E-05 2.2E-09 86.7 9.8 66 298-364 103-171 (389)
67 cd00992 PDZ_signaling PDZ doma 97.7 0.00011 2.3E-09 66.1 7.3 53 297-351 26-81 (82)
68 PF04495 GRASP55_65: GRASP55/6 97.6 0.0002 4.2E-09 71.0 8.8 73 1008-1081 43-117 (138)
69 PF00089 Trypsin: Trypsin; In 97.5 0.0018 4E-08 69.1 15.2 169 649-839 24-220 (220)
70 COG0793 Prc Periplasmic protea 97.5 0.00029 6.3E-09 82.8 9.6 78 1009-1088 113-194 (406)
71 COG0793 Prc Periplasmic protea 97.4 0.00036 7.9E-09 81.9 8.6 67 298-364 112-183 (406)
72 PF14685 Tricorn_PDZ: Tricorn 97.3 0.002 4.2E-08 58.6 10.0 64 900-968 12-87 (88)
73 PF04495 GRASP55_65: GRASP55/6 97.2 0.00081 1.8E-08 66.7 7.2 86 260-365 25-114 (138)
74 KOG3834 Golgi reassembly stack 97.2 0.0046 1E-07 70.1 13.8 163 300-475 17-185 (462)
75 KOG3605 Beta amyloid precursor 97.2 0.0007 1.5E-08 79.4 7.3 115 304-441 679-802 (829)
76 KOG3553 Tax interaction protei 97.2 0.00035 7.5E-09 62.7 3.5 57 1008-1068 59-117 (124)
77 KOG3605 Beta amyloid precursor 97.1 0.00064 1.4E-08 79.8 6.5 120 904-1052 677-802 (829)
78 COG3480 SdrC Predicted secrete 97.1 0.0013 2.9E-08 71.8 8.4 71 296-367 129-201 (342)
79 KOG3129 26S proteasome regulat 97.1 0.0012 2.6E-08 67.8 7.4 73 297-369 138-214 (231)
80 PRK09681 putative type II secr 97.1 0.0017 3.6E-08 71.4 9.1 68 296-364 203-275 (276)
81 PRK09681 putative type II secr 97.0 0.0017 3.7E-08 71.2 8.3 62 906-971 210-275 (276)
82 COG3480 SdrC Predicted secrete 97.0 0.0021 4.6E-08 70.3 8.3 69 1008-1077 130-198 (342)
83 PRK11186 carboxy-terminal prot 97.0 0.0022 4.9E-08 79.3 9.4 69 1009-1079 256-335 (667)
84 cd00190 Tryp_SPc Trypsin-like 96.9 0.012 2.6E-07 63.3 14.0 94 648-748 23-133 (232)
85 COG3975 Predicted protease wit 96.9 0.0013 2.9E-08 76.5 6.2 86 263-368 439-526 (558)
86 PRK11186 carboxy-terminal prot 96.9 0.0026 5.7E-08 78.7 9.0 66 298-363 255-332 (667)
87 PF00863 Peptidase_C4: Peptida 96.8 0.017 3.7E-07 62.1 13.3 176 624-842 15-196 (235)
88 KOG3129 26S proteasome regulat 96.7 0.005 1.1E-07 63.4 7.8 69 1009-1079 140-211 (231)
89 smart00020 Tryp_SPc Trypsin-li 96.7 0.023 4.9E-07 61.3 13.5 93 648-748 24-133 (229)
90 COG3031 PulC Type II secretory 96.4 0.0074 1.6E-07 63.4 6.9 66 901-970 208-274 (275)
91 COG3031 PulC Type II secretory 96.2 0.0082 1.8E-07 63.0 6.2 62 302-363 211-274 (275)
92 KOG3553 Tax interaction protei 95.9 0.02 4.3E-07 51.8 6.2 46 396-441 56-105 (124)
93 PF10459 Peptidase_S46: Peptid 95.8 0.027 5.8E-07 70.3 8.8 42 117-158 200-252 (698)
94 PF05579 Peptidase_S32: Equine 95.7 0.072 1.6E-06 57.2 10.4 116 67-221 111-229 (297)
95 COG3975 Predicted protease wit 95.7 0.017 3.7E-07 67.5 6.3 76 984-1081 451-526 (558)
96 PF05580 Peptidase_S55: SpoIVB 95.3 0.18 3.9E-06 53.1 11.7 168 66-236 18-216 (218)
97 PF02122 Peptidase_S39: Peptid 94.6 0.0096 2.1E-07 62.8 0.2 144 66-232 28-181 (203)
98 PF10459 Peptidase_S46: Peptid 94.6 0.037 8E-07 69.0 5.0 53 191-243 624-687 (698)
99 KOG3532 Predicted protein kina 94.3 0.097 2.1E-06 62.3 7.3 51 295-345 395-446 (1051)
100 COG3591 V8-like Glu-specific e 94.1 0.93 2E-05 49.5 13.7 167 651-843 65-250 (251)
101 KOG3550 Receptor targeting pro 94.0 0.23 4.9E-06 48.5 7.9 54 297-352 115-172 (207)
102 KOG3532 Predicted protein kina 93.6 0.14 3.1E-06 60.9 7.0 46 900-945 398-444 (1051)
103 KOG3552 FERM domain protein FR 93.5 0.074 1.6E-06 65.3 4.6 53 300-353 77-131 (1298)
104 KOG3542 cAMP-regulated guanine 93.0 0.097 2.1E-06 62.0 4.3 55 1007-1062 561-615 (1283)
105 PF00949 Peptidase_S7: Peptida 93.0 0.083 1.8E-06 51.8 3.2 31 191-221 88-118 (132)
106 KOG3550 Receptor targeting pro 92.7 0.27 5.8E-06 48.0 6.1 52 1009-1062 116-170 (207)
107 PF00548 Peptidase_C3: 3C cyst 92.4 1.3 2.8E-05 46.0 11.3 139 66-220 23-170 (172)
108 KOG1892 Actin filament-binding 92.1 0.19 4.1E-06 61.9 5.3 61 295-356 958-1021(1629)
109 KOG3571 Dishevelled 3 and rela 91.2 0.63 1.4E-05 54.2 7.9 86 377-484 261-351 (626)
110 KOG3542 cAMP-regulated guanine 91.1 0.18 4E-06 59.8 3.7 53 399-452 562-616 (1283)
111 PF08192 Peptidase_S64: Peptid 90.6 0.99 2.2E-05 54.8 9.2 121 114-242 540-688 (695)
112 PF03761 DUF316: Domain of unk 90.1 8 0.00017 43.4 15.9 109 115-236 159-272 (282)
113 KOG3571 Dishevelled 3 and rela 89.9 0.9 1.9E-05 53.0 7.7 72 983-1062 260-335 (626)
114 KOG3552 FERM domain protein FR 89.5 0.41 8.9E-06 59.2 4.9 56 900-961 75-132 (1298)
115 KOG3651 Protein kinase C, alph 87.8 0.99 2.1E-05 49.2 5.8 54 297-352 30-87 (429)
116 KOG0606 Microtubule-associated 86.9 0.9 2E-05 58.0 5.7 51 1011-1063 661-713 (1205)
117 COG0750 Predicted membrane-ass 86.6 1.9 4.2E-05 50.6 8.2 56 304-359 135-195 (375)
118 KOG3606 Cell polarity protein 86.5 1.1 2.5E-05 48.0 5.4 54 1009-1062 195-251 (358)
119 PF11874 DUF3394: Domain of un 86.4 2.5 5.5E-05 43.9 7.7 83 934-1035 62-149 (183)
120 KOG1892 Actin filament-binding 86.4 0.43 9.2E-06 59.0 2.4 65 895-963 955-1021(1629)
121 KOG3627 Trypsin [Amino acid tr 86.0 17 0.00038 39.8 15.0 147 69-222 39-229 (256)
122 COG0750 Predicted membrane-ass 84.6 3.3 7.1E-05 48.6 8.8 58 1011-1070 132-193 (375)
123 KOG2921 Intramembrane metallop 84.5 1.3 2.9E-05 50.2 5.0 46 1007-1052 219-265 (484)
124 PF00944 Peptidase_S3: Alphavi 83.7 0.93 2E-05 43.8 2.9 33 190-222 96-128 (158)
125 KOG0609 Calcium/calmodulin-dep 83.2 2 4.3E-05 51.0 5.9 74 1009-1084 147-226 (542)
126 KOG3551 Syntrophins (type beta 82.7 0.88 1.9E-05 51.3 2.7 52 300-351 112-166 (506)
127 PF00548 Peptidase_C3: 3C cyst 82.6 20 0.00043 37.2 12.5 151 623-809 9-169 (172)
128 KOG3606 Cell polarity protein 81.4 2.1 4.6E-05 46.1 4.8 46 399-444 194-244 (358)
129 KOG2921 Intramembrane metallop 77.1 3.4 7.4E-05 47.0 5.0 46 295-341 218-265 (484)
130 PF08192 Peptidase_S64: Peptid 76.2 19 0.00042 44.2 11.2 125 699-842 540-688 (695)
131 KOG0609 Calcium/calmodulin-dep 75.0 5.5 0.00012 47.4 6.2 53 299-352 147-203 (542)
132 KOG3549 Syntrophins (type gamm 73.6 3.8 8.1E-05 45.7 4.1 53 300-352 82-137 (505)
133 KOG3551 Syntrophins (type beta 72.8 3.5 7.7E-05 46.7 3.7 52 1009-1062 111-165 (506)
134 PF11874 DUF3394: Domain of un 71.1 22 0.00049 37.0 8.8 79 333-424 63-149 (183)
135 KOG3938 RGS-GAIP interacting p 70.3 10 0.00022 41.1 6.3 51 405-455 157-210 (334)
136 PF01732 DUF31: Putative pepti 68.2 3.3 7.2E-05 48.7 2.5 29 191-219 346-374 (374)
137 PF03510 Peptidase_C24: 2C end 67.6 18 0.0004 34.0 6.7 52 72-135 3-54 (105)
138 KOG3651 Protein kinase C, alph 65.8 14 0.00031 40.6 6.3 56 898-959 28-87 (429)
139 KOG0606 Microtubule-associated 64.3 9.4 0.0002 49.3 5.4 49 299-349 660-711 (1205)
140 KOG3549 Syntrophins (type gamm 63.3 6.1 0.00013 44.1 3.1 68 1009-1078 81-151 (505)
141 PF05416 Peptidase_C37: Southa 58.1 18 0.00039 41.8 5.7 137 68-222 379-528 (535)
142 PF02907 Peptidase_S29: Hepati 55.1 8.3 0.00018 37.6 2.1 114 71-220 15-128 (148)
143 PF12381 Peptidase_C3G: Tungro 52.1 18 0.0004 38.3 4.2 57 188-244 168-230 (231)
144 KOG3938 RGS-GAIP interacting p 51.6 13 0.00029 40.2 3.2 56 1010-1065 151-209 (334)
145 PF00949 Peptidase_S7: Peptida 49.4 14 0.0003 36.5 2.7 27 782-809 90-116 (132)
146 COG5233 GRH1 Peripheral Golgi 47.8 35 0.00077 38.0 5.7 68 1016-1083 195-265 (417)
147 COG0298 HypC Hydrogenase matur 38.0 57 0.0012 29.1 4.4 48 690-745 4-52 (82)
148 KOG4371 Membrane-associated pr 34.7 78 0.0017 40.9 6.5 116 314-432 1186-1306(1332)
149 cd01735 LSm12_N LSm12 belongs 31.8 99 0.0021 26.3 4.7 32 679-711 8-39 (61)
150 PF00947 Pico_P2A: Picornaviru 31.2 56 0.0012 31.9 3.6 34 187-221 77-110 (127)
151 KOG4407 Predicted Rho GTPase-a 29.4 36 0.00078 44.7 2.5 86 303-443 101-191 (1973)
152 KOG1738 Membrane-associated gu 28.9 32 0.00069 42.0 1.9 37 297-333 224-262 (638)
153 cd01726 LSm6 The eukaryotic Sm 26.1 97 0.0021 26.6 4.0 30 679-709 12-41 (67)
154 cd00600 Sm_like The eukaryotic 25.4 1.2E+02 0.0026 25.3 4.4 31 678-709 7-37 (63)
155 cd01732 LSm5 The eukaryotic Sm 25.3 1.1E+02 0.0024 27.2 4.2 30 678-708 14-43 (76)
156 PF01455 HupF_HypC: HupF/HypC 25.2 1.5E+02 0.0034 25.7 5.0 44 690-742 4-47 (68)
157 PF14275 DUF4362: Domain of un 25.1 2E+02 0.0044 26.9 6.0 53 416-470 1-53 (98)
158 cd01735 LSm12_N LSm12 belongs 24.5 1.9E+02 0.0041 24.6 5.2 32 95-126 8-39 (61)
159 PF00944 Peptidase_S3: Alphavi 24.2 1E+02 0.0023 30.2 4.0 23 791-813 107-129 (158)
160 cd06168 LSm9 The eukaryotic Sm 23.7 1.3E+02 0.0028 26.6 4.4 29 679-708 12-40 (75)
161 cd01717 Sm_B The eukaryotic Sm 23.5 1.1E+02 0.0024 27.3 4.0 29 679-708 12-40 (79)
162 cd01722 Sm_F The eukaryotic Sm 23.2 1.2E+02 0.0026 26.2 4.0 30 679-709 13-42 (68)
163 cd01730 LSm3 The eukaryotic Sm 22.5 1.1E+02 0.0024 27.6 3.7 29 678-707 12-40 (82)
164 cd01719 Sm_G The eukaryotic Sm 21.8 1.5E+02 0.0032 26.0 4.3 56 679-743 12-67 (72)
165 PRK00737 small nuclear ribonuc 21.6 1.4E+02 0.003 26.1 4.1 30 679-709 16-45 (72)
166 cd01731 archaeal_Sm1 The archa 21.6 1.4E+02 0.003 25.7 4.1 31 678-709 11-41 (68)
167 cd01728 LSm1 The eukaryotic Sm 21.3 1.6E+02 0.0034 26.1 4.3 60 678-743 13-72 (74)
168 cd01729 LSm7 The eukaryotic Sm 21.1 1.5E+02 0.0032 26.7 4.3 30 678-708 13-42 (81)
169 PF05579 Peptidase_S32: Equine 20.9 2.2E+02 0.0048 31.5 6.1 19 791-809 209-227 (297)
170 KOG1738 Membrane-associated gu 20.2 1.2E+02 0.0025 37.4 4.3 45 900-945 225-271 (638)
No 1
>KOG1421 consensus Predicted signaling-associated protein (contains a PDZ domain) [General function prediction only]
Probab=100.00 E-value=8.3e-155 Score=1297.17 Aligned_cols=917 Identities=45% Similarity=0.715 Sum_probs=855.0
Q ss_pred cccccCCCCCcCCcCCcchHHHHHHHhCCceEEEEEEeeeccCCCCCCccEEEEEEEeCCCcEEEeCccccCCCCeEEEE
Q 001276 19 DMCMEVDPPLRENVATADDWRKALNKVVPAVVVLRTTACRAFDTEAAGASYATGFVVDKRRGIILTNRHVVKPGPVVAEA 98 (1109)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sVV~I~~~~~~~~d~~~~~~~~GSGfvV~~~~G~IlTn~HVv~~~~~~~~v 98 (1109)
+.+.+..|+.....+...+|+..+..+.+|||+|++++.+.||++.++.+.||||+|++..|||||||||++.++....+
T Consensus 35 el~~e~~p~~~~s~~~~e~w~~~ia~VvksvVsI~~S~v~~fdtesag~~~atgfvvd~~~gyiLtnrhvv~pgP~va~a 114 (955)
T KOG1421|consen 35 ELVIEPDPPLNESLATSEDWRNTIANVVKSVVSIRFSAVRAFDTESAGESEATGFVVDKKLGYILTNRHVVAPGPFVASA 114 (955)
T ss_pred ccccccCCCCCcccchhhhhhhhhhhhcccEEEEEehheeecccccccccceeEEEEecccceEEEeccccCCCCceeEE
Confidence 34555555555556667799999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCeEEEEEEEEEcCCCcEEEEEEcCCCcccccccCCCCCCccCCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCC
Q 001276 99 MFVNREEIPVYPIYRDPVHDFGFFRYDPSAIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHY 178 (1109)
Q Consensus 99 ~~~~~~~~~a~vv~~d~~~DlAlLk~~~~~~~~~~l~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~vs~~~~~~~~~ 178 (1109)
.|.|.++++..++|+||.|||+++|++|+.+.+..+..++++++.+++|.+++++||++++++++..|++++++|++|.|
T Consensus 115 vf~n~ee~ei~pvyrDpVhdfGf~r~dps~ir~s~vt~i~lap~~akvgseirvvgNDagEklsIlagflSrldr~apdy 194 (955)
T KOG1421|consen 115 VFDNHEEIEIYPVYRDPVHDFGFFRYDPSTIRFSIVTEICLAPELAKVGSEIRVVGNDAGEKLSILAGFLSRLDRNAPDY 194 (955)
T ss_pred EecccccCCcccccCCchhhcceeecChhhcceeeeeccccCccccccCCceEEecCCccceEEeehhhhhhccCCCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccccceeeEEEeeccCCCCCCCceecCCCcEEEEeccccCCCCCccccchHHHHHHHHHHHhcCCccccccccccc
Q 001276 179 KKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSSSASAFFLPLERVVRALRFLQERRDCNIHNWEAVSI 258 (1109)
Q Consensus 179 ~~~~~~~~~~~~iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~~~~~falP~~~i~~~l~~l~~~~~~~~~~~~~~~v 258 (1109)
+...|+|||++|+|..+..++|+||+||+|.+|++|+++++++..++.+|+||+++++|+|.++++++ ++
T Consensus 195 g~~~yndfnTfy~QaasstsggssgspVv~i~gyAVAl~agg~~ssas~ffLpLdrV~RaL~clq~n~----------PI 264 (955)
T KOG1421|consen 195 GEDTYNDFNTFYIQAASSTSGGSSGSPVVDIPGYAVALNAGGSISSASDFFLPLDRVVRALRCLQNNT----------PI 264 (955)
T ss_pred cccccccccceeeeehhcCCCCCCCCceecccceEEeeecCCcccccccceeeccchhhhhhhhhcCC----------Cc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999 89
Q ss_pred CCCccceEEEEcChhHHHHcCCChhHHHhhhcCCCCCCCceEEEEEecCCCccccCCCCCCEEEEECCEEeCChhHHHHH
Q 001276 259 PRGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHLRLEPGDVLVRVNGEVITQFLKLETL 338 (1109)
Q Consensus 259 ~rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~gL~~GD~Il~VnG~~v~~~~~l~~~ 338 (1109)
+||+|+++|.+++|||||||||+.|||+.+|.++| ..+|||||+.|+++|||++.|++||++++||+..+.+|..+..+
T Consensus 265 tRGtLqvefl~k~~de~rrlGL~sE~eqv~r~k~P-~~tgmLvV~~vL~~gpa~k~Le~GDillavN~t~l~df~~l~~i 343 (955)
T KOG1421|consen 265 TRGTLQVEFLHKLFDECRRLGLSSEWEQVVRTKFP-ERTGMLVVETVLPEGPAEKKLEPGDILLAVNSTCLNDFEALEQI 343 (955)
T ss_pred ccceEEEEEehhhhHHHHhcCCcHHHHHHHHhcCc-ccceeEEEEEeccCCchhhccCCCcEEEEEcceehHHHHHHHHH
Confidence 99999999999999999999999999999999999 89999999999999999999999999999999999999999999
Q ss_pred HhcCCCCeEEEEEEECCEEEEEEEEeecCCCCCCCccccccceEEecCCHHHhhccCCCCCeEEEEcCCChhHHcCCCCC
Q 001276 339 LDDGVDKNIELLIERGGISMTVNLVVQDLHSITPDYFLEVSGAVIHPLSYQQARNFRFPCGLVYVAEPGYMLFRAGVPRH 418 (1109)
Q Consensus 339 l~~~~g~~v~l~v~R~g~~~~~~v~l~~~~~~~~~~~~~~~G~~~~~l~~~~~~~~~~~~~gv~v~~pg~~a~~aGl~~G 418 (1109)
|++.+|+.+.|+|+|+|++.+++++++++|.++|+||+++||++||+++||++|.|.+|++|+||+++++.++..+-.-|
T Consensus 344 LDegvgk~l~LtI~Rggqelel~vtvqdlh~itp~R~levcGav~hdlsyq~ar~y~lP~~GvyVa~~~gsf~~~~~~y~ 423 (955)
T KOG1421|consen 344 LDEGVGKNLELTIQRGGQELELTVTVQDLHGITPDRFLEVCGAVFHDLSYQLARLYALPVEGVYVASPGGSFRHRGPRYG 423 (955)
T ss_pred HhhccCceEEEEEEeCCEEEEEEEEeccccCCCCceEEEEcceEecCCCHHHHhhcccccCcEEEccCCCCccccCCcce
Confidence 99999999999999999999999999999999999999999999999999999999999999999998655544443339
Q ss_pred CEEEEcCCeecCCHHHHHHHHHhcCCCCeEeEEEEeecccccceEEEEEEecCCCCCCCeeeeecCCCCCceecccCCCC
Q 001276 419 AIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYSSYTDRHRRKSVLVTIDRHEWYAPPQIYTRNDSSGLWSANPAILSE 498 (1109)
Q Consensus 419 D~I~~Vng~~v~~l~~~~~~i~~~~~g~~v~l~~~~~~~~~~~~~~~l~i~R~~~~~~~~~~~r~d~~g~W~~~~~~~~~ 498 (1109)
++|.+||++++++|++|+++++++++|+||+++|+|++|+|+.++..++||| ||||++++++|||++|+||+.++.+|.
T Consensus 424 ~ii~~vanK~tPdLdaFidvlk~L~dg~rV~vry~hl~dkh~p~v~~v~iDr-Hwy~p~~~~trndetglWdrk~L~~pq 502 (955)
T KOG1421|consen 424 QIIDSVANKPTPDLDAFIDVLKELPDGARVPVRYHHLTDKHSPRVTTVTIDR-HWYWPFREYTRNDETGLWDRKNLKDPQ 502 (955)
T ss_pred EEEEeecCCcCCCHHHHHHHHHhccCCCeeeEEEEEecCCCCceEEEEEEec-cccccceeeeeCCCcccccccccCCCC
Confidence 9999999999999999999999999999999999999999999999999999 999999999999999999999999998
Q ss_pred CCCCCCCCCCCccCcccccccccccccccccccccCccccccCccccccccccccccccccCCCcccccccceeeccccC
Q 001276 499 VLMPSSGINGGVQGVASQTVSICGELVHMEHMHQRNNQELTDGVTSMETACEHASAESISRGESDNGRKKRRVEENISAD 578 (1109)
Q Consensus 499 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 578 (1109)
| +.+.+|.+.+..+
T Consensus 503 P--------------a~~~kP~s~~ip~---------------------------------------------------- 516 (955)
T KOG1421|consen 503 P--------------AISIKPASVSIPS---------------------------------------------------- 516 (955)
T ss_pred c--------------ccccCCccccCCC----------------------------------------------------
Confidence 7 3456665544220
Q ss_pred CccccCCCCCCCCccccccccccccCCCCCCCCCcccCccccccccccccEEEEEEEcCcccccCCcccceeeEEEEEEE
Q 001276 579 GVVADCSPHESGDARLEDSSTMENAGSRDYFGAPAATTNASFAESVIEPTLVMFEVHVPPSCMIDGVHSQHFFGTGVIIY 658 (1109)
Q Consensus 579 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~SvV~V~~~~~~~~~~dg~~~~~~~GsG~VId 658 (1109)
++ ..++..+++..++|.|.+.+| ..+||..+....|||+|++
T Consensus 517 ---------------i~---------------------~~~~~~~~i~~~~~~v~~~~~--~~l~g~s~~i~kgt~~i~d 558 (955)
T KOG1421|consen 517 ---------------IG---------------------VNNFPSADISNCLVDVEPMMP--VNLDGVSSDIYKGTALIMD 558 (955)
T ss_pred ---------------cC---------------------cCCcchhHHhhhhhhheecee--eccccchhhhhcCceEEEE
Confidence 11 112234668899999999999 5999999988999999999
Q ss_pred eeCCceEEEEeCceecCCCCcEEEEeecCCeEEeEEEEEeeCCCcEEEEEECCCCCCcccccceeceecCCCccCCCCCe
Q 001276 659 HSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGEVVFLHPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDS 738 (1109)
Q Consensus 659 ~~~~~G~IlTn~~~V~~~~~di~V~~~d~~~~~~a~vv~~dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~ 738 (1109)
..+|+++++|.+|+.+++|++|+++| +..++|.+.|+||.+|+|++||||+..-. ++|.+.. +++||+
T Consensus 559 --~~~g~~vvsr~~vp~d~~d~~vt~~d-S~~i~a~~~fL~~t~n~a~~kydp~~~~~--------~kl~~~~-v~~gD~ 626 (955)
T KOG1421|consen 559 --TSKGLGVVSRSVVPSDAKDQRVTEAD-SDGIPANVSFLHPTENVASFKYDPALEVQ--------LKLTDTT-VLRGDE 626 (955)
T ss_pred --ccCCceeEecccCCchhhceEEeecc-cccccceeeEecCccceeEeccChhHhhh--------hccceee-EecCCc
Confidence 47999999999999999999999998 99999999999999999999999986643 7887765 999999
Q ss_pred EEEEeeCCCCcceeeeeeEeccccccccCCCCCCcccccceeEEEEecccCCCC-CceEEcCCeeEEEEEeecccccccc
Q 001276 739 VYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRAMNMEVIELDTDFGSTF-SGVLTDEHGRVQAIWGSFSTQVKFG 817 (1109)
Q Consensus 739 V~~iG~p~~~~~~~~~~~vt~i~~~~~i~~~~~~~y~~~~~~~I~~d~~ig~~s-GGpL~d~~G~VvGi~~~~~~~~~~g 817 (1109)
+.+.|+..+++.++++++|++++ ..++++...||||++|+++|.++++++..| .|.|.|.||+|+|+|+.+.++.
T Consensus 627 ~~f~g~~~~~r~ltaktsv~dvs-~~~~ps~~~pr~r~~n~e~Is~~~nlsT~c~sg~ltdddg~vvalwl~~~ge~--- 702 (955)
T KOG1421|consen 627 CTFEGFTEDLRALTAKTSVTDVS-VVIIPSSVMPRFRATNLEVISFMDNLSTSCLSGRLTDDDGEVVALWLSVVGED--- 702 (955)
T ss_pred eeEecccccchhhcccceeeeeE-EEEecCCCCcceeecceEEEEEeccccccccceEEECCCCeEEEEEeeeeccc---
Confidence 99999999999999999999987 778999999999999999999999998767 9999999999999999988873
Q ss_pred CCCCCCceeEecccHHHHHHHHHHHHcCCCCCcccccccccCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCC
Q 001276 818 CSSSEDHQFVRGIPIYTISRVLDKIISGASGPSLLINGVKRPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPV 897 (1109)
Q Consensus 818 ~~~~~~~~~~~aipi~~i~~~l~~l~~~~~~~~~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~ 897 (1109)
.++.+..|.+|+.+.+++++|++|+.+.+ +..+++|+||..|++.+||.+|+|.|||-++++....
T Consensus 703 -~~~kd~~y~~gl~~~~~l~vl~rlk~g~~-------------~rp~i~~vef~~i~laqar~lglp~e~imk~e~es~~ 768 (955)
T KOG1421|consen 703 -VGGKDYTYKYGLSMSYILPVLERLKLGPS-------------ARPTIAGVEFSHITLAQARTLGLPSEFIMKSEEESTI 768 (955)
T ss_pred -cCCceeEEEeccchHHHHHHHHHHhcCCC-------------CCceeeccceeeEEeehhhccCCCHHHHhhhhhcCCC
Confidence 45688889999999999999999999953 3456999999999999999999999999999999999
Q ss_pred ccceEEEEeecCCCHHhhhccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeeeecCCC
Q 001276 898 RRQVLRVKGCLAGSKAENMLEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGN 977 (1109)
Q Consensus 898 ~~~~~~V~~V~~~spA~~aL~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~l~~~~~~ 977 (1109)
++|+++|++|.+..+- .|..||+|+++|||.|+.++||.. + ..++++|+|+|.++++++++.+..
T Consensus 769 ~~ql~~ishv~~~~~k--il~~gdiilsvngk~itr~~dl~d-~----------~eid~~ilrdg~~~~ikipt~p~~-- 833 (955)
T KOG1421|consen 769 PRQLYVISHVRPLLHK--ILGVGDIILSVNGKMITRLSDLHD-F----------EEIDAVILRDGIEMEIKIPTYPEY-- 833 (955)
T ss_pred cceEEEEEeeccCccc--ccccccEEEEecCeEEeeehhhhh-h----------hhhheeeeecCcEEEEEecccccc--
Confidence 9999999999886652 399999999999999999999986 3 358899999999999999987665
Q ss_pred CcceEEeecCccccCCchhhhh-ccCCCCCCCcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCC
Q 001276 978 GTTRVINWCGCIVQDPHPAVRA-LGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHG 1056 (1109)
Q Consensus 978 ~t~~~~~~~G~~~~~p~~~~r~-~~~lp~~~~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~ 1056 (1109)
+++|.+.|.|+++|+||+++++ ...+|. ||||+.+..||||.+ +|.+..||++|||..++++|+|..+++++|+|
T Consensus 834 et~r~vi~~gailq~ph~av~~q~edlp~---gvyvt~rg~gspalq-~l~aa~fitavng~~t~~lddf~~~~~~ipdn 909 (955)
T KOG1421|consen 834 ETSRAVIWMGAILQPPHSAVFEQVEDLPE---GVYVTSRGYGSPALQ-MLRAAHFITAVNGHDTNTLDDFYHMLLEIPDN 909 (955)
T ss_pred ccceEEEEEeccccCchHHHHHHHhccCC---ceEEeecccCChhHh-hcchheeEEEecccccCcHHHHHHHHhhCCCC
Confidence 8999999999999999999998 488998 999999999999999 99999999999999999999999999999999
Q ss_pred ceEEEEEEEeCCeEEEEEEeeCCccCcceEEEEcCCCCCeEEEEe
Q 001276 1057 EFVRVRTVHLNGKPRVLTLKQDLHYWPTWELIFDPDTALWRRKSV 1101 (1109)
Q Consensus 1057 ~~v~l~~v~rdg~~~~i~lk~~~~y~pt~e~~~~~~~~~w~~~~~ 1101 (1109)
.||+++.++|||.+..+++|+|+|||||.+|.+|..+. |+.++.
T Consensus 910 syv~v~~mtfd~vp~~~s~k~n~hyfpt~~l~rd~~~~-wi~kev 953 (955)
T KOG1421|consen 910 SYVQVKQMTFDGVPSIVSVKPNPHYFPTCILERDSNGR-WITKEV 953 (955)
T ss_pred ceEEEEEeccCCCceEEEeccCCccCceeEEEecccCc-eeeeec
Confidence 99999999999999999999999999999999998655 977663
No 2
>PRK10139 serine endoprotease; Provisional
Probab=100.00 E-value=6.8e-53 Score=496.11 Aligned_cols=378 Identities=19% Similarity=0.314 Sum_probs=311.7
Q ss_pred chHHHHHHHhCCceEEEEEEeeec------------cCC------CCCCccEEEEEEEeCCCcEEEeCccccCCCCeEEE
Q 001276 36 DDWRKALNKVVPAVVVLRTTACRA------------FDT------EAAGASYATGFVVDKRRGIILTNRHVVKPGPVVAE 97 (1109)
Q Consensus 36 ~~~~~~~~~~~~sVV~I~~~~~~~------------~d~------~~~~~~~GSGfvV~~~~G~IlTn~HVv~~~~~~~~ 97 (1109)
++|.++++++.||||.|.+..... |.. .....+.||||||++++||||||+|||. +...+.
T Consensus 40 ~~~~~~~~~~~pavV~i~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~GSG~ii~~~~g~IlTn~HVv~-~a~~i~ 118 (455)
T PRK10139 40 PSLAPMLEKVLPAVVSVRVEGTASQGQKIPEEFKKFFGDDLPDQPAQPFEGLGSGVIIDAAKGYVLTNNHVIN-QAQKIS 118 (455)
T ss_pred ccHHHHHHHhCCcEEEEEEEEeecccccCchhHHHhccccCCccccccccceEEEEEEECCCCEEEeChHHhC-CCCEEE
Confidence 479999999999999999875321 211 1123578999999865799999999999 567899
Q ss_pred EEecCCeEEEEEEEEEcCCCcEEEEEEcC-CCcccccccCCCCCCccCCCCCEEEEEecCCCCCCeEEEEEEEEecCCCC
Q 001276 98 AMFVNREEIPVYPIYRDPVHDFGFFRYDP-SAIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAP 176 (1109)
Q Consensus 98 v~~~~~~~~~a~vv~~d~~~DlAlLk~~~-~~~~~~~l~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~vs~~~~~~~ 176 (1109)
|++.|+++++|++++.|+.+||||||++. ..++++.+++ +..+++||+|+++|||+|...+++.|+||++.|...
T Consensus 119 V~~~dg~~~~a~vvg~D~~~DlAvlkv~~~~~l~~~~lg~----s~~~~~G~~V~aiG~P~g~~~tvt~GivS~~~r~~~ 194 (455)
T PRK10139 119 IQLNDGREFDAKLIGSDDQSDIALLQIQNPSKLTQIAIAD----SDKLRVGDFAVAVGNPFGLGQTATSGIISALGRSGL 194 (455)
T ss_pred EEECCCCEEEEEEEEEcCCCCEEEEEecCCCCCceeEecC----ccccCCCCEEEEEecCCCCCCceEEEEEcccccccc
Confidence 99999999999999999999999999974 5566666665 778999999999999999999999999999988632
Q ss_pred CCCCCCccccceeeEEEeeccCCCCCCCceecCCCcEEEEeccccCC----CCCccccchHHHHHHHHHHHhcCCccccc
Q 001276 177 HYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSS----SASAFFLPLERVVRALRFLQERRDCNIHN 252 (1109)
Q Consensus 177 ~~~~~~~~~~~~~~iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~----~~~~falP~~~i~~~l~~l~~~~~~~~~~ 252 (1109)
.. .++. .|||+|+++++|||||||||.+|+||||+++.... .+++|+||++.+++++++|.+++
T Consensus 195 ~~--~~~~----~~iqtda~in~GnSGGpl~n~~G~vIGi~~~~~~~~~~~~gigfaIP~~~~~~v~~~l~~~g------ 262 (455)
T PRK10139 195 NL--EGLE----NFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSVGIGFAIPSNMARTLAQQLIDFG------ 262 (455)
T ss_pred CC--CCcc----eEEEECCccCCCCCcceEECCCCeEEEEEEEEEcCCCCccceEEEEEhHHHHHHHHHHhhcC------
Confidence 22 1232 46999999999999999999999999999875432 57899999999999999999988
Q ss_pred ccccccCCCccceEEEEcChhHHHHcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCC
Q 001276 253 WEAVSIPRGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQ 331 (1109)
Q Consensus 253 ~~~~~v~rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~ 331 (1109)
.+.|||||+.++.++.+.++.|||+ ...|++| ..|.++|||++ |||+||+|++|||++|.+
T Consensus 263 ----~v~r~~LGv~~~~l~~~~~~~lgl~-------------~~~Gv~V-~~V~~~SpA~~AGL~~GDvIl~InG~~V~s 324 (455)
T PRK10139 263 ----EIKRGLLGIKGTEMSADIAKAFNLD-------------VQRGAFV-SEVLPNSGSAKAGVKAGDIITSLNGKPLNS 324 (455)
T ss_pred ----cccccceeEEEEECCHHHHHhcCCC-------------CCCceEE-EEECCCChHHHCCCCCCCEEEEECCEECCC
Confidence 8999999999999999999999987 4578887 79999999999 999999999999999999
Q ss_pred hhHHHHHHhc-CCCCeEEEEEEECCEEEEEEEEeecCCCCCCCcc---ccccceEEecCCHHHhhccCCCCCeEEEEc--
Q 001276 332 FLKLETLLDD-GVDKNIELLIERGGISMTVNLVVQDLHSITPDYF---LEVSGAVIHPLSYQQARNFRFPCGLVYVAE-- 405 (1109)
Q Consensus 332 ~~~l~~~l~~-~~g~~v~l~v~R~g~~~~~~v~l~~~~~~~~~~~---~~~~G~~~~~l~~~~~~~~~~~~~gv~v~~-- 405 (1109)
|.++...+.. .+|+.+.++|.|+|+.+++++++........... ..+.|+.+.+. ..+. ...|++|..
T Consensus 325 ~~dl~~~l~~~~~g~~v~l~V~R~G~~~~l~v~~~~~~~~~~~~~~~~~~~~g~~l~~~---~~~~---~~~Gv~V~~V~ 398 (455)
T PRK10139 325 FAELRSRIATTEPGTKVKLGLLRNGKPLEVEVTLDTSTSSSASAEMITPALQGATLSDG---QLKD---GTKGIKIDEVV 398 (455)
T ss_pred HHHHHHHHHhcCCCCEEEEEEEECCEEEEEEEEECCCCCcccccccccccccccEeccc---cccc---CCCceEEEEeC
Confidence 9999988855 7899999999999999999998754432111111 11334444431 1111 125788874
Q ss_pred CCChhHHcCCCCCCEEEEcCCeecCCHHHHHHHHHhcCCCCeEeEEEEeec
Q 001276 406 PGYMLFRAGVPRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYSSYT 456 (1109)
Q Consensus 406 pg~~a~~aGl~~GD~I~~Vng~~v~~l~~~~~~i~~~~~g~~v~l~~~~~~ 456 (1109)
++++|+++||++||+|++|||+++.+|++|.+++++.+ +.+.|++.|-+
T Consensus 399 ~~spA~~aGL~~GD~I~~Ing~~v~~~~~~~~~l~~~~--~~v~l~v~R~g 447 (455)
T PRK10139 399 KGSPAAQAGLQKDDVIIGVNRDRVNSIAEMRKVLAAKP--AIIALQIVRGN 447 (455)
T ss_pred CCChHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhCC--CeEEEEEEECC
Confidence 89999999999999999999999999999999998843 56777666543
No 3
>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=1.3e-52 Score=495.92 Aligned_cols=384 Identities=25% Similarity=0.380 Sum_probs=333.4
Q ss_pred hHHHHHHHhCCceEEEEEEeee---------------ccCC----------CCCCccEEEEEEEeCCCcEEEeCccccCC
Q 001276 37 DWRKALNKVVPAVVVLRTTACR---------------AFDT----------EAAGASYATGFVVDKRRGIILTNRHVVKP 91 (1109)
Q Consensus 37 ~~~~~~~~~~~sVV~I~~~~~~---------------~~d~----------~~~~~~~GSGfvV~~~~G~IlTn~HVv~~ 91 (1109)
++.++++++.||||.|.+.... .|.. .....+.||||+|++ +||||||+||+.
T Consensus 2 ~~~~~~~~~~p~vv~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GSGfii~~-~G~IlTn~Hvv~- 79 (428)
T TIGR02037 2 SFAPLVEKVAPAVVNISVEGTVKRRNRPPALPPFFRQFFGDDMPNFPRQQRERKVRGLGSGVIISA-DGYILTNNHVVD- 79 (428)
T ss_pred cHHHHHHHhCCceEEEEEEEEecccCCCcccchhHHHhhcccccCcccccccccccceeeEEEECC-CCEEEEcHHHcC-
Confidence 4789999999999999986421 1211 112457899999998 699999999999
Q ss_pred CCeEEEEEecCCeEEEEEEEEEcCCCcEEEEEEcCC-CcccccccCCCCCCccCCCCCEEEEEecCCCCCCeEEEEEEEE
Q 001276 92 GPVVAEAMFVNREEIPVYPIYRDPVHDFGFFRYDPS-AIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLAR 170 (1109)
Q Consensus 92 ~~~~~~v~~~~~~~~~a~vv~~d~~~DlAlLk~~~~-~~~~~~l~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~vs~ 170 (1109)
++..+.|++.|+++++|++++.|+.+||||||++.. .++++.+.+ +..+++|++|+++|||++...+++.|+|++
T Consensus 80 ~~~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~~~~~~~~~~l~~----~~~~~~G~~v~aiG~p~g~~~~~t~G~vs~ 155 (428)
T TIGR02037 80 GADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVIKLGD----SDKLRVGDWVLAIGNPFGLGQTVTSGIVSA 155 (428)
T ss_pred CCCeEEEEeCCCCEEEEEEEEecCCCCEEEEEecCCCCceEEEccC----CCCCCCCCEEEEEECCCcCCCcEEEEEEEe
Confidence 577899999999999999999999999999999875 566666654 678999999999999999999999999999
Q ss_pred ecCCCCCCCCCCccccceeeEEEeeccCCCCCCCceecCCCcEEEEeccccCC----CCCccccchHHHHHHHHHHHhcC
Q 001276 171 LDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSS----SASAFFLPLERVVRALRFLQERR 246 (1109)
Q Consensus 171 ~~~~~~~~~~~~~~~~~~~~iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~----~~~~falP~~~i~~~l~~l~~~~ 246 (1109)
..+... ....|.+ +||+++++++|+|||||||.+|+||||+++.... .+.+|+||++.+++++++|++++
T Consensus 156 ~~~~~~--~~~~~~~----~i~tda~i~~GnSGGpl~n~~G~viGI~~~~~~~~g~~~g~~faiP~~~~~~~~~~l~~~g 229 (428)
T TIGR02037 156 LGRSGL--GIGDYEN----FIQTDAAINPGNSGGPLVNLRGEVIGINTAIYSPSGGNVGIGFAIPSNMAKNVVDQLIEGG 229 (428)
T ss_pred cccCcc--CCCCccc----eEEECCCCCCCCCCCceECCCCeEEEEEeEEEcCCCCccceEEEEEhHHHHHHHHHHHhcC
Confidence 988632 1123333 5999999999999999999999999999775432 46899999999999999999998
Q ss_pred CcccccccccccCCCccceEEEEcChhHHHHcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEEC
Q 001276 247 DCNIHNWEAVSIPRGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVN 325 (1109)
Q Consensus 247 ~~~~~~~~~~~v~rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~Vn 325 (1109)
.+.|+|||+.++..+.+.++.||++ ...|++| ..|.++|||++ ||++||+|++||
T Consensus 230 ----------~~~~~~lGi~~~~~~~~~~~~lgl~-------------~~~Gv~V-~~V~~~spA~~aGL~~GDvI~~Vn 285 (428)
T TIGR02037 230 ----------KVQRGWLGVTIQEVTSDLAKSLGLE-------------KQRGALV-AQVLPGSPAEKAGLKAGDVILSVN 285 (428)
T ss_pred ----------cCcCCcCceEeecCCHHHHHHcCCC-------------CCCceEE-EEccCCCChHHcCCCCCCEEEEEC
Confidence 7899999999999999999999997 4578777 79999999999 999999999999
Q ss_pred CEEeCChhHHHHHHhc-CCCCeEEEEEEECCEEEEEEEEeecCCCCCCCccccccceEEecCCHHHhhccCCCC--CeEE
Q 001276 326 GEVITQFLKLETLLDD-GVDKNIELLIERGGISMTVNLVVQDLHSITPDYFLEVSGAVIHPLSYQQARNFRFPC--GLVY 402 (1109)
Q Consensus 326 G~~v~~~~~l~~~l~~-~~g~~v~l~v~R~g~~~~~~v~l~~~~~~~~~~~~~~~G~~~~~l~~~~~~~~~~~~--~gv~ 402 (1109)
|+++.++.++...+.. ..|+.+++++.|+|+.+++++++..++.....+...+.|+.+++++....+.++++. .|++
T Consensus 286 g~~i~~~~~~~~~l~~~~~g~~v~l~v~R~g~~~~~~v~l~~~~~~~~~~~~~~lGi~~~~l~~~~~~~~~l~~~~~Gv~ 365 (428)
T TIGR02037 286 GKPISSFADLRRAIGTLKPGKKVTLGILRKGKEKTITVTLGASPEEQASSSNPFLGLTVANLSPEIRKELRLKGDVKGVV 365 (428)
T ss_pred CEEcCCHHHHHHHHHhcCCCCEEEEEEEECCEEEEEEEEECcCCCccccccccccceEEecCCHHHHHHcCCCcCcCceE
Confidence 9999999999988854 788999999999999999999988766544455667899999999998888888875 6999
Q ss_pred EEc--CCChhHHcCCCCCCEEEEcCCeecCCHHHHHHHHHhcCCCCeEeEEEEeec
Q 001276 403 VAE--PGYMLFRAGVPRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYSSYT 456 (1109)
Q Consensus 403 v~~--pg~~a~~aGl~~GD~I~~Vng~~v~~l~~~~~~i~~~~~g~~v~l~~~~~~ 456 (1109)
|.+ ++|+|+++||++||+|++|||+++.++++|.++++..+.++++.|++.|-+
T Consensus 366 V~~V~~~SpA~~aGL~~GDvI~~Ing~~V~s~~d~~~~l~~~~~g~~v~l~v~R~g 421 (428)
T TIGR02037 366 VTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLDRAKKGGRVALLILRGG 421 (428)
T ss_pred EEEeCCCCHHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhcCCCCEEEEEEEECC
Confidence 984 899999999999999999999999999999999999877888888887754
No 4
>PRK10942 serine endoprotease; Provisional
Probab=100.00 E-value=1.1e-50 Score=479.79 Aligned_cols=378 Identities=20% Similarity=0.324 Sum_probs=311.2
Q ss_pred chHHHHHHHhCCceEEEEEEeee-------------ccCC----------------------------CCCCccEEEEEE
Q 001276 36 DDWRKALNKVVPAVVVLRTTACR-------------AFDT----------------------------EAAGASYATGFV 74 (1109)
Q Consensus 36 ~~~~~~~~~~~~sVV~I~~~~~~-------------~~d~----------------------------~~~~~~~GSGfv 74 (1109)
+++.++++++.||||.|.+.... .|.. .....+.|||||
T Consensus 38 ~~~~~~~~~~~pavv~i~~~~~~~~~~~~~~~~~~~ff~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GSG~i 117 (473)
T PRK10942 38 PSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRQFQQFFGDNSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVI 117 (473)
T ss_pred ccHHHHHHHhCCceEEEEEEEeccccCCCCChhHHHhhcccccccccccccccccccccccccccccccccccceEEEEE
Confidence 46999999999999999876521 0210 001246899999
Q ss_pred EeCCCcEEEeCccccCCCCeEEEEEecCCeEEEEEEEEEcCCCcEEEEEEc-CCCcccccccCCCCCCccCCCCCEEEEE
Q 001276 75 VDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYPIYRDPVHDFGFFRYD-PSAIQFLNYDEIPLAPEAACVGLEIRVV 153 (1109)
Q Consensus 75 V~~~~G~IlTn~HVv~~~~~~~~v~~~~~~~~~a~vv~~d~~~DlAlLk~~-~~~~~~~~l~~l~l~~~~~~~G~~V~~i 153 (1109)
|++++||||||+|||. +.+.+.|++.|+++++|++++.|+.+||||||++ +..++++.+++ ++.+++|++|+++
T Consensus 118 i~~~~G~IlTn~HVv~-~a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki~~~~~l~~~~lg~----s~~l~~G~~V~ai 192 (473)
T PRK10942 118 IDADKGYVVTNNHVVD-NATKIKVQLSDGRKFDAKVVGKDPRSDIALIQLQNPKNLTAIKMAD----SDALRVGDYTVAI 192 (473)
T ss_pred EECCCCEEEeChhhcC-CCCEEEEEECCCCEEEEEEEEecCCCCEEEEEecCCCCCceeEecC----ccccCCCCEEEEE
Confidence 9975699999999999 6678999999999999999999999999999996 45566666665 7789999999999
Q ss_pred ecCCCCCCeEEEEEEEEecCCCCCCCCCCccccceeeEEEeeccCCCCCCCceecCCCcEEEEeccccCC----CCCccc
Q 001276 154 GNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSS----SASAFF 229 (1109)
Q Consensus 154 G~p~g~~~si~~G~vs~~~~~~~~~~~~~~~~~~~~~iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~----~~~~fa 229 (1109)
|||++...+++.|+|+++.|.... ...|.+ |||+|+++++|||||||+|.+|+||||+++.... .+.+|+
T Consensus 193 G~P~g~~~tvt~GiVs~~~r~~~~--~~~~~~----~iqtda~i~~GnSGGpL~n~~GeviGI~t~~~~~~g~~~g~gfa 266 (473)
T PRK10942 193 GNPYGLGETVTSGIVSALGRSGLN--VENYEN----FIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFA 266 (473)
T ss_pred cCCCCCCcceeEEEEEEeecccCC--cccccc----eEEeccccCCCCCcCccCCCCCeEEEEEEEEEcCCCCcccEEEE
Confidence 999999999999999999876321 123333 5999999999999999999999999999875532 468999
Q ss_pred cchHHHHHHHHHHHhcCCcccccccccccCCCccceEEEEcChhHHHHcCCChhHHHhhhcCCCCCCCceEEEEEecCCC
Q 001276 230 LPLERVVRALRFLQERRDCNIHNWEAVSIPRGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGG 309 (1109)
Q Consensus 230 lP~~~i~~~l~~l~~~~~~~~~~~~~~~v~rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~s 309 (1109)
||++.+++++++|++++ .+.|||||+.++.++.+.++.|||+ ...|++| ..|.++|
T Consensus 267 IP~~~~~~v~~~l~~~g----------~v~rg~lGv~~~~l~~~~a~~~~l~-------------~~~GvlV-~~V~~~S 322 (473)
T PRK10942 267 IPSNMVKNLTSQMVEYG----------QVKRGELGIMGTELNSELAKAMKVD-------------AQRGAFV-SQVLPNS 322 (473)
T ss_pred EEHHHHHHHHHHHHhcc----------ccccceeeeEeeecCHHHHHhcCCC-------------CCCceEE-EEECCCC
Confidence 99999999999999998 8999999999999999999999987 5689888 7999999
Q ss_pred cccc-CCCCCCEEEEECCEEeCChhHHHHHHh-cCCCCeEEEEEEECCEEEEEEEEeecCCCCCCCccccccceEEecCC
Q 001276 310 PAHL-RLEPGDVLVRVNGEVITQFLKLETLLD-DGVDKNIELLIERGGISMTVNLVVQDLHSITPDYFLEVSGAVIHPLS 387 (1109)
Q Consensus 310 pA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~-~~~g~~v~l~v~R~g~~~~~~v~l~~~~~~~~~~~~~~~G~~~~~l~ 387 (1109)
||++ ||++||+|++|||++|.+|.++...+. ...|+.+.+++.|+|+.+++.+++.........+...+.|+....+.
T Consensus 323 pA~~AGL~~GDvIl~InG~~V~s~~dl~~~l~~~~~g~~v~l~v~R~G~~~~v~v~l~~~~~~~~~~~~~~lGl~g~~l~ 402 (473)
T PRK10942 323 SAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNVELQQSSQNQVDSSNIFNGIEGAELS 402 (473)
T ss_pred hHHHcCCCCCCEEEEECCEECCCHHHHHHHHHhcCCCCEEEEEEEECCeEEEEEEEeCcCcccccccccccccceeeecc
Confidence 9999 999999999999999999999998884 47789999999999999999988865422111122223444333332
Q ss_pred HHHhhccCCCCCeEEEEc--CCChhHHcCCCCCCEEEEcCCeecCCHHHHHHHHHhcCCCCeEeEEEEeec
Q 001276 388 YQQARNFRFPCGLVYVAE--PGYMLFRAGVPRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYSSYT 456 (1109)
Q Consensus 388 ~~~~~~~~~~~~gv~v~~--pg~~a~~aGl~~GD~I~~Vng~~v~~l~~~~~~i~~~~~g~~v~l~~~~~~ 456 (1109)
... ...|++|.+ ++++|+++||++||+|++|||++|.++++|.+++++.+ +.+.|+++|-+
T Consensus 403 ~~~------~~~gvvV~~V~~~S~A~~aGL~~GDvIv~VNg~~V~s~~dl~~~l~~~~--~~v~l~V~R~g 465 (473)
T PRK10942 403 NKG------GDKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAELRKILDSKP--SVLALNIQRGD 465 (473)
T ss_pred ccc------CCCCeEEEEeCCCChHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhCC--CeEEEEEEECC
Confidence 210 114788874 89999999999999999999999999999999999832 57777776644
No 5
>PRK10139 serine endoprotease; Provisional
Probab=100.00 E-value=3.1e-50 Score=473.60 Aligned_cols=390 Identities=20% Similarity=0.272 Sum_probs=309.5
Q ss_pred ccccccccccEEEEEEEcCccc----------ccCC-c-----ccceeeEEEEEEEeeCCceEEEEeCceecCCCCcEEE
Q 001276 619 SFAESVIEPTLVMFEVHVPPSC----------MIDG-V-----HSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVML 682 (1109)
Q Consensus 619 ~~~~~~~~~SvV~V~~~~~~~~----------~~dg-~-----~~~~~~GsG~VId~~~~~G~IlTn~~~V~~~~~di~V 682 (1109)
...++++.||||.|.+...... .+.. . ....+.||||||+ +++|||||| +||+.++..|.|
T Consensus 43 ~~~~~~~~pavV~i~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~GSG~ii~--~~~g~IlTn-~HVv~~a~~i~V 119 (455)
T PRK10139 43 APMLEKVLPAVVSVRVEGTASQGQKIPEEFKKFFGDDLPDQPAQPFEGLGSGVIID--AAKGYVLTN-NHVINQAQKISI 119 (455)
T ss_pred HHHHHHhCCcEEEEEEEEeecccccCchhHHHhccccCCccccccccceEEEEEEE--CCCCEEEeC-hHHhCCCCEEEE
Confidence 3478899999999987532100 1110 0 1224679999998 247999999 667888899999
Q ss_pred EeecCCeEEeEEEEEeeCCCcEEEEEEC-CCCCCcccccceeceecCCCccCCCCCeEEEEeeCCCCcceeeeeeEeccc
Q 001276 683 SFAAFPIEIPGEVVFLHPVHNFALIAYD-PSSLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPC 761 (1109)
Q Consensus 683 ~~~d~~~~~~a~vv~~dp~~dlAilk~d-~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~iG~p~~~~~~~~~~~vt~i~ 761 (1109)
+|.| +++++|+|++.|+.+||||||++ +..+++ ++|+++..+++||+|++||||+++... +|
T Consensus 120 ~~~d-g~~~~a~vvg~D~~~DlAvlkv~~~~~l~~--------~~lg~s~~~~~G~~V~aiG~P~g~~~t-----vt--- 182 (455)
T PRK10139 120 QLND-GREFDAKLIGSDDQSDIALLQIQNPSKLTQ--------IAIADSDKLRVGDFAVAVGNPFGLGQT-----AT--- 182 (455)
T ss_pred EECC-CCEEEEEEEEEcCCCCEEEEEecCCCCCce--------eEecCccccCCCCEEEEEecCCCCCCc-----eE---
Confidence 9998 99999999999999999999997 456665 899999889999999999999998654 44
Q ss_pred cccccCCCCCCccc-ccceeEEEEecccCC-CCCceEEcCCeeEEEEEeeccccccccCCCCCCceeEecccHHHHHHHH
Q 001276 762 AALNISSADCPRYR-AMNMEVIELDTDFGS-TFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVL 839 (1109)
Q Consensus 762 ~~~~i~~~~~~~y~-~~~~~~I~~d~~ig~-~sGGpL~d~~G~VvGi~~~~~~~~~~g~~~~~~~~~~~aipi~~i~~~l 839 (1109)
.|++++..+..+. .....+||+|+++++ ||||||+|.+|+||||+++.... + ....+. .||||++.+++++
T Consensus 183 -~GivS~~~r~~~~~~~~~~~iqtda~in~GnSGGpl~n~~G~vIGi~~~~~~~---~-~~~~gi--gfaIP~~~~~~v~ 255 (455)
T PRK10139 183 -SGIISALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAP---G-GGSVGI--GFAIPSNMARTLA 255 (455)
T ss_pred -EEEEccccccccCCCCcceEEEECCccCCCCCcceEECCCCeEEEEEEEEEcC---C-CCccce--EEEEEhHHHHHHH
Confidence 4555544432211 113478999999976 79999999999999999985433 0 123344 4889999999999
Q ss_pred HHHHcCCCCCcccccccccCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCHHhhh-cc
Q 001276 840 DKIISGASGPSLLINGVKRPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSKAENM-LE 918 (1109)
Q Consensus 840 ~~l~~~~~~~~~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~spA~~a-L~ 918 (1109)
++|+++++ +.|+ |||+.++.++...++.+|++.. .+++|..|.++|||+++ |+
T Consensus 256 ~~l~~~g~--------v~r~-----~LGv~~~~l~~~~~~~lgl~~~-------------~Gv~V~~V~~~SpA~~AGL~ 309 (455)
T PRK10139 256 QQLIDFGE--------IKRG-----LLGIKGTEMSADIAKAFNLDVQ-------------RGAFVSEVLPNSGSAKAGVK 309 (455)
T ss_pred HHHhhcCc--------cccc-----ceeEEEEECCHHHHHhcCCCCC-------------CceEEEEECCCChHHHCCCC
Confidence 99999887 7788 9999999999888888888654 67889999999999999 99
Q ss_pred CCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeeeecCCCCcceE---EeecCccccCCch
Q 001276 919 QGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGNGTTRV---INWCGCIVQDPHP 995 (1109)
Q Consensus 919 ~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~l~~~~~~~t~~~---~~~~G~~~~~p~~ 995 (1109)
+||+|++|||++|.+|.++...+....++ +.+.++|.|+|+.+++.+++........... ..+.|+.+++.
T Consensus 310 ~GDvIl~InG~~V~s~~dl~~~l~~~~~g----~~v~l~V~R~G~~~~l~v~~~~~~~~~~~~~~~~~~~~g~~l~~~-- 383 (455)
T PRK10139 310 AGDIITSLNGKPLNSFAELRSRIATTEPG----TKVKLGLLRNGKPLEVEVTLDTSTSSSASAEMITPALQGATLSDG-- 383 (455)
T ss_pred CCCEEEEECCEECCCHHHHHHHHHhcCCC----CEEEEEEEECCEEEEEEEEECCCCCcccccccccccccccEeccc--
Confidence 99999999999999999999988655665 7899999999999999998754432211111 12345554431
Q ss_pred hhhhccCCCCCCCcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEeCCeEEEEEE
Q 001276 996 AVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTL 1075 (1109)
Q Consensus 996 ~~r~~~~lp~~~~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i~l 1075 (1109)
+ ++....|++|..|.++|||+++||++||+|++|||+++.+|++|.+++++. ++.+.|+ +.|+|..+++.+
T Consensus 384 ---~---~~~~~~Gv~V~~V~~~spA~~aGL~~GD~I~~Ing~~v~~~~~~~~~l~~~--~~~v~l~-v~R~g~~~~~~~ 454 (455)
T PRK10139 384 ---Q---LKDGTKGIKIDEVVKGSPAAQAGLQKDDVIIGVNRDRVNSIAEMRKVLAAK--PAIIALQ-IVRGNESIYLLL 454 (455)
T ss_pred ---c---cccCCCceEEEEeCCCChHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhC--CCeEEEE-EEECCEEEEEEe
Confidence 1 111124899999999999999999999999999999999999999999984 3688888 899999888876
Q ss_pred e
Q 001276 1076 K 1076 (1109)
Q Consensus 1076 k 1076 (1109)
+
T Consensus 455 ~ 455 (455)
T PRK10139 455 R 455 (455)
T ss_pred C
Confidence 3
No 6
>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=6.2e-50 Score=473.11 Aligned_cols=395 Identities=24% Similarity=0.329 Sum_probs=326.4
Q ss_pred ccccccccEEEEEEEcCccc-------------ccCC----c------ccceeeEEEEEEEeeCCceEEEEeCceecCCC
Q 001276 621 AESVIEPTLVMFEVHVPPSC-------------MIDG----V------HSQHFFGTGVIIYHSQSMGLVVVDKNTVAISA 677 (1109)
Q Consensus 621 ~~~~~~~SvV~V~~~~~~~~-------------~~dg----~------~~~~~~GsG~VId~~~~~G~IlTn~~~V~~~~ 677 (1109)
+++++.||||.|.+...... .+.. . ....+.||||||+ ++|||||| +||+.++
T Consensus 6 ~~~~~~p~vv~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GSGfii~---~~G~IlTn-~Hvv~~~ 81 (428)
T TIGR02037 6 LVEKVAPAVVNISVEGTVKRRNRPPALPPFFRQFFGDDMPNFPRQQRERKVRGLGSGVIIS---ADGYILTN-NHVVDGA 81 (428)
T ss_pred HHHHhCCceEEEEEEEEecccCCCcccchhHHHhhcccccCcccccccccccceeeEEEEC---CCCEEEEc-HHHcCCC
Confidence 67889999999987542100 1111 0 1134679999999 57999999 6688889
Q ss_pred CcEEEEeecCCeEEeEEEEEeeCCCcEEEEEECCC-CCCcccccceeceecCCCccCCCCCeEEEEeeCCCCcceeeeee
Q 001276 678 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAYDPS-SLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSI 756 (1109)
Q Consensus 678 ~di~V~~~d~~~~~~a~vv~~dp~~dlAilk~d~~-~l~~~~~~~v~~~~l~~~~~l~~G~~V~~iG~p~~~~~~~~~~~ 756 (1109)
+++.|++++ ++.++|++++.|+.+||||||++.. .+++ ++|+++..+++||+|+++|||+++....+.+.
T Consensus 82 ~~i~V~~~~-~~~~~a~vv~~d~~~DlAllkv~~~~~~~~--------~~l~~~~~~~~G~~v~aiG~p~g~~~~~t~G~ 152 (428)
T TIGR02037 82 DEITVTLSD-GREFKAKLVGKDPRTDIAVLKIDAKKNLPV--------IKLGDSDKLRVGDWVLAIGNPFGLGQTVTSGI 152 (428)
T ss_pred CeEEEEeCC-CCEEEEEEEEecCCCCEEEEEecCCCCceE--------EEccCCCCCCCCCEEEEEECCCcCCCcEEEEE
Confidence 999999998 9999999999999999999999865 5555 89998888999999999999999866555555
Q ss_pred EeccccccccCCCCCCcc-cccceeEEEEecccCC-CCCceEEcCCeeEEEEEeeccccccccCCCCCCceeEecccHHH
Q 001276 757 VTNPCAALNISSADCPRY-RAMNMEVIELDTDFGS-TFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYT 834 (1109)
Q Consensus 757 vt~i~~~~~i~~~~~~~y-~~~~~~~I~~d~~ig~-~sGGpL~d~~G~VvGi~~~~~~~~~~g~~~~~~~~~~~aipi~~ 834 (1109)
|+ ...+... ......+|++|+++++ +|||||+|.+|+|+|||++.... +....++.||||++.
T Consensus 153 vs---------~~~~~~~~~~~~~~~i~tda~i~~GnSGGpl~n~~G~viGI~~~~~~~------~g~~~g~~faiP~~~ 217 (428)
T TIGR02037 153 VS---------ALGRSGLGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAIYSP------SGGNVGIGFAIPSNM 217 (428)
T ss_pred EE---------ecccCccCCCCccceEEECCCCCCCCCCCceECCCCeEEEEEeEEEcC------CCCccceEEEEEhHH
Confidence 55 2222110 0112368999999955 79999999999999999885432 122345568999999
Q ss_pred HHHHHHHHHcCCCCCcccccccccCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCHHh
Q 001276 835 ISRVLDKIISGASGPSLLINGVKRPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSKAE 914 (1109)
Q Consensus 835 i~~~l~~l~~~~~~~~~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~spA~ 914 (1109)
+++++++|+++++ +.|+ |||+.++.++...++.+|++.. .+++|.+|.++|||+
T Consensus 218 ~~~~~~~l~~~g~--------~~~~-----~lGi~~~~~~~~~~~~lgl~~~-------------~Gv~V~~V~~~spA~ 271 (428)
T TIGR02037 218 AKNVVDQLIEGGK--------VQRG-----WLGVTIQEVTSDLAKSLGLEKQ-------------RGALVAQVLPGSPAE 271 (428)
T ss_pred HHHHHHHHHhcCc--------CcCC-----cCceEeecCCHHHHHHcCCCCC-------------CceEEEEccCCCChH
Confidence 9999999999986 6777 9999999999999999998765 678899999999999
Q ss_pred hh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeeeecCCCCcceEEeecCccccCC
Q 001276 915 NM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGNGTTRVINWCGCIVQDP 993 (1109)
Q Consensus 915 ~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~l~~~~~~~t~~~~~~~G~~~~~p 993 (1109)
++ |+.||+|++|||++|.++.++..++.....+ +.+.++|.|+|+.+++++++...++....+...|+|+.++.+
T Consensus 272 ~aGL~~GDvI~~Vng~~i~~~~~~~~~l~~~~~g----~~v~l~v~R~g~~~~~~v~l~~~~~~~~~~~~~~lGi~~~~l 347 (428)
T TIGR02037 272 KAGLKAGDVILSVNGKPISSFADLRRAIGTLKPG----KKVTLGILRKGKEKTITVTLGASPEEQASSSNPFLGLTVANL 347 (428)
T ss_pred HcCCCCCCEEEEECCEEcCCHHHHHHHHHhcCCC----CEEEEEEEECCEEEEEEEEECcCCCccccccccccceEEecC
Confidence 99 9999999999999999999999998666665 889999999999999999887665444455667899999999
Q ss_pred chhhhhccCCCCCCCcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEeCCeEEEE
Q 001276 994 HPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVL 1073 (1109)
Q Consensus 994 ~~~~r~~~~lp~~~~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i 1073 (1109)
+...++...++....|++|+.|.++|||+++||++||+|++|||+++.++++|.+++++.+.++.++|+ +.|+|+..++
T Consensus 348 ~~~~~~~~~l~~~~~Gv~V~~V~~~SpA~~aGL~~GDvI~~Ing~~V~s~~d~~~~l~~~~~g~~v~l~-v~R~g~~~~~ 426 (428)
T TIGR02037 348 SPEIRKELRLKGDVKGVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLDRAKKGGRVALL-ILRGGATIFV 426 (428)
T ss_pred CHHHHHHcCCCcCcCceEEEEeCCCCHHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhcCCCCEEEEE-EEECCEEEEE
Confidence 888877544554335999999999999999999999999999999999999999999987778999999 8999988766
Q ss_pred E
Q 001276 1074 T 1074 (1109)
Q Consensus 1074 ~ 1074 (1109)
.
T Consensus 427 ~ 427 (428)
T TIGR02037 427 T 427 (428)
T ss_pred E
Confidence 5
No 7
>KOG1421 consensus Predicted signaling-associated protein (contains a PDZ domain) [General function prediction only]
Probab=100.00 E-value=7.1e-50 Score=450.81 Aligned_cols=442 Identities=29% Similarity=0.420 Sum_probs=386.5
Q ss_pred ccccccccEEEEEEEcCcccccCCcccceeeEEEEEEEeeCCceEEEEeCceecCCCCcEEEEeecCCeEEeEEEEEeeC
Q 001276 621 AESVIEPTLVMFEVHVPPSCMIDGVHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGEVVFLHP 700 (1109)
Q Consensus 621 ~~~~~~~SvV~V~~~~~~~~~~dg~~~~~~~GsG~VId~~~~~G~IlTn~~~V~~~~~di~V~~~d~~~~~~a~vv~~dp 700 (1109)
.++.+.+|+|.|+...- ..+|.-....+.|+|||+| +..||||||||+|..+...-.+.|.+ -.+++--.++.||
T Consensus 57 ~ia~VvksvVsI~~S~v--~~fdtesag~~~atgfvvd--~~~gyiLtnrhvv~pgP~va~avf~n-~ee~ei~pvyrDp 131 (955)
T KOG1421|consen 57 TIANVVKSVVSIRFSAV--RAFDTESAGESEATGFVVD--KKLGYILTNRHVVAPGPFVASAVFDN-HEEIEIYPVYRDP 131 (955)
T ss_pred hhhhhcccEEEEEehhe--eecccccccccceeEEEEe--cccceEEEeccccCCCCceeEEEecc-cccCCcccccCCc
Confidence 77889999999987665 4677777888999999999 58999999999999999989999998 8888888999999
Q ss_pred CCcEEEEEECCCCCCcccccceeceecCCCccCCCCCeEEEEeeCCCCcceeeeeeEeccccccccCC--CCCCcccccc
Q 001276 701 VHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISS--ADCPRYRAMN 778 (1109)
Q Consensus 701 ~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~iG~p~~~~~~~~~~~vt~i~~~~~i~~--~~~~~y~~~~ 778 (1109)
.||+.+++|||+.+.. ..|+.+.+.++. .+.|-++..+|+..+--+..-.+.++ +..-.. -.-..|-..|
T Consensus 132 VhdfGf~r~dps~ir~---s~vt~i~lap~~-akvgseirvvgNDagEklsIlagflS----rldr~apdyg~~~yndfn 203 (955)
T KOG1421|consen 132 VHDFGFFRYDPSTIRF---SIVTEICLAPEL-AKVGSEIRVVGNDAGEKLSILAGFLS----RLDRNAPDYGEDTYNDFN 203 (955)
T ss_pred hhhcceeecChhhcce---eeeeccccCccc-cccCCceEEecCCccceEEeehhhhh----hccCCCcccccccccccc
Confidence 9999999999998876 788888998876 79999999999987664322222222 221111 1223344467
Q ss_pred eeEEEEeccc-CCCCCceEEcCCeeEEEEEeeccccccccCCCCCCceeEecccHHHHHHHHHHHHcCCCCCcccccccc
Q 001276 779 MEVIELDTDF-GSTFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLDKIISGASGPSLLINGVK 857 (1109)
Q Consensus 779 ~~~I~~d~~i-g~~sGGpL~d~~G~VvGi~~~~~~~~~~g~~~~~~~~~~~aipi~~i~~~l~~l~~~~~~~~~~~~~v~ 857 (1109)
..++|.-+.- |++||.|++|.+|..|+++... ....... |.+|++.+++.|..|+++.. +.
T Consensus 204 Tfy~QaasstsggssgspVv~i~gyAVAl~agg--------~~ssas~--ffLpLdrV~RaL~clq~n~P--------It 265 (955)
T KOG1421|consen 204 TFYIQAASSTSGGSSGSPVVDIPGYAVALNAGG--------SISSASD--FFLPLDRVVRALRCLQNNTP--------IT 265 (955)
T ss_pred ceeeeehhcCCCCCCCCceecccceEEeeecCC--------ccccccc--ceeeccchhhhhhhhhcCCC--------cc
Confidence 8888887766 4457999999999999997653 2334556 55999999999999998865 88
Q ss_pred cCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCHHhhhccCCCEEEEECCEEcCChhHH
Q 001276 858 RPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSKAENMLEQGDMMLAINKQPVTCFHDI 937 (1109)
Q Consensus 858 r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~spA~~aL~~GDiIlsVnG~~V~~~~dl 937 (1109)
|+ +|.++|.....+++|.+||+.||++.+..++|.+.+.++|..|.+++||++.|++||++++||+.-+.++..+
T Consensus 266 RG-----tLqvefl~k~~de~rrlGL~sE~eqv~r~k~P~~tgmLvV~~vL~~gpa~k~Le~GDillavN~t~l~df~~l 340 (955)
T KOG1421|consen 266 RG-----TLQVEFLHKLFDECRRLGLSSEWEQVVRTKFPERTGMLVVETVLPEGPAEKKLEPGDILLAVNSTCLNDFEAL 340 (955)
T ss_pred cc-----eEEEEEehhhhHHHHhcCCcHHHHHHHHhcCcccceeEEEEEeccCCchhhccCCCcEEEEEcceehHHHHHH
Confidence 88 9999999999999999999999999999999999999999999999999999999999999998888888777
Q ss_pred HHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeeeecCCCCcceEEeecCccccCCchhhhhccCCCCCCCcEEEEEecC
Q 001276 938 ENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGNGTTRVINWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCH 1017 (1109)
Q Consensus 938 ~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~l~~~~~~~t~~~~~~~G~~~~~p~~~~r~~~~lp~~~~gV~V~~v~~ 1017 (1109)
...+. .+ .++.+.++|+|+|++.++++++...++..+.|++.|||+.+|+||+++++++.+|- .|+||++..
T Consensus 341 ~~iLD---eg--vgk~l~LtI~Rggqelel~vtvqdlh~itp~R~levcGav~hdlsyq~ar~y~lP~--~GvyVa~~~- 412 (955)
T KOG1421|consen 341 EQILD---EG--VGKNLELTIQRGGQELELTVTVQDLHGITPDRFLEVCGAVFHDLSYQLARLYALPV--EGVYVASPG- 412 (955)
T ss_pred HHHHh---hc--cCceEEEEEEeCCEEEEEEEEeccccCCCCceEEEEcceEecCCCHHHHhhccccc--CcEEEccCC-
Confidence 77762 22 45899999999999999999999999999999999999999999999999999987 599999999
Q ss_pred CChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEeC--CeEEEEEEeeCCc-cCcceEEEEcCCCC
Q 001276 1018 GSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLN--GKPRVLTLKQDLH-YWPTWELIFDPDTA 1094 (1109)
Q Consensus 1018 gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~rd--g~~~~i~lk~~~~-y~pt~e~~~~~~~~ 1094 (1109)
||+++.++++ +-+|.+||+++++++++|.++++++++|++|+++++..+ +++++++++.|.| |||+|++.||++++
T Consensus 413 gsf~~~~~~y-~~ii~~vanK~tPdLdaFidvlk~L~dg~rV~vry~hl~dkh~p~v~~v~iDrHwy~p~~~~trndetg 491 (955)
T KOG1421|consen 413 GSFRHRGPRY-GQIIDSVANKPTPDLDAFIDVLKELPDGARVPVRYHHLTDKHSPRVTTVTIDRHWYWPFREYTRNDETG 491 (955)
T ss_pred CCccccCCcc-eEEEEeecCCcCCCHHHHHHHHHhccCCCeeeEEEEEecCCCCceEEEEEEeccccccceeeeeCCCcc
Confidence 9999999999 999999999999999999999999999999999999888 7899999999999 99999999999999
Q ss_pred CeEEEEecccCCC
Q 001276 1095 LWRRKSVKALNSS 1107 (1109)
Q Consensus 1095 ~w~~~~~~~~~~~ 1107 (1109)
.|++...+.+||.
T Consensus 492 lWdrk~L~~pqPa 504 (955)
T KOG1421|consen 492 LWDRKNLKDPQPA 504 (955)
T ss_pred cccccccCCCCcc
Confidence 9999999999885
No 8
>PRK10942 serine endoprotease; Provisional
Probab=100.00 E-value=7.3e-49 Score=464.12 Aligned_cols=360 Identities=19% Similarity=0.269 Sum_probs=292.7
Q ss_pred eeeEEEEEEEeeCCceEEEEeCceecCCCCcEEEEeecCCeEEeEEEEEeeCCCcEEEEEEC-CCCCCcccccceeceec
Q 001276 649 HFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGEVVFLHPVHNFALIAYD-PSSLGVAGASVVRAAEL 727 (1109)
Q Consensus 649 ~~~GsG~VId~~~~~G~IlTn~~~V~~~~~di~V~~~d~~~~~~a~vv~~dp~~dlAilk~d-~~~l~~~~~~~v~~~~l 727 (1109)
.+.||||||+ .++|||||| +||+.++++|+|+|+| +++++|+|++.|+.+||||||++ +..+++ ++|
T Consensus 110 ~~~GSG~ii~--~~~G~IlTn-~HVv~~a~~i~V~~~d-g~~~~a~vv~~D~~~DlAvlki~~~~~l~~--------~~l 177 (473)
T PRK10942 110 MALGSGVIID--ADKGYVVTN-NHVVDNATKIKVQLSD-GRKFDAKVVGKDPRSDIALIQLQNPKNLTA--------IKM 177 (473)
T ss_pred cceEEEEEEE--CCCCEEEeC-hhhcCCCCEEEEEECC-CCEEEEEEEEecCCCCEEEEEecCCCCCce--------eEe
Confidence 3579999998 346999999 5678888999999998 99999999999999999999995 556665 899
Q ss_pred CCCccCCCCCeEEEEeeCCCCcceeeeeeEeccccccccCCCCCCcccccceeEEEEecccCC-CCCceEEcCCeeEEEE
Q 001276 728 LPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRAMNMEVIELDTDFGS-TFSGVLTDEHGRVQAI 806 (1109)
Q Consensus 728 ~~~~~l~~G~~V~~iG~p~~~~~~~~~~~vt~i~~~~~i~~~~~~~y~~~~~~~I~~d~~ig~-~sGGpL~d~~G~VvGi 806 (1109)
+++..+++||+|++||+|+++..+.+.+.|+.+. .+......| ..+||+|+++++ ||||||+|.+|+||||
T Consensus 178 g~s~~l~~G~~V~aiG~P~g~~~tvt~GiVs~~~----r~~~~~~~~----~~~iqtda~i~~GnSGGpL~n~~GeviGI 249 (473)
T PRK10942 178 ADSDALRVGDYTVAIGNPYGLGETVTSGIVSALG----RSGLNVENY----ENFIQTDAAINRGNSGGALVNLNGELIGI 249 (473)
T ss_pred cCccccCCCCEEEEEcCCCCCCcceeEEEEEEee----cccCCcccc----cceEEeccccCCCCCcCccCCCCCeEEEE
Confidence 9998899999999999999986655555555211 111111233 378999999966 7999999999999999
Q ss_pred EeeccccccccCCCCCCceeEecccHHHHHHHHHHHHcCCCCCcccccccccCCCceeeeeeEEEEcChHhHHHcCCCHH
Q 001276 807 WGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLDKIISGASGPSLLINGVKRPMPLVRILEVELYPTLLSKARSFGLSDD 886 (1109)
Q Consensus 807 ~~~~~~~~~~g~~~~~~~~~~~aipi~~i~~~l~~l~~~~~~~~~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~ 886 (1109)
|+++... +....++.|+||++.+++++++|+++++ +.|+ |||+.++.++...++.+|++..
T Consensus 250 ~t~~~~~------~g~~~g~gfaIP~~~~~~v~~~l~~~g~--------v~rg-----~lGv~~~~l~~~~a~~~~l~~~ 310 (473)
T PRK10942 250 NTAILAP------DGGNIGIGFAIPSNMVKNLTSQMVEYGQ--------VKRG-----ELGIMGTELNSELAKAMKVDAQ 310 (473)
T ss_pred EEEEEcC------CCCcccEEEEEEHHHHHHHHHHHHhccc--------cccc-----eeeeEeeecCHHHHHhcCCCCC
Confidence 9986543 1222345588999999999999999887 7788 9999999999888888888754
Q ss_pred HHHHHHhcCCCccceEEEEeecCCCHHhhh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEE
Q 001276 887 WVQALVKKDPVRRQVLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREI 965 (1109)
Q Consensus 887 wi~~~~~~~~~~~~~~~V~~V~~~spA~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~ 965 (1109)
.+++|..|.++|||+++ |++||+|++|||++|.+++++...+.....+ +.+.++|.|+|+.+
T Consensus 311 -------------~GvlV~~V~~~SpA~~AGL~~GDvIl~InG~~V~s~~dl~~~l~~~~~g----~~v~l~v~R~G~~~ 373 (473)
T PRK10942 311 -------------RGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVG----SKLTLGLLRDGKPV 373 (473)
T ss_pred -------------CceEEEEECCCChHHHcCCCCCCEEEEECCEECCCHHHHHHHHHhcCCC----CEEEEEEEECCeEE
Confidence 67889999999999999 9999999999999999999999998766665 78999999999999
Q ss_pred EEEEeeeecCCCCcceEEeecCccccCCchhhhhccCCCCCCCcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHH
Q 001276 966 ELQVGTDVRDGNGTTRVINWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEA 1045 (1109)
Q Consensus 966 ~l~v~l~~~~~~~t~~~~~~~G~~~~~p~~~~r~~~~lp~~~~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~ 1045 (1109)
++.+++.........+...++|+........ .+ ..+++|+.|.++|||+++||++||+|++|||++|.++++
T Consensus 374 ~v~v~l~~~~~~~~~~~~~~lGl~g~~l~~~------~~--~~gvvV~~V~~~S~A~~aGL~~GDvIv~VNg~~V~s~~d 445 (473)
T PRK10942 374 NVNVELQQSSQNQVDSSNIFNGIEGAELSNK------GG--DKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAE 445 (473)
T ss_pred EEEEEeCcCcccccccccccccceeeecccc------cC--CCCeEEEEeCCCChHHHcCCCCCCEEEEECCEEcCCHHH
Confidence 9999876543222222223455443322210 01 137999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCCceEEEEEEEeCCeEEEEEE
Q 001276 1046 FVNVTKEIEHGEFVRVRTVHLNGKPRVLTL 1075 (1109)
Q Consensus 1046 f~~~l~~~~~~~~v~l~~v~rdg~~~~i~l 1075 (1109)
|.+++++. ++.+.|+ +.|+|..+++.+
T Consensus 446 l~~~l~~~--~~~v~l~-V~R~g~~~~v~~ 472 (473)
T PRK10942 446 LRKILDSK--PSVLALN-IQRGDSSIYLLM 472 (473)
T ss_pred HHHHHHhC--CCeEEEE-EEECCEEEEEEe
Confidence 99999983 3688888 899999888776
No 9
>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=3.3e-44 Score=411.40 Aligned_cols=300 Identities=19% Similarity=0.296 Sum_probs=258.2
Q ss_pred cCCcchHHHHHHHhCCceEEEEEEeeec-cCCCCCCccEEEEEEEeCCCcEEEeCccccCCCCeEEEEEecCCeEEEEEE
Q 001276 32 VATADDWRKALNKVVPAVVVLRTTACRA-FDTEAAGASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYP 110 (1109)
Q Consensus 32 ~~~~~~~~~~~~~~~~sVV~I~~~~~~~-~d~~~~~~~~GSGfvV~~~~G~IlTn~HVv~~~~~~~~v~~~~~~~~~a~v 110 (1109)
.+.+.++.++++++.||||.|+...... ........+.||||+|++ +||||||+|||. +...+.++|.|++.++|++
T Consensus 41 ~~~~~~~~~~~~~~~psVV~I~~~~~~~~~~~~~~~~~~GSG~vi~~-~G~IlTn~HVV~-~~~~i~V~~~dg~~~~a~v 118 (351)
T TIGR02038 41 NTVEISFNKAVRRAAPAVVNIYNRSISQNSLNQLSIQGLGSGVIMSK-EGYILTNYHVIK-KADQIVVALQDGRKFEAEL 118 (351)
T ss_pred cccchhHHHHHHhcCCcEEEEEeEeccccccccccccceEEEEEEeC-CeEEEecccEeC-CCCEEEEEECCCCEEEEEE
Confidence 3445589999999999999999864321 112223457899999997 799999999999 5678999999999999999
Q ss_pred EEEcCCCcEEEEEEcCCCcccccccCCCCCCccCCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCccccceee
Q 001276 111 IYRDPVHDFGFFRYDPSAIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFY 190 (1109)
Q Consensus 111 v~~d~~~DlAlLk~~~~~~~~~~l~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~vs~~~~~~~~~~~~~~~~~~~~~ 190 (1109)
+++|+.+||||||++...++++++.. +..+++||+|+++|||++...+++.|+|+++.|... ...++ ..+
T Consensus 119 v~~d~~~DlAvlkv~~~~~~~~~l~~----s~~~~~G~~V~aiG~P~~~~~s~t~GiIs~~~r~~~--~~~~~----~~~ 188 (351)
T TIGR02038 119 VGSDPLTDLAVLKIEGDNLPTIPVNL----DRPPHVGDVVLAIGNPYNLGQTITQGIISATGRNGL--SSVGR----QNF 188 (351)
T ss_pred EEecCCCCEEEEEecCCCCceEeccC----cCccCCCCEEEEEeCCCCCCCcEEEEEEEeccCccc--CCCCc----ceE
Confidence 99999999999999987776666654 678999999999999999999999999999988642 11122 246
Q ss_pred EEEeeccCCCCCCCceecCCCcEEEEeccccC------CCCCccccchHHHHHHHHHHHhcCCcccccccccccCCCccc
Q 001276 191 MQAASGTKGGSSGSPVIDWQGRAVALNAGSKS------SSASAFFLPLERVVRALRFLQERRDCNIHNWEAVSIPRGTLQ 264 (1109)
Q Consensus 191 iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~------~~~~~falP~~~i~~~l~~l~~~~~~~~~~~~~~~v~rg~lg 264 (1109)
||+|+++++|||||||||.+|+||||+++... ..+.+|+||++.+++++++|++++ .+.|+|||
T Consensus 189 iqtda~i~~GnSGGpl~n~~G~vIGI~~~~~~~~~~~~~~g~~faIP~~~~~~vl~~l~~~g----------~~~r~~lG 258 (351)
T TIGR02038 189 IQTDAAINAGNSGGALINTNGELVGINTASFQKGGDEGGEGINFAIPIKLAHKIMGKIIRDG----------RVIRGYIG 258 (351)
T ss_pred EEECCccCCCCCcceEECCCCeEEEEEeeeecccCCCCccceEEEecHHHHHHHHHHHhhcC----------cccceEee
Confidence 99999999999999999999999999975432 147899999999999999999988 78899999
Q ss_pred eEEEEcChhHHHHcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhc-C
Q 001276 265 VTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDD-G 342 (1109)
Q Consensus 265 ~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~-~ 342 (1109)
+.++.+....++.||++ ...|++| ..|.++|||++ ||++||+|++|||++|.++.++...+.. .
T Consensus 259 v~~~~~~~~~~~~lgl~-------------~~~Gv~V-~~V~~~spA~~aGL~~GDvI~~Ing~~V~s~~dl~~~l~~~~ 324 (351)
T TIGR02038 259 VSGEDINSVVAQGLGLP-------------DLRGIVI-TGVDPNGPAARAGILVRDVILKYDGKDVIGAEELMDRIAETR 324 (351)
T ss_pred eEEEECCHHHHHhcCCC-------------ccccceE-eecCCCChHHHCCCCCCCEEEEECCEEcCCHHHHHHHHHhcC
Confidence 99999988888899987 4578777 69999999999 9999999999999999999999988854 7
Q ss_pred CCCeEEEEEEECCEEEEEEEEeecC
Q 001276 343 VDKNIELLIERGGISMTVNLVVQDL 367 (1109)
Q Consensus 343 ~g~~v~l~v~R~g~~~~~~v~l~~~ 367 (1109)
.|+.+.+++.|+|+.+++++++..+
T Consensus 325 ~g~~v~l~v~R~g~~~~~~v~l~~~ 349 (351)
T TIGR02038 325 PGSKVMVTVLRQGKQLELPVTIDEK 349 (351)
T ss_pred CCCEEEEEEEECCEEEEEEEEecCC
Confidence 8999999999999999999888654
No 10
>PRK10898 serine endoprotease; Provisional
Probab=100.00 E-value=1.4e-43 Score=405.72 Aligned_cols=301 Identities=18% Similarity=0.295 Sum_probs=256.5
Q ss_pred cCCcchHHHHHHHhCCceEEEEEEeeeccC-CCCCCccEEEEEEEeCCCcEEEeCccccCCCCeEEEEEecCCeEEEEEE
Q 001276 32 VATADDWRKALNKVVPAVVVLRTTACRAFD-TEAAGASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYP 110 (1109)
Q Consensus 32 ~~~~~~~~~~~~~~~~sVV~I~~~~~~~~d-~~~~~~~~GSGfvV~~~~G~IlTn~HVv~~~~~~~~v~~~~~~~~~a~v 110 (1109)
.....++.++++++.+|||.|.......+. ......+.||||+|++ +||||||+|||. +...+.|++.|++.++|++
T Consensus 41 ~~~~~~~~~~~~~~~psvV~v~~~~~~~~~~~~~~~~~~GSGfvi~~-~G~IlTn~HVv~-~a~~i~V~~~dg~~~~a~v 118 (353)
T PRK10898 41 DETPASYNQAVRRAAPAVVNVYNRSLNSTSHNQLEIRTLGSGVIMDQ-RGYILTNKHVIN-DADQIIVALQDGRVFEALL 118 (353)
T ss_pred ccccchHHHHHHHhCCcEEEEEeEeccccCcccccccceeeEEEEeC-CeEEEecccEeC-CCCEEEEEeCCCCEEEEEE
Confidence 344458999999999999999987643322 2333457899999997 799999999999 5678999999999999999
Q ss_pred EEEcCCCcEEEEEEcCCCcccccccCCCCCCccCCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCccccceee
Q 001276 111 IYRDPVHDFGFFRYDPSAIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFY 190 (1109)
Q Consensus 111 v~~d~~~DlAlLk~~~~~~~~~~l~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~vs~~~~~~~~~~~~~~~~~~~~~ 190 (1109)
+++|+.+||||||++...++++++.+ +..+++|++|+++|||++...+++.|+|++..|..... .++ ..+
T Consensus 119 v~~d~~~DlAvl~v~~~~l~~~~l~~----~~~~~~G~~V~aiG~P~g~~~~~t~Giis~~~r~~~~~--~~~----~~~ 188 (353)
T PRK10898 119 VGSDSLTDLAVLKINATNLPVIPINP----KRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLSP--TGR----QNF 188 (353)
T ss_pred EEEcCCCCEEEEEEcCCCCCeeeccC----cCcCCCCCEEEEEeCCCCcCCCcceeEEEeccccccCC--ccc----cce
Confidence 99999999999999987777666654 56789999999999999999999999999988754221 122 246
Q ss_pred EEEeeccCCCCCCCceecCCCcEEEEeccccC-------CCCCccccchHHHHHHHHHHHhcCCcccccccccccCCCcc
Q 001276 191 MQAASGTKGGSSGSPVIDWQGRAVALNAGSKS-------SSASAFFLPLERVVRALRFLQERRDCNIHNWEAVSIPRGTL 263 (1109)
Q Consensus 191 iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~-------~~~~~falP~~~i~~~l~~l~~~~~~~~~~~~~~~v~rg~l 263 (1109)
||+|+++++|||||||+|.+|+||||+++... ..+.+|+||++.+++++++|++++ .+.|+||
T Consensus 189 iqtda~i~~GnSGGPl~n~~G~vvGI~~~~~~~~~~~~~~~g~~faIP~~~~~~~~~~l~~~G----------~~~~~~l 258 (353)
T PRK10898 189 LQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPTQLATKIMDKLIRDG----------RVIRGYI 258 (353)
T ss_pred EEeccccCCCCCcceEECCCCeEEEEEEEEecccCCCCcccceEEEEchHHHHHHHHHHhhcC----------ccccccc
Confidence 99999999999999999999999999976432 146899999999999999999888 7899999
Q ss_pred ceEEEEcChhHHHHcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhc-
Q 001276 264 QVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDD- 341 (1109)
Q Consensus 264 g~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~- 341 (1109)
|+..+..+......+|++ ...|++| ..|.++|||++ ||++||+|++|||++|.++.++...+..
T Consensus 259 Gi~~~~~~~~~~~~~~~~-------------~~~Gv~V-~~V~~~spA~~aGL~~GDvI~~Ing~~V~s~~~l~~~l~~~ 324 (353)
T PRK10898 259 GIGGREIAPLHAQGGGID-------------QLQGIVV-NEVSPDGPAAKAGIQVNDLIISVNNKPAISALETMDQVAEI 324 (353)
T ss_pred ceEEEECCHHHHHhcCCC-------------CCCeEEE-EEECCCChHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhc
Confidence 999998876666666665 4578887 69999999999 9999999999999999999999888854
Q ss_pred CCCCeEEEEEEECCEEEEEEEEeecCC
Q 001276 342 GVDKNIELLIERGGISMTVNLVVQDLH 368 (1109)
Q Consensus 342 ~~g~~v~l~v~R~g~~~~~~v~l~~~~ 368 (1109)
.+|+.+.+++.|+|+.+++.+++..++
T Consensus 325 ~~g~~v~l~v~R~g~~~~~~v~l~~~p 351 (353)
T PRK10898 325 RPGSVIPVVVMRDDKQLTLQVTIQEYP 351 (353)
T ss_pred CCCCEEEEEEEECCEEEEEEEEeccCC
Confidence 789999999999999999999887654
No 11
>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=4e-39 Score=369.42 Aligned_cols=299 Identities=19% Similarity=0.236 Sum_probs=241.7
Q ss_pred ccccccccccEEEEEEEcCcccccCCcccceeeEEEEEEEeeCCceEEEEeCceecCCCCcEEEEeecCCeEEeEEEEEe
Q 001276 619 SFAESVIEPTLVMFEVHVPPSCMIDGVHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGEVVFL 698 (1109)
Q Consensus 619 ~~~~~~~~~SvV~V~~~~~~~~~~dg~~~~~~~GsG~VId~~~~~G~IlTn~~~V~~~~~di~V~~~d~~~~~~a~vv~~ 698 (1109)
..+++++.||+|.|.+...... ........+.||||||+ ++|||||| +||+.++..+.|+|.| ++.++|++++.
T Consensus 48 ~~~~~~~~psVV~I~~~~~~~~-~~~~~~~~~~GSG~vi~---~~G~IlTn-~HVV~~~~~i~V~~~d-g~~~~a~vv~~ 121 (351)
T TIGR02038 48 NKAVRRAAPAVVNIYNRSISQN-SLNQLSIQGLGSGVIMS---KEGYILTN-YHVIKKADQIVVALQD-GRKFEAELVGS 121 (351)
T ss_pred HHHHHhcCCcEEEEEeEecccc-ccccccccceEEEEEEe---CCeEEEec-ccEeCCCCEEEEEECC-CCEEEEEEEEe
Confidence 3478899999999987654211 11112234679999999 68999999 5566778889999998 99999999999
Q ss_pred eCCCcEEEEEECCCCCCcccccceeceecCCCccCCCCCeEEEEeeCCCCcceeeeeeEeccccccccCCCCCCcccc-c
Q 001276 699 HPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRA-M 777 (1109)
Q Consensus 699 dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~iG~p~~~~~~~~~~~vt~i~~~~~i~~~~~~~y~~-~ 777 (1109)
|+.+||||||++...+++ ++++++..+++||+|++||||+++....+.+.|+ ...+..+.. .
T Consensus 122 d~~~DlAvlkv~~~~~~~--------~~l~~s~~~~~G~~V~aiG~P~~~~~s~t~GiIs---------~~~r~~~~~~~ 184 (351)
T TIGR02038 122 DPLTDLAVLKIEGDNLPT--------IPVNLDRPPHVGDVVLAIGNPYNLGQTITQGIIS---------ATGRNGLSSVG 184 (351)
T ss_pred cCCCCEEEEEecCCCCce--------EeccCcCccCCCCEEEEEeCCCCCCCcEEEEEEE---------eccCcccCCCC
Confidence 999999999998877765 7888887899999999999999987655555554 332221111 1
Q ss_pred ceeEEEEecccCC-CCCceEEcCCeeEEEEEeeccccccccCCCCCCceeEecccHHHHHHHHHHHHcCCCCCccccccc
Q 001276 778 NMEVIELDTDFGS-TFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLDKIISGASGPSLLINGV 856 (1109)
Q Consensus 778 ~~~~I~~d~~ig~-~sGGpL~d~~G~VvGi~~~~~~~~~~g~~~~~~~~~~~aipi~~i~~~l~~l~~~~~~~~~~~~~v 856 (1109)
..++||+|+++++ ||||||+|.+|+|||||++..... ......++.|+||++.+++++++|+++++ +
T Consensus 185 ~~~~iqtda~i~~GnSGGpl~n~~G~vIGI~~~~~~~~----~~~~~~g~~faIP~~~~~~vl~~l~~~g~--------~ 252 (351)
T TIGR02038 185 RQNFIQTDAAINAGNSGGALINTNGELVGINTASFQKG----GDEGGEGINFAIPIKLAHKIMGKIIRDGR--------V 252 (351)
T ss_pred cceEEEECCccCCCCCcceEECCCCeEEEEEeeeeccc----CCCCccceEEEecHHHHHHHHHHHhhcCc--------c
Confidence 2478999999976 799999999999999998743220 11222455589999999999999999876 5
Q ss_pred ccCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCHHhhh-ccCCCEEEEECCEEcCChh
Q 001276 857 KRPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFH 935 (1109)
Q Consensus 857 ~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~spA~~a-L~~GDiIlsVnG~~V~~~~ 935 (1109)
.|+ |||+.++.++...++.+|++.. ++++|..|.++|||+++ |++||+|++|||++|.++.
T Consensus 253 ~r~-----~lGv~~~~~~~~~~~~lgl~~~-------------~Gv~V~~V~~~spA~~aGL~~GDvI~~Ing~~V~s~~ 314 (351)
T TIGR02038 253 IRG-----YIGVSGEDINSVVAQGLGLPDL-------------RGIVITGVDPNGPAARAGILVRDVILKYDGKDVIGAE 314 (351)
T ss_pred cce-----EeeeEEEECCHHHHHhcCCCcc-------------ccceEeecCCCChHHHCCCCCCCEEEEECCEEcCCHH
Confidence 667 9999999999888888888754 67889999999999999 9999999999999999999
Q ss_pred HHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeeeec
Q 001276 936 DIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVR 974 (1109)
Q Consensus 936 dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~l~~~ 974 (1109)
++...+...+++ +.+.++|.|+|+.+++.+++.+.
T Consensus 315 dl~~~l~~~~~g----~~v~l~v~R~g~~~~~~v~l~~~ 349 (351)
T TIGR02038 315 ELMDRIAETRPG----SKVMVTVLRQGKQLELPVTIDEK 349 (351)
T ss_pred HHHHHHHhcCCC----CEEEEEEEECCEEEEEEEEecCC
Confidence 999998665665 78999999999999999887543
No 12
>PRK10898 serine endoprotease; Provisional
Probab=100.00 E-value=1.7e-38 Score=363.71 Aligned_cols=300 Identities=15% Similarity=0.218 Sum_probs=238.6
Q ss_pred cccccccccEEEEEEEcCcccccCCcccceeeEEEEEEEeeCCceEEEEeCceecCCCCcEEEEeecCCeEEeEEEEEee
Q 001276 620 FAESVIEPTLVMFEVHVPPSCMIDGVHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGEVVFLH 699 (1109)
Q Consensus 620 ~~~~~~~~SvV~V~~~~~~~~~~dg~~~~~~~GsG~VId~~~~~G~IlTn~~~V~~~~~di~V~~~d~~~~~~a~vv~~d 699 (1109)
..++++.+|+|.|.+.... ..........+.||||||+ ++|||||| +||+.++.++.|++.| +..++|++++.|
T Consensus 49 ~~~~~~~psvV~v~~~~~~-~~~~~~~~~~~~GSGfvi~---~~G~IlTn-~HVv~~a~~i~V~~~d-g~~~~a~vv~~d 122 (353)
T PRK10898 49 QAVRRAAPAVVNVYNRSLN-STSHNQLEIRTLGSGVIMD---QRGYILTN-KHVINDADQIIVALQD-GRVFEALLVGSD 122 (353)
T ss_pred HHHHHhCCcEEEEEeEecc-ccCcccccccceeeEEEEe---CCeEEEec-ccEeCCCCEEEEEeCC-CCEEEEEEEEEc
Confidence 4788999999999887652 1111122334789999999 68999999 5566788899999998 999999999999
Q ss_pred CCCcEEEEEECCCCCCcccccceeceecCCCccCCCCCeEEEEeeCCCCcceeeeeeEeccccccccCCCCCCccc-ccc
Q 001276 700 PVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYR-AMN 778 (1109)
Q Consensus 700 p~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~iG~p~~~~~~~~~~~vt~i~~~~~i~~~~~~~y~-~~~ 778 (1109)
+.+||||||++...+++ ++|+++..+++||+|+++|||+++....+.+.|+ +..+..+. ...
T Consensus 123 ~~~DlAvl~v~~~~l~~--------~~l~~~~~~~~G~~V~aiG~P~g~~~~~t~Giis---------~~~r~~~~~~~~ 185 (353)
T PRK10898 123 SLTDLAVLKINATNLPV--------IPINPKRVPHIGDVVLAIGNPYNLGQTITQGIIS---------ATGRIGLSPTGR 185 (353)
T ss_pred CCCCEEEEEEcCCCCCe--------eeccCcCcCCCCCEEEEEeCCCCcCCCcceeEEE---------eccccccCCccc
Confidence 99999999998877776 8888887899999999999999876644455554 32221111 112
Q ss_pred eeEEEEecccCC-CCCceEEcCCeeEEEEEeeccccccccCCCCCCceeEecccHHHHHHHHHHHHcCCCCCcccccccc
Q 001276 779 MEVIELDTDFGS-TFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLDKIISGASGPSLLINGVK 857 (1109)
Q Consensus 779 ~~~I~~d~~ig~-~sGGpL~d~~G~VvGi~~~~~~~~~~g~~~~~~~~~~~aipi~~i~~~l~~l~~~~~~~~~~~~~v~ 857 (1109)
.++||+|+++++ ||||||+|.+|+||||+++..... + ......++.|+||++.+++++++|+++++ +.
T Consensus 186 ~~~iqtda~i~~GnSGGPl~n~~G~vvGI~~~~~~~~--~-~~~~~~g~~faIP~~~~~~~~~~l~~~G~--------~~ 254 (353)
T PRK10898 186 QNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKS--N-DGETPEGIGFAIPTQLATKIMDKLIRDGR--------VI 254 (353)
T ss_pred cceEEeccccCCCCCcceEECCCCeEEEEEEEEeccc--C-CCCcccceEEEEchHHHHHHHHHHhhcCc--------cc
Confidence 368999999966 799999999999999998754330 0 01112345588999999999999998886 67
Q ss_pred cCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCHHhhh-ccCCCEEEEECCEEcCChhH
Q 001276 858 RPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHD 936 (1109)
Q Consensus 858 r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~spA~~a-L~~GDiIlsVnG~~V~~~~d 936 (1109)
|+ |||+.++.+....+..++++.. .+++|..|.++|||+++ |++||+|++|||++|.++.+
T Consensus 255 ~~-----~lGi~~~~~~~~~~~~~~~~~~-------------~Gv~V~~V~~~spA~~aGL~~GDvI~~Ing~~V~s~~~ 316 (353)
T PRK10898 255 RG-----YIGIGGREIAPLHAQGGGIDQL-------------QGIVVNEVSPDGPAAKAGIQVNDLIISVNNKPAISALE 316 (353)
T ss_pred cc-----ccceEEEECCHHHHHhcCCCCC-------------CeEEEEEECCCChHHHcCCCCCCEEEEECCEEcCCHHH
Confidence 77 9999999887665555554433 78889999999999999 99999999999999999999
Q ss_pred HHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeeeecC
Q 001276 937 IENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRD 975 (1109)
Q Consensus 937 l~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~l~~~~ 975 (1109)
+...+.....+ +.+.++|.|+|+.+++.+++.+.+
T Consensus 317 l~~~l~~~~~g----~~v~l~v~R~g~~~~~~v~l~~~p 351 (353)
T PRK10898 317 TMDQVAEIRPG----SVIPVVVMRDDKQLTLQVTIQEYP 351 (353)
T ss_pred HHHHHHhcCCC----CEEEEEEEECCEEEEEEEEeccCC
Confidence 99888665665 789999999999999998876543
No 13
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2e-33 Score=324.10 Aligned_cols=295 Identities=24% Similarity=0.414 Sum_probs=255.1
Q ss_pred chHHHHHHHhCCceEEEEEEeeecc----CCCC--C-CccEEEEEEEeCCCcEEEeCccccCCCCeEEEEEecCCeEEEE
Q 001276 36 DDWRKALNKVVPAVVVLRTTACRAF----DTEA--A-GASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPV 108 (1109)
Q Consensus 36 ~~~~~~~~~~~~sVV~I~~~~~~~~----d~~~--~-~~~~GSGfvV~~~~G~IlTn~HVv~~~~~~~~v~~~~~~~~~a 108 (1109)
..+...++++.++||.+........ .... . ..+.||||++++ +|||+||.||+.. +..+.+.+.|++++++
T Consensus 33 ~~~~~~~~~~~~~vV~~~~~~~~~~~~~~~~~~~~~~~~~~gSg~i~~~-~g~ivTn~hVi~~-a~~i~v~l~dg~~~~a 110 (347)
T COG0265 33 LSFATAVEKVAPAVVSIATGLTAKLRSFFPSDPPLRSAEGLGSGFIISS-DGYIVTNNHVIAG-AEEITVTLADGREVPA 110 (347)
T ss_pred cCHHHHHHhcCCcEEEEEeeeeecchhcccCCcccccccccccEEEEcC-CeEEEecceecCC-cceEEEEeCCCCEEEE
Confidence 6999999999999999998754321 1111 0 158899999996 8999999999995 8889999999999999
Q ss_pred EEEEEcCCCcEEEEEEcCCC-cccccccCCCCCCccCCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCccccc
Q 001276 109 YPIYRDPVHDFGFFRYDPSA-IQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFN 187 (1109)
Q Consensus 109 ~vv~~d~~~DlAlLk~~~~~-~~~~~l~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~vs~~~~~~~~~~~~~~~~~~ 187 (1109)
++++.|+..|+|+||++... ++++.+.. +..+++|++++++|+|+++..+++.|+++.+.|. .+....+ .
T Consensus 111 ~~vg~d~~~dlavlki~~~~~~~~~~~~~----s~~l~vg~~v~aiGnp~g~~~tvt~Givs~~~r~--~v~~~~~---~ 181 (347)
T COG0265 111 KLVGKDPISDLAVLKIDGAGGLPVIALGD----SDKLRVGDVVVAIGNPFGLGQTVTSGIVSALGRT--GVGSAGG---Y 181 (347)
T ss_pred EEEecCCccCEEEEEeccCCCCceeeccC----CCCcccCCEEEEecCCCCcccceeccEEeccccc--cccCccc---c
Confidence 99999999999999999765 66666665 7788999999999999999999999999999997 2222111 2
Q ss_pred eeeEEEeeccCCCCCCCceecCCCcEEEEeccccCCC----CCccccchHHHHHHHHHHHhcCCcccccccccccCCCcc
Q 001276 188 TFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSSS----ASAFFLPLERVVRALRFLQERRDCNIHNWEAVSIPRGTL 263 (1109)
Q Consensus 188 ~~~iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~~----~~~falP~~~i~~~l~~l~~~~~~~~~~~~~~~v~rg~l 263 (1109)
..+||+|+++++|+||||++|.+|++|||++...... +.+|++|++.+++++.++...+ ++.|+++
T Consensus 182 ~~~IqtdAain~gnsGgpl~n~~g~~iGint~~~~~~~~~~gigfaiP~~~~~~v~~~l~~~G----------~v~~~~l 251 (347)
T COG0265 182 VNFIQTDAAINPGNSGGPLVNIDGEVVGINTAIIAPSGGSSGIGFAIPVNLVAPVLDELISKG----------KVVRGYL 251 (347)
T ss_pred cchhhcccccCCCCCCCceEcCCCcEEEEEEEEecCCCCcceeEEEecHHHHHHHHHHHHHcC----------Ccccccc
Confidence 3469999999999999999999999999998877653 4799999999999999999876 7999999
Q ss_pred ceEEEEcChhHHHHcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHh-c
Q 001276 264 QVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLD-D 341 (1109)
Q Consensus 264 g~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~-~ 341 (1109)
|+.+..+..+.+ +|++ ...|++| ..|.+++||++ |++.||+|+++||+++.+..++...+. .
T Consensus 252 gv~~~~~~~~~~--~g~~-------------~~~G~~V-~~v~~~spa~~agi~~Gdii~~vng~~v~~~~~l~~~v~~~ 315 (347)
T COG0265 252 GVIGEPLTADIA--LGLP-------------VAAGAVV-LGVLPGSPAAKAGIKAGDIITAVNGKPVASLSDLVAAVASN 315 (347)
T ss_pred ceEEEEcccccc--cCCC-------------CCCceEE-EecCCCChHHHcCCCCCCEEEEECCEEccCHHHHHHHHhcc
Confidence 999998887777 7765 5688776 79999999999 999999999999999999999998884 4
Q ss_pred CCCCeEEEEEEECCEEEEEEEEeecC
Q 001276 342 GVDKNIELLIERGGISMTVNLVVQDL 367 (1109)
Q Consensus 342 ~~g~~v~l~v~R~g~~~~~~v~l~~~ 367 (1109)
.+|+.+.+++.|+|+.+++.+++.++
T Consensus 316 ~~g~~v~~~~~r~g~~~~~~v~l~~~ 341 (347)
T COG0265 316 RPGDEVALKLLRGGKERELAVTLGDR 341 (347)
T ss_pred CCCCEEEEEEEECCEEEEEEEEecCc
Confidence 68999999999999999999999873
No 14
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=1.2e-28 Score=284.40 Aligned_cols=294 Identities=27% Similarity=0.353 Sum_probs=239.0
Q ss_pred cccccccccEEEEEEEcCccc--ccCC---cccceeeEEEEEEEeeCCceEEEEeCceecCCCCcEEEEeecCCeEEeEE
Q 001276 620 FAESVIEPTLVMFEVHVPPSC--MIDG---VHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGE 694 (1109)
Q Consensus 620 ~~~~~~~~SvV~V~~~~~~~~--~~dg---~~~~~~~GsG~VId~~~~~G~IlTn~~~V~~~~~di~V~~~d~~~~~~a~ 694 (1109)
...+++.+++|.+........ .+.. .......||||+++ ..|||+|| +||+.++..+.+++.| ++.++|+
T Consensus 37 ~~~~~~~~~vV~~~~~~~~~~~~~~~~~~~~~~~~~~gSg~i~~---~~g~ivTn-~hVi~~a~~i~v~l~d-g~~~~a~ 111 (347)
T COG0265 37 TAVEKVAPAVVSIATGLTAKLRSFFPSDPPLRSAEGLGSGFIIS---SDGYIVTN-NHVIAGAEEITVTLAD-GREVPAK 111 (347)
T ss_pred HHHHhcCCcEEEEEeeeeecchhcccCCcccccccccccEEEEc---CCeEEEec-ceecCCcceEEEEeCC-CCEEEEE
Confidence 377888999999988654211 0000 01114789999999 79999999 6666669999999987 9999999
Q ss_pred EEEeeCCCcEEEEEECCCC-CCcccccceeceecCCCccCCCCCeEEEEeeCCCCcceeeeeeEeccccccccCCCCCCc
Q 001276 695 VVFLHPVHNFALIAYDPSS-LGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPR 773 (1109)
Q Consensus 695 vv~~dp~~dlAilk~d~~~-l~~~~~~~v~~~~l~~~~~l~~G~~V~~iG~p~~~~~~~~~~~vt~i~~~~~i~~~~~~~ 773 (1109)
+++.|+.+|+|++|++... ++. +.++++..++.||+++++|+|+++. .+|+ .|+++...+..
T Consensus 112 ~vg~d~~~dlavlki~~~~~~~~--------~~~~~s~~l~vg~~v~aiGnp~g~~-----~tvt----~Givs~~~r~~ 174 (347)
T COG0265 112 LVGKDPISDLAVLKIDGAGGLPV--------IALGDSDKLRVGDVVVAIGNPFGLG-----QTVT----SGIVSALGRTG 174 (347)
T ss_pred EEecCCccCEEEEEeccCCCCce--------eeccCCCCcccCCEEEEecCCCCcc-----ccee----ccEEecccccc
Confidence 9999999999999998764 665 7999999999999999999999964 4555 55566555531
Q ss_pred cc--ccceeEEEEecccCC-CCCceEEcCCeeEEEEEeeccccccccCCCCCCceeEecccHHHHHHHHHHHHcCCCCCc
Q 001276 774 YR--AMNMEVIELDTDFGS-TFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLDKIISGASGPS 850 (1109)
Q Consensus 774 y~--~~~~~~I~~d~~ig~-~sGGpL~d~~G~VvGi~~~~~~~~~~g~~~~~~~~~~~aipi~~i~~~l~~l~~~~~~~~ 850 (1109)
+. .....+||+|+++++ +|||||+|.+|+++||+++..... + +..+++ |+||++.+++++.++...++
T Consensus 175 v~~~~~~~~~IqtdAain~gnsGgpl~n~~g~~iGint~~~~~~--~--~~~gig--faiP~~~~~~v~~~l~~~G~--- 245 (347)
T COG0265 175 VGSAGGYVNFIQTDAAINPGNSGGPLVNIDGEVVGINTAIIAPS--G--GSSGIG--FAIPVNLVAPVLDELISKGK--- 245 (347)
T ss_pred ccCcccccchhhcccccCCCCCCCceEcCCCcEEEEEEEEecCC--C--CcceeE--EEecHHHHHHHHHHHHHcCC---
Confidence 11 125689999999977 899999999999999998854430 1 134455 78999999999999998655
Q ss_pred ccccccccCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCHHhhh-ccCCCEEEEECCE
Q 001276 851 LLINGVKRPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSKAENM-LEQGDMMLAINKQ 929 (1109)
Q Consensus 851 ~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~spA~~a-L~~GDiIlsVnG~ 929 (1109)
+.|+ ++|+.+..+....+ +|++.. .+.+|..|.+++||+++ ++.||+|+++||+
T Consensus 246 -----v~~~-----~lgv~~~~~~~~~~--~g~~~~-------------~G~~V~~v~~~spa~~agi~~Gdii~~vng~ 300 (347)
T COG0265 246 -----VVRG-----YLGVIGEPLTADIA--LGLPVA-------------AGAVVLGVLPGSPAAKAGIKAGDIITAVNGK 300 (347)
T ss_pred -----cccc-----ccceEEEEcccccc--cCCCCC-------------CceEEEecCCCChHHHcCCCCCCEEEEECCE
Confidence 7888 89999998877666 665533 66889999999999999 9999999999999
Q ss_pred EcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeeee
Q 001276 930 PVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDV 973 (1109)
Q Consensus 930 ~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~l~~ 973 (1109)
++.+..++...+....++ +.+.+++.|+|+++++.+++.+
T Consensus 301 ~v~~~~~l~~~v~~~~~g----~~v~~~~~r~g~~~~~~v~l~~ 340 (347)
T COG0265 301 PVASLSDLVAAVASNRPG----DEVALKLLRGGKERELAVTLGD 340 (347)
T ss_pred EccCHHHHHHHHhccCCC----CEEEEEEEECCEEEEEEEEecC
Confidence 999999999999766665 8999999999999999998876
No 15
>KOG1320 consensus Serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=1.4e-22 Score=231.67 Aligned_cols=316 Identities=19% Similarity=0.254 Sum_probs=237.2
Q ss_pred CcchHHHHHHHhCCceEEEEEEee----eccCCCCCCccEEEEEEEeCCCcEEEeCccccCCCCe----------EEEEE
Q 001276 34 TADDWRKALNKVVPAVVVLRTTAC----RAFDTEAAGASYATGFVVDKRRGIILTNRHVVKPGPV----------VAEAM 99 (1109)
Q Consensus 34 ~~~~~~~~~~~~~~sVV~I~~~~~----~~~d~~~~~~~~GSGfvV~~~~G~IlTn~HVv~~~~~----------~~~v~ 99 (1109)
.....+...++...|+|.|..... .+|....-....||||||+. +|+|+||+||+..... .+.+.
T Consensus 126 ~~~~v~~~~~~cd~Avv~Ie~~~f~~~~~~~e~~~ip~l~~S~~Vv~g-d~i~VTnghV~~~~~~~y~~~~~~l~~vqi~ 204 (473)
T KOG1320|consen 126 YKAFVAAVFEECDLAVVYIESEEFWKGMNPFELGDIPSLNGSGFVVGG-DGIIVTNGHVVRVEPRIYAHSSTVLLRVQID 204 (473)
T ss_pred hhhhHHHhhhcccceEEEEeeccccCCCcccccCCCcccCccEEEEcC-CcEEEEeeEEEEEEeccccCCCcceeeEEEE
Confidence 345788899999999999996422 22555566778899999997 8999999999985433 35666
Q ss_pred ecCC--eEEEEEEEEEcCCCcEEEEEEcCC-C-cccccccCCCCCCccCCCCCEEEEEecCCCCCCeEEEEEEEEecCCC
Q 001276 100 FVNR--EEIPVYPIYRDPVHDFGFFRYDPS-A-IQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDA 175 (1109)
Q Consensus 100 ~~~~--~~~~a~vv~~d~~~DlAlLk~~~~-~-~~~~~l~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~vs~~~~~~ 175 (1109)
.+++ ..+.+.+++.|+..|+|+++++.. . ++.+++.. ...++.|+++..+|+|++...+.+.|+++...|..
T Consensus 205 aa~~~~~s~ep~i~g~d~~~gvA~l~ik~~~~i~~~i~~~~----~~~~~~G~~~~a~~~~f~~~nt~t~g~vs~~~R~~ 280 (473)
T KOG1320|consen 205 AAIGPGNSGEPVIVGVDKVAGVAFLKIKTPENILYVIPLGV----SSHFRTGVEVSAIGNGFGLLNTLTQGMVSGQLRKS 280 (473)
T ss_pred EeecCCccCCCeEEccccccceEEEEEecCCcccceeecce----eeeecccceeeccccCceeeeeeeecccccccccc
Confidence 6665 889999999999999999999644 2 44444444 78899999999999999999999999999999976
Q ss_pred CCCCCCCccccceeeEEEeeccCCCCCCCceecCCCcEEEEeccccCC----CCCccccchHHHHHHHHHHHhcCCcccc
Q 001276 176 PHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSS----SASAFFLPLERVVRALRFLQERRDCNIH 251 (1109)
Q Consensus 176 ~~~~~~~~~~~~~~~iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~----~~~~falP~~~i~~~l~~l~~~~~~~~~ 251 (1109)
...+.. ......+++|++++++.|+||+|++|.+|++||+++..... .+.+|++|.+.++.++.+.-+.+ +-+.
T Consensus 281 ~~lg~~-~g~~i~~~~qtd~ai~~~nsg~~ll~~DG~~IgVn~~~~~ri~~~~~iSf~~p~d~vl~~v~r~~e~~-~~lr 358 (473)
T KOG1320|consen 281 FKLGLE-TGVLISKINQTDAAINPGNSGGPLLNLDGEVIGVNTRKVTRIGFSHGISFKIPIDTVLVIVLRLGEFQ-ISLR 358 (473)
T ss_pred cccCcc-cceeeeeecccchhhhcccCCCcEEEecCcEeeeeeeeeEEeeccccceeccCchHhhhhhhhhhhhc-eeec
Confidence 544333 22234578999999999999999999999999999876653 68899999999999887663222 1111
Q ss_pred cccccccCCCccceEEEEcChhHH-HHcCCChhHHHhhhcCCCCCCC-ceEEEEEecCCCcccc-CCCCCCEEEEECCEE
Q 001276 252 NWEAVSIPRGTLQVTFVHKGFDET-RRLGLQSATEQMVRHASPPGET-GLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEV 328 (1109)
Q Consensus 252 ~~~~~~v~rg~lg~~~~~~~~~~~-r~lGl~~~~~~~~~~~~~~~~~-G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~ 328 (1109)
+.......+.++|+.......... ..++.++ .+|.... ++++ ..|.|++++.. ++.+||+|++|||++
T Consensus 359 ~~~~~~p~~~~~g~~s~~i~~g~vf~~~~~~~--------~~~~~~~q~v~i-s~Vlp~~~~~~~~~~~g~~V~~vng~~ 429 (473)
T KOG1320|consen 359 PVKPLVPVHQYIGLPSYYIFAGLVFVPLTKSY--------IFPSGVVQLVLV-SQVLPGSINGGYGLKPGDQVVKVNGKP 429 (473)
T ss_pred cccCcccccccCCceeEEEecceEEeecCCCc--------cccccceeEEEE-EEeccCCCcccccccCCCEEEEECCEE
Confidence 111112234566666543322111 1122221 2332233 4555 79999999999 999999999999999
Q ss_pred eCChhHHHHHHhc-CCCCeEEEEEEECCEEEEEEEEee
Q 001276 329 ITQFLKLETLLDD-GVDKNIELLIERGGISMTVNLVVQ 365 (1109)
Q Consensus 329 v~~~~~l~~~l~~-~~g~~v~l~v~R~g~~~~~~v~l~ 365 (1109)
|.+..++..++.. ..+++|.+..+|..+..++.+...
T Consensus 430 V~n~~~l~~~i~~~~~~~~v~vl~~~~~e~~tl~Il~~ 467 (473)
T KOG1320|consen 430 VKNLKHLYELIEECSTEDKVAVLDRRSAEDATLEILPE 467 (473)
T ss_pred eechHHHHHHHHhcCcCceEEEEEecCccceeEEeccc
Confidence 9999999999954 667888888888888888877654
No 16
>KOG1320 consensus Serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.80 E-value=3.2e-18 Score=196.05 Aligned_cols=309 Identities=17% Similarity=0.164 Sum_probs=218.3
Q ss_pred ccccccccEEEEEEEc--CcccccCCcccceeeEEEEEEEeeCCceEEEEeCceecCCCC----------cEEEEeecCC
Q 001276 621 AESVIEPTLVMFEVHV--PPSCMIDGVHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISAS----------DVMLSFAAFP 688 (1109)
Q Consensus 621 ~~~~~~~SvV~V~~~~--~~~~~~dg~~~~~~~GsG~VId~~~~~G~IlTn~~~V~~~~~----------di~V~~~d~~ 688 (1109)
..++...++|.|+..- ....++.+..-....|||+||+ .+|+++||.|++..... .|.|+.++ +
T Consensus 133 ~~~~cd~Avv~Ie~~~f~~~~~~~e~~~ip~l~~S~~Vv~---gd~i~VTnghV~~~~~~~y~~~~~~l~~vqi~aa~-~ 208 (473)
T KOG1320|consen 133 VFEECDLAVVYIESEEFWKGMNPFELGDIPSLNGSGFVVG---GDGIIVTNGHVVRVEPRIYAHSSTVLLRVQIDAAI-G 208 (473)
T ss_pred hhhcccceEEEEeeccccCCCcccccCCCcccCccEEEEc---CCcEEEEeeEEEEEEeccccCCCcceeeEEEEEee-c
Confidence 3344557788887521 1111255555666789999999 79999999776654333 48888887 6
Q ss_pred --eEEeEEEEEeeCCCcEEEEEECCC-C-CCcccccceeceecCCCccCCCCCeEEEEeeCCCCcceeeeeeEecccccc
Q 001276 689 --IEIPGEVVFLHPVHNFALIAYDPS-S-LGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAAL 764 (1109)
Q Consensus 689 --~~~~a~vv~~dp~~dlAilk~d~~-~-l~~~~~~~v~~~~l~~~~~l~~G~~V~~iG~p~~~~~~~~~~~vt~i~~~~ 764 (1109)
...++.+++.|+..|+|+++++.. . ++. ++++-+..++.|+++.++|+|+++. .+++ .+
T Consensus 209 ~~~s~ep~i~g~d~~~gvA~l~ik~~~~i~~~--------i~~~~~~~~~~G~~~~a~~~~f~~~-----nt~t----~g 271 (473)
T KOG1320|consen 209 PGNSGEPVIVGVDKVAGVAFLKIKTPENILYV--------IPLGVSSHFRTGVEVSAIGNGFGLL-----NTLT----QG 271 (473)
T ss_pred CCccCCCeEEccccccceEEEEEecCCcccce--------eecceeeeecccceeeccccCceee-----eeee----ec
Confidence 899999999999999999999533 2 332 6777777799999999999999984 4555 66
Q ss_pred ccCCCCCCccc------ccceeEEEEecccCC-CCCceEEcCCeeEEEEEeeccccccccCCCCCCceeEecccHHHHHH
Q 001276 765 NISSADCPRYR------AMNMEVIELDTDFGS-TFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISR 837 (1109)
Q Consensus 765 ~i~~~~~~~y~------~~~~~~I~~d~~ig~-~sGGpL~d~~G~VvGi~~~~~~~~~~g~~~~~~~~~~~aipi~~i~~ 837 (1109)
.++...|..|. -...+++|+|++++. ++||||+|.+|++||+++...... .-..+.+ |++|.+.++.
T Consensus 272 ~vs~~~R~~~~lg~~~g~~i~~~~qtd~ai~~~nsg~~ll~~DG~~IgVn~~~~~ri----~~~~~iS--f~~p~d~vl~ 345 (473)
T KOG1320|consen 272 MVSGQLRKSFKLGLETGVLISKINQTDAAINPGNSGGPLLNLDGEVIGVNTRKVTRI----GFSHGIS--FKIPIDTVLV 345 (473)
T ss_pred ccccccccccccCcccceeeeeecccchhhhcccCCCcEEEecCcEeeeeeeeeEEe----eccccce--eccCchHhhh
Confidence 66666555543 244689999999966 799999999999999988733210 0123445 8899999999
Q ss_pred HHHHHHcCCCCCcccccccccCCCceeeeeeEEEEcChHhHHH-cCCCHHHHHHHHhcCC-CccceEEEEeecCCCHHhh
Q 001276 838 VLDKIISGASGPSLLINGVKRPMPLVRILEVELYPTLLSKARS-FGLSDDWVQALVKKDP-VRRQVLRVKGCLAGSKAEN 915 (1109)
Q Consensus 838 ~l~~l~~~~~~~~~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~-~Gl~~~wi~~~~~~~~-~~~~~~~V~~V~~~spA~~ 915 (1109)
++.+.......- ..+++..|.-+|+|.....+.....-. .+.+.. ++ ...|++++..|.+++++..
T Consensus 346 ~v~r~~e~~~~l----r~~~~~~p~~~~~g~~s~~i~~g~vf~~~~~~~~--------~~~~~~q~v~is~Vlp~~~~~~ 413 (473)
T KOG1320|consen 346 IVLRLGEFQISL----RPVKPLVPVHQYIGLPSYYIFAGLVFVPLTKSYI--------FPSGVVQLVLVSQVLPGSINGG 413 (473)
T ss_pred hhhhhhhhceee----ccccCcccccccCCceeEEEecceEEeecCCCcc--------ccccceeEEEEEEeccCCCccc
Confidence 888874332100 012222334456666555433221110 111111 11 2337888999999999999
Q ss_pred h-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeee
Q 001276 916 M-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTD 972 (1109)
Q Consensus 916 a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~l~ 972 (1109)
. +++||+|++|||++|.+..++..++.....+ ++|.+...|..|..++.+...
T Consensus 414 ~~~~~g~~V~~vng~~V~n~~~l~~~i~~~~~~----~~v~vl~~~~~e~~tl~Il~~ 467 (473)
T KOG1320|consen 414 YGLKPGDQVVKVNGKPVKNLKHLYELIEECSTE----DKVAVLDRRSAEDATLEILPE 467 (473)
T ss_pred ccccCCCEEEEECCEEeechHHHHHHHHhcCcC----ceEEEEEecCccceeEEeccc
Confidence 9 9999999999999999999999999655543 678888888888888888543
No 17
>KOG3209 consensus WW domain-containing protein [General function prediction only]
Probab=99.73 E-value=1.1e-15 Score=175.47 Aligned_cols=178 Identities=20% Similarity=0.275 Sum_probs=109.7
Q ss_pred ccCCCccceEEEEcChhHHHHcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChhH
Q 001276 257 SIPRGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFLK 334 (1109)
Q Consensus 257 ~v~rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~~ 334 (1109)
.+.+++.|+-|....-|.. ...-.|.|+.|+.++||++ .|+.||+|+.|||+.+-...+
T Consensus 349 ~LvKg~~GFGfTliGGdd~-------------------~gDefLqVKsvl~DGPAa~dGkle~GDviV~INg~cvlGhTH 409 (984)
T KOG3209|consen 349 KLVKGYMGFGFTLIGGDDV-------------------RGDEFLQVKSVLKDGPAAQDGKLETGDVIVHINGECVLGHTH 409 (984)
T ss_pred EEeecccccceEEecCCcC-------------------CCCceeeeeecccCCchhhcCccccCcEEEEECCceeccccH
Confidence 4566777777776542221 2345677899999999999 599999999999999987766
Q ss_pred HH--HHHhc-CCCCeEEEEEEECCE-----EE----EEEEEeecCCCCCCCccccccceEEe------------cCCHHH
Q 001276 335 LE--TLLDD-GVDKNIELLIERGGI-----SM----TVNLVVQDLHSITPDYFLEVSGAVIH------------PLSYQQ 390 (1109)
Q Consensus 335 l~--~~l~~-~~g~~v~l~v~R~g~-----~~----~~~v~l~~~~~~~~~~~~~~~G~~~~------------~l~~~~ 390 (1109)
.+ .++.. -+|+.|.|++.|+=+ .. ...--+..|+...+ ...|.-+. +-++..
T Consensus 410 AqaV~~fqaiPvg~~V~L~lcRgyelp~dp~dp~~sp~~~iv~~~P~~~~----~~~gp~v~~~~sss~~~a~~~~~~el 485 (984)
T KOG3209|consen 410 AQAVKRFQAIPVGQSVDLVLCRGYELPFDPEDPVGSPRVAIVPSWPDSST----DKGGPMVTGRPSSSTHLAQHDGPPEL 485 (984)
T ss_pred HHHHHHhhccccCCeeeEEEecCccCCCCCcccCCCCccccccCCCCCCC----CCCCCeeecCCCCccccccCCCCccc
Confidence 55 44433 579999999999421 11 11111222221111 11111110 000000
Q ss_pred --------hhccCCC----CCeEEEEcCCChhHHcCCCCCCEEEEcCCeecCCH--HHHHHHHHhcCCCCeEeEEEEeec
Q 001276 391 --------ARNFRFP----CGLVYVAEPGYMLFRAGVPRHAIIKKFAGEEISRL--EDLISVLSKLSRGARVPIEYSSYT 456 (1109)
Q Consensus 391 --------~~~~~~~----~~gv~v~~pg~~a~~aGl~~GD~I~~Vng~~v~~l--~~~~~~i~~~~~g~~v~l~~~~~~ 456 (1109)
..-|++. ..|.-|...-.+-+.-||..||+|+.+|++.+..+ .+++++++..+-|.++.|.+.|-+
T Consensus 486 ~ti~i~kgpegfgftiADsPtgqrvK~ilDp~~c~gl~eGd~IVei~~rnvr~L~h~qvvdmlke~piG~r~~Llv~RGg 565 (984)
T KOG3209|consen 486 TTIKIVKGPEGFGFTIADSPTGQRVKQILDPQDCPGLSEGDLIVEINERNVRALTHTQVVDMLKECPIGSRVHLLVKRGG 565 (984)
T ss_pred EEEeeecCCCCCCceeccCCCCCceeeecCcccCCCCCCCCeEEecccccccccchHHHHHHHHhccCCcceeEEEecCC
Confidence 0011110 01111221223445568999999999999999988 689999999999999999888876
Q ss_pred c
Q 001276 457 D 457 (1109)
Q Consensus 457 ~ 457 (1109)
-
T Consensus 566 p 566 (984)
T KOG3209|consen 566 P 566 (984)
T ss_pred C
Confidence 5
No 18
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=99.70 E-value=3.2e-16 Score=186.36 Aligned_cols=157 Identities=20% Similarity=0.223 Sum_probs=127.3
Q ss_pred EEEeecCCCHHhhh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeeeecCCC---C
Q 001276 903 RVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGN---G 978 (1109)
Q Consensus 903 ~V~~V~~~spA~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~l~~~~~~---~ 978 (1109)
+|..|.++|||+++ ||+||+|++|||++|.+|+++...+....++ ++++++|.|+|+.+++++++...+.. .
T Consensus 129 lV~~V~~~SpA~kAGLk~GDvI~~vnG~~V~~~~~l~~~v~~~~~g----~~v~v~v~R~gk~~~~~v~l~~~~~~~~~~ 204 (449)
T PRK10779 129 VVGEIAPNSIAAQAQIAPGTELKAVDGIETPDWDAVRLALVSKIGD----ESTTITVAPFGSDQRRDKTLDLRHWAFEPD 204 (449)
T ss_pred cccccCCCCHHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhhccC----CceEEEEEeCCccceEEEEecccccccCcc
Confidence 48999999999999 9999999999999999999999988665554 78999999999998888887543211 1
Q ss_pred cceEEeecCccccCCchhhhhccCCCCCCCcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCce
Q 001276 979 TTRVINWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEF 1058 (1109)
Q Consensus 979 t~~~~~~~G~~~~~p~~~~r~~~~lp~~~~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~ 1058 (1109)
+.......|+.... + ..+++|+.|.++|||+++||++||.|++|||+++.+++++.+.+++. .++.
T Consensus 205 ~~~~~~~lGl~~~~-----------~--~~~~vV~~V~~~SpA~~AGL~~GDvIl~Ing~~V~s~~dl~~~l~~~-~~~~ 270 (449)
T PRK10779 205 KQDPVSSLGIRPRG-----------P--QIEPVLAEVQPNSAASKAGLQAGDRIVKVDGQPLTQWQTFVTLVRDN-PGKP 270 (449)
T ss_pred ccchhhcccccccC-----------C--CcCcEEEeeCCCCHHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhC-CCCE
Confidence 11111123332111 1 11468999999999999999999999999999999999999999984 5788
Q ss_pred EEEEEEEeCCeEEEEEEeeC
Q 001276 1059 VRVRTVHLNGKPRVLTLKQD 1078 (1109)
Q Consensus 1059 v~l~~v~rdg~~~~i~lk~~ 1078 (1109)
+.++ +.|+|+.+.++++++
T Consensus 271 v~l~-v~R~g~~~~~~v~~~ 289 (449)
T PRK10779 271 LALE-IERQGSPLSLTLTPD 289 (449)
T ss_pred EEEE-EEECCEEEEEEEEee
Confidence 9998 899999999988875
No 19
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=99.55 E-value=6.8e-14 Score=164.87 Aligned_cols=144 Identities=22% Similarity=0.322 Sum_probs=119.6
Q ss_pred ceEEEEeecCCCHHhhh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeeeecCCCC
Q 001276 900 QVLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGNG 978 (1109)
Q Consensus 900 ~~~~V~~V~~~spA~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~l~~~~~~~ 978 (1109)
.+.+|.+|.++|||+++ |++||+|+++||+++.++.++...+.... +++.+++.|+++...+.+++.
T Consensus 128 ~g~~V~~V~~~SpA~~AGL~~GDvI~~vng~~v~~~~dl~~~ia~~~------~~v~~~I~r~g~~~~l~v~l~------ 195 (420)
T TIGR00054 128 VGPVIELLDKNSIALEAGIEPGDEILSVNGNKIPGFKDVRQQIADIA------GEPMVEILAERENWTFEVMKE------ 195 (420)
T ss_pred CCceeeccCCCCHHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhhc------ccceEEEEEecCceEeccccc------
Confidence 34569999999999999 99999999999999999999998885433 457899999888766554322
Q ss_pred cceEEeecCccccCCchhhhhccCCCCCCCcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCce
Q 001276 979 TTRVINWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEF 1058 (1109)
Q Consensus 979 t~~~~~~~G~~~~~p~~~~r~~~~lp~~~~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~ 1058 (1109)
+.... |. .+++|..|.++|||+++||++||.|++|||+++.+++++.+.+++. .++.
T Consensus 196 ---------~~~~~-----------~~--~g~vV~~V~~~SpA~~aGL~~GD~Iv~Vng~~V~s~~dl~~~l~~~-~~~~ 252 (420)
T TIGR00054 196 ---------LIPRG-----------PK--IEPVLSDVTPNSPAEKAGLKEGDYIQSINGEKLRSWTDFVSAVKEN-PGKS 252 (420)
T ss_pred ---------ceecC-----------CC--cCcEEEEECCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHHHhC-CCCc
Confidence 11001 10 2578999999999999999999999999999999999999999985 4778
Q ss_pred EEEEEEEeCCeEEEEEEeeCC
Q 001276 1059 VRVRTVHLNGKPRVLTLKQDL 1079 (1109)
Q Consensus 1059 v~l~~v~rdg~~~~i~lk~~~ 1079 (1109)
+.++ +.|+|+.+.++++++.
T Consensus 253 v~l~-v~R~g~~~~~~v~~~~ 272 (420)
T TIGR00054 253 MDIK-VERNGETLSISLTPEA 272 (420)
T ss_pred eEEE-EEECCEEEEEEEEEcC
Confidence 9998 7999999999998854
No 20
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=99.54 E-value=7.1e-14 Score=166.43 Aligned_cols=143 Identities=18% Similarity=0.236 Sum_probs=111.7
Q ss_pred EEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHh-cCCCCeEEEEEEECCEEEEEEEEeecCCCC-CC--Cccc
Q 001276 302 VDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLD-DGVDKNIELLIERGGISMTVNLVVQDLHSI-TP--DYFL 376 (1109)
Q Consensus 302 v~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~-~~~g~~v~l~v~R~g~~~~~~v~l~~~~~~-~~--~~~~ 376 (1109)
|..|.++|||++ |||+||+|++|||++|.+|.++...+. ..+|+++++++.|+|+.++.++++...+.. .+ ....
T Consensus 130 V~~V~~~SpA~kAGLk~GDvI~~vnG~~V~~~~~l~~~v~~~~~g~~v~v~v~R~gk~~~~~v~l~~~~~~~~~~~~~~~ 209 (449)
T PRK10779 130 VGEIAPNSIAAQAQIAPGTELKAVDGIETPDWDAVRLALVSKIGDESTTITVAPFGSDQRRDKTLDLRHWAFEPDKQDPV 209 (449)
T ss_pred ccccCCCCHHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhhccCCceEEEEEeCCccceEEEEecccccccCccccchh
Confidence 479999999999 999999999999999999999998774 467788999999999998888877533211 01 1111
Q ss_pred cccceEEecCCHHHhhccCCCCCeEEEE--cCCChhHHcCCCCCCEEEEcCCeecCCHHHHHHHHHhcCCCCeEeEEEEe
Q 001276 377 EVSGAVIHPLSYQQARNFRFPCGLVYVA--EPGYMLFRAGVPRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYSS 454 (1109)
Q Consensus 377 ~~~G~~~~~l~~~~~~~~~~~~~gv~v~--~pg~~a~~aGl~~GD~I~~Vng~~v~~l~~~~~~i~~~~~g~~v~l~~~~ 454 (1109)
...| +.++.++ .++.|. .++|+|++|||++||+|++|||+++.+|+++.+.++. ..++.+.+++.|
T Consensus 210 ~~lG--l~~~~~~---------~~~vV~~V~~~SpA~~AGL~~GDvIl~Ing~~V~s~~dl~~~l~~-~~~~~v~l~v~R 277 (449)
T PRK10779 210 SSLG--IRPRGPQ---------IEPVLAEVQPNSAASKAGLQAGDRIVKVDGQPLTQWQTFVTLVRD-NPGKPLALEIER 277 (449)
T ss_pred hccc--ccccCCC---------cCcEEEeeCCCCHHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHh-CCCCEEEEEEEE
Confidence 1223 2332221 134555 4899999999999999999999999999999999988 467788888887
Q ss_pred ec
Q 001276 455 YT 456 (1109)
Q Consensus 455 ~~ 456 (1109)
-+
T Consensus 278 ~g 279 (449)
T PRK10779 278 QG 279 (449)
T ss_pred CC
Confidence 54
No 21
>PF12812 PDZ_1: PDZ-like domain
Probab=99.51 E-value=3.3e-14 Score=125.59 Aligned_cols=76 Identities=46% Similarity=0.706 Sum_probs=70.9
Q ss_pred CCCCCccccccceEEecCCHHHhhccCCCCCeEEEEcCCChhHHcC-CCCCCEEEEcCCeecCCHHHHHHHHHhcCC
Q 001276 369 SITPDYFLEVSGAVIHPLSYQQARNFRFPCGLVYVAEPGYMLFRAG-VPRHAIIKKFAGEEISRLEDLISVLSKLSR 444 (1109)
Q Consensus 369 ~~~~~~~~~~~G~~~~~l~~~~~~~~~~~~~gv~v~~pg~~a~~aG-l~~GD~I~~Vng~~v~~l~~~~~~i~~~~~ 444 (1109)
+++|+|+++++|++||+|+||++|.|+++++|+|++.+++....++ +.+|++|++|||+||+|+++|+++|+++||
T Consensus 1 ~itp~r~v~~~Ga~f~~Ls~q~aR~~~~~~~gv~v~~~~g~~~~~~~i~~g~iI~~Vn~kpt~~Ld~f~~vvk~ipd 77 (78)
T PF12812_consen 1 AITPSRFVEVCGAVFHDLSYQQARQYGIPVGGVYVAVSGGSLAFAGGISKGFIITSVNGKPTPDLDDFIKVVKKIPD 77 (78)
T ss_pred CccCCEEEEEcCeecccCCHHHHHHhCCCCCEEEEEecCCChhhhCCCCCCeEEEeECCcCCcCHHHHHHHHHhCCC
Confidence 3789999999999999999999999999999999998766666666 999999999999999999999999999997
No 22
>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=99.49 E-value=1.9e-13 Score=132.48 Aligned_cols=110 Identities=33% Similarity=0.576 Sum_probs=74.9
Q ss_pred EEEEEEeCCCcEEEeCccccCC-------CCeEEEEEecCCeEEE--EEEEEEcCC-CcEEEEEEcCCCcccccccCCCC
Q 001276 70 ATGFVVDKRRGIILTNRHVVKP-------GPVVAEAMFVNREEIP--VYPIYRDPV-HDFGFFRYDPSAIQFLNYDEIPL 139 (1109)
Q Consensus 70 GSGfvV~~~~G~IlTn~HVv~~-------~~~~~~v~~~~~~~~~--a~vv~~d~~-~DlAlLk~~~~~~~~~~l~~l~l 139 (1109)
||||+|++ +|+||||+||+.. ....+.+.+.++..+. +++++.|+. +|+|||+++.
T Consensus 1 GTGf~i~~-~g~ilT~~Hvv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~All~v~~------------- 66 (120)
T PF13365_consen 1 GTGFLIGP-DGYILTAAHVVEDWNDGKQPDNSSVEVVFPDGRRVPPVAEVVYFDPDDYDLALLKVDP------------- 66 (120)
T ss_dssp EEEEEEET-TTEEEEEHHHHTCCTT--G-TCSEEEEEETTSCEEETEEEEEEEETT-TTEEEEEESC-------------
T ss_pred CEEEEEcC-CceEEEchhheecccccccCCCCEEEEEecCCCEEeeeEEEEEECCccccEEEEEEec-------------
Confidence 79999997 6899999999995 3456888888888888 999999999 9999999980
Q ss_pred CCccCCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCccccceeeEEEeeccCCCCCCCceecCCCcEEEE
Q 001276 140 APEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVAL 216 (1109)
Q Consensus 140 ~~~~~~~G~~V~~iG~p~g~~~si~~G~vs~~~~~~~~~~~~~~~~~~~~~iq~~a~~~~G~SGgPv~n~~G~vVGi 216 (1109)
....+... ...+......... .......+| +++.+.+|+|||||||.+|+||||
T Consensus 67 ----------~~~~~~~~-----~~~~~~~~~~~~~-------~~~~~~~~~-~~~~~~~G~SGgpv~~~~G~vvGi 120 (120)
T PF13365_consen 67 ----------WTGVGGGV-----RVPGSTSGVSPTS-------TNDNRMLYI-TDADTRPGSSGGPVFDSDGRVVGI 120 (120)
T ss_dssp ----------EEEEEEEE-----EEEEEEEEEEEEE-------EEETEEEEE-ESSS-STTTTTSEEEETTSEEEEE
T ss_pred ----------ccceeeee-----Eeeeecccccccc-------CcccceeEe-eecccCCCcEeHhEECCCCEEEeC
Confidence 00000000 0000011110000 000011124 799999999999999999999997
No 23
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=99.39 E-value=3.3e-12 Score=150.69 Aligned_cols=131 Identities=19% Similarity=0.242 Sum_probs=106.1
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEECCEEEEEEEEeecCCCCCCCcc
Q 001276 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIERGGISMTVNLVVQDLHSITPDYF 375 (1109)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~v~R~g~~~~~~v~l~~~~~~~~~~~ 375 (1109)
.|.+| ..|.++|||++ ||++||+|++|||+++.++.++...+.... +++.+++.|+++..++.+++.
T Consensus 128 ~g~~V-~~V~~~SpA~~AGL~~GDvI~~vng~~v~~~~dl~~~ia~~~-~~v~~~I~r~g~~~~l~v~l~---------- 195 (420)
T TIGR00054 128 VGPVI-ELLDKNSIALEAGIEPGDEILSVNGNKIPGFKDVRQQIADIA-GEPMVEILAERENWTFEVMKE---------- 195 (420)
T ss_pred CCcee-eccCCCCHHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhhc-ccceEEEEEecCceEeccccc----------
Confidence 66676 79999999999 999999999999999999999998886555 678899999888766544322
Q ss_pred ccccceEEecCCHHHhhccCCCCCeEEEE--cCCChhHHcCCCCCCEEEEcCCeecCCHHHHHHHHHhcCCCCeEeEEEE
Q 001276 376 LEVSGAVIHPLSYQQARNFRFPCGLVYVA--EPGYMLFRAGVPRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYS 453 (1109)
Q Consensus 376 ~~~~G~~~~~l~~~~~~~~~~~~~gv~v~--~pg~~a~~aGl~~GD~I~~Vng~~v~~l~~~~~~i~~~~~g~~v~l~~~ 453 (1109)
+.+..+ ..++.|. .++|+|+++||++||+|++|||+++.+|+++.+.++.. .++.+.+++.
T Consensus 196 -------~~~~~~---------~~g~vV~~V~~~SpA~~aGL~~GD~Iv~Vng~~V~s~~dl~~~l~~~-~~~~v~l~v~ 258 (420)
T TIGR00054 196 -------LIPRGP---------KIEPVLSDVTPNSPAEKAGLKEGDYIQSINGEKLRSWTDFVSAVKEN-PGKSMDIKVE 258 (420)
T ss_pred -------ceecCC---------CcCcEEEEECCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHHHhC-CCCceEEEEE
Confidence 111111 1245555 48999999999999999999999999999999999984 5677888888
Q ss_pred eec
Q 001276 454 SYT 456 (1109)
Q Consensus 454 ~~~ 456 (1109)
|-+
T Consensus 259 R~g 261 (420)
T TIGR00054 259 RNG 261 (420)
T ss_pred ECC
Confidence 754
No 24
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=99.22 E-value=7.3e-11 Score=106.72 Aligned_cols=68 Identities=31% Similarity=0.581 Sum_probs=60.9
Q ss_pred CCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHH-hcCCCCeEEEEEEECCEEEEEEEEe
Q 001276 296 ETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLL-DDGVDKNIELLIERGGISMTVNLVV 364 (1109)
Q Consensus 296 ~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l-~~~~g~~v~l~v~R~g~~~~~~v~l 364 (1109)
..|++| ..|.++|||++ ||++||+|++|||++|.++.++...+ ...+|++++|++.|+|+.++++++|
T Consensus 13 ~~g~~V-~~V~~~spA~~aGl~~GD~I~~ing~~v~~~~~~~~~l~~~~~g~~v~l~v~R~g~~~~~~v~l 82 (82)
T PF13180_consen 13 TGGVVV-VSVIPGSPAAKAGLQPGDIILAINGKPVNSSEDLVNILSKGKPGDTVTLTVLRDGEELTVEVTL 82 (82)
T ss_dssp SSSEEE-EEESTTSHHHHTTS-TTEEEEEETTEESSSHHHHHHHHHCSSTTSEEEEEEEETTEEEEEEEE-
T ss_pred CCeEEE-EEeCCCCcHHHCCCCCCcEEEEECCEEcCCHHHHHHHHHhCCCCCEEEEEEEECCEEEEEEEEC
Confidence 367787 58999999999 99999999999999999999999888 5689999999999999999998875
No 25
>PF12812 PDZ_1: PDZ-like domain
Probab=99.15 E-value=1.3e-10 Score=102.90 Aligned_cols=76 Identities=30% Similarity=0.484 Sum_probs=66.5
Q ss_pred CCcceEEeecCccccC-CchhhhhccCCCCCCCcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCC
Q 001276 977 NGTTRVINWCGCIVQD-PHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEH 1055 (1109)
Q Consensus 977 ~~t~~~~~~~G~~~~~-p~~~~r~~~~lp~~~~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~ 1055 (1109)
..++|++.|+|+.|++ +++.+|++. ++. ++++.+...|+++.++|+.+|-+|++|||+||+|+|+|.++++++||
T Consensus 2 itp~r~v~~~Ga~f~~Ls~q~aR~~~-~~~---~gv~v~~~~g~~~~~~~i~~g~iI~~Vn~kpt~~Ld~f~~vvk~ipd 77 (78)
T PF12812_consen 2 ITPSRFVEVCGAVFHDLSYQQARQYG-IPV---GGVYVAVSGGSLAFAGGISKGFIITSVNGKPTPDLDDFIKVVKKIPD 77 (78)
T ss_pred ccCCEEEEEcCeecccCCHHHHHHhC-CCC---CEEEEEecCCChhhhCCCCCCeEEEeECCcCCcCHHHHHHHHHhCCC
Confidence 4578999999999999 777777765 454 45666789999999999999999999999999999999999999997
Q ss_pred C
Q 001276 1056 G 1056 (1109)
Q Consensus 1056 ~ 1056 (1109)
+
T Consensus 78 ~ 78 (78)
T PF12812_consen 78 N 78 (78)
T ss_pred C
Confidence 5
No 26
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=99.10 E-value=6.1e-10 Score=100.70 Aligned_cols=69 Identities=29% Similarity=0.377 Sum_probs=64.1
Q ss_pred CcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEeCCeEEEEEEee
Q 001276 1008 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQ 1077 (1109)
Q Consensus 1008 ~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i~lk~ 1077 (1109)
.+++|..+.++|||+++||++||.|++|||+++.++.+|.+.+...+.|+.++|+ +.|+|+.+.++++.
T Consensus 14 ~g~~V~~V~~~spA~~aGl~~GD~I~~ing~~v~~~~~~~~~l~~~~~g~~v~l~-v~R~g~~~~~~v~l 82 (82)
T PF13180_consen 14 GGVVVVSVIPGSPAAKAGLQPGDIILAINGKPVNSSEDLVNILSKGKPGDTVTLT-VLRDGEELTVEVTL 82 (82)
T ss_dssp SSEEEEEESTTSHHHHTTS-TTEEEEEETTEESSSHHHHHHHHHCSSTTSEEEEE-EEETTEEEEEEEE-
T ss_pred CeEEEEEeCCCCcHHHCCCCCCcEEEEECCEEcCCHHHHHHHHHhCCCCCEEEEE-EEECCEEEEEEEEC
Confidence 4899999999999999999999999999999999999999999888889999999 89999999998873
No 27
>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=99.03 E-value=1.3e-09 Score=105.42 Aligned_cols=55 Identities=31% Similarity=0.512 Sum_probs=47.2
Q ss_pred EEEEEEEeeCCceEEEEeCceecC-------CCCcEEEEeecCCeEEe--EEEEEeeCC-CcEEEEEEC
Q 001276 652 GTGVIIYHSQSMGLVVVDKNTVAI-------SASDVMLSFAAFPIEIP--GEVVFLHPV-HNFALIAYD 710 (1109)
Q Consensus 652 GsG~VId~~~~~G~IlTn~~~V~~-------~~~di~V~~~d~~~~~~--a~vv~~dp~-~dlAilk~d 710 (1109)
||||+|+ ++|||||++|++.. ....+.+.+.+ +...+ |++++.|+. .|||||+++
T Consensus 1 GTGf~i~---~~g~ilT~~Hvv~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~D~All~v~ 65 (120)
T PF13365_consen 1 GTGFLIG---PDGYILTAAHVVEDWNDGKQPDNSSVEVVFPD-GRRVPPVAEVVYFDPDDYDLALLKVD 65 (120)
T ss_dssp EEEEEEE---TTTEEEEEHHHHTCCTT--G-TCSEEEEEETT-SCEEETEEEEEEEETT-TTEEEEEES
T ss_pred CEEEEEc---CCceEEEchhheecccccccCCCCEEEEEecC-CCEEeeeEEEEEECCccccEEEEEEe
Confidence 8999999 67799999665553 45668888887 77788 999999999 999999999
No 28
>cd00987 PDZ_serine_protease PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.95 E-value=7.3e-09 Score=95.17 Aligned_cols=87 Identities=37% Similarity=0.540 Sum_probs=71.6
Q ss_pred CccceEEEEcChhHHHHcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHH
Q 001276 261 GTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLL 339 (1109)
Q Consensus 261 g~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l 339 (1109)
+++|+.++.......++++++ ...|++| ..|.++|||+. ||++||+|++|||+++.++.++...+
T Consensus 1 ~~~G~~~~~~~~~~~~~~~~~-------------~~~g~~V-~~v~~~s~a~~~gl~~GD~I~~Ing~~i~~~~~~~~~l 66 (90)
T cd00987 1 PWLGVTVQDLTPDLAEELGLK-------------DTKGVLV-ASVDPGSPAAKAGLKPGDVILAVNGKPVKSVADLRRAL 66 (90)
T ss_pred CccceEEeECCHHHHHHcCCC-------------CCCEEEE-EEECCCCHHHHcCCCcCCEEEEECCEECCCHHHHHHHH
Confidence 478999998776656655554 3456555 79999999998 99999999999999999999999888
Q ss_pred hc-CCCCeEEEEEEECCEEEEEE
Q 001276 340 DD-GVDKNIELLIERGGISMTVN 361 (1109)
Q Consensus 340 ~~-~~g~~v~l~v~R~g~~~~~~ 361 (1109)
.. ..++.+.+++.|+|+..++.
T Consensus 67 ~~~~~~~~i~l~v~r~g~~~~~~ 89 (90)
T cd00987 67 AELKPGDKVTLTVLRGGKELTVT 89 (90)
T ss_pred HhcCCCCEEEEEEEECCEEEEee
Confidence 55 45889999999999876543
No 29
>cd00987 PDZ_serine_protease PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.93 E-value=8e-09 Score=94.92 Aligned_cols=88 Identities=31% Similarity=0.404 Sum_probs=74.5
Q ss_pred ecCccccCCchhhhhccCCCCCCCcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEE
Q 001276 985 WCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTV 1064 (1109)
Q Consensus 985 ~~G~~~~~p~~~~r~~~~lp~~~~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v 1064 (1109)
|+|+.++.++...+....++ ...|++|..+.++|||+++||++||.|++|||+++.+++++.+++.....+..+.+. +
T Consensus 2 ~~G~~~~~~~~~~~~~~~~~-~~~g~~V~~v~~~s~a~~~gl~~GD~I~~Ing~~i~~~~~~~~~l~~~~~~~~i~l~-v 79 (90)
T cd00987 2 WLGVTVQDLTPDLAEELGLK-DTKGVLVASVDPGSPAAKAGLKPGDVILAVNGKPVKSVADLRRALAELKPGDKVTLT-V 79 (90)
T ss_pred ccceEEeECCHHHHHHcCCC-CCCEEEEEEECCCCHHHHcCCCcCCEEEEECCEECCCHHHHHHHHHhcCCCCEEEEE-E
Confidence 78999999887766532222 245899999999999999999999999999999999999999999987668899999 6
Q ss_pred EeCCeEEEEE
Q 001276 1065 HLNGKPRVLT 1074 (1109)
Q Consensus 1065 ~rdg~~~~i~ 1074 (1109)
.|+|..+.++
T Consensus 80 ~r~g~~~~~~ 89 (90)
T cd00987 80 LRGGKELTVT 89 (90)
T ss_pred EECCEEEEee
Confidence 8999876654
No 30
>cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ domains a C-terminal beta-strand is thought to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.84 E-value=2.5e-08 Score=89.43 Aligned_cols=70 Identities=24% Similarity=0.440 Sum_probs=63.0
Q ss_pred CceEEEEEecCCCccccCCCCCCEEEEECCEEeCChhHHHHHHhc-CCCCeEEEEEEECCEEEEEEEEeecC
Q 001276 297 TGLLVVDSVVPGGPAHLRLEPGDVLVRVNGEVITQFLKLETLLDD-GVDKNIELLIERGGISMTVNLVVQDL 367 (1109)
Q Consensus 297 ~G~lVv~~V~~~spA~~gL~~GD~Il~VnG~~v~~~~~l~~~l~~-~~g~~v~l~v~R~g~~~~~~v~l~~~ 367 (1109)
.|++| ..|.++|||+.||++||+|++|||+++.+|.++...+.. ..|+.+.+++.|+|+..++++++..+
T Consensus 8 ~Gv~V-~~V~~~s~A~~gL~~GD~I~~Ing~~v~~~~~~~~~l~~~~~~~~v~l~v~r~g~~~~~~v~l~~~ 78 (79)
T cd00986 8 HGVYV-TSVVEGMPAAGKLKAGDHIIAVDGKPFKEAEELIDYIQSKKEGDTVKLKVKREEKELPEDLILKTF 78 (79)
T ss_pred cCEEE-EEECCCCchhhCCCCCCEEEEECCEECCCHHHHHHHHHhCCCCCEEEEEEEECCEEEEEEEEEecc
Confidence 57666 799999999889999999999999999999999988864 67889999999999999999988754
No 31
>cd00991 PDZ_archaeal_metalloprotease PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.82 E-value=2.9e-08 Score=89.08 Aligned_cols=68 Identities=26% Similarity=0.268 Sum_probs=61.7
Q ss_pred CcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEeCCeEEEEEEe
Q 001276 1008 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLK 1076 (1109)
Q Consensus 1008 ~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i~lk 1076 (1109)
.|++|..+.++|||+++||++||.|++|||+++.++++|...+.....++.+.|+ +.|+|+...+++.
T Consensus 10 ~Gv~V~~V~~~spa~~aGL~~GDiI~~Ing~~v~~~~d~~~~l~~~~~g~~v~l~-v~r~g~~~~~~~~ 77 (79)
T cd00991 10 AGVVIVGVIVGSPAENAVLHTGDVIYSINGTPITTLEDFMEALKPTKPGEVITVT-VLPSTTKLTNVST 77 (79)
T ss_pred CcEEEEEECCCChHHhcCCCCCCEEEEECCEEcCCHHHHHHHHhcCCCCCEEEEE-EEECCEEEEEEEE
Confidence 4899999999999999999999999999999999999999999986558889998 7899988777654
No 32
>cd00991 PDZ_archaeal_metalloprotease PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.82 E-value=2.7e-08 Score=89.27 Aligned_cols=68 Identities=24% Similarity=0.324 Sum_probs=60.1
Q ss_pred CCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhc-CCCCeEEEEEEECCEEEEEEEE
Q 001276 295 GETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDD-GVDKNIELLIERGGISMTVNLV 363 (1109)
Q Consensus 295 ~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~-~~g~~v~l~v~R~g~~~~~~v~ 363 (1109)
...|++| ..|.++|||++ ||++||+|++|||+++.+|.++...+.. ..|+.+.+++.|+|+..+++++
T Consensus 8 ~~~Gv~V-~~V~~~spa~~aGL~~GDiI~~Ing~~v~~~~d~~~~l~~~~~g~~v~l~v~r~g~~~~~~~~ 77 (79)
T cd00991 8 AVAGVVI-VGVIVGSPAENAVLHTGDVIYSINGTPITTLEDFMEALKPTKPGEVITVTVLPSTTKLTNVST 77 (79)
T ss_pred cCCcEEE-EEECCCChHHhcCCCCCCEEEEECCEEcCCHHHHHHHHhcCCCCCEEEEEEEECCEEEEEEEE
Confidence 4568776 79999999998 9999999999999999999999998865 4688999999999998877664
No 33
>cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ domains a C-terminal beta-strand is thought to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.72 E-value=9.8e-08 Score=85.60 Aligned_cols=69 Identities=26% Similarity=0.398 Sum_probs=62.3
Q ss_pred CcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEeCCeEEEEEEeeC
Q 001276 1008 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQD 1078 (1109)
Q Consensus 1008 ~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i~lk~~ 1078 (1109)
.|++|..+.++|||++ ||++||.|++|||+++.++++|.+.+...+.+..+.|+ +.|+|+...+++++.
T Consensus 8 ~Gv~V~~V~~~s~A~~-gL~~GD~I~~Ing~~v~~~~~~~~~l~~~~~~~~v~l~-v~r~g~~~~~~v~l~ 76 (79)
T cd00986 8 HGVYVTSVVEGMPAAG-KLKAGDHIIAVDGKPFKEAEELIDYIQSKKEGDTVKLK-VKREEKELPEDLILK 76 (79)
T ss_pred cCEEEEEECCCCchhh-CCCCCCEEEEECCEECCCHHHHHHHHHhCCCCCEEEEE-EEECCEEEEEEEEEe
Confidence 4899999999999997 89999999999999999999999999976668889999 789999988887764
No 34
>cd00990 PDZ_glycyl_aminopeptidase PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand is presumed to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.70 E-value=1e-07 Score=85.59 Aligned_cols=66 Identities=26% Similarity=0.178 Sum_probs=53.9
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEECCEEEEEEEEee
Q 001276 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIERGGISMTVNLVVQ 365 (1109)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~v~R~g~~~~~~v~l~ 365 (1109)
.|++| ..|.++|||+. ||++||+|++|||+++.+|.++... ...++.+.+++.|+|+..++.+.+.
T Consensus 12 ~~~~V-~~V~~~s~a~~aGl~~GD~I~~Ing~~v~~~~~~l~~--~~~~~~v~l~v~r~g~~~~~~v~~~ 78 (80)
T cd00990 12 GLGKV-TFVRDDSPADKAGLVAGDELVAVNGWRVDALQDRLKE--YQAGDPVELTVFRDDRLIEVPLTLA 78 (80)
T ss_pred CcEEE-EEECCCChHHHhCCCCCCEEEEECCEEhHHHHHHHHh--cCCCCEEEEEEEECCEEEEEEEEec
Confidence 45554 79999999999 9999999999999999986654222 2467889999999999888877664
No 35
>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.67 E-value=1.6e-07 Score=84.10 Aligned_cols=66 Identities=30% Similarity=0.421 Sum_probs=59.0
Q ss_pred cEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEeCCeEEEEEEe
Q 001276 1009 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLK 1076 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i~lk 1076 (1109)
.++|+.+.++|||+++||++||.|++|||+++.+++++...++... ++.+.++ +.|+|..+.+.++
T Consensus 13 ~~~V~~v~~~s~a~~~gl~~GD~I~~ing~~i~~~~~~~~~l~~~~-~~~~~l~-v~r~~~~~~~~l~ 78 (79)
T cd00989 13 EPVIGEVVPGSPAAKAGLKAGDRILAINGQKIKSWEDLVDAVQENP-GKPLTLT-VERNGETITLTLT 78 (79)
T ss_pred CcEEEeECCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHHHHCC-CceEEEE-EEECCEEEEEEec
Confidence 3689999999999999999999999999999999999999998854 7788998 6889988777765
No 36
>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=98.65 E-value=5.3e-07 Score=96.70 Aligned_cols=176 Identities=21% Similarity=0.268 Sum_probs=107.4
Q ss_pred CceEEEEEEeeeccCCCCCCccEEEEEEEeCCCcEEEeCccccCCCCeEEEEEec-------CC--eEEEEEEEEEcC--
Q 001276 47 PAVVVLRTTACRAFDTEAAGASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFV-------NR--EEIPVYPIYRDP-- 115 (1109)
Q Consensus 47 ~sVV~I~~~~~~~~d~~~~~~~~GSGfvV~~~~G~IlTn~HVv~~~~~~~~v~~~-------~~--~~~~a~vv~~d~-- 115 (1109)
|.+|.|.... ....|+|++|+++ +|||++|++.. .....+.+. ++ ..+...-+..++
T Consensus 13 p~~v~i~~~~---------~~~~C~G~li~~~--~vLTaahC~~~-~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~h~~~ 80 (220)
T PF00089_consen 13 PWVVSIRYSN---------GRFFCTGTLISPR--WVLTAAHCVDG-ASDIKVRLGTYSIRNSDGSEQTIKVSKIIIHPKY 80 (220)
T ss_dssp TTEEEEEETT---------TEEEEEEEEEETT--EEEEEGGGHTS-GGSEEEEESESBTTSTTTTSEEEEEEEEEEETTS
T ss_pred CeEEEEeeCC---------CCeeEeEEecccc--ccccccccccc-cccccccccccccccccccccccccccccccccc
Confidence 6677777631 1678999999964 99999999995 333444332 22 345555554533
Q ss_pred -----CCcEEEEEEcCCCcccccccCCCCCC--ccCCCCCEEEEEecCCCCC----CeEEEEEEEEecCC--CCCCCCCC
Q 001276 116 -----VHDFGFFRYDPSAIQFLNYDEIPLAP--EAACVGLEIRVVGNDSGEK----VSILAGTLARLDRD--APHYKKDG 182 (1109)
Q Consensus 116 -----~~DlAlLk~~~~~~~~~~l~~l~l~~--~~~~~G~~V~~iG~p~g~~----~si~~G~vs~~~~~--~~~~~~~~ 182 (1109)
.+|+|||+++..-.....+.++.+.. ..++.|+.+.++|++.... ..+....+....+. ...+...
T Consensus 81 ~~~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~- 159 (220)
T PF00089_consen 81 DPSTYDNDIALLKLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNGYSSNLQSVTVPVVSRKTCRSSYNDN- 159 (220)
T ss_dssp BTTTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTTSBTSBEEEEEEEEEEHHHHHHHTTTT-
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-
Confidence 47999999986521111223333333 4468999999999986532 23444444333221 0001110
Q ss_pred ccccceeeEEEee----ccCCCCCCCceecCCCcEEEEeccccCCCC---CccccchHHHHHH
Q 001276 183 YNDFNTFYMQAAS----GTKGGSSGSPVIDWQGRAVALNAGSKSSSA---SAFFLPLERVVRA 238 (1109)
Q Consensus 183 ~~~~~~~~iq~~a----~~~~G~SGgPv~n~~G~vVGi~~~~~~~~~---~~falP~~~i~~~ 238 (1109)
+...++.+.. ....|+|||||++.++.++||.+.+..... ..++.++...+..
T Consensus 160 ---~~~~~~c~~~~~~~~~~~g~sG~pl~~~~~~lvGI~s~~~~c~~~~~~~v~~~v~~~~~W 219 (220)
T PF00089_consen 160 ---LTPNMICAGSSGSGDACQGDSGGPLICNNNYLVGIVSFGENCGSPNYPGVYTRVSSYLDW 219 (220)
T ss_dssp ---STTTEEEEETTSSSBGGTTTTTSEEEETTEEEEEEEEEESSSSBTTSEEEEEEGGGGHHH
T ss_pred ---cccccccccccccccccccccccccccceeeecceeeecCCCCCCCcCEEEEEHHHhhcc
Confidence 1222455554 678899999999988899999988743322 3666777655543
No 37
>TIGR01713 typeII_sec_gspC general secretion pathway protein C. This model represents GspC, protein C of the main terminal branch of the general secretion pathway, also called type II secretion. This system transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=98.65 E-value=3e-07 Score=101.08 Aligned_cols=99 Identities=17% Similarity=0.119 Sum_probs=82.2
Q ss_pred HHHHHHHHHHHhcCCcccccccccccCCCccceEEEEcChhHHHHcCCChhHHHhhhcCCCCCCCceEEEEEecCCCccc
Q 001276 233 ERVVRALRFLQERRDCNIHNWEAVSIPRGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAH 312 (1109)
Q Consensus 233 ~~i~~~l~~l~~~~~~~~~~~~~~~v~rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~ 312 (1109)
..++++++++.+.+ .+-++++|+.-.... | ...|.+| ..+.+++||+
T Consensus 159 ~~~~~v~~~l~~~g----------~~~~~~lgi~p~~~~-------g---------------~~~G~~v-~~v~~~s~a~ 205 (259)
T TIGR01713 159 VVSRRIIEELTKDP----------QKMFDYIRLSPVMKN-------D---------------KLEGYRL-NPGKDPSLFY 205 (259)
T ss_pred hhHHHHHHHHHHCH----------HhhhheEeEEEEEeC-------C---------------ceeEEEE-EecCCCCHHH
Confidence 46677888888877 678889998865321 1 2467776 7999999999
Q ss_pred c-CCCCCCEEEEECCEEeCChhHHHHHHhc-CCCCeEEEEEEECCEEEEEEEEe
Q 001276 313 L-RLEPGDVLVRVNGEVITQFLKLETLLDD-GVDKNIELLIERGGISMTVNLVV 364 (1109)
Q Consensus 313 ~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~-~~g~~v~l~v~R~g~~~~~~v~l 364 (1109)
+ ||++||+|++|||+++.++.++..++.. ..++.++|+|+|+|+.+++.+.+
T Consensus 206 ~aGLr~GDvIv~ING~~i~~~~~~~~~l~~~~~~~~v~l~V~R~G~~~~i~v~~ 259 (259)
T TIGR01713 206 KSGLQDGDIAVALNGLDLRDPEQAFQALQMLREETNLTLTVERDGQREDIYVRF 259 (259)
T ss_pred HcCCCCCCEEEEECCEEcCCHHHHHHHHHhcCCCCeEEEEEEECCEEEEEEEEC
Confidence 9 9999999999999999999999998865 67789999999999998887653
No 38
>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.59 E-value=2.1e-07 Score=83.31 Aligned_cols=63 Identities=33% Similarity=0.588 Sum_probs=55.5
Q ss_pred EEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEECCEEEEEEE
Q 001276 300 LVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIERGGISMTVNL 362 (1109)
Q Consensus 300 lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~v~R~g~~~~~~v 362 (1109)
++|..|.++|||++ ||++||+|++|||+++.++.++...+....++.+.+++.|+|+..++.+
T Consensus 14 ~~V~~v~~~s~a~~~gl~~GD~I~~ing~~i~~~~~~~~~l~~~~~~~~~l~v~r~~~~~~~~l 77 (79)
T cd00989 14 PVIGEVVPGSPAAKAGLKAGDRILAINGQKIKSWEDLVDAVQENPGKPLTLTVERNGETITLTL 77 (79)
T ss_pred cEEEeECCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHHHHCCCceEEEEEEECCEEEEEEe
Confidence 44579999999998 9999999999999999999999988866667889999999998766654
No 39
>cd00988 PDZ_CTP_protease PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.57 E-value=3.5e-07 Score=83.14 Aligned_cols=66 Identities=32% Similarity=0.617 Sum_probs=57.0
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCCh--hHHHHHHhcCCCCeEEEEEEEC-CEEEEEEEE
Q 001276 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQF--LKLETLLDDGVDKNIELLIERG-GISMTVNLV 363 (1109)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g~~v~l~v~R~-g~~~~~~v~ 363 (1109)
.+++| ..|.++|||++ ||++||+|++|||+++.+| .++..++....|+.+.+++.|+ |+..++++.
T Consensus 13 ~~~~V-~~v~~~s~a~~~gl~~GD~I~~vng~~i~~~~~~~~~~~l~~~~~~~i~l~v~r~~~~~~~~~~~ 82 (85)
T cd00988 13 GGLVI-TSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGKAGTKVRLTLKRGDGEPREVTLT 82 (85)
T ss_pred CeEEE-EEecCCCCHHHcCCCCCCEEEEECCEEcCCCCHHHHHHHhcCCCCCEEEEEEEcCCCCEEEEEEE
Confidence 45554 79999999999 9999999999999999999 8888877666788999999998 887777654
No 40
>cd00988 PDZ_CTP_protease PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.51 E-value=5.7e-07 Score=81.69 Aligned_cols=68 Identities=31% Similarity=0.478 Sum_probs=60.9
Q ss_pred CcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEEEEEeC-CeEEEEEEee
Q 001276 1008 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVHLN-GKPRVLTLKQ 1077 (1109)
Q Consensus 1008 ~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~~v~rd-g~~~~i~lk~ 1077 (1109)
.+++|..+.++|||+++||++||.|++|||+++.++ +++...++.. .++.+.|+ +.|+ |..+.+++++
T Consensus 13 ~~~~V~~v~~~s~a~~~gl~~GD~I~~vng~~i~~~~~~~~~~~l~~~-~~~~i~l~-v~r~~~~~~~~~~~~ 83 (85)
T cd00988 13 GGLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGK-AGTKVRLT-LKRGDGEPREVTLTR 83 (85)
T ss_pred CeEEEEEecCCCCHHHcCCCCCCEEEEECCEEcCCCCHHHHHHHhcCC-CCCEEEEE-EEcCCCCEEEEEEEE
Confidence 378999999999999999999999999999999999 9999999874 47889998 6788 8888888875
No 41
>cd00990 PDZ_glycyl_aminopeptidase PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand is presumed to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.49 E-value=7.7e-07 Score=79.88 Aligned_cols=66 Identities=26% Similarity=0.224 Sum_probs=56.2
Q ss_pred cEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEeCCeEEEEEEeeC
Q 001276 1009 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQD 1078 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i~lk~~ 1078 (1109)
+++|+.+.++|||+++||++||.|++|||+++.++.++ ++....++.+.|. +.|+|+.+.+.+++.
T Consensus 13 ~~~V~~V~~~s~a~~aGl~~GD~I~~Ing~~v~~~~~~---l~~~~~~~~v~l~-v~r~g~~~~~~v~~~ 78 (80)
T cd00990 13 LGKVTFVRDDSPADKAGLVAGDELVAVNGWRVDALQDR---LKEYQAGDPVELT-VFRDDRLIEVPLTLA 78 (80)
T ss_pred cEEEEEECCCChHHHhCCCCCCEEEEECCEEhHHHHHH---HHhcCCCCEEEEE-EEECCEEEEEEEEec
Confidence 68999999999999999999999999999999986655 4443357789998 789999988888764
No 42
>TIGR01713 typeII_sec_gspC general secretion pathway protein C. This model represents GspC, protein C of the main terminal branch of the general secretion pathway, also called type II secretion. This system transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=98.49 E-value=1.1e-06 Score=96.51 Aligned_cols=99 Identities=16% Similarity=0.166 Sum_probs=80.8
Q ss_pred HHHHHHHHHHHcCCCCCcccccccccCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCH
Q 001276 833 YTISRVLDKIISGASGPSLLINGVKRPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSK 912 (1109)
Q Consensus 833 ~~i~~~l~~l~~~~~~~~~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~sp 912 (1109)
..+++++++|.+.++ +-|. |+|+...... ....|++|..+.++++
T Consensus 159 ~~~~~v~~~l~~~g~--------~~~~-----~lgi~p~~~~----------------------g~~~G~~v~~v~~~s~ 203 (259)
T TIGR01713 159 VVSRRIIEELTKDPQ--------KMFD-----YIRLSPVMKN----------------------DKLEGYRLNPGKDPSL 203 (259)
T ss_pred hhHHHHHHHHHHCHH--------hhhh-----eEeEEEEEeC----------------------CceeEEEEEecCCCCH
Confidence 456788889887754 4444 7888654321 1236899999999999
Q ss_pred Hhhh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEe
Q 001276 913 AENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVG 970 (1109)
Q Consensus 913 A~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~ 970 (1109)
|+++ |++||+|++|||+++.++.++..++..++.+ +.+.++|.|+|+.+++.+.
T Consensus 204 a~~aGLr~GDvIv~ING~~i~~~~~~~~~l~~~~~~----~~v~l~V~R~G~~~~i~v~ 258 (259)
T TIGR01713 204 FYKSGLQDGDIAVALNGLDLRDPEQAFQALQMLREE----TNLTLTVERDGQREDIYVR 258 (259)
T ss_pred HHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhcCCC----CeEEEEEEECCEEEEEEEE
Confidence 9999 9999999999999999999999999776665 7899999999999888875
No 43
>KOG3580 consensus Tight junction proteins [Signal transduction mechanisms]
Probab=98.49 E-value=6.3e-07 Score=102.42 Aligned_cols=56 Identities=30% Similarity=0.366 Sum_probs=51.9
Q ss_pred CcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEEE
Q 001276 1008 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRT 1063 (1109)
Q Consensus 1008 ~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~~ 1063 (1109)
-|++|+.|..||||++.||+.||.|+.||.++..++ ++.+..|-.+|+|+.++|..
T Consensus 429 VGIFVaGvqegspA~~eGlqEGDQIL~VN~vdF~nl~REeAVlfLL~lPkGEevtila 486 (1027)
T KOG3580|consen 429 VGIFVAGVQEGSPAEQEGLQEGDQILKVNTVDFRNLVREEAVLFLLELPKGEEVTILA 486 (1027)
T ss_pred eeEEEeecccCCchhhccccccceeEEeccccchhhhHHHHHHHHhcCCCCcEEeehh
Confidence 389999999999999999999999999999999998 78888888899999999864
No 44
>KOG3209 consensus WW domain-containing protein [General function prediction only]
Probab=98.39 E-value=2.5e-06 Score=99.75 Aligned_cols=146 Identities=20% Similarity=0.212 Sum_probs=88.7
Q ss_pred EEEEEecCCCcccc-C-CCCCCEEEEECCEEeCChhH--HHHHHhc-CCCCeEEEEEEECCEEE-EEEEEeecCCCCCCC
Q 001276 300 LVVDSVVPGGPAHL-R-LEPGDVLVRVNGEVITQFLK--LETLLDD-GVDKNIELLIERGGISM-TVNLVVQDLHSITPD 373 (1109)
Q Consensus 300 lVv~~V~~~spA~~-g-L~~GD~Il~VnG~~v~~~~~--l~~~l~~-~~g~~v~l~v~R~g~~~-~~~v~l~~~~~~~~~ 373 (1109)
+.|..|.+.+.|+. | |++||.|+.|||.+|..-.+ +..++.. +-...|.|+|.|.-..- ...-+..+.....+.
T Consensus 676 i~iG~Iv~lGaAe~DGRL~~gDElv~iDG~pV~GksH~~vv~Lm~~AArnghV~LtVRRkv~~~~~~rsp~~s~~~~~~y 755 (984)
T KOG3209|consen 676 IYIGAIVPLGAAEEDGRLREGDELVCIDGIPVEGKSHSEVVDLMEAAARNGHVNLTVRRKVRTGPARRSPRNSAAPSGPY 755 (984)
T ss_pred eEEeeeeecccccccCcccCCCeEEEecCeeccCccHHHHHHHHHHHHhcCceEEEEeeeeeeccccCCcccccCCCCCe
Confidence 44589999999999 5 99999999999999976544 4445533 34467999998831100 000001111111222
Q ss_pred ccc----cccceEEecCCHHHhhccCCCCCeEEEEcCCChhHHcC-CCCCCEEEEcCCeecCCH--HHHHHHHHhcCCCC
Q 001276 374 YFL----EVSGAVIHPLSYQQARNFRFPCGLVYVAEPGYMLFRAG-VPRHAIIKKFAGEEISRL--EDLISVLSKLSRGA 446 (1109)
Q Consensus 374 ~~~----~~~G~~~~~l~~~~~~~~~~~~~gv~v~~pg~~a~~aG-l~~GD~I~~Vng~~v~~l--~~~~~~i~~~~~g~ 446 (1109)
+.+ +--|+.|.-++-+-.. ..|+=-..+||||++-| |++||+|++|||+.|-++ .+.++.||. .|-
T Consensus 756 DV~lhR~ENeGFGFVi~sS~~kp-----~sgiGrIieGSPAdRCgkLkVGDrilAVNG~sI~~lsHadiv~LIKd--aGl 828 (984)
T KOG3209|consen 756 DVVLHRKENEGFGFVIMSSQNKP-----ESGIGRIIEGSPADRCGKLKVGDRILAVNGQSILNLSHADIVSLIKD--AGL 828 (984)
T ss_pred eeEEecccCCceeEEEEecccCC-----CCCccccccCChhHhhccccccceEEEecCeeeeccCchhHHHHHHh--cCc
Confidence 211 1223333333332211 12321123899999988 999999999999999988 577888887 344
Q ss_pred eEeEEE
Q 001276 447 RVPIEY 452 (1109)
Q Consensus 447 ~v~l~~ 452 (1109)
.|+|++
T Consensus 829 sVtLtI 834 (984)
T KOG3209|consen 829 SVTLTI 834 (984)
T ss_pred eEEEEE
Confidence 444444
No 45
>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=98.34 E-value=8.3e-06 Score=88.13 Aligned_cols=162 Identities=19% Similarity=0.207 Sum_probs=93.1
Q ss_pred CCceEEEEEEeeeccCCCCCCccEEEEEEEeCCCcEEEeCccccCCC-CeEEEEEecC---------CeEEEEEEEEEcC
Q 001276 46 VPAVVVLRTTACRAFDTEAAGASYATGFVVDKRRGIILTNRHVVKPG-PVVAEAMFVN---------REEIPVYPIYRDP 115 (1109)
Q Consensus 46 ~~sVV~I~~~~~~~~d~~~~~~~~GSGfvV~~~~G~IlTn~HVv~~~-~~~~~v~~~~---------~~~~~a~vv~~d~ 115 (1109)
.|.+|.|.... ....++|.+|++ .+|||++|++... .....+.+.. ...+.++-+..+|
T Consensus 12 ~Pw~v~i~~~~---------~~~~C~GtlIs~--~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp 80 (232)
T cd00190 12 FPWQVSLQYTG---------GRHFCGGSLISP--RWVLTAAHCVYSSAPSNYTVRLGSHDLSSNEGGGQVIKVKKVIVHP 80 (232)
T ss_pred CCCEEEEEccC---------CcEEEEEEEeeC--CEEEECHHhcCCCCCccEEEEeCcccccCCCCceEEEEEEEEEECC
Confidence 45677776531 467899999996 4999999999853 1334444431 2334455555554
Q ss_pred -------CCcEEEEEEcCCCcccccccCCCCCCc--cCCCCCEEEEEecCCCCCC-----eEEEEEEEEecCC--CCCCC
Q 001276 116 -------VHDFGFFRYDPSAIQFLNYDEIPLAPE--AACVGLEIRVVGNDSGEKV-----SILAGTLARLDRD--APHYK 179 (1109)
Q Consensus 116 -------~~DlAlLk~~~~~~~~~~l~~l~l~~~--~~~~G~~V~~iG~p~g~~~-----si~~G~vs~~~~~--~~~~~ 179 (1109)
.+|+|||+++..--....+.++.|... .+..|+.+.++|+...... ......+..+.+. ...+.
T Consensus 81 ~y~~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~ 160 (232)
T cd00190 81 NYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEGGPLPDVLQEVNVPIVSNAECKRAYS 160 (232)
T ss_pred CCCCCCCcCCEEEEEECCcccCCCcccceECCCccccCCCCCEEEEEeCCcCCCCCCCCceeeEEEeeeECHHHhhhhcc
Confidence 489999999853211112444445444 6788999999998754321 1222222222210 00010
Q ss_pred C-CCccccceeeEEE-----eeccCCCCCCCceecCC---CcEEEEecccc
Q 001276 180 K-DGYNDFNTFYMQA-----ASGTKGGSSGSPVIDWQ---GRAVALNAGSK 221 (1109)
Q Consensus 180 ~-~~~~~~~~~~iq~-----~a~~~~G~SGgPv~n~~---G~vVGi~~~~~ 221 (1109)
. ..... ..+-. ......|.|||||+... +.++||.+.+.
T Consensus 161 ~~~~~~~---~~~C~~~~~~~~~~c~gdsGgpl~~~~~~~~~lvGI~s~g~ 208 (232)
T cd00190 161 YGGTITD---NMLCAGGLEGGKDACQGDSGGPLVCNDNGRGVLVGIVSWGS 208 (232)
T ss_pred CcccCCC---ceEeeCCCCCCCccccCCCCCcEEEEeCCEEEEEEEEehhh
Confidence 0 00001 01111 23345699999999765 88999998765
No 46
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos
Probab=98.28 E-value=2.8e-06 Score=74.01 Aligned_cols=53 Identities=36% Similarity=0.619 Sum_probs=47.2
Q ss_pred ceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCCh--hHHHHHHhcCCCCeEEEEE
Q 001276 298 GLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQF--LKLETLLDDGVDKNIELLI 351 (1109)
Q Consensus 298 G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g~~v~l~v 351 (1109)
|++| ..|.++|||+. ||++||+|++|||+++.++ .++..++....|+.++|++
T Consensus 14 ~~~V-~~v~~~s~a~~~gl~~GD~I~~Ing~~v~~~~~~~~~~~l~~~~g~~v~l~v 69 (70)
T cd00136 14 GVVV-LSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEVGEKVTLTV 69 (70)
T ss_pred CEEE-EEeCCCCHHHHcCCCCCCEEEEECCEECCCCCHHHHHHHHhhCCCCeEEEEE
Confidence 5555 79999999999 9999999999999999999 8888888777788888876
No 47
>KOG3580 consensus Tight junction proteins [Signal transduction mechanisms]
Probab=98.25 E-value=7.5e-06 Score=93.88 Aligned_cols=158 Identities=22% Similarity=0.319 Sum_probs=108.1
Q ss_pred CCceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChh--HHHHHHhcCCCCeEEEEEEECCEEEEEEEEeecC----
Q 001276 296 ETGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFL--KLETLLDDGVDKNIELLIERGGISMTVNLVVQDL---- 367 (1109)
Q Consensus 296 ~~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~--~l~~~l~~~~g~~v~l~v~R~g~~~~~~v~l~~~---- 367 (1109)
...++| +.+...|.|++ +||+||+|+.|||....++. +...++..+- .+++|.|+|+.....+.|+--..
T Consensus 218 gSqIFv-Keit~~gLAardgnlqEGDiiLkINGtvteNmSLtDar~LIEkS~-GKL~lvVlRD~~qtLiNiP~l~d~dSe 295 (1027)
T KOG3580|consen 218 GSQIFV-KEITRTGLAARDGNLQEGDIILKINGTVTENMSLTDARKLIEKSR-GKLQLVVLRDSQQTLINIPSLNDSDSE 295 (1027)
T ss_pred cchhhh-hhhcccchhhccCCcccccEEEEECcEeeccccchhHHHHHHhcc-CceEEEEEecCCceeeecCCCcccccc
Confidence 355666 78999999988 79999999999999887753 4444544443 46899999987766665542110
Q ss_pred ----CCC--------------------------------------CCCccccccce------------------------
Q 001276 368 ----HSI--------------------------------------TPDYFLEVSGA------------------------ 381 (1109)
Q Consensus 368 ----~~~--------------------------------------~~~~~~~~~G~------------------------ 381 (1109)
..+ ++.| +...|+
T Consensus 296 ~~disEi~tms~rs~spp~rrs~~~s~d~~s~s~h~p~~Ps~r~~~~~R-~s~~gat~tPvks~~d~~~~~V~e~t~e~~ 374 (1027)
T KOG3580|consen 296 IEDISEIETMSDRSFSPPERRSQYSSYDYHSSSEHLPERPSSREDTPSR-LSRMGATPTPVKSTGDIAGTVVPETTKEPR 374 (1027)
T ss_pred ccchhhhhccccccCCCchhhhhccCccccCchhcCCCCCCccccchhh-cccCCCCCCCccCccccCCccccccccCcc
Confidence 000 0000 000011
Q ss_pred ---------------EEecCCHHHhhccCCC----------------------CCeEEEE--cCCChhHHcCCCCCCEEE
Q 001276 382 ---------------VIHPLSYQQARNFRFP----------------------CGLVYVA--EPGYMLFRAGVPRHAIIK 422 (1109)
Q Consensus 382 ---------------~~~~l~~~~~~~~~~~----------------------~~gv~v~--~pg~~a~~aGl~~GD~I~ 422 (1109)
+|.-++.+....|+.. .-|+||+ ..|+||+.-||+.||.|+
T Consensus 375 ~~q~p~lP~pk~~~~~~~~pS~~~m~~ygysP~tk~VrF~KGdSvGLRLAGGNDVGIFVaGvqegspA~~eGlqEGDQIL 454 (1027)
T KOG3580|consen 375 YQQEPPLPQPKAAPRTFLRPSPEDMAIYGYSPNTKMVRFKKGDSVGLRLAGGNDVGIFVAGVQEGSPAEQEGLQEGDQIL 454 (1027)
T ss_pred cccCCCCCCcccCcceeeecCHHHHHHhcCCCCceeEEeecCCeeeeEeccCCceeEEEeecccCCchhhccccccceeE
Confidence 1222333333334421 1388988 589999999999999999
Q ss_pred EcCCeecCCH--HHHHHHHHhcCCCCeEeEEEEeec
Q 001276 423 KFAGEEISRL--EDLISVLSKLSRGARVPIEYSSYT 456 (1109)
Q Consensus 423 ~Vng~~v~~l--~~~~~~i~~~~~g~~v~l~~~~~~ 456 (1109)
+||.++..|+ ++.+..|-.+|.|+.|+|...+-.
T Consensus 455 ~VN~vdF~nl~REeAVlfLL~lPkGEevtilaQ~k~ 490 (1027)
T KOG3580|consen 455 KVNTVDFRNLVREEAVLFLLELPKGEEVTILAQSKA 490 (1027)
T ss_pred EeccccchhhhHHHHHHHHhcCCCCcEEeehhhhhh
Confidence 9999999999 789999999999999999765433
No 48
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos
Probab=98.24 E-value=3.6e-06 Score=73.35 Aligned_cols=53 Identities=36% Similarity=0.441 Sum_probs=50.0
Q ss_pred cEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEE
Q 001276 1009 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVR 1062 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~ 1062 (1109)
+++|..+.++|||+++||++||.|++|||+++.++ +++.+.++..+ ++.++|+
T Consensus 14 ~~~V~~v~~~s~a~~~gl~~GD~I~~Ing~~v~~~~~~~~~~~l~~~~-g~~v~l~ 68 (70)
T cd00136 14 GVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEV-GEKVTLT 68 (70)
T ss_pred CEEEEEeCCCCHHHHcCCCCCCEEEEECCEECCCCCHHHHHHHHhhCC-CCeEEEE
Confidence 78999999999999999999999999999999999 99999999865 8888887
No 49
>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=98.19 E-value=4e-05 Score=82.86 Aligned_cols=153 Identities=15% Similarity=0.148 Sum_probs=88.0
Q ss_pred CccEEEEEEEeCCCcEEEeCccccCCCC-eEEEEEecCC--------eEEEEEEEEEc-------CCCcEEEEEEcCCC-
Q 001276 66 GASYATGFVVDKRRGIILTNRHVVKPGP-VVAEAMFVNR--------EEIPVYPIYRD-------PVHDFGFFRYDPSA- 128 (1109)
Q Consensus 66 ~~~~GSGfvV~~~~G~IlTn~HVv~~~~-~~~~v~~~~~--------~~~~a~vv~~d-------~~~DlAlLk~~~~~- 128 (1109)
....++|.+|++ .+|||++|++.... ....+.+... ..+.+.-+..+ ..+|+|||+++..-
T Consensus 24 ~~~~C~GtlIs~--~~VLTaahC~~~~~~~~~~v~~g~~~~~~~~~~~~~~v~~~~~~p~~~~~~~~~DiAll~L~~~i~ 101 (229)
T smart00020 24 GRHFCGGSLISP--RWVLTAAHCVYGSDPSNIRVRLGSHDLSSGEEGQVIKVSKVIIHPNYNPSTYDNDIALLKLKSPVT 101 (229)
T ss_pred CCcEEEEEEecC--CEEEECHHHcCCCCCcceEEEeCcccCCCCCCceEEeeEEEEECCCCCCCCCcCCEEEEEECcccC
Confidence 467899999995 59999999998542 3556665532 34455555543 35899999997541
Q ss_pred cccccccCCCCCC--ccCCCCCEEEEEecCCCCC------CeEEEEEEEEecC--CCCCCCCC-CccccceeeEE--Eee
Q 001276 129 IQFLNYDEIPLAP--EAACVGLEIRVVGNDSGEK------VSILAGTLARLDR--DAPHYKKD-GYNDFNTFYMQ--AAS 195 (1109)
Q Consensus 129 ~~~~~l~~l~l~~--~~~~~G~~V~~iG~p~g~~------~si~~G~vs~~~~--~~~~~~~~-~~~~~~~~~iq--~~a 195 (1109)
+.. .+.++.|.. ..+..|+.+.+.|++.... .......+..+.+ -...+... .......+... ...
T Consensus 102 ~~~-~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~ 180 (229)
T smart00020 102 LSD-NVRPICLPSSNYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNVPIVSNATCRRAYSGGGAITDNMLCAGGLEGGK 180 (229)
T ss_pred CCC-ceeeccCCCcccccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEEEEeCHHHhhhhhccccccCCCcEeecCCCCCC
Confidence 111 233444433 3677899999999876542 1222222322222 00001000 01110001111 124
Q ss_pred ccCCCCCCCceecCCC--cEEEEecccc
Q 001276 196 GTKGGSSGSPVIDWQG--RAVALNAGSK 221 (1109)
Q Consensus 196 ~~~~G~SGgPv~n~~G--~vVGi~~~~~ 221 (1109)
...+|.||||++...+ .++||.+.+.
T Consensus 181 ~~c~gdsG~pl~~~~~~~~l~Gi~s~g~ 208 (229)
T smart00020 181 DACQGDSGGPLVCNDGRWVLVGIVSWGS 208 (229)
T ss_pred cccCCCCCCeeEEECCCEEEEEEEEECC
Confidence 4567999999997654 8999998765
No 50
>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=98.04 E-value=0.0001 Score=78.91 Aligned_cols=165 Identities=19% Similarity=0.235 Sum_probs=91.6
Q ss_pred HhCCceEEEEEEeeeccCCCCCCccEEEEEEEeCCCcEEEeCccccCCCCeEEEEEecCCeEEEEE-----EEEEcCCCc
Q 001276 44 KVVPAVVVLRTTACRAFDTEAAGASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVY-----PIYRDPVHD 118 (1109)
Q Consensus 44 ~~~~sVV~I~~~~~~~~d~~~~~~~~GSGfvV~~~~G~IlTn~HVv~~~~~~~~v~~~~~~~~~a~-----vv~~d~~~D 118 (1109)
-+...|..|.... ......--||...+ +|+||+|....+...+.+...-|. |... -+..=+..|
T Consensus 15 ~Ia~~ic~l~n~s-------~~~~~~l~gigyG~---~iItn~HLf~~nng~L~i~s~hG~-f~v~nt~~lkv~~i~~~D 83 (235)
T PF00863_consen 15 PIASNICRLTNES-------DGGTRSLYGIGYGS---YIITNAHLFKRNNGELTIKSQHGE-FTVPNTTQLKVHPIEGRD 83 (235)
T ss_dssp HHHTTEEEEEEEE-------TTEEEEEEEEEETT---EEEEEGGGGSSTTCEEEEEETTEE-EEECEGGGSEEEE-TCSS
T ss_pred hhhheEEEEEEEe-------CCCeEEEEEEeECC---EEEEChhhhccCCCeEEEEeCceE-EEcCCccccceEEeCCcc
Confidence 3456677777542 12233345666754 999999999876667777766653 2222 234446799
Q ss_pred EEEEEEcCCCcccccccCCCCCCccCCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCccccceeeEEEeeccC
Q 001276 119 FGFFRYDPSAIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAASGTK 198 (1109)
Q Consensus 119 lAlLk~~~~~~~~~~l~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~vs~~~~~~~~~~~~~~~~~~~~~iq~~a~~~ 198 (1109)
|.++|.. +++|+.+- .+.-..++.|++|..||.-+..+...+ .||......|. . +..+...-.++.
T Consensus 84 iviirmP-kDfpPf~~---kl~FR~P~~~e~v~mVg~~fq~k~~~s--~vSesS~i~p~----~----~~~fWkHwIsTk 149 (235)
T PF00863_consen 84 IVIIRMP-KDFPPFPQ---KLKFRAPKEGERVCMVGSNFQEKSISS--TVSESSWIYPE----E----NSHFWKHWISTK 149 (235)
T ss_dssp EEEEE---TTS----S------B----TT-EEEEEEEECSSCCCEE--EEEEEEEEEEE----T----TTTEEEE-C---
T ss_pred EEEEeCC-cccCCcch---hhhccCCCCCCEEEEEEEEEEcCCeeE--EECCceEEeec----C----CCCeeEEEecCC
Confidence 9999994 45543221 122456899999999998665543211 12222111110 1 123578888899
Q ss_pred CCCCCCceec-CCCcEEEEeccccCCCCCccccchH
Q 001276 199 GGSSGSPVID-WQGRAVALNAGSKSSSASAFFLPLE 233 (1109)
Q Consensus 199 ~G~SGgPv~n-~~G~vVGi~~~~~~~~~~~falP~~ 233 (1109)
.|+-|+|+++ .||++|||++........+|+.|+.
T Consensus 150 ~G~CG~PlVs~~Dg~IVGiHsl~~~~~~~N~F~~f~ 185 (235)
T PF00863_consen 150 DGDCGLPLVSTKDGKIVGIHSLTSNTSSRNYFTPFP 185 (235)
T ss_dssp TT-TT-EEEETTT--EEEEEEEEETTTSSEEEEE--
T ss_pred CCccCCcEEEcCCCcEEEEEcCccCCCCeEEEEcCC
Confidence 9999999998 6899999999888778889997763
No 51
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=98.03 E-value=2.8e-05 Score=83.72 Aligned_cols=178 Identities=15% Similarity=0.110 Sum_probs=99.5
Q ss_pred CceEEEEEEeeeccCC-----CCCCccEEEEEEEeCCCcEEEeCccccCCCCeE-EE-EEec-----CCe---EEEEEEE
Q 001276 47 PAVVVLRTTACRAFDT-----EAAGASYATGFVVDKRRGIILTNRHVVKPGPVV-AE-AMFV-----NRE---EIPVYPI 111 (1109)
Q Consensus 47 ~sVV~I~~~~~~~~d~-----~~~~~~~GSGfvV~~~~G~IlTn~HVv~~~~~~-~~-v~~~-----~~~---~~~a~vv 111 (1109)
..+..|.-....+|.. ...++..+++|+|.++ .+||++||+-..... .. ..+. ++. .+.....
T Consensus 38 d~r~~V~dt~~~Py~av~~~~~~tG~~~~~~~lI~pn--tvLTa~Hc~~s~~~G~~~~~~~p~g~~~~~~~~~~~~~~~~ 115 (251)
T COG3591 38 DDRTQVTDTTQFPYSAVVQFEAATGRLCTAATLIGPN--TVLTAGHCIYSPDYGEDDIAAAPPGVNSDGGPFYGITKIEI 115 (251)
T ss_pred CCeeecccCCCCCcceeEEeecCCCcceeeEEEEcCc--eEEEeeeEEecCCCChhhhhhcCCcccCCCCCCCceeeEEE
Confidence 5555555444334332 1222334566999975 999999999743321 11 1111 111 1111222
Q ss_pred EEc-C---CCcEEEEEEcCCCcc----cc---cccCCCCCCccCCCCCEEEEEecCCCCCCe----EEEEEEEEecCCCC
Q 001276 112 YRD-P---VHDFGFFRYDPSAIQ----FL---NYDEIPLAPEAACVGLEIRVVGNDSGEKVS----ILAGTLARLDRDAP 176 (1109)
Q Consensus 112 ~~d-~---~~DlAlLk~~~~~~~----~~---~l~~l~l~~~~~~~G~~V~~iG~p~g~~~s----i~~G~vs~~~~~~~ 176 (1109)
... . ..|.+...+.+..+. +. .....++ ....+.++.+.++|||.+.... ...+.+.....
T Consensus 116 ~~~~g~~~~~d~~~~~v~~~~~~~g~~~~~~~~~~~~~~-~~~~~~~d~i~v~GYP~dk~~~~~~~e~t~~v~~~~~--- 191 (251)
T COG3591 116 RVYPGELYKEDGASYDVGEAALESGINIGDVVNYLKRNT-ASEAKANDRITVIGYPGDKPNIGTMWESTGKVNSIKG--- 191 (251)
T ss_pred EecCCceeccCCceeeccHHHhccCCCcccccccccccc-ccccccCceeEEEeccCCCCcceeEeeecceeEEEec---
Confidence 122 2 345555555432221 11 1111222 3567899999999999876532 33344433322
Q ss_pred CCCCCCccccceeeEEEeeccCCCCCCCceecCCCcEEEEeccccCCC---CCccc-cchHHHHHHHHHH
Q 001276 177 HYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSSS---ASAFF-LPLERVVRALRFL 242 (1109)
Q Consensus 177 ~~~~~~~~~~~~~~iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~~---~~~fa-lP~~~i~~~l~~l 242 (1109)
.+++.++.+.+|+||+||++.+.++||+++.+.... ..+++ .=...++.+++++
T Consensus 192 ------------~~l~y~~dT~pG~SGSpv~~~~~~vigv~~~g~~~~~~~~~n~~vr~t~~~~~~I~~~ 249 (251)
T COG3591 192 ------------NKLFYDADTLPGSSGSPVLISKDEVIGVHYNGPGANGGSLANNAVRLTPEILNFIQQN 249 (251)
T ss_pred ------------ceEEEEecccCCCCCCceEecCceEEEEEecCCCcccccccCcceEecHHHHHHHHHh
Confidence 258999999999999999999999999998766532 23333 3335566655543
No 52
>PF14685 Tricorn_PDZ: Tricorn protease PDZ domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A.
Probab=97.98 E-value=4.6e-05 Score=69.06 Aligned_cols=64 Identities=25% Similarity=0.372 Sum_probs=47.6
Q ss_pred CceEEEEEecCC--------Ccccc-C--CCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEECC-EEEEE
Q 001276 297 TGLLVVDSVVPG--------GPAHL-R--LEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIERGG-ISMTV 360 (1109)
Q Consensus 297 ~G~lVv~~V~~~--------spA~~-g--L~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~v~R~g-~~~~~ 360 (1109)
.|.+.|.+|.++ ||..+ | +++||.|++|||+++..-.++..+|....|+.|.|+|.+.+ +.+++
T Consensus 11 ~~~y~I~~I~~gd~~~~~~~sPL~~pGv~v~~GD~I~aInG~~v~~~~~~~~lL~~~agk~V~Ltv~~~~~~~R~v 86 (88)
T PF14685_consen 11 NGGYRIARIYPGDPWNPNARSPLAQPGVDVREGDYILAINGQPVTADANPYRLLEGKAGKQVLLTVNRKPGGARTV 86 (88)
T ss_dssp TTEEEEEEE-BS-TTSSS-B-GGGGGS----TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEEE-STT-EEEE
T ss_pred CCEEEEEEEeCCCCCCccccCCccCCCCCCCCCCEEEEECCEECCCCCCHHHHhcccCCCEEEEEEecCCCCceEE
Confidence 577778899886 78888 6 55999999999999999999999999999999999999966 44444
No 53
>smart00228 PDZ Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
Probab=97.95 E-value=3.6e-05 Score=69.47 Aligned_cols=58 Identities=38% Similarity=0.615 Sum_probs=47.4
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHh-cCCCCeEEEEEEECC
Q 001276 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLD-DGVDKNIELLIERGG 355 (1109)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~-~~~g~~v~l~v~R~g 355 (1109)
.|++| ..|.++|||+. ||++||+|++|||+.+.++.+...... ...+..+.|++.|++
T Consensus 26 ~~~~i-~~v~~~s~a~~~gl~~GD~I~~In~~~v~~~~~~~~~~~~~~~~~~~~l~i~r~~ 85 (85)
T smart00228 26 GGVVV-SSVVPGSPAAKAGLKVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85 (85)
T ss_pred CCEEE-EEECCCCHHHHcCCCCCCEEEEECCEECCCCCHHHHHHHHHhCCCeEEEEEEeCC
Confidence 56665 89999999999 999999999999999998877665542 334568899998864
No 54
>PF00595 PDZ: PDZ domain (Also known as DHR or GLGF) Coordinates are not yet available; InterPro: IPR001478 PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [, ]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences []. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated. PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (beta-A to beta-F) and two alpha-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands.; GO: 0005515 protein binding; PDB: 3AXA_A 1WF8_A 1QAV_B 1QAU_A 1B8Q_A 1MC7_A 2KAW_A 1I16_A 1VB7_A 1WI4_A ....
Probab=97.94 E-value=2.9e-05 Score=69.90 Aligned_cols=54 Identities=33% Similarity=0.612 Sum_probs=43.2
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHH--HHhcCCCCeEEEEEE
Q 001276 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLET--LLDDGVDKNIELLIE 352 (1109)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~--~l~~~~g~~v~l~v~ 352 (1109)
.+++| ..|.++|||+. ||++||+|++|||+.+.++.+.+. ++... +..++|+|+
T Consensus 25 ~~~~V-~~v~~~~~a~~~gl~~GD~Il~INg~~v~~~~~~~~~~~l~~~-~~~v~L~V~ 81 (81)
T PF00595_consen 25 KGVFV-SSVVPGSPAERAGLKVGDRILEINGQSVRGMSHDEVVQLLKSA-SNPVTLTVQ 81 (81)
T ss_dssp EEEEE-EEECTTSHHHHHTSSTTEEEEEETTEESTTSBHHHHHHHHHHS-TSEEEEEEE
T ss_pred CCEEE-EEEeCCChHHhcccchhhhhheeCCEeCCCCCHHHHHHHHHCC-CCcEEEEEC
Confidence 46666 79999999999 999999999999999999866553 34443 348888764
No 55
>TIGR00225 prc C-terminal peptidase (prc). A C-terminal peptidase with different substrates in different species including processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in E.coli E.coli and H influenza have the most distal branch of the tree and their proteins have an N-terminal 200 amino acids that show no homology to other proteins in the database.
Probab=97.92 E-value=2.7e-05 Score=89.76 Aligned_cols=67 Identities=24% Similarity=0.453 Sum_probs=56.0
Q ss_pred EEEEEecCCCcccc-CCCCCCEEEEECCEEeCCh--hHHHHHHhcCCCCeEEEEEEECCEEEEEEEEeec
Q 001276 300 LVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQF--LKLETLLDDGVDKNIELLIERGGISMTVNLVVQD 366 (1109)
Q Consensus 300 lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g~~v~l~v~R~g~~~~~~v~l~~ 366 (1109)
++|..|.++|||++ ||++||+|++|||+++.+| .++...+....|+.+.+++.|+|+...+++++..
T Consensus 64 ~~V~~V~~~spA~~aGL~~GD~I~~Ing~~v~~~~~~~~~~~l~~~~g~~v~l~v~R~g~~~~~~v~l~~ 133 (334)
T TIGR00225 64 IVIVSPFEGSPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALIRGKKGTKVSLEILRAGKSKPLTFTLKR 133 (334)
T ss_pred EEEEEeCCCChHHHcCCCCCCEEEEECCEECCCCCHHHHHHhccCCCCCEEEEEEEeCCCCceEEEEEEE
Confidence 44479999999999 9999999999999999987 4555666566788999999999887777776654
No 56
>PF00595 PDZ: PDZ domain (Also known as DHR or GLGF) Coordinates are not yet available; InterPro: IPR001478 PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [, ]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences []. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated. PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (beta-A to beta-F) and two alpha-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands.; GO: 0005515 protein binding; PDB: 3AXA_A 1WF8_A 1QAV_B 1QAU_A 1B8Q_A 1MC7_A 2KAW_A 1I16_A 1VB7_A 1WI4_A ....
Probab=97.90 E-value=3.5e-05 Score=69.34 Aligned_cols=53 Identities=32% Similarity=0.494 Sum_probs=46.5
Q ss_pred CcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEE
Q 001276 1008 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVR 1062 (1109)
Q Consensus 1008 ~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~ 1062 (1109)
.++||+.+.++|||+++||++||.|++|||+++.++ ++..+.++..+ ..++|+
T Consensus 25 ~~~~V~~v~~~~~a~~~gl~~GD~Il~INg~~v~~~~~~~~~~~l~~~~--~~v~L~ 79 (81)
T PF00595_consen 25 KGVFVSSVVPGSPAERAGLKVGDRILEINGQSVRGMSHDEVVQLLKSAS--NPVTLT 79 (81)
T ss_dssp EEEEEEEECTTSHHHHHTSSTTEEEEEETTEESTTSBHHHHHHHHHHST--SEEEEE
T ss_pred CCEEEEEEeCCChHHhcccchhhhhheeCCEeCCCCCHHHHHHHHHCCC--CcEEEE
Confidence 389999999999999999999999999999999976 77788888743 377776
No 57
>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
Probab=97.89 E-value=4.4e-05 Score=68.56 Aligned_cols=53 Identities=30% Similarity=0.412 Sum_probs=47.0
Q ss_pred CcEEEEEecCCChhhhcCCCCCCeEEEECCeeCC--CHHHHHHHHHhCCCCceEEEE
Q 001276 1008 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTP--DLEAFVNVTKEIEHGEFVRVR 1062 (1109)
Q Consensus 1008 ~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~--~l~~f~~~l~~~~~~~~v~l~ 1062 (1109)
.+++|..+.++|||+++||++||.|++|||+++. +++++.+.++... ..++|.
T Consensus 26 ~~~~V~~v~~~s~a~~~gl~~GD~I~~ing~~i~~~~~~~~~~~l~~~~--~~v~l~ 80 (82)
T cd00992 26 GGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHEEAVELLKNSG--DEVTLT 80 (82)
T ss_pred CCeEEEEECCCChHHhCCCCCCCEEEEECCEEcCccCHHHHHHHHHhCC--CeEEEE
Confidence 3789999999999999999999999999999999 9999999999743 256655
No 58
>KOG3834 consensus Golgi reassembly stacking protein GRASP65, contains PDZ domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.87 E-value=0.00018 Score=81.14 Aligned_cols=164 Identities=18% Similarity=0.140 Sum_probs=109.3
Q ss_pred cceEEEEeecCCCHHhhh-ccC-CCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCC--EEEEEEEeeeec
Q 001276 899 RQVLRVKGCLAGSKAENM-LEQ-GDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQG--REIELQVGTDVR 974 (1109)
Q Consensus 899 ~~~~~V~~V~~~spA~~a-L~~-GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g--~~~~l~v~l~~~ 974 (1109)
..++-|-+|..+|+|.++ |++ =|-|++|||..+..-.|...++..... ++|+++|+... ..+.++|+....
T Consensus 14 teg~hvlkVqedSpa~~aglepffdFIvSI~g~rL~~dnd~Lk~llk~~s-----ekVkltv~n~kt~~~R~v~I~ps~~ 88 (462)
T KOG3834|consen 14 TEGYHVLKVQEDSPAHKAGLEPFFDFIVSINGIRLNKDNDTLKALLKANS-----EKVKLTVYNSKTQEVRIVEIVPSNN 88 (462)
T ss_pred ceeEEEEEeecCChHHhcCcchhhhhhheeCcccccCchHHHHHHHHhcc-----cceEEEEEecccceeEEEEeccccc
Confidence 456778999999999999 665 799999999999977666555522222 55999998533 233344432221
Q ss_pred CCCCcceEEeecCccccCCchhhhhccCCCCCCCcEEEEEecCCChhhhcCCC-CCCeEEEECCeeCCCHHHHHHHHHhC
Q 001276 975 DGNGTTRVINWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLY-ALQWIVEINGKRTPDLEAFVNVTKEI 1053 (1109)
Q Consensus 975 ~~~~t~~~~~~~G~~~~~p~~~~r~~~~lp~~~~gV~V~~v~~gSPA~~~GL~-~gD~I~~VNg~~v~~l~~f~~~l~~~ 1053 (1109)
.. .. ++|..++- ..+-.....---|-+|.+.|||+.+||+ -+|.|+.+-+.-..+.+||...|+.+
T Consensus 89 wg---gq---llGvsvrF-------csf~~A~~~vwHvl~V~p~SPaalAgl~~~~DYivG~~~~~~~~~eDl~~lIesh 155 (462)
T KOG3834|consen 89 WG---GQ---LLGVSVRF-------CSFDGAVESVWHVLSVEPNSPAALAGLRPYTDYIVGIWDAVMHEEEDLFTLIESH 155 (462)
T ss_pred cc---cc---ccceEEEe-------ccCccchhheeeeeecCCCCHHHhcccccccceEecchhhhccchHHHHHHHHhc
Confidence 11 01 23333211 0000000001136789999999999998 78999999555566778999999986
Q ss_pred CCCceEEEEEEEeC-CeEEEEEEeeCCcc
Q 001276 1054 EHGEFVRVRTVHLN-GKPRVLTLKQDLHY 1081 (1109)
Q Consensus 1054 ~~~~~v~l~~v~rd-g~~~~i~lk~~~~y 1081 (1109)
. ++.++|.+.+.| ...+.+++++|.+|
T Consensus 156 e-~kpLklyVYN~D~d~~ReVti~pn~aw 183 (462)
T KOG3834|consen 156 E-GKPLKLYVYNHDTDSCREVTITPNSAW 183 (462)
T ss_pred c-CCCcceeEeecCCCccceEEeeccccc
Confidence 5 888998755554 45789999999884
No 59
>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=97.87 E-value=9.4e-05 Score=85.17 Aligned_cols=68 Identities=24% Similarity=0.385 Sum_probs=59.5
Q ss_pred CcEEEEEec--------CCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEeCCeEEEEEEee
Q 001276 1008 HGVYVARWC--------HGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQ 1077 (1109)
Q Consensus 1008 ~gV~V~~v~--------~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i~lk~ 1077 (1109)
.||+|.... .+|||+++||++||.|++|||+++.++++|.+++++.. ++.+.|+ +.|+|+...+++++
T Consensus 105 ~GVlVvg~~~v~~~~g~~~SPAa~AGLq~GDiIvsING~~V~s~~DL~~iL~~~~-g~~V~Lt-V~R~Ge~~tv~V~P 180 (402)
T TIGR02860 105 KGVLVVGFSDIETEKGKIHSPGEEAGIQIGDRILKINGEKIKNMDDLANLINKAG-GEKLTLT-IERGGKIIETVIKP 180 (402)
T ss_pred CEEEEEEEEcccccCCCCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHHHhCC-CCeEEEE-EEECCEEEEEEEEE
Confidence 477775442 36999999999999999999999999999999999975 8889999 78999999888875
No 60
>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase. Members of this protein family are predicted FeS-containing oxidoreductases of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cutoff score for this model, 700 bits, excludes homologs from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialized, conserved function, perhaps related to photosynthesis. A distantly related protein family, TIGR03278, in universal in and restricted to archaeal methanogens, and may be linked to methanogenesis.
Probab=97.87 E-value=2.8e-05 Score=89.98 Aligned_cols=64 Identities=22% Similarity=0.328 Sum_probs=55.4
Q ss_pred EEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEeCCeEEEEEEeeCC
Q 001276 1012 VARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQDL 1079 (1109)
Q Consensus 1012 V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i~lk~~~ 1079 (1109)
|..|.++|||+++||++||.|++|||+++.+|.++...+. ++.+.|++..|+|+.+.+.+.+++
T Consensus 2 I~~V~pgSpAe~AGLe~GD~IlsING~~V~Dw~D~~~~l~----~e~l~L~V~~rdGe~~~l~Ie~~~ 65 (433)
T TIGR03279 2 ISAVLPGSIAEELGFEPGDALVSINGVAPRDLIDYQFLCA----DEELELEVLDANGESHQIEIEKDL 65 (433)
T ss_pred cCCcCCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHhc----CCcEEEEEEcCCCeEEEEEEecCC
Confidence 5678999999999999999999999999999999888884 356888844589999888888753
No 61
>smart00228 PDZ Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
Probab=97.87 E-value=4.4e-05 Score=68.92 Aligned_cols=59 Identities=29% Similarity=0.317 Sum_probs=46.7
Q ss_pred CcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEeC
Q 001276 1008 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLN 1067 (1109)
Q Consensus 1008 ~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~rd 1067 (1109)
.+++|..+.++|||+++||++||.|++|||+++.++.+..........+..++|. +.|+
T Consensus 26 ~~~~i~~v~~~s~a~~~gl~~GD~I~~In~~~v~~~~~~~~~~~~~~~~~~~~l~-i~r~ 84 (85)
T smart00228 26 GGVVVSSVVPGSPAAKAGLKVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLT-VLRG 84 (85)
T ss_pred CCEEEEEECCCCHHHHcCCCCCCEEEEECCEECCCCCHHHHHHHHHhCCCeEEEE-EEeC
Confidence 3899999999999999999999999999999999875544443332335578887 5554
No 62
>PLN00049 carboxyl-terminal processing protease; Provisional
Probab=97.87 E-value=6.9e-05 Score=88.02 Aligned_cols=76 Identities=21% Similarity=0.273 Sum_probs=63.7
Q ss_pred cEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEEEEEeCCeEEEEEEeeCCccCcceE
Q 001276 1009 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQDLHYWPTWE 1086 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i~lk~~~~y~pt~e 1086 (1109)
+++|..+.++|||+++||++||+|++|||+++.++ +++...++. +.++.+.|+ +.|+|..+.++|+...-..+++.
T Consensus 103 g~~V~~V~~~SPA~~aGl~~GD~Iv~InG~~v~~~~~~~~~~~l~g-~~g~~v~lt-v~r~g~~~~~~l~r~~v~~~~v~ 180 (389)
T PLN00049 103 GLVVVAPAPGGPAARAGIRPGDVILAIDGTSTEGLSLYEAADRLQG-PEGSSVELT-LRRGPETRLVTLTREKVSLNPVK 180 (389)
T ss_pred cEEEEEeCCCChHHHcCCCCCCEEEEECCEECCCCCHHHHHHHHhc-CCCCEEEEE-EEECCEEEEEEEEeeeEecccee
Confidence 68899999999999999999999999999999864 777888865 458899999 78999988888876554445443
No 63
>TIGR00225 prc C-terminal peptidase (prc). A C-terminal peptidase with different substrates in different species including processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in E.coli E.coli and H influenza have the most distal branch of the tree and their proteins have an N-terminal 200 amino acids that show no homology to other proteins in the database.
Probab=97.80 E-value=9.3e-05 Score=85.35 Aligned_cols=77 Identities=25% Similarity=0.356 Sum_probs=61.9
Q ss_pred cEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEEEEEeCCeEEE--EEEeeCCccCcc
Q 001276 1009 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVHLNGKPRV--LTLKQDLHYWPT 1084 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~~v~rdg~~~~--i~lk~~~~y~pt 1084 (1109)
+++|..|.++|||+++||++||.|++|||+++.++ +++...+.. +.++.+.|+ +.|+|.... +++.....+.|+
T Consensus 63 ~~~V~~V~~~spA~~aGL~~GD~I~~Ing~~v~~~~~~~~~~~l~~-~~g~~v~l~-v~R~g~~~~~~v~l~~~~~~~~~ 140 (334)
T TIGR00225 63 EIVIVSPFEGSPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALIRG-KKGTKVSLE-ILRAGKSKPLTFTLKRDRIELQT 140 (334)
T ss_pred EEEEEEeCCCChHHHcCCCCCCEEEEECCEECCCCCHHHHHHhccC-CCCCEEEEE-EEeCCCCceEEEEEEEEEeeccc
Confidence 68899999999999999999999999999999986 577777766 458899999 788876544 445555456666
Q ss_pred eEE
Q 001276 1085 WEL 1087 (1109)
Q Consensus 1085 ~e~ 1087 (1109)
.+.
T Consensus 141 v~~ 143 (334)
T TIGR00225 141 VKA 143 (334)
T ss_pred eEE
Confidence 654
No 64
>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase. Members of this protein family are predicted FeS-containing oxidoreductases of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cutoff score for this model, 700 bits, excludes homologs from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialized, conserved function, perhaps related to photosynthesis. A distantly related protein family, TIGR03278, in universal in and restricted to archaeal methanogens, and may be linked to methanogenesis.
Probab=97.79 E-value=5.3e-05 Score=87.69 Aligned_cols=59 Identities=31% Similarity=0.503 Sum_probs=50.9
Q ss_pred EEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEE-ECCEEEEEEEEe
Q 001276 303 DSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIE-RGGISMTVNLVV 364 (1109)
Q Consensus 303 ~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~v~-R~g~~~~~~v~l 364 (1109)
..|.|+|||++ ||++||+|++|||+++.+|.++...+. ++.+.++|. |+|+..++++..
T Consensus 3 ~~V~pgSpAe~AGLe~GD~IlsING~~V~Dw~D~~~~l~---~e~l~L~V~~rdGe~~~l~Ie~ 63 (433)
T TIGR03279 3 SAVLPGSIAEELGFEPGDALVSINGVAPRDLIDYQFLCA---DEELELEVLDANGESHQIEIEK 63 (433)
T ss_pred CCcCCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHhc---CCcEEEEEEcCCCeEEEEEEec
Confidence 68999999999 999999999999999999999887773 357889986 788777776654
No 65
>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=97.76 E-value=0.0001 Score=84.80 Aligned_cols=68 Identities=28% Similarity=0.453 Sum_probs=58.8
Q ss_pred CCceEEEEEec-------CCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEECCEEEEEEEE
Q 001276 296 ETGLLVVDSVV-------PGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIERGGISMTVNLV 363 (1109)
Q Consensus 296 ~~G~lVv~~V~-------~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~v~R~g~~~~~~v~ 363 (1109)
..|+||+..-. .+|||++ |||+||+|++|||+++.+|.++..++....++.+.+++.|+|+..++++.
T Consensus 104 t~GVlVvg~~~v~~~~g~~~SPAa~AGLq~GDiIvsING~~V~s~~DL~~iL~~~~g~~V~LtV~R~Ge~~tv~V~ 179 (402)
T TIGR02860 104 TKGVLVVGFSDIETEKGKIHSPGEEAGIQIGDRILKINGEKIKNMDDLANLINKAGGEKLTLTIERGGKIIETVIK 179 (402)
T ss_pred cCEEEEEEEEcccccCCCCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHHHhCCCCeEEEEEEECCEEEEEEEE
Confidence 48999975422 2589999 99999999999999999999999999776788999999999988887775
No 66
>PLN00049 carboxyl-terminal processing protease; Provisional
Probab=97.73 E-value=9.9e-05 Score=86.69 Aligned_cols=66 Identities=30% Similarity=0.527 Sum_probs=55.3
Q ss_pred ceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCCh--hHHHHHHhcCCCCeEEEEEEECCEEEEEEEEe
Q 001276 298 GLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQF--LKLETLLDDGVDKNIELLIERGGISMTVNLVV 364 (1109)
Q Consensus 298 G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g~~v~l~v~R~g~~~~~~v~l 364 (1109)
|++| ..|.++|||++ ||++||+|++|||++|.++ .++..++....|+.+.|+|.|+|+..+++++-
T Consensus 103 g~~V-~~V~~~SPA~~aGl~~GD~Iv~InG~~v~~~~~~~~~~~l~g~~g~~v~ltv~r~g~~~~~~l~r 171 (389)
T PLN00049 103 GLVV-VAPAPGGPAARAGIRPGDVILAIDGTSTEGLSLYEAADRLQGPEGSSVELTLRRGPETRLVTLTR 171 (389)
T ss_pred cEEE-EEeCCCChHHHcCCCCCCEEEEECCEECCCCCHHHHHHHHhcCCCCEEEEEEEECCEEEEEEEEe
Confidence 6555 69999999999 9999999999999999865 56666666667889999999999877766654
No 67
>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
Probab=97.70 E-value=0.00011 Score=66.06 Aligned_cols=53 Identities=34% Similarity=0.577 Sum_probs=43.5
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeC--ChhHHHHHHhcCCCCeEEEEE
Q 001276 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVIT--QFLKLETLLDDGVDKNIELLI 351 (1109)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~--~~~~l~~~l~~~~g~~v~l~v 351 (1109)
.|++| ..|.++|||+. ||++||+|++|||+++. ++.++...+....+ .++|++
T Consensus 26 ~~~~V-~~v~~~s~a~~~gl~~GD~I~~ing~~i~~~~~~~~~~~l~~~~~-~v~l~v 81 (82)
T cd00992 26 GGIFV-SRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHEEAVELLKNSGD-EVTLTV 81 (82)
T ss_pred CCeEE-EEECCCChHHhCCCCCCCEEEEECCEEcCccCHHHHHHHHHhCCC-eEEEEE
Confidence 46665 79999999999 99999999999999999 88888887765433 566554
No 68
>PF04495 GRASP55_65: GRASP55/65 PDZ-like domain ; InterPro: IPR007583 GRASP55 (Golgi reassembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide-sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system [].; PDB: 3RLE_A 4EDJ_A.
Probab=97.65 E-value=0.0002 Score=71.03 Aligned_cols=73 Identities=19% Similarity=0.309 Sum_probs=53.8
Q ss_pred CcEEEEEecCCChhhhcCCCC-CCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEe-CCeEEEEEEeeCCcc
Q 001276 1008 HGVYVARWCHGSPVHRYGLYA-LQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHL-NGKPRVLTLKQDLHY 1081 (1109)
Q Consensus 1008 ~gV~V~~v~~gSPA~~~GL~~-gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~r-dg~~~~i~lk~~~~y 1081 (1109)
.+.-|.+|.++|||+++||.+ .|+|+.+++....+.++|.+.+++.. ++.+.|.+.+. ....+.+++.|+.++
T Consensus 43 ~~~~Vl~V~p~SPA~~AGL~p~~DyIig~~~~~l~~~~~l~~~v~~~~-~~~l~L~Vyns~~~~vR~V~i~P~~~W 117 (138)
T PF04495_consen 43 EGWHVLRVAPNSPAAKAGLEPFFDYIIGIDGGLLDDEDDLFELVEANE-NKPLQLYVYNSKTDSVREVTITPSRNW 117 (138)
T ss_dssp CEEEEEEE-TTSHHHHTT--TTTEEEEEETTCE--STCHHHHHHHHTT-TS-EEEEEEETTTTCEEEEEE---TTS
T ss_pred ceEEEeEecCCCHHHHCCccccccEEEEccceecCCHHHHHHHHHHcC-CCcEEEEEEECCCCeEEEEEEEcCCCC
Confidence 467899999999999999998 69999999999999999999999965 88899985443 355678888886543
No 69
>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=97.52 E-value=0.0018 Score=69.14 Aligned_cols=169 Identities=20% Similarity=0.226 Sum_probs=96.1
Q ss_pred eeeEEEEEEEeeCCceEEEEeCceecCCCCcEEEEeec------CC--eEEeEEEEEeeC-------CCcEEEEEECCC-
Q 001276 649 HFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAA------FP--IEIPGEVVFLHP-------VHNFALIAYDPS- 712 (1109)
Q Consensus 649 ~~~GsG~VId~~~~~G~IlTn~~~V~~~~~di~V~~~d------~~--~~~~a~vv~~dp-------~~dlAilk~d~~- 712 (1109)
...++|++|. +-+|||.+|.+.. ..++.+.+.. .+ ..+..+-+..|| .+|+|||+++..
T Consensus 24 ~~~C~G~li~----~~~vLTaahC~~~-~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~h~~~~~~~~~~DiAll~L~~~~ 98 (220)
T PF00089_consen 24 RFFCTGTLIS----PRWVLTAAHCVDG-ASDIKVRLGTYSIRNSDGSEQTIKVSKIIIHPKYDPSTYDNDIALLKLDRPI 98 (220)
T ss_dssp EEEEEEEEEE----TTEEEEEGGGHTS-GGSEEEEESESBTTSTTTTSEEEEEEEEEEETTSBTTTTTTSEEEEEESSSS
T ss_pred CeeEeEEecc----ccccccccccccc-cccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 6789999999 5599999776665 4456564432 01 244444454543 469999999766
Q ss_pred CCCcccccceeceecCC-CccCCCCCeEEEEeeCCCCcce----eeeeeEeccccccccCCCCCCc-ccc-cceeEEEEe
Q 001276 713 SLGVAGASVVRAAELLP-EPALRRGDSVYLVGLSRSLQAT----SRKSIVTNPCAALNISSADCPR-YRA-MNMEVIELD 785 (1109)
Q Consensus 713 ~l~~~~~~~v~~~~l~~-~~~l~~G~~V~~iG~p~~~~~~----~~~~~vt~i~~~~~i~~~~~~~-y~~-~~~~~I~~d 785 (1109)
.+. ..+.++.+.. ...++.|+.+.++|++...... .....+. .++...... |.. .....+...
T Consensus 99 ~~~----~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~------~~~~~~c~~~~~~~~~~~~~c~~ 168 (220)
T PF00089_consen 99 TFG----DNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNGYSSNLQSVTVP------VVSRKTCRSSYNDNLTPNMICAG 168 (220)
T ss_dssp EHB----SSBEESBBTSTTHTTTTTSEEEEEESSBSSTTSBTSBEEEEEEE------EEEHHHHHHHTTTTSTTTEEEEE
T ss_pred ccc----cccccccccccccccccccccccccccccccccccccccccccc------ccccccccccccccccccccccc
Confidence 222 3556677766 2346899999999998753221 1111121 111100000 110 122344444
Q ss_pred c----cc-CCCCCceEEcCCeeEEEEEeeccccccccCCCCCCceeEecccHHHHHHHH
Q 001276 786 T----DF-GSTFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVL 839 (1109)
Q Consensus 786 ~----~i-g~~sGGpL~d~~G~VvGi~~~~~~~~~~g~~~~~~~~~~~aipi~~i~~~l 839 (1109)
. .. ...|||||+..++.|+||.+....- ....... +..++...+++|
T Consensus 169 ~~~~~~~~~g~sG~pl~~~~~~lvGI~s~~~~c-----~~~~~~~--v~~~v~~~~~WI 220 (220)
T PF00089_consen 169 SSGSGDACQGDSGGPLICNNNYLVGIVSFGENC-----GSPNYPG--VYTRVSSYLDWI 220 (220)
T ss_dssp TTSSSBGGTTTTTSEEEETTEEEEEEEEEESSS-----SBTTSEE--EEEEGGGGHHHH
T ss_pred ccccccccccccccccccceeeecceeeecCCC-----CCCCcCE--EEEEHHHhhccC
Confidence 3 22 2248999999999999998764111 1111223 447777666553
No 70
>COG0793 Prc Periplasmic protease [Cell envelope biogenesis, outer membrane]
Probab=97.52 E-value=0.00029 Score=82.76 Aligned_cols=78 Identities=24% Similarity=0.318 Sum_probs=67.0
Q ss_pred cEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEEEEEeC--CeEEEEEEeeCCccCcc
Q 001276 1009 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVHLN--GKPRVLTLKQDLHYWPT 1084 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~~v~rd--g~~~~i~lk~~~~y~pt 1084 (1109)
++.|.+..+|+||+++|+++||.|+.|||+++.+. ++.++.++. +.|+.|+|+ +.|. ++++.++++-+.-.-++
T Consensus 113 ~~~V~s~~~~~PA~kagi~~GD~I~~IdG~~~~~~~~~~av~~irG-~~Gt~V~L~-i~r~~~~k~~~v~l~Re~i~l~~ 190 (406)
T COG0793 113 GVKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRG-KPGTKVTLT-ILRAGGGKPFTVTLTREEIELED 190 (406)
T ss_pred CcEEEecCCCChHHHcCCCCCCEEEEECCEEccCCCHHHHHHHhCC-CCCCeEEEE-EEEcCCCceeEEEEEEEEEeccc
Confidence 67899999999999999999999999999999988 667888887 569999999 6775 67899998887777666
Q ss_pred eEEE
Q 001276 1085 WELI 1088 (1109)
Q Consensus 1085 ~e~~ 1088 (1109)
..++
T Consensus 191 v~~~ 194 (406)
T COG0793 191 VAAK 194 (406)
T ss_pred eeee
Confidence 6654
No 71
>COG0793 Prc Periplasmic protease [Cell envelope biogenesis, outer membrane]
Probab=97.42 E-value=0.00036 Score=81.94 Aligned_cols=67 Identities=28% Similarity=0.472 Sum_probs=52.6
Q ss_pred ceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChh--HHHHHHhcCCCCeEEEEEEECC--EEEEEEEEe
Q 001276 298 GLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFL--KLETLLDDGVDKNIELLIERGG--ISMTVNLVV 364 (1109)
Q Consensus 298 G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~--~l~~~l~~~~g~~v~l~v~R~g--~~~~~~v~l 364 (1109)
+.+.|..+.+++||++ ||++||+|++|||+++.... +....+....|..|+|++.|.+ +..++++.-
T Consensus 112 ~~~~V~s~~~~~PA~kagi~~GD~I~~IdG~~~~~~~~~~av~~irG~~Gt~V~L~i~r~~~~k~~~v~l~R 183 (406)
T COG0793 112 GGVKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTILRAGGGKPFTVTLTR 183 (406)
T ss_pred CCcEEEecCCCChHHHcCCCCCCEEEEECCEEccCCCHHHHHHHhCCCCCCeEEEEEEEcCCCceeEEEEEE
Confidence 4444469999999999 99999999999999998863 3555666788999999999974 444544443
No 72
>PF14685 Tricorn_PDZ: Tricorn protease PDZ domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A.
Probab=97.30 E-value=0.002 Score=58.60 Aligned_cols=64 Identities=23% Similarity=0.239 Sum_probs=42.9
Q ss_pred ceEEEEeecCC--------CHHhhh---ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCC-EEEEE
Q 001276 900 QVLRVKGCLAG--------SKAENM---LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQG-REIEL 967 (1109)
Q Consensus 900 ~~~~V~~V~~~--------spA~~a---L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g-~~~~l 967 (1109)
+++.|.++.++ ||..+. +++||+|++|||+++..-.++..+|. -+.+ ..+.++|.+.+ +.+++
T Consensus 12 ~~y~I~~I~~gd~~~~~~~sPL~~pGv~v~~GD~I~aInG~~v~~~~~~~~lL~-~~ag----k~V~Ltv~~~~~~~R~v 86 (88)
T PF14685_consen 12 GGYRIARIYPGDPWNPNARSPLAQPGVDVREGDYILAINGQPVTADANPYRLLE-GKAG----KQVLLTVNRKPGGARTV 86 (88)
T ss_dssp TEEEEEEE-BS-TTSSS-B-GGGGGS----TT-EEEEETTEE-BTTB-HHHHHH-TTTT----SEEEEEEE-STT-EEEE
T ss_pred CEEEEEEEeCCCCCCccccCCccCCCCCCCCCCEEEEECCEECCCCCCHHHHhc-ccCC----CEEEEEEecCCCCceEE
Confidence 66888888764 677665 77999999999999999989988883 3333 88999999865 45555
Q ss_pred E
Q 001276 968 Q 968 (1109)
Q Consensus 968 ~ 968 (1109)
.
T Consensus 87 ~ 87 (88)
T PF14685_consen 87 V 87 (88)
T ss_dssp E
T ss_pred E
Confidence 4
No 73
>PF04495 GRASP55_65: GRASP55/65 PDZ-like domain ; InterPro: IPR007583 GRASP55 (Golgi reassembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide-sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system [].; PDB: 3RLE_A 4EDJ_A.
Probab=97.22 E-value=0.00081 Score=66.68 Aligned_cols=86 Identities=23% Similarity=0.371 Sum_probs=58.0
Q ss_pred CCccceEEEEcChhHHHHcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCC-CCEEEEECCEEeCChhHHHH
Q 001276 260 RGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEP-GDVLVRVNGEVITQFLKLET 337 (1109)
Q Consensus 260 rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~-GD~Il~VnG~~v~~~~~l~~ 337 (1109)
.|.||+.++.-.+..+ ...+.-| -.|.|+|||+. ||++ .|.|+.+|+..+.+.++|..
T Consensus 25 ~g~LG~sv~~~~~~~~-------------------~~~~~~V-l~V~p~SPA~~AGL~p~~DyIig~~~~~l~~~~~l~~ 84 (138)
T PF04495_consen 25 QGLLGISVRFESFEGA-------------------EEEGWHV-LRVAPNSPAAKAGLEPFFDYIIGIDGGLLDDEDDLFE 84 (138)
T ss_dssp SSSS-EEEEEEE-TTG-------------------CCCEEEE-EEE-TTSHHHHTT--TTTEEEEEETTCE--STCHHHH
T ss_pred CCCCcEEEEEeccccc-------------------ccceEEE-eEecCCCHHHHCCccccccEEEEccceecCCHHHHHH
Confidence 3778888886543222 2345455 59999999999 9999 69999999999999999999
Q ss_pred HHhcCCCCeEEEEEEECC--EEEEEEEEee
Q 001276 338 LLDDGVDKNIELLIERGG--ISMTVNLVVQ 365 (1109)
Q Consensus 338 ~l~~~~g~~v~l~v~R~g--~~~~~~v~l~ 365 (1109)
.+..+.++.+.|.|+... ..+++++...
T Consensus 85 ~v~~~~~~~l~L~Vyns~~~~vR~V~i~P~ 114 (138)
T PF04495_consen 85 LVEANENKPLQLYVYNSKTDSVREVTITPS 114 (138)
T ss_dssp HHHHTTTS-EEEEEEETTTTCEEEEEE---
T ss_pred HHHHcCCCcEEEEEEECCCCeEEEEEEEcC
Confidence 998899999999998754 3455555444
No 74
>KOG3834 consensus Golgi reassembly stacking protein GRASP65, contains PDZ domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.21 E-value=0.0046 Score=70.07 Aligned_cols=163 Identities=21% Similarity=0.242 Sum_probs=104.7
Q ss_pred EEEEEecCCCcccc-CCCC-CCEEEEECCEEeCChhH-HHHHHhcCCCCeEEEEEEECCEE--EEEEEEeecCCCCCCCc
Q 001276 300 LVVDSVVPGGPAHL-RLEP-GDVLVRVNGEVITQFLK-LETLLDDGVDKNIELLIERGGIS--MTVNLVVQDLHSITPDY 374 (1109)
Q Consensus 300 lVv~~V~~~spA~~-gL~~-GD~Il~VnG~~v~~~~~-l~~~l~~~~g~~v~l~v~R~g~~--~~~~v~l~~~~~~~~~~ 374 (1109)
+-|-.|..+|||++ ||++ -|-|++|||..+..-.+ |.+.|..+..+ |++++.-.... +.+.|+..+...
T Consensus 17 ~hvlkVqedSpa~~aglepffdFIvSI~g~rL~~dnd~Lk~llk~~sek-Vkltv~n~kt~~~R~v~I~ps~~wg----- 90 (462)
T KOG3834|consen 17 YHVLKVQEDSPAHKAGLEPFFDFIVSINGIRLNKDNDTLKALLKANSEK-VKLTVYNSKTQEVRIVEIVPSNNWG----- 90 (462)
T ss_pred EEEEEeecCChHHhcCcchhhhhhheeCcccccCchHHHHHHHHhcccc-eEEEEEecccceeEEEEeccccccc-----
Confidence 44469999999999 9887 57899999999986554 44555555544 99998864433 333333322211
Q ss_pred cccccceEEecCCHHHhhccCCCCCeEEEEcCCChhHHcCCC-CCCEEEEcCCeecCCHHHHHHHHHhcCCCCeEeEEEE
Q 001276 375 FLEVSGAVIHPLSYQQARNFRFPCGLVYVAEPGYMLFRAGVP-RHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYS 453 (1109)
Q Consensus 375 ~~~~~G~~~~~l~~~~~~~~~~~~~gv~v~~pg~~a~~aGl~-~GD~I~~Vng~~v~~l~~~~~~i~~~~~g~~v~l~~~ 453 (1109)
- .++|.+++..+...+-... -=++-..+.++|++|||. -+|.|+-+-+.-...-++|...|.. ..++.+.|-++
T Consensus 91 g-qllGvsvrFcsf~~A~~~v---wHvl~V~p~SPaalAgl~~~~DYivG~~~~~~~~~eDl~~lIes-he~kpLklyVY 165 (462)
T KOG3834|consen 91 G-QLLGVSVRFCSFDGAVESV---WHVLSVEPNSPAALAGLRPYTDYIVGIWDAVMHEEEDLFTLIES-HEGKPLKLYVY 165 (462)
T ss_pred c-cccceEEEeccCccchhhe---eeeeecCCCCHHHhcccccccceEecchhhhccchHHHHHHHHh-ccCCCcceeEe
Confidence 0 1455555433221110000 012233589999999999 7899999955556677788888888 45788888777
Q ss_pred eecccccceEEEEEEecCCCCC
Q 001276 454 SYTDRHRRKSVLVTIDRHEWYA 475 (1109)
Q Consensus 454 ~~~~~~~~~~~~l~i~R~~~~~ 475 (1109)
..+. ...+.+.++-++ .|-.
T Consensus 166 N~D~-d~~ReVti~pn~-awGg 185 (462)
T KOG3834|consen 166 NHDT-DSCREVTITPNS-AWGG 185 (462)
T ss_pred ecCC-CccceEEeeccc-cccc
Confidence 6654 344556666667 7754
No 75
>KOG3605 consensus Beta amyloid precursor-binding protein [General function prediction only]
Probab=97.18 E-value=0.0007 Score=79.41 Aligned_cols=115 Identities=23% Similarity=0.359 Sum_probs=75.0
Q ss_pred EecCCCcccc--CCCCCCEEEEECCEEeCCh--hHHHHHHhcCCC-CeEEEEEEECCEEEEEEEEeecCCCCCCCccccc
Q 001276 304 SVVPGGPAHL--RLEPGDVLVRVNGEVITQF--LKLETLLDDGVD-KNIELLIERGGISMTVNLVVQDLHSITPDYFLEV 378 (1109)
Q Consensus 304 ~V~~~spA~~--gL~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g-~~v~l~v~R~g~~~~~~v~l~~~~~~~~~~~~~~ 378 (1109)
....++||++ .|..||.|++|||..+-.. ..-+.++...-. ..|+++|.+=--..++.|.-.+
T Consensus 679 nmm~~GpAarsgkLnIGDQiiaING~SLVGLPLstcQs~Ik~~KnQT~VkltiV~cpPV~~V~I~RPd------------ 746 (829)
T KOG3605|consen 679 NMMHGGPAARSGKLNIGDQIMSINGTSLVGLPLSTCQSIIKGLKNQTAVKLNIVSCPPVTTVLIRRPD------------ 746 (829)
T ss_pred hcccCChhhhcCCccccceeEeecCceeccccHHHHHHHHhcccccceEEEEEecCCCceEEEeeccc------------
Confidence 4567899999 5999999999999977653 233344433222 3477776654333333222111
Q ss_pred cceEEecCCHHHhhccCCCC-CeEEEE-cCCChhHHcCCCCCCEEEEcCCeecCCH--HHHHHHHHh
Q 001276 379 SGAVIHPLSYQQARNFRFPC-GLVYVA-EPGYMLFRAGVPRHAIIKKFAGEEISRL--EDLISVLSK 441 (1109)
Q Consensus 379 ~G~~~~~l~~~~~~~~~~~~-~gv~v~-~pg~~a~~aGl~~GD~I~~Vng~~v~~l--~~~~~~i~~ 441 (1109)
+.|| +||.+ .||+.+ ..|+-|++.|+++|-+|++|||+.|--. +..++.|..
T Consensus 747 -------~kyQ----LGFSVQNGiICSLlRGGIAERGGVRVGHRIIEINgQSVVA~pHekIV~lLs~ 802 (829)
T KOG3605|consen 747 -------LRYQ----LGFSVQNGIICSLLRGGIAERGGVRVGHRIIEINGQSVVATPHEKIVQLLSN 802 (829)
T ss_pred -------chhh----ccceeeCcEeehhhcccchhccCceeeeeEEEECCceEEeccHHHHHHHHHH
Confidence 1122 23333 477666 3899999999999999999999988433 456666655
No 76
>KOG3553 consensus Tax interaction protein TIP1 [Cell wall/membrane/envelope biogenesis]
Probab=97.16 E-value=0.00035 Score=62.75 Aligned_cols=57 Identities=28% Similarity=0.394 Sum_probs=43.6
Q ss_pred CcEEEEEecCCChhhhcCCCCCCeEEEECCeeCC--CHHHHHHHHHhCCCCceEEEEEEEeCC
Q 001276 1008 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTP--DLEAFVNVTKEIEHGEFVRVRTVHLNG 1068 (1109)
Q Consensus 1008 ~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~--~l~~f~~~l~~~~~~~~v~l~~v~rdg 1068 (1109)
.|+||++|.+||||+.+||+.+|.|+.|||.... +-+..++.+++ ++-+++. |.|.+
T Consensus 59 ~GiYvT~V~eGsPA~~AGLrihDKIlQvNG~DfTMvTHd~Avk~i~k---~~vl~mL-VaR~~ 117 (124)
T KOG3553|consen 59 KGIYVTRVSEGSPAEIAGLRIHDKILQVNGWDFTMVTHDQAVKRITK---EEVLRML-VARQS 117 (124)
T ss_pred ccEEEEEeccCChhhhhcceecceEEEecCceeEEEEhHHHHHHhhH---hHHHHHH-HHhhc
Confidence 4999999999999999999999999999998754 44666666665 4444443 44444
No 77
>KOG3605 consensus Beta amyloid precursor-binding protein [General function prediction only]
Probab=97.15 E-value=0.00064 Score=79.75 Aligned_cols=120 Identities=20% Similarity=0.327 Sum_probs=78.4
Q ss_pred EEeecCCCHHhhh--ccCCCEEEEECCEEcCC--hhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeeeecCCCCc
Q 001276 904 VKGCLAGSKAENM--LEQGDMMLAINKQPVTC--FHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGNGT 979 (1109)
Q Consensus 904 V~~V~~~spA~~a--L~~GDiIlsVnG~~V~~--~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~l~~~~~~~t 979 (1109)
+.....++||+.. |.-||.|++|||...-. .+.-+.++...+.. ..|+|+|++=--..++.|
T Consensus 677 iAnmm~~GpAarsgkLnIGDQiiaING~SLVGLPLstcQs~Ik~~KnQ----T~VkltiV~cpPV~~V~I---------- 742 (829)
T KOG3605|consen 677 IANMMHGGPAARSGKLNIGDQIMSINGTSLVGLPLSTCQSIIKGLKNQ----TAVKLNIVSCPPVTTVLI---------- 742 (829)
T ss_pred HHhcccCChhhhcCCccccceeEeecCceeccccHHHHHHHHhccccc----ceEEEEEecCCCceEEEe----------
Confidence 3455678899976 99999999999987754 33334555444443 678888887443334433
Q ss_pred ceEEeecCccccCCchhhhhccCCCCCCCcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCH--HHHHHHHHh
Q 001276 980 TRVINWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKE 1052 (1109)
Q Consensus 980 ~~~~~~~G~~~~~p~~~~r~~~~lp~~~~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~l~~ 1052 (1109)
.+|+ ...|++|-- ..||++ ....|+-|++-|++.|-+|++|||+.|--. +-++++|..
T Consensus 743 -----------~RPd-~kyQLGFSV--QNGiIC-SLlRGGIAERGGVRVGHRIIEINgQSVVA~pHekIV~lLs~ 802 (829)
T KOG3605|consen 743 -----------RRPD-LRYQLGFSV--QNGIIC-SLLRGGIAERGGVRVGHRIIEINGQSVVATPHEKIVQLLSN 802 (829)
T ss_pred -----------eccc-chhhcccee--eCcEee-hhhcccchhccCceeeeeEEEECCceEEeccHHHHHHHHHH
Confidence 2222 112233221 126654 578999999999999999999999986432 555666554
No 78
>COG3480 SdrC Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms]
Probab=97.14 E-value=0.0013 Score=71.79 Aligned_cols=71 Identities=24% Similarity=0.349 Sum_probs=63.0
Q ss_pred CCceEEEEEecCCCccccCCCCCCEEEEECCEEeCChhHHHHHHh-cCCCCeEEEEEEE-CCEEEEEEEEeecC
Q 001276 296 ETGLLVVDSVVPGGPAHLRLEPGDVLVRVNGEVITQFLKLETLLD-DGVDKNIELLIER-GGISMTVNLVVQDL 367 (1109)
Q Consensus 296 ~~G~lVv~~V~~~spA~~gL~~GD~Il~VnG~~v~~~~~l~~~l~-~~~g~~v~l~v~R-~g~~~~~~v~l~~~ 367 (1109)
-.|++++ .|..++||...|+.||.|++|||+++.+..++.+.+. ..+|++|+|++.| +++....++++...
T Consensus 129 y~gvyv~-~v~~~~~~~gkl~~gD~i~avdg~~f~s~~e~i~~v~~~k~Gd~VtI~~~r~~~~~~~~~~tl~~~ 201 (342)
T COG3480 129 YAGVYVL-SVIDNSPFKGKLEAGDTIIAVDGEPFTSSDELIDYVSSKKPGDEVTIDYERHNETPEIVTITLIKN 201 (342)
T ss_pred EeeEEEE-EccCCcchhceeccCCeEEeeCCeecCCHHHHHHHHhccCCCCeEEEEEEeccCCCceEEEEEEee
Confidence 4799996 8999999999999999999999999999999999885 5899999999997 77777788877655
No 79
>KOG3129 consensus 26S proteasome regulatory complex, subunit PSMD9 [Posttranslational modification, protein turnover, chaperones]
Probab=97.13 E-value=0.0012 Score=67.85 Aligned_cols=73 Identities=27% Similarity=0.445 Sum_probs=62.2
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHH---HHhcCCCCeEEEEEEECCEEEEEEEEeecCCC
Q 001276 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLET---LLDDGVDKNIELLIERGGISMTVNLVVQDLHS 369 (1109)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~---~l~~~~g~~v~l~v~R~g~~~~~~v~l~~~~~ 369 (1109)
.-+.+|..|.|+|||+. ||+.||.|+++....--+|..|.. ....+.++.+.++|.|.|+...+.++...|..
T Consensus 138 ~~Fa~V~sV~~~SPA~~aGl~~gD~il~fGnV~sgn~~~lq~i~~~v~~~e~~~v~v~v~R~g~~v~L~ltP~~W~G 214 (231)
T KOG3129|consen 138 RPFAVVDSVVPGSPADEAGLCVGDEILKFGNVHSGNFLPLQNIAAVVQSNEDQIVSVTVIREGQKVVLSLTPKKWQG 214 (231)
T ss_pred cceEEEeecCCCChhhhhCcccCceEEEecccccccchhHHHHHHHHHhccCcceeEEEecCCCEEEEEeCcccccC
Confidence 45677899999999999 999999999999888888776664 33668889999999999999999888877753
No 80
>PRK09681 putative type II secretion protein GspC; Provisional
Probab=97.12 E-value=0.0017 Score=71.38 Aligned_cols=68 Identities=21% Similarity=0.350 Sum_probs=53.5
Q ss_pred CCceEEEEEecCCCcc---cc-CCCCCCEEEEECCEEeCChhHHHHHHhc-CCCCeEEEEEEECCEEEEEEEEe
Q 001276 296 ETGLLVVDSVVPGGPA---HL-RLEPGDVLVRVNGEVITQFLKLETLLDD-GVDKNIELLIERGGISMTVNLVV 364 (1109)
Q Consensus 296 ~~G~lVv~~V~~~spA---~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~-~~g~~v~l~v~R~g~~~~~~v~l 364 (1109)
+.| ++==.+.|+..+ .+ |||+||++++|||.++++..+...++.. +....++|+|+|+|+.+++.+.+
T Consensus 203 ~~G-l~GYrl~Pgkd~~lF~~~GLq~GDva~sING~dL~D~~qa~~l~~~L~~~tei~ltVeRdGq~~~i~i~l 275 (276)
T PRK09681 203 KEG-IVGYAVKPGADRSLFDASGFKEGDIAIALNQQDFTDPRAMIALMRQLPSMDSIQLTVLRKGARHDISIAL 275 (276)
T ss_pred eCC-ceEEEECCCCcHHHHHHcCCCCCCEEEEeCCeeCCCHHHHHHHHHHhccCCeEEEEEEECCEEEEEEEEc
Confidence 345 432245576544 34 9999999999999999999988888754 66678999999999999988765
No 81
>PRK09681 putative type II secretion protein GspC; Provisional
Probab=97.05 E-value=0.0017 Score=71.24 Aligned_cols=62 Identities=18% Similarity=0.345 Sum_probs=51.8
Q ss_pred eecCCC---HHhhh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEee
Q 001276 906 GCLAGS---KAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGT 971 (1109)
Q Consensus 906 ~V~~~s---pA~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~l 971 (1109)
++.|+. -...+ ||+||++++|||..+++.++...+++.+... ..++++|.|+|+..++.+.+
T Consensus 210 rl~Pgkd~~lF~~~GLq~GDva~sING~dL~D~~qa~~l~~~L~~~----tei~ltVeRdGq~~~i~i~l 275 (276)
T PRK09681 210 AVKPGADRSLFDASGFKEGDIAIALNQQDFTDPRAMIALMRQLPSM----DSIQLTVLRKGARHDISIAL 275 (276)
T ss_pred EECCCCcHHHHHHcCCCCCCEEEEeCCeeCCCHHHHHHHHHHhccC----CeEEEEEEECCEEEEEEEEc
Confidence 445654 34466 9999999999999999999988888777765 88999999999999988754
No 82
>COG3480 SdrC Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms]
Probab=97.00 E-value=0.0021 Score=70.30 Aligned_cols=69 Identities=22% Similarity=0.335 Sum_probs=61.2
Q ss_pred CcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEEEEeCCeEEEEEEee
Q 001276 1008 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQ 1077 (1109)
Q Consensus 1008 ~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i~lk~ 1077 (1109)
.|||+..+..+|||..- |.+||.|++|||+++.+.++|...++..+.|+.|+|.+-+.++.+...+++.
T Consensus 130 ~gvyv~~v~~~~~~~gk-l~~gD~i~avdg~~f~s~~e~i~~v~~~k~Gd~VtI~~~r~~~~~~~~~~tl 198 (342)
T COG3480 130 AGVYVLSVIDNSPFKGK-LEAGDTIIAVDGEPFTSSDELIDYVSSKKPGDEVTIDYERHNETPEIVTITL 198 (342)
T ss_pred eeEEEEEccCCcchhce-eccCCeEEeeCCeecCCHHHHHHHHhccCCCCeEEEEEEeccCCCceEEEEE
Confidence 59999999999999864 9999999999999999999999999999999999999544588887666554
No 83
>PRK11186 carboxy-terminal protease; Provisional
Probab=96.97 E-value=0.0022 Score=79.28 Aligned_cols=69 Identities=28% Similarity=0.364 Sum_probs=55.9
Q ss_pred cEEEEEecCCChhhhc-CCCCCCeEEEEC--CeeCCC-----HHHHHHHHHhCCCCceEEEEEEEe---CCeEEEEEEee
Q 001276 1009 GVYVARWCHGSPVHRY-GLYALQWIVEIN--GKRTPD-----LEAFVNVTKEIEHGEFVRVRTVHL---NGKPRVLTLKQ 1077 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~-GL~~gD~I~~VN--g~~v~~-----l~~f~~~l~~~~~~~~v~l~~v~r---dg~~~~i~lk~ 1077 (1109)
+++|..+.+||||+++ ||++||+|++|| |+++.+ +++..+.++. +.|+.|+|+ +.| ++.++.++|.-
T Consensus 256 ~~~V~~vipGsPA~ka~gLk~GD~IlaVn~~g~~~~dv~g~~~~~vv~lirG-~~Gt~V~Lt-V~r~~~~~~~~~vtl~R 333 (667)
T PRK11186 256 YTVINSLVAGGPAAKSKKLSVGDKIVGVGQDGKPIVDVIGWRLDDVVALIKG-PKGSKVRLE-ILPAGKGTKTRIVTLTR 333 (667)
T ss_pred eEEEEEccCCChHHHhCCCCCCCEEEEECCCCCcccccccCCHHHHHHHhcC-CCCCEEEEE-EEeCCCCCceEEEEEEe
Confidence 5789999999999998 999999999999 555443 4688888887 679999999 666 45677777765
Q ss_pred CC
Q 001276 1078 DL 1079 (1109)
Q Consensus 1078 ~~ 1079 (1109)
+.
T Consensus 334 ~~ 335 (667)
T PRK11186 334 DK 335 (667)
T ss_pred ee
Confidence 54
No 84
>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=96.95 E-value=0.012 Score=63.31 Aligned_cols=94 Identities=21% Similarity=0.230 Sum_probs=62.5
Q ss_pred ceeeEEEEEEEeeCCceEEEEeCceecCC-CCcEEEEeecC--------CeEEeEEEEEeeC-------CCcEEEEEECC
Q 001276 648 QHFFGTGVIIYHSQSMGLVVVDKNTVAIS-ASDVMLSFAAF--------PIEIPGEVVFLHP-------VHNFALIAYDP 711 (1109)
Q Consensus 648 ~~~~GsG~VId~~~~~G~IlTn~~~V~~~-~~di~V~~~d~--------~~~~~a~vv~~dp-------~~dlAilk~d~ 711 (1109)
....++|.+|+ +.+|||.+|.+... ...+.|.+... ...+..+-+..|| ..|+|||+++.
T Consensus 23 ~~~~C~GtlIs----~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp~y~~~~~~~DiAll~L~~ 98 (232)
T cd00190 23 GRHFCGGSLIS----PRWVLTAAHCVYSSAPSNYTVRLGSHDLSSNEGGGQVIKVKKVIVHPNYNPSTYDNDIALLKLKR 98 (232)
T ss_pred CcEEEEEEEee----CCEEEECHHhcCCCCCccEEEEeCcccccCCCCceEEEEEEEEEECCCCCCCCCcCCEEEEEECC
Confidence 34679999999 67999998877653 23455555421 2234455566675 57999999975
Q ss_pred CCCCcccccceeceecCCCc-cCCCCCeEEEEeeCCCC
Q 001276 712 SSLGVAGASVVRAAELLPEP-ALRRGDSVYLVGLSRSL 748 (1109)
Q Consensus 712 ~~l~~~~~~~v~~~~l~~~~-~l~~G~~V~~iG~p~~~ 748 (1109)
..-.. ..+.++.|.... .+..|+.+.++|+....
T Consensus 99 ~~~~~---~~v~picl~~~~~~~~~~~~~~~~G~g~~~ 133 (232)
T cd00190 99 PVTLS---DNVRPICLPSSGYNLPAGTTCTVSGWGRTS 133 (232)
T ss_pred cccCC---CcccceECCCccccCCCCCEEEEEeCCcCC
Confidence 42211 345666775542 47889999999986543
No 85
>COG3975 Predicted protease with the C-terminal PDZ domain [General function prediction only]
Probab=96.91 E-value=0.0013 Score=76.47 Aligned_cols=86 Identities=30% Similarity=0.394 Sum_probs=67.5
Q ss_pred cceEEEEcChhHHHHcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHH-h
Q 001276 263 LQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLL-D 340 (1109)
Q Consensus 263 lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l-~ 340 (1109)
.|+.+..++.. .-.||+.- .++.|..+|..|.++|||++ ||.+||.|++|||. ...+ +
T Consensus 439 ~gL~~~~~~~~-~~~LGl~v-----------~~~~g~~~i~~V~~~gPA~~AGl~~Gd~ivai~G~--------s~~l~~ 498 (558)
T COG3975 439 FGLTFTPKPRE-AYYLGLKV-----------KSEGGHEKITFVFPGGPAYKAGLSPGDKIVAINGI--------SDQLDR 498 (558)
T ss_pred cceEEEecCCC-CcccceEe-----------cccCCeeEEEecCCCChhHhccCCCccEEEEEcCc--------cccccc
Confidence 67777777654 44577651 14567777789999999999 99999999999999 2233 4
Q ss_pred cCCCCeEEEEEEECCEEEEEEEEeecCC
Q 001276 341 DGVDKNIELLIERGGISMTVNLVVQDLH 368 (1109)
Q Consensus 341 ~~~g~~v~l~v~R~g~~~~~~v~l~~~~ 368 (1109)
..+++.+++++.|.|+.+++.+++....
T Consensus 499 ~~~~d~i~v~~~~~~~L~e~~v~~~~~~ 526 (558)
T COG3975 499 YKVNDKIQVHVFREGRLREFLVKLGGDP 526 (558)
T ss_pred cccccceEEEEccCCceEEeecccCCCc
Confidence 5788999999999999999988776543
No 86
>PRK11186 carboxy-terminal protease; Provisional
Probab=96.89 E-value=0.0026 Score=78.68 Aligned_cols=66 Identities=29% Similarity=0.423 Sum_probs=49.3
Q ss_pred ceEEEEEecCCCcccc--CCCCCCEEEEEC--CEEeCC-----hhHHHHHHhcCCCCeEEEEEEEC---CEEEEEEEE
Q 001276 298 GLLVVDSVVPGGPAHL--RLEPGDVLVRVN--GEVITQ-----FLKLETLLDDGVDKNIELLIERG---GISMTVNLV 363 (1109)
Q Consensus 298 G~lVv~~V~~~spA~~--gL~~GD~Il~Vn--G~~v~~-----~~~l~~~l~~~~g~~v~l~v~R~---g~~~~~~v~ 363 (1109)
+.++|..|.|||||++ ||++||+|++|| |+++.+ ..++..++....|..|.|+|.|+ ++..++++.
T Consensus 255 ~~~~V~~vipGsPA~ka~gLk~GD~IlaVn~~g~~~~dv~g~~~~~vv~lirG~~Gt~V~LtV~r~~~~~~~~~vtl~ 332 (667)
T PRK11186 255 DYTVINSLVAGGPAAKSKKLSVGDKIVGVGQDGKPIVDVIGWRLDDVVALIKGPKGSKVRLEILPAGKGTKTRIVTLT 332 (667)
T ss_pred CeEEEEEccCCChHHHhCCCCCCCEEEEECCCCCcccccccCCHHHHHHHhcCCCCCEEEEEEEeCCCCCceEEEEEE
Confidence 3355579999999998 899999999999 554433 23566677777899999999984 445555554
No 87
>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=96.81 E-value=0.017 Score=62.06 Aligned_cols=176 Identities=11% Similarity=0.082 Sum_probs=86.8
Q ss_pred cccccEEEEEEEcCcccccCCcccceeeEEEEEEEeeCCceEEEEeCceecCCCCcEEEEeecCCeEEeEE---E--EEe
Q 001276 624 VIEPTLVMFEVHVPPSCMIDGVHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGE---V--VFL 698 (1109)
Q Consensus 624 ~~~~SvV~V~~~~~~~~~~dg~~~~~~~GsG~VId~~~~~G~IlTn~~~V~~~~~di~V~~~d~~~~~~a~---v--v~~ 698 (1109)
-+...++.++.... .....=.|+... .+|+||+|....+...++|...- |.- ... - +.-
T Consensus 15 ~Ia~~ic~l~n~s~---------~~~~~l~gigyG-----~~iItn~HLf~~nng~L~i~s~h-G~f-~v~nt~~lkv~~ 78 (235)
T PF00863_consen 15 PIASNICRLTNESD---------GGTRSLYGIGYG-----SYIITNAHLFKRNNGELTIKSQH-GEF-TVPNTTQLKVHP 78 (235)
T ss_dssp HHHTTEEEEEEEET---------TEEEEEEEEEET-----TEEEEEGGGGSSTTCEEEEEETT-EEE-EECEGGGSEEEE
T ss_pred hhhheEEEEEEEeC---------CCeEEEEEEeEC-----CEEEEChhhhccCCCeEEEEeCc-eEE-EcCCccccceEE
Confidence 35667787765543 122334455554 49999988877777778777764 432 111 1 222
Q ss_pred eCCCcEEEEEECCCCCCcccccceeceecCCCccCCCCCeEEEEeeCCCCcceeeeeeEeccccccccCCCCCCcccccc
Q 001276 699 HPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRAMN 778 (1109)
Q Consensus 699 dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~iG~p~~~~~~~~~~~vt~i~~~~~i~~~~~~~y~~~~ 778 (1109)
=+..|+.|++.. +++|+ --+-++|. ..+.||.|..||..+..... ..+||+.+ .+.+......+
T Consensus 79 i~~~DiviirmP-kDfpP----f~~kl~FR---~P~~~e~v~mVg~~fq~k~~--~s~vSesS--~i~p~~~~~fW---- 142 (235)
T PF00863_consen 79 IEGRDIVIIRMP-KDFPP----FPQKLKFR---APKEGERVCMVGSNFQEKSI--SSTVSESS--WIYPEENSHFW---- 142 (235)
T ss_dssp -TCSSEEEEE---TTS--------S---B-------TT-EEEEEEEECSSCCC--EEEEEEEE--EEEEETTTTEE----
T ss_pred eCCccEEEEeCC-cccCC----cchhhhcc---CCCCCCEEEEEEEEEEcCCe--eEEECCce--EEeecCCCCee----
Confidence 346799999974 34443 00113342 25899999999987644321 33333211 11111111111
Q ss_pred eeEEEEecccCCCCCceEEcCC-eeEEEEEeeccccccccCCCCCCceeEecccHHHHHHHHHHH
Q 001276 779 MEVIELDTDFGSTFSGVLTDEH-GRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLDKI 842 (1109)
Q Consensus 779 ~~~I~~d~~ig~~sGGpL~d~~-G~VvGi~~~~~~~~~~g~~~~~~~~~~~aipi~~i~~~l~~l 842 (1109)
.-.+++.-|. ||.||++.. |.+|||.+.... ....+|+-++|-+.+..+++..
T Consensus 143 --kHwIsTk~G~-CG~PlVs~~Dg~IVGiHsl~~~--------~~~~N~F~~f~~~f~~~~l~~~ 196 (235)
T PF00863_consen 143 --KHWISTKDGD-CGLPLVSTKDGKIVGIHSLTSN--------TSSRNYFTPFPDDFEEFYLENI 196 (235)
T ss_dssp --EE-C---TT--TT-EEEETTT--EEEEEEEEET--------TTSSEEEEE--TTHHHHHCC-C
T ss_pred --EEEecCCCCc-cCCcEEEcCCCcEEEEEcCccC--------CCCeEEEEcCCHHHHHHHhccc
Confidence 1234444466 999999865 999999876432 3456677777766666555543
No 88
>KOG3129 consensus 26S proteasome regulatory complex, subunit PSMD9 [Posttranslational modification, protein turnover, chaperones]
Probab=96.70 E-value=0.005 Score=63.36 Aligned_cols=69 Identities=23% Similarity=0.267 Sum_probs=55.8
Q ss_pred cEEEEEecCCChhhhcCCCCCCeEEEECCeeCCC---HHHHHHHHHhCCCCceEEEEEEEeCCeEEEEEEeeCC
Q 001276 1009 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPD---LEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQDL 1079 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~---l~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i~lk~~~ 1079 (1109)
-++|+.|.++|||+.+||..||.|+++..+..-+ +.....+++.. .++.+.++ +.|.|....++|.|..
T Consensus 140 Fa~V~sV~~~SPA~~aGl~~gD~il~fGnV~sgn~~~lq~i~~~v~~~-e~~~v~v~-v~R~g~~v~L~ltP~~ 211 (231)
T KOG3129|consen 140 FAVVDSVVPGSPADEAGLCVGDEILKFGNVHSGNFLPLQNIAAVVQSN-EDQIVSVT-VIREGQKVVLSLTPKK 211 (231)
T ss_pred eEEEeecCCCChhhhhCcccCceEEEecccccccchhHHHHHHHHHhc-cCcceeEE-EecCCCEEEEEeCccc
Confidence 4689999999999999999999999976555444 45555666664 58889999 8999999988888743
No 89
>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=96.68 E-value=0.023 Score=61.31 Aligned_cols=93 Identities=22% Similarity=0.275 Sum_probs=63.7
Q ss_pred ceeeEEEEEEEeeCCceEEEEeCceecCCC-CcEEEEeecCC-------eEEeEEEEEeeC-------CCcEEEEEECCC
Q 001276 648 QHFFGTGVIIYHSQSMGLVVVDKNTVAISA-SDVMLSFAAFP-------IEIPGEVVFLHP-------VHNFALIAYDPS 712 (1109)
Q Consensus 648 ~~~~GsG~VId~~~~~G~IlTn~~~V~~~~-~di~V~~~d~~-------~~~~a~vv~~dp-------~~dlAilk~d~~ 712 (1109)
....++|.+|+ +.+|||.+|.+.... ..+.|.+.... ......-+..|| .+|+|||+++..
T Consensus 24 ~~~~C~GtlIs----~~~VLTaahC~~~~~~~~~~v~~g~~~~~~~~~~~~~~v~~~~~~p~~~~~~~~~DiAll~L~~~ 99 (229)
T smart00020 24 GRHFCGGSLIS----PRWVLTAAHCVYGSDPSNIRVRLGSHDLSSGEEGQVIKVSKVIIHPNYNPSTYDNDIALLKLKSP 99 (229)
T ss_pred CCcEEEEEEec----CCEEEECHHHcCCCCCcceEEEeCcccCCCCCCceEEeeEEEEECCCCCCCCCcCCEEEEEECcc
Confidence 35679999999 779999988776553 56777776522 334445455554 579999999654
Q ss_pred -CCCcccccceeceecCCC-ccCCCCCeEEEEeeCCCC
Q 001276 713 -SLGVAGASVVRAAELLPE-PALRRGDSVYLVGLSRSL 748 (1109)
Q Consensus 713 -~l~~~~~~~v~~~~l~~~-~~l~~G~~V~~iG~p~~~ 748 (1109)
.+. ..++++.|... ..+..|+.+.+.|+....
T Consensus 100 i~~~----~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~ 133 (229)
T smart00020 100 VTLS----DNVRPICLPSSNYNVPAGTTCTVSGWGRTS 133 (229)
T ss_pred cCCC----CceeeccCCCcccccCCCCEEEEEeCCCCC
Confidence 232 24556666543 236789999999987654
No 90
>COG3031 PulC Type II secretory pathway, component PulC [Intracellular trafficking and secretion]
Probab=96.39 E-value=0.0074 Score=63.36 Aligned_cols=66 Identities=27% Similarity=0.334 Sum_probs=54.8
Q ss_pred eEEEEeecCCCHHhhh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEe
Q 001276 901 VLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVG 970 (1109)
Q Consensus 901 ~~~V~~V~~~spA~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~l~v~ 970 (1109)
|+.+.-...++..++. ||.||+.+++|+..+++.+++..+++.+..- ..+.++|.|+|+..++.|.
T Consensus 208 Gyr~~pgkd~slF~~sglq~GDIavaiNnldltdp~~m~~llq~l~~m----~s~qlTv~R~G~rhdInV~ 274 (275)
T COG3031 208 GYRFEPGKDGSLFYKSGLQRGDIAVAINNLDLTDPEDMFRLLQMLRNM----PSLQLTVIRRGKRHDINVR 274 (275)
T ss_pred EEEecCCCCcchhhhhcCCCcceEEEecCcccCCHHHHHHHHHhhhcC----cceEEEEEecCccceeeec
Confidence 4444444556777777 9999999999999999999999999877765 7899999999999888774
No 91
>COG3031 PulC Type II secretory pathway, component PulC [Intracellular trafficking and secretion]
Probab=96.24 E-value=0.0082 Score=63.02 Aligned_cols=62 Identities=21% Similarity=0.200 Sum_probs=51.3
Q ss_pred EEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhc-CCCCeEEEEEEECCEEEEEEEE
Q 001276 302 VDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDD-GVDKNIELLIERGGISMTVNLV 363 (1109)
Q Consensus 302 v~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~-~~g~~v~l~v~R~g~~~~~~v~ 363 (1109)
++...+++..+. |||+||+.+++|+..+++-.+...+|.. .--+.++++|.|+|+.+.+.+.
T Consensus 211 ~~pgkd~slF~~sglq~GDIavaiNnldltdp~~m~~llq~l~~m~s~qlTv~R~G~rhdInV~ 274 (275)
T COG3031 211 FEPGKDGSLFYKSGLQRGDIAVAINNLDLTDPEDMFRLLQMLRNMPSLQLTVIRRGKRHDINVR 274 (275)
T ss_pred ecCCCCcchhhhhcCCCcceEEEecCcccCCHHHHHHHHHhhhcCcceEEEEEecCccceeeec
Confidence 355556677777 9999999999999999999998888743 4456799999999999887764
No 92
>KOG3553 consensus Tax interaction protein TIP1 [Cell wall/membrane/envelope biogenesis]
Probab=95.93 E-value=0.02 Score=51.79 Aligned_cols=46 Identities=20% Similarity=0.250 Sum_probs=37.0
Q ss_pred CCCCeEEEE--cCCChhHHcCCCCCCEEEEcCCeec--CCHHHHHHHHHh
Q 001276 396 FPCGLVYVA--EPGYMLFRAGVPRHAIIKKFAGEEI--SRLEDLISVLSK 441 (1109)
Q Consensus 396 ~~~~gv~v~--~pg~~a~~aGl~~GD~I~~Vng~~v--~~l~~~~~~i~~ 441 (1109)
-+..|+||. +.||||+.|||+.+|.|++|||-.. -+-+..++.+++
T Consensus 56 ytD~GiYvT~V~eGsPA~~AGLrihDKIlQvNG~DfTMvTHd~Avk~i~k 105 (124)
T KOG3553|consen 56 YTDKGIYVTRVSEGSPAEIAGLRIHDKILQVNGWDFTMVTHDQAVKRITK 105 (124)
T ss_pred cCCccEEEEEeccCChhhhhcceecceEEEecCceeEEEEhHHHHHHhhH
Confidence 345799998 4899999999999999999999654 344666666665
No 93
>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=95.76 E-value=0.027 Score=70.26 Aligned_cols=42 Identities=19% Similarity=0.270 Sum_probs=33.5
Q ss_pred CcEEEEEEcCC-----------CcccccccCCCCCCccCCCCCEEEEEecCCC
Q 001276 117 HDFGFFRYDPS-----------AIQFLNYDEIPLAPEAACVGLEIRVVGNDSG 158 (1109)
Q Consensus 117 ~DlAlLk~~~~-----------~~~~~~l~~l~l~~~~~~~G~~V~~iG~p~g 158 (1109)
-||+|+|+=.. +.|+-+-.-++++.+.++.||.++++|||..
T Consensus 200 gDfs~fRvY~~~dg~PA~Ys~dnvP~~p~~~l~is~~G~keGD~vmv~GyPG~ 252 (698)
T PF10459_consen 200 GDFSFFRVYADKDGKPADYSKDNVPYKPKHFLKISLKGVKEGDFVMVAGYPGR 252 (698)
T ss_pred CceEEEEEEeCCCCCccccCcCCCCCCCccccccCCCCCCCCCeEEEccCCCc
Confidence 49999999322 4666555668888899999999999999944
No 94
>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=95.70 E-value=0.072 Score=57.23 Aligned_cols=116 Identities=22% Similarity=0.209 Sum_probs=58.2
Q ss_pred ccEEEEEEEeCC-CcEEEeCccccCCCCeEEEEEecCCeEEEEEEEEEcCCCcEEEEEEcCC--CcccccccCCCCCCcc
Q 001276 67 ASYATGFVVDKR-RGIILTNRHVVKPGPVVAEAMFVNREEIPVYPIYRDPVHDFGFFRYDPS--AIQFLNYDEIPLAPEA 143 (1109)
Q Consensus 67 ~~~GSGfvV~~~-~G~IlTn~HVv~~~~~~~~v~~~~~~~~~a~vv~~d~~~DlAlLk~~~~--~~~~~~l~~l~l~~~~ 143 (1109)
++.|||=++.-+ +-.|+|+.||+..+ ..++...+- .. ..-++..-|||.-.++.- ..|..++.+ +
T Consensus 111 ss~Gsggvft~~~~~vvvTAtHVlg~~--~a~v~~~g~-~~---~~tF~~~GDfA~~~~~~~~G~~P~~k~a~----~-- 178 (297)
T PF05579_consen 111 SSVGSGGVFTIGGNTVVVTATHVLGGN--TARVSGVGT-RR---MLTFKKNGDFAEADITNWPGAAPKYKFAQ----N-- 178 (297)
T ss_dssp SSEEEEEEEECTTEEEEEEEHHHCBTT--EEEEEETTE-EE---EEEEEEETTEEEEEETTS-S---B--B-T----T--
T ss_pred ecccccceEEECCeEEEEEEEEEcCCC--eEEEEecce-EE---EEEEeccCcEEEEECCCCCCCCCceeecC----C--
Confidence 456666555531 34999999999943 344444332 22 234556679999999432 222222211 0
Q ss_pred CCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCccccceeeEEEeeccCCCCCCCceecCCCcEEEEecccc
Q 001276 144 ACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSK 221 (1109)
Q Consensus 144 ~~~G~~V~~iG~p~g~~~si~~G~vs~~~~~~~~~~~~~~~~~~~~~iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~ 221 (1109)
..| .+.=.+ ..-+..|.|..- ..=+=+.+|.||+||+..+|.+||++++..
T Consensus 179 -~~G---rAyW~t---~tGvE~G~ig~~--------------------~~~~fT~~GDSGSPVVt~dg~liGVHTGSn 229 (297)
T PF05579_consen 179 -YTG---RAYWLT---STGVEPGFIGGG--------------------GAVCFTGPGDSGSPVVTEDGDLIGVHTGSN 229 (297)
T ss_dssp --SE---EEEEEE---TTEEEEEEEETT--------------------EEEESS-GGCTT-EEEETTC-EEEEEEEEE
T ss_pred -ccc---ceEEEc---ccCcccceecCc--------------------eEEEEcCCCCCCCccCcCCCCEEEEEecCC
Confidence 001 010000 011222222111 111335679999999999999999999854
No 95
>COG3975 Predicted protease with the C-terminal PDZ domain [General function prediction only]
Probab=95.70 E-value=0.017 Score=67.53 Aligned_cols=76 Identities=22% Similarity=0.242 Sum_probs=58.7
Q ss_pred eecCccccCCchhhhhccCCCCCCCcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEEE
Q 001276 984 NWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRT 1063 (1109)
Q Consensus 984 ~~~G~~~~~p~~~~r~~~~lp~~~~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~ 1063 (1109)
.|+|+.+..- .....|+.|.++|||++|||.+||.|++|||. .+.+.....|..+.+.
T Consensus 451 ~~LGl~v~~~-------------~g~~~i~~V~~~gPA~~AGl~~Gd~ivai~G~--------s~~l~~~~~~d~i~v~- 508 (558)
T COG3975 451 YYLGLKVKSE-------------GGHEKITFVFPGGPAYKAGLSPGDKIVAINGI--------SDQLDRYKVNDKIQVH- 508 (558)
T ss_pred cccceEeccc-------------CCeeEEEecCCCChhHhccCCCccEEEEEcCc--------cccccccccccceEEE-
Confidence 4778776442 23568999999999999999999999999999 2333444567888888
Q ss_pred EEeCCeEEEEEEeeCCcc
Q 001276 1064 VHLNGKPRVLTLKQDLHY 1081 (1109)
Q Consensus 1064 v~rdg~~~~i~lk~~~~y 1081 (1109)
+.+.|.-+.+.+|..-.+
T Consensus 509 ~~~~~~L~e~~v~~~~~~ 526 (558)
T COG3975 509 VFREGRLREFLVKLGGDP 526 (558)
T ss_pred EccCCceEEeecccCCCc
Confidence 777888777777776554
No 96
>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=95.34 E-value=0.18 Score=53.07 Aligned_cols=168 Identities=15% Similarity=0.078 Sum_probs=87.5
Q ss_pred CccEEEEEEEeCCCcEEEeCccccCCCCeEEEEEecCCeEEEEEEEEEcCC----------------CcEEEEEEc----
Q 001276 66 GASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYPIYRDPV----------------HDFGFFRYD---- 125 (1109)
Q Consensus 66 ~~~~GSGfvV~~~~G~IlTn~HVv~~~~~~~~v~~~~~~~~~a~vv~~d~~----------------~DlAlLk~~---- 125 (1109)
..+.||=-+++++++..--=-|.+.+......+.+.+|+.+++++....+. .-++-+.-+
T Consensus 18 ~aGiGTlTf~dp~~~~fgALGH~I~D~dt~~~~~i~~G~I~~a~I~~I~kg~~G~PGe~~G~~~~~~~~~G~I~~Nt~~G 97 (218)
T PF05580_consen 18 TAGIGTLTFYDPETGTFGALGHGISDVDTGQLIPIKNGEIYEASITSIKKGKKGQPGEKIGVFDNESNILGTIEKNTQFG 97 (218)
T ss_pred CcCeEEEEEEECCCCcEEecCCeEEcCCCCceeEecCCEEEEEEEEEEecCCCcCCceEEEEECCCCceEEEEEeccccc
Confidence 456777778887667777777888755445566777888888777555322 112222221
Q ss_pred ------CCC-cccccccCCCCC-CccCCCCCEEEEEecCCCCC-CeEEEEEEEEecCCC-CCCCCCCccccceeeEEEee
Q 001276 126 ------PSA-IQFLNYDEIPLA-PEAACVGLEIRVVGNDSGEK-VSILAGTLARLDRDA-PHYKKDGYNDFNTFYMQAAS 195 (1109)
Q Consensus 126 ------~~~-~~~~~l~~l~l~-~~~~~~G~~V~~iG~p~g~~-~si~~G~vs~~~~~~-~~~~~~~~~~~~~~~iq~~a 195 (1109)
... .....-.++|++ .+.+++|..-.. --=.|.. -.... .|..+.++. +.....-+.-...+++....
T Consensus 98 I~G~~~~~~~~~~~~~~~~pva~~~evk~G~A~i~-Tv~~G~~ie~f~i-eI~~v~~~~~~~~k~~vi~vtd~~Ll~~TG 175 (218)
T PF05580_consen 98 IYGTLDQDDISNPSYNEPIPVAPKQEVKPGPAYIL-TVIDGTKIEEFDI-EIEKVLPQSSPSGKGMVIKVTDPRLLEKTG 175 (218)
T ss_pred eeEEeccccccccccCceeEEEEHHHceEccEEEE-EEEcCCeEEEeEE-EEEEEccCCCCCCCcEEEEECCcchhhhhC
Confidence 110 111122333333 456777764322 1111221 11111 222232221 11111000000112344445
Q ss_pred ccCCCCCCCceecCCCcEEEEeccccCC-CCCccccchHHHH
Q 001276 196 GTKGGSSGSPVIDWQGRAVALNAGSKSS-SASAFFLPLERVV 236 (1109)
Q Consensus 196 ~~~~G~SGgPv~n~~G~vVGi~~~~~~~-~~~~falP~~~i~ 236 (1109)
-+-.||||||++ .+|++||=++....+ ...+|.++++..+
T Consensus 176 GIvqGMSGSPI~-qdGKLiGAVthvf~~dp~~Gygi~ie~ML 216 (218)
T PF05580_consen 176 GIVQGMSGSPII-QDGKLIGAVTHVFVNDPTKGYGIFIEWML 216 (218)
T ss_pred CEEecccCCCEE-ECCEEEEEEEEEEecCCCceeeecHHHHh
Confidence 577899999998 599999998766644 5678888876554
No 97
>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=94.63 E-value=0.0096 Score=62.81 Aligned_cols=144 Identities=24% Similarity=0.298 Sum_probs=52.4
Q ss_pred CccEEEEEEEeCCCc--EEEeCccccCCCCeEEEEEecCCeEEEE---EEEEEcCCCcEEEEEEcCCCcccccccCCCCC
Q 001276 66 GASYATGFVVDKRRG--IILTNRHVVKPGPVVAEAMFVNREEIPV---YPIYRDPVHDFGFFRYDPSAIQFLNYDEIPLA 140 (1109)
Q Consensus 66 ~~~~GSGfvV~~~~G--~IlTn~HVv~~~~~~~~v~~~~~~~~~a---~vv~~d~~~DlAlLk~~~~~~~~~~l~~l~l~ 140 (1109)
..++|+. |...+| .++|++||... +... ..+.+++.++. +.++.+...|++||+..+.-...+....+.|.
T Consensus 28 hvGya~c--v~l~~g~~~L~ta~Hv~~~-~~~~-~~~k~g~kipl~~f~~~~~~~~~D~~il~~P~n~~s~Lg~k~~~~~ 103 (203)
T PF02122_consen 28 HVGYATC--VRLFDGEDALLTARHVWSR-PSKV-TSLKTGEKIPLAEFTDLLESRIADFVILRGPPNWESKLGVKAAQLS 103 (203)
T ss_dssp ------E--EEE----EEEEE-HHHHTS-SS----EEETTEEEE--S-EEEEE-TTT-EEEEE--HHHHHHHT-----B-
T ss_pred ccccceE--EECcCCccceecccccCCC-ccce-eEcCCCCcccchhChhhhCCCccCEEEEecCcCHHHHhCccccccc
Confidence 3455555 432245 99999999995 4433 34456666554 46677899999999998431111222222221
Q ss_pred C-ccCCCCCEEEEEecCCCCCCeEEEE-EEEEecCCCCCCCCCCccccceeeEEEeeccCCCCCCCceecCCCcEEEEec
Q 001276 141 P-EAACVGLEIRVVGNDSGEKVSILAG-TLARLDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNA 218 (1109)
Q Consensus 141 ~-~~~~~G~~V~~iG~p~g~~~si~~G-~vs~~~~~~~~~~~~~~~~~~~~~iq~~a~~~~G~SGgPv~n~~G~vVGi~~ 218 (1109)
. ..+..| .+..+ ....+ ..+.-.. ++. -.+ .++..-+...+|.||.|.++.+ +++|++.
T Consensus 104 ~~~~~~~g----~~~~y-----~~~~~~~~~~sa~-i~g-----~~~---~~~~vls~T~~G~SGtp~y~g~-~vvGvH~ 164 (203)
T PF02122_consen 104 QNSQLAKG----PVSFY-----GFSSGEWPCSSAK-IPG-----TEG---KFASVLSNTSPGWSGTPYYSGK-NVVGVHT 164 (203)
T ss_dssp ---SEEEE----ESSTT-----SEEEEEEEEEE-S----------ST---TEEEE-----TT-TT-EEE-SS--EEEEEE
T ss_pred chhhhCCC----Ceeee-----eecCCCceeccCc-ccc-----ccC---cCCceEcCCCCCCCCCCeEECC-CceEeec
Confidence 1 110000 01111 11121 1111111 111 111 1477888999999999999998 9999999
Q ss_pred cc---cCCCCCccccch
Q 001276 219 GS---KSSSASAFFLPL 232 (1109)
Q Consensus 219 ~~---~~~~~~~falP~ 232 (1109)
+. ....+.++.-|+
T Consensus 165 G~~~~~~~~n~n~~spi 181 (203)
T PF02122_consen 165 GSPSGSNRENNNRMSPI 181 (203)
T ss_dssp EE---------------
T ss_pred Ccccccccccccccccc
Confidence 84 333455554444
No 98
>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=94.57 E-value=0.037 Score=69.03 Aligned_cols=53 Identities=25% Similarity=0.369 Sum_probs=40.6
Q ss_pred EEEeeccCCCCCCCceecCCCcEEEEeccccCC-----------CCCccccchHHHHHHHHHHH
Q 001276 191 MQAASGTKGGSSGSPVIDWQGRAVALNAGSKSS-----------SASAFFLPLERVVRALRFLQ 243 (1109)
Q Consensus 191 iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~-----------~~~~falP~~~i~~~l~~l~ 243 (1109)
+.++..+.+|||||||+|.+|++|||+.-+.-. ...+..+-+..|+.+|+++-
T Consensus 624 FlstnDitGGNSGSPvlN~~GeLVGl~FDgn~Esl~~D~~fdp~~~R~I~VDiRyvL~~ldkv~ 687 (698)
T PF10459_consen 624 FLSTNDITGGNSGSPVLNAKGELVGLAFDGNWESLSGDIAFDPELNRTIHVDIRYVLWALDKVY 687 (698)
T ss_pred EEeccCcCCCCCCCccCCCCceEEEEeecCchhhcccccccccccceeEEEEHHHHHHHHHHHh
Confidence 577888999999999999999999999654321 22344577778888887764
No 99
>KOG3532 consensus Predicted protein kinase [General function prediction only]
Probab=94.33 E-value=0.097 Score=62.25 Aligned_cols=51 Identities=24% Similarity=0.266 Sum_probs=43.9
Q ss_pred CCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCC
Q 001276 295 GETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDK 345 (1109)
Q Consensus 295 ~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~ 345 (1109)
+...++-|..|++++||.+ .|++||++++|||.+|++..+....+....|+
T Consensus 395 ~~~~~v~v~tv~~ns~a~k~~~~~gdvlvai~~~pi~s~~q~~~~~~s~~~~ 446 (1051)
T KOG3532|consen 395 NTNRAVKVCTVEDNSLADKAAFKPGDVLVAINNVPIRSERQATRFLQSTTGD 446 (1051)
T ss_pred CCceEEEEEEecCCChhhHhcCCCcceEEEecCccchhHHHHHHHHHhcccc
Confidence 3455666789999999999 99999999999999999999888888776554
No 100
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=94.07 E-value=0.93 Score=49.47 Aligned_cols=167 Identities=11% Similarity=0.022 Sum_probs=84.5
Q ss_pred eEEEEEEEeeCCceEEEEeCceecCCC-C-cEEEEeecCCe--------EEeEEEEEeeC----CCcEEEEEECCCCCC-
Q 001276 651 FGTGVIIYHSQSMGLVVVDKNTVAISA-S-DVMLSFAAFPI--------EIPGEVVFLHP----VHNFALIAYDPSSLG- 715 (1109)
Q Consensus 651 ~GsG~VId~~~~~G~IlTn~~~V~~~~-~-di~V~~~d~~~--------~~~a~vv~~dp----~~dlAilk~d~~~l~- 715 (1109)
..++|+|. +-.+||+.|++.... . +....+.. ++ .+.....+..+ ..|.+...+.+..+.
T Consensus 65 ~~~~~lI~----pntvLTa~Hc~~s~~~G~~~~~~~p~-g~~~~~~~~~~~~~~~~~~~~g~~~~~d~~~~~v~~~~~~~ 139 (251)
T COG3591 65 CTAATLIG----PNTVLTAGHCIYSPDYGEDDIAAAPP-GVNSDGGPFYGITKIEIRVYPGELYKEDGASYDVGEAALES 139 (251)
T ss_pred eeeEEEEc----CceEEEeeeEEecCCCChhhhhhcCC-cccCCCCCCCceeeEEEEecCCceeccCCceeeccHHHhcc
Confidence 34669999 779999977765433 1 11122211 11 12222222222 345666666544332
Q ss_pred -cccccceeceecCCCccCCCCCeEEEEeeCCCCcceeeeeeEeccccccccCCCCCCcccccceeEEEEecc--cCCCC
Q 001276 716 -VAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRAMNMEVIELDTD--FGSTF 792 (1109)
Q Consensus 716 -~~~~~~v~~~~l~~~~~l~~G~~V~~iG~p~~~~~~~~~~~vt~i~~~~~i~~~~~~~y~~~~~~~I~~d~~--ig~~s 792 (1109)
......+....+.....++.+|.+-.+|||.........-.-+ +-+ ++ .....++-|+. .|+ |
T Consensus 140 g~~~~~~~~~~~~~~~~~~~~~d~i~v~GYP~dk~~~~~~~e~t-----~~v------~~--~~~~~l~y~~dT~pG~-S 205 (251)
T COG3591 140 GINIGDVVNYLKRNTASEAKANDRITVIGYPGDKPNIGTMWEST-----GKV------NS--IKGNKLFYDADTLPGS-S 205 (251)
T ss_pred CCCccccccccccccccccccCceeEEEeccCCCCcceeEeeec-----cee------EE--EecceEEEEecccCCC-C
Confidence 1001122222333344579999999999998764211110111 000 00 11123444444 455 9
Q ss_pred CceEEcCCeeEEEEEeeccccccccCCCCCCceeE-ecccHHHHHHHHHHHH
Q 001276 793 SGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFV-RGIPIYTISRVLDKII 843 (1109)
Q Consensus 793 GGpL~d~~G~VvGi~~~~~~~~~~g~~~~~~~~~~-~aipi~~i~~~l~~l~ 843 (1109)
|.|+++.+.+|+|++...... .++..|+ ...-...++++|.++.
T Consensus 206 GSpv~~~~~~vigv~~~g~~~-------~~~~~~n~~vr~t~~~~~~I~~~~ 250 (251)
T COG3591 206 GSPVLISKDEVIGVHYNGPGA-------NGGSLANNAVRLTPEILNFIQQNI 250 (251)
T ss_pred CCceEecCceEEEEEecCCCc-------ccccccCcceEecHHHHHHHHHhh
Confidence 999999999999999875442 1112222 1233456666666553
No 101
>KOG3550 consensus Receptor targeting protein Lin-7 [Extracellular structures]
Probab=94.00 E-value=0.23 Score=48.45 Aligned_cols=54 Identities=28% Similarity=0.515 Sum_probs=40.1
Q ss_pred CceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChhHHH--HHHhcCCCCeEEEEEE
Q 001276 297 TGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFLKLE--TLLDDGVDKNIELLIE 352 (1109)
Q Consensus 297 ~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~~l~--~~l~~~~g~~v~l~v~ 352 (1109)
+-+++ +.+.||+.|+. ||+-||.+++|||..+..-.+-. ++|....| +|+|.|.
T Consensus 115 spiyi-sriipggvadrhgglkrgdqllsvngvsvege~hekavellkaa~g-svklvvr 172 (207)
T KOG3550|consen 115 SPIYI-SRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKAAVG-SVKLVVR 172 (207)
T ss_pred CceEE-EeecCCccccccCcccccceeEeecceeecchhhHHHHHHHHHhcC-cEEEEEe
Confidence 44555 89999999999 89999999999999998754433 44555544 4566553
No 102
>KOG3532 consensus Predicted protein kinase [General function prediction only]
Probab=93.65 E-value=0.14 Score=60.90 Aligned_cols=46 Identities=22% Similarity=0.324 Sum_probs=41.9
Q ss_pred ceEEEEeecCCCHHhhh-ccCCCEEEEECCEEcCChhHHHHHHHhcc
Q 001276 900 QVLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHDIENACQALD 945 (1109)
Q Consensus 900 ~~~~V~~V~~~spA~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~ 945 (1109)
+.+.|-.|.+++||.++ |++||++++|||.+|++.++....++...
T Consensus 398 ~~v~v~tv~~ns~a~k~~~~~gdvlvai~~~pi~s~~q~~~~~~s~~ 444 (1051)
T KOG3532|consen 398 RAVKVCTVEDNSLADKAAFKPGDVLVAINNVPIRSERQATRFLQSTT 444 (1051)
T ss_pred eEEEEEEecCCChhhHhcCCCcceEEEecCccchhHHHHHHHHHhcc
Confidence 67889999999999999 99999999999999999999999885443
No 103
>KOG3552 consensus FERM domain protein FRM-8 [General function prediction only]
Probab=93.54 E-value=0.074 Score=65.33 Aligned_cols=53 Identities=28% Similarity=0.547 Sum_probs=41.2
Q ss_pred EEEEEecCCCccccCCCCCCEEEEECCEEeCCh--hHHHHHHhcCCCCeEEEEEEE
Q 001276 300 LVVDSVVPGGPAHLRLEPGDVLVRVNGEVITQF--LKLETLLDDGVDKNIELLIER 353 (1109)
Q Consensus 300 lVv~~V~~~spA~~gL~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g~~v~l~v~R 353 (1109)
+||..|.+|||+..+|++||.|+.|||++|.+. +++-+++.. .-+.|.|+|.+
T Consensus 77 viVr~VT~GGps~GKL~PGDQIl~vN~Epv~daprervIdlvRa-ce~sv~ltV~q 131 (1298)
T KOG3552|consen 77 VIVRFVTEGGPSIGKLQPGDQILAVNGEPVKDAPRERVIDLVRA-CESSVNLTVCQ 131 (1298)
T ss_pred eEEEEecCCCCccccccCCCeEEEecCcccccccHHHHHHHHHH-HhhhcceEEec
Confidence 555899999999999999999999999999874 444455432 33467777766
No 104
>KOG3542 consensus cAMP-regulated guanine nucleotide exchange factor [Signal transduction mechanisms]
Probab=92.97 E-value=0.097 Score=61.97 Aligned_cols=55 Identities=25% Similarity=0.421 Sum_probs=42.8
Q ss_pred CCcEEEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCceEEEE
Q 001276 1007 GHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVR 1062 (1109)
Q Consensus 1007 ~~gV~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~v~l~ 1062 (1109)
+.|+||..|.|||.|++.||+.||.|++|||+...++.. .++..-...++.+.|+
T Consensus 561 GfgifV~~V~pgskAa~~GlKRgDqilEVNgQnfenis~-~KA~eiLrnnthLtlt 615 (1283)
T KOG3542|consen 561 GFGIFVAEVFPGSKAAREGLKRGDQILEVNGQNFENISA-KKAEEILRNNTHLTLT 615 (1283)
T ss_pred cceeEEeeecCCchHHHhhhhhhhhhhhccccchhhhhH-HHHHHHhcCCceEEEE
Confidence 348999999999999999999999999999999988753 3333333345555554
No 105
>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=92.97 E-value=0.083 Score=51.77 Aligned_cols=31 Identities=29% Similarity=0.359 Sum_probs=22.0
Q ss_pred EEEeeccCCCCCCCceecCCCcEEEEecccc
Q 001276 191 MQAASGTKGGSSGSPVIDWQGRAVALNAGSK 221 (1109)
Q Consensus 191 iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~ 221 (1109)
...+....+|+||+|+||.+|++|||...+.
T Consensus 88 ~~~~~d~~~GsSGSpi~n~~g~ivGlYg~g~ 118 (132)
T PF00949_consen 88 GAIDLDFPKGSSGSPIFNQNGEIVGLYGNGV 118 (132)
T ss_dssp EEE---S-TTGTT-EEEETTSCEEEEEEEEE
T ss_pred EeeecccCCCCCCCceEcCCCcEEEEEccce
Confidence 4445557889999999999999999986654
No 106
>KOG3550 consensus Receptor targeting protein Lin-7 [Extracellular structures]
Probab=92.71 E-value=0.27 Score=48.00 Aligned_cols=52 Identities=23% Similarity=0.286 Sum_probs=42.1
Q ss_pred cEEEEEecCCChhhhc-CCCCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEE
Q 001276 1009 GVYVARWCHGSPVHRY-GLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVR 1062 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~-GL~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~ 1062 (1109)
.+||+++.||+-|++- ||+.||.+++|||+.+..- +-.++++++. -..|+|.
T Consensus 116 piyisriipggvadrhgglkrgdqllsvngvsvege~hekavellkaa--~gsvklv 170 (207)
T KOG3550|consen 116 PIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKAA--VGSVKLV 170 (207)
T ss_pred ceEEEeecCCccccccCcccccceeEeecceeecchhhHHHHHHHHHh--cCcEEEE
Confidence 5799999999999986 7999999999999888754 6677778873 3446665
No 107
>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=92.36 E-value=1.3 Score=46.00 Aligned_cols=139 Identities=14% Similarity=0.140 Sum_probs=77.4
Q ss_pred CccEEEEEEEeCCCcEEEeCccccCCCCeEEEEEecCCeEEEEE--EEEEcCC---CcEEEEEEcCCCcccccccC-CCC
Q 001276 66 GASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVY--PIYRDPV---HDFGFFRYDPSAIQFLNYDE-IPL 139 (1109)
Q Consensus 66 ~~~~GSGfvV~~~~G~IlTn~HVv~~~~~~~~v~~~~~~~~~a~--vv~~d~~---~DlAlLk~~~~~~~~~~l~~-l~l 139 (1109)
+...++++.|- +.++|.++|.-. ...+.+ ++..++.. +...+.. .|+++++++.. -++-++.. ++
T Consensus 23 g~~t~l~~gi~--~~~~lvp~H~~~----~~~i~i-~g~~~~~~d~~~lv~~~~~~~Dl~~v~l~~~-~kfrDIrk~~~- 93 (172)
T PF00548_consen 23 GEFTMLALGIY--DRYFLVPTHEEP----EDTIYI-DGVEYKVDDSVVLVDRDGVDTDLTLVKLPRN-PKFRDIRKFFP- 93 (172)
T ss_dssp EEEEEEEEEEE--BTEEEEEGGGGG----CSEEEE-TTEEEEEEEEEEEEETTSSEEEEEEEEEESS-S-B--GGGGSB-
T ss_pred ceEEEecceEe--eeEEEEECcCCC----cEEEEE-CCEEEEeeeeEEEecCCCcceeEEEEEccCC-cccCchhhhhc-
Confidence 46678888887 459999999322 223333 35554332 3334544 59999999642 22222221 11
Q ss_pred CCccCCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCccccceeeEEEeeccCCCCCCCceec---CCCcEEEE
Q 001276 140 APEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVID---WQGRAVAL 216 (1109)
Q Consensus 140 ~~~~~~~G~~V~~iG~p~g~~~si~~G~vs~~~~~~~~~~~~~~~~~~~~~iq~~a~~~~G~SGgPv~n---~~G~vVGi 216 (1109)
.......+...++-++......+..+.+...+.- ... . ......+...+++.+|+-||||+. ..++++||
T Consensus 94 -~~~~~~~~~~l~v~~~~~~~~~~~v~~v~~~~~i-~~~-g----~~~~~~~~Y~~~t~~G~CG~~l~~~~~~~~~i~Gi 166 (172)
T PF00548_consen 94 -ESIPEYPECVLLVNSTKFPRMIVEVGFVTNFGFI-NLS-G----TTTPRSLKYKAPTKPGMCGSPLVSRIGGQGKIIGI 166 (172)
T ss_dssp -SSGGTEEEEEEEEESSSSTCEEEEEEEEEEEEEE-EET-T----EEEEEEEEEESEEETTGTTEEEEESCGGTTEEEEE
T ss_pred -cccccCCCcEEEEECCCCccEEEEEEEEeecCcc-ccC-C----CEeeEEEEEccCCCCCccCCeEEEeeccCccEEEE
Confidence 1222445555555444333334444444433321 000 0 012346888899999999999984 36889999
Q ss_pred eccc
Q 001276 217 NAGS 220 (1109)
Q Consensus 217 ~~~~ 220 (1109)
+.++
T Consensus 167 HvaG 170 (172)
T PF00548_consen 167 HVAG 170 (172)
T ss_dssp EEEE
T ss_pred Eecc
Confidence 9875
No 108
>KOG1892 consensus Actin filament-binding protein Afadin [Cytoskeleton]
Probab=92.10 E-value=0.19 Score=61.94 Aligned_cols=61 Identities=30% Similarity=0.442 Sum_probs=49.3
Q ss_pred CCCceEEEEEecCCCcccc-C-CCCCCEEEEECCEEeCChhHHH-HHHhcCCCCeEEEEEEECCE
Q 001276 295 GETGLLVVDSVVPGGPAHL-R-LEPGDVLVRVNGEVITQFLKLE-TLLDDGVDKNIELLIERGGI 356 (1109)
Q Consensus 295 ~~~G~lVv~~V~~~spA~~-g-L~~GD~Il~VnG~~v~~~~~l~-~~l~~~~g~~v~l~v~R~g~ 356 (1109)
..-|++| +.|.+|++|+. | |+.||.+++|||..+-...+-+ ..|+...|..|.+.|...|-
T Consensus 958 ~klGIYv-KsVV~GgaAd~DGRL~aGDQLLsVdG~SLiGisQErAA~lmtrtg~vV~leVaKqgA 1021 (1629)
T KOG1892|consen 958 RKLGIYV-KSVVEGGAADHDGRLEAGDQLLSVDGHSLIGISQERAARLMTRTGNVVHLEVAKQGA 1021 (1629)
T ss_pred cccceEE-EEeccCCccccccccccCceeeeecCcccccccHHHHHHHHhccCCeEEEehhhhhh
Confidence 4578888 89999999999 5 9999999999999887765544 34566778889998876543
No 109
>KOG3571 consensus Dishevelled 3 and related proteins [General function prediction only]
Probab=91.21 E-value=0.63 Score=54.17 Aligned_cols=86 Identities=20% Similarity=0.264 Sum_probs=61.7
Q ss_pred cccceEEecCCHHHhhccCCCCCeEEEEc--CCChhHHcC-CCCCCEEEEcCCeecCCH--HHHHHHHHhcCCCCeEeEE
Q 001276 377 EVSGAVIHPLSYQQARNFRFPCGLVYVAE--PGYMLFRAG-VPRHAIIKKFAGEEISRL--EDLISVLSKLSRGARVPIE 451 (1109)
Q Consensus 377 ~~~G~~~~~l~~~~~~~~~~~~~gv~v~~--pg~~a~~aG-l~~GD~I~~Vng~~v~~l--~~~~~~i~~~~~g~~v~l~ 451 (1109)
.|+|+++.--+. .-...|+||.+ ++++-+..| +.+||.|++||.....|+ ++.+++|+..-.
T Consensus 261 nfLGiSivgqsn------~rgDggIYVgsImkgGAVA~DGRIe~GDMiLQVNevsFENmSNd~AVrvLREaV~------- 327 (626)
T KOG3571|consen 261 NFLGISIVGQSN------ARGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNEVSFENMSNDQAVRVLREAVS------- 327 (626)
T ss_pred ccceeEeecccC------cCCCCceEEeeeccCceeeccCccCccceEEEeeecchhhcCchHHHHHHHHHhc-------
Confidence 567877654332 11236999995 788887777 999999999999999998 789999988643
Q ss_pred EEeecccccceEEEEEEecCCCCCCCeeeeecC
Q 001276 452 YSSYTDRHRRKSVLVTIDRHEWYAPPQIYTRND 484 (1109)
Q Consensus 452 ~~~~~~~~~~~~~~l~i~R~~~~~~~~~~~r~d 484 (1109)
+..++.+++-. .|.+..+-+.+.+
T Consensus 328 --------~~gPi~ltvAk-~~DP~~q~~fTip 351 (626)
T KOG3571|consen 328 --------RPGPIKLTVAK-CWDPNPQSYFTIP 351 (626)
T ss_pred --------cCCCeEEEEee-ccCCCCcccccCC
Confidence 23556677766 7765555554443
No 110
>KOG3542 consensus cAMP-regulated guanine nucleotide exchange factor [Signal transduction mechanisms]
Probab=91.13 E-value=0.18 Score=59.77 Aligned_cols=53 Identities=21% Similarity=0.299 Sum_probs=43.1
Q ss_pred CeEEEEc--CCChhHHcCCCCCCEEEEcCCeecCCHHHHHHHHHhcCCCCeEeEEE
Q 001276 399 GLVYVAE--PGYMLFRAGVPRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEY 452 (1109)
Q Consensus 399 ~gv~v~~--pg~~a~~aGl~~GD~I~~Vng~~v~~l~~~~~~i~~~~~g~~v~l~~ 452 (1109)
-|+||.+ ||+.|.++|||.||.|++||||...++ .+.+++.-+.+...++|++
T Consensus 562 fgifV~~V~pgskAa~~GlKRgDqilEVNgQnfeni-s~~KA~eiLrnnthLtltv 616 (1283)
T KOG3542|consen 562 FGIFVAEVFPGSKAAREGLKRGDQILEVNGQNFENI-SAKKAEEILRNNTHLTLTV 616 (1283)
T ss_pred ceeEEeeecCCchHHHhhhhhhhhhhhccccchhhh-hHHHHHHHhcCCceEEEEE
Confidence 3899985 999999999999999999999999998 5666666666655555544
No 111
>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=90.62 E-value=0.99 Score=54.79 Aligned_cols=121 Identities=19% Similarity=0.316 Sum_probs=72.6
Q ss_pred cCCCcEEEEEEcCCC---------ccccccc-CCCCC-------CccCCCCCEEEEEecCCCCCCeEEEEEEEEecCCCC
Q 001276 114 DPVHDFGFFRYDPSA---------IQFLNYD-EIPLA-------PEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAP 176 (1109)
Q Consensus 114 d~~~DlAlLk~~~~~---------~~~~~l~-~l~l~-------~~~~~~G~~V~~iG~p~g~~~si~~G~vs~~~~~~~ 176 (1109)
....|+||+++++.- +.+-... .+.+. -..+..|.+|+=+|.-.|. +.|.|.+..- .
T Consensus 540 ~~LsD~AIIkV~~~~~~~N~LGddi~f~~~dP~l~f~NlyV~~~~~~~~~G~~VfK~GrTTgy----T~G~lNg~kl-v- 613 (695)
T PF08192_consen 540 KRLSDWAIIKVNKERKCQNYLGDDIQFNEPDPTLMFQNLYVREVVSNLVPGMEVFKVGRTTGY----TTGILNGIKL-V- 613 (695)
T ss_pred ccccceEEEEeCCCceecCCCCccccccCCCccccccccchhhhhhccCCCCeEEEecccCCc----cceEecceEE-E-
Confidence 445799999998532 1100000 01111 2346789999999988776 4555544421 0
Q ss_pred CCCCCCccccceeeEEEe----eccCCCCCCCceecCCCc------EEEEeccccCC-CCCccccchHHHHHHHHHH
Q 001276 177 HYKKDGYNDFNTFYMQAA----SGTKGGSSGSPVIDWQGR------AVALNAGSKSS-SASAFFLPLERVVRALRFL 242 (1109)
Q Consensus 177 ~~~~~~~~~~~~~~iq~~----a~~~~G~SGgPv~n~~G~------vVGi~~~~~~~-~~~~falP~~~i~~~l~~l 242 (1109)
.+.. +-.. -.+++... +=..+|.||+=|++.-+. |+||..+.... ..++++.|+..|+.-|+..
T Consensus 614 yw~d-G~i~-s~efvV~s~~~~~Fa~~GDSGS~VLtk~~d~~~gLgvvGMlhsydge~kqfglftPi~~il~rl~~v 688 (695)
T PF08192_consen 614 YWAD-GKIQ-SSEFVVSSDNNPAFASGGDSGSWVLTKLEDNNKGLGVVGMLHSYDGEQKQFGLFTPINEILDRLEEV 688 (695)
T ss_pred EecC-CCeE-EEEEEEecCCCccccCCCCcccEEEecccccccCceeeEEeeecCCccceeeccCcHHHHHHHHHHh
Confidence 0111 1111 13344444 335679999999987555 99998774433 4688899999888777665
No 112
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=90.13 E-value=8 Score=43.40 Aligned_cols=109 Identities=11% Similarity=0.138 Sum_probs=58.2
Q ss_pred CCCcEEEEEEcCCCcccccccCCCCCCccCCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCccccceeeEEEe
Q 001276 115 PVHDFGFFRYDPSAIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAA 194 (1109)
Q Consensus 115 ~~~DlAlLk~~~~~~~~~~l~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~vs~~~~~~~~~~~~~~~~~~~~~iq~~ 194 (1109)
...++.||.++..........-|+=.+.....|+.+.+.|+.......-..-.+..... ....+...
T Consensus 159 ~~~~~mIlEl~~~~~~~~~~~Cl~~~~~~~~~~~~~~~yg~~~~~~~~~~~~~i~~~~~-------------~~~~~~~~ 225 (282)
T PF03761_consen 159 RPYSPMILELEEDFSKNVSPPCLADSSTNWEKGDEVDVYGFNSTGKLKHRKLKITNCTK-------------CAYSICTK 225 (282)
T ss_pred cccceEEEEEcccccccCCCEEeCCCccccccCceEEEeecCCCCeEEEEEEEEEEeec-------------cceeEecc
Confidence 34788899997661111122223323455788999999998322221111111111111 11234555
Q ss_pred eccCCCCCCCcee-cCCC--cEEEEeccccCCC--CCccccchHHHH
Q 001276 195 SGTKGGSSGSPVI-DWQG--RAVALNAGSKSSS--ASAFFLPLERVV 236 (1109)
Q Consensus 195 a~~~~G~SGgPv~-n~~G--~vVGi~~~~~~~~--~~~falP~~~i~ 236 (1109)
.....|.+|||++ +.+| .|||+.+.+.... ...+++.+...+
T Consensus 226 ~~~~~~d~Gg~lv~~~~gr~tlIGv~~~~~~~~~~~~~~f~~v~~~~ 272 (282)
T PF03761_consen 226 QYSCKGDRGGPLVKNINGRWTLIGVGASGNYECNKNNSYFFNVSWYQ 272 (282)
T ss_pred cccCCCCccCeEEEEECCCEEEEEEEccCCCcccccccEEEEHHHhh
Confidence 5667899999997 3445 4999987655332 245556555443
No 113
>KOG3571 consensus Dishevelled 3 and related proteins [General function prediction only]
Probab=89.92 E-value=0.9 Score=52.95 Aligned_cols=72 Identities=18% Similarity=0.285 Sum_probs=51.9
Q ss_pred EeecCccccCCchhhhhccCCCCCCCcEEEEEecCCChhhhcC-CCCCCeEEEECCeeCCCH--HHHHHHHHhCCCC-ce
Q 001276 983 INWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYG-LYALQWIVEINGKRTPDL--EAFVNVTKEIEHG-EF 1058 (1109)
Q Consensus 983 ~~~~G~~~~~p~~~~r~~~~lp~~~~gV~V~~v~~gSPA~~~G-L~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~-~~ 1058 (1109)
+.|+|+.+..-. ......|+||..+.+|++-+.-| +.+||.|+.||.+...++ ++.+.+|+++-.. ..
T Consensus 260 vnfLGiSivgqs--------n~rgDggIYVgsImkgGAVA~DGRIe~GDMiLQVNevsFENmSNd~AVrvLREaV~~~gP 331 (626)
T KOG3571|consen 260 VNFLGISIVGQS--------NARGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNEVSFENMSNDQAVRVLREAVSRPGP 331 (626)
T ss_pred cccceeEeeccc--------CcCCCCceEEeeeccCceeeccCccCccceEEEeeecchhhcCchHHHHHHHHHhccCCC
Confidence 457787764422 11112489999999999877766 799999999999999988 7888888875222 22
Q ss_pred EEEE
Q 001276 1059 VRVR 1062 (1109)
Q Consensus 1059 v~l~ 1062 (1109)
++|+
T Consensus 332 i~lt 335 (626)
T KOG3571|consen 332 IKLT 335 (626)
T ss_pred eEEE
Confidence 5555
No 114
>KOG3552 consensus FERM domain protein FRM-8 [General function prediction only]
Probab=89.51 E-value=0.41 Score=59.18 Aligned_cols=56 Identities=21% Similarity=0.344 Sum_probs=43.1
Q ss_pred ceEEEEeecCCCHHhhhccCCCEEEEECCEEcCC--hhHHHHHHHhccCCCCCCCeEEEEEEeC
Q 001276 900 QVLRVKGCLAGSKAENMLEQGDMMLAINKQPVTC--FHDIENACQALDKDGEDNGKLDITIFRQ 961 (1109)
Q Consensus 900 ~~~~V~~V~~~spA~~aL~~GDiIlsVnG~~V~~--~~dl~~~l~~~~~g~~~~~~v~l~V~R~ 961 (1109)
.-++|..|.+|+|+...|++||.|++|||++|.. |+.+..++..- .+.|.++|.+-
T Consensus 75 rPviVr~VT~GGps~GKL~PGDQIl~vN~Epv~daprervIdlvRac------e~sv~ltV~qP 132 (1298)
T KOG3552|consen 75 RPVIVRFVTEGGPSIGKLQPGDQILAVNGEPVKDAPRERVIDLVRAC------ESSVNLTVCQP 132 (1298)
T ss_pred CceEEEEecCCCCccccccCCCeEEEecCcccccccHHHHHHHHHHH------hhhcceEEecc
Confidence 3467999999999998899999999999999986 44444444222 25688888874
No 115
>KOG3651 consensus Protein kinase C, alpha binding protein [Signal transduction mechanisms]
Probab=87.78 E-value=0.99 Score=49.16 Aligned_cols=54 Identities=24% Similarity=0.371 Sum_probs=40.0
Q ss_pred CceEEEEEecCCCcccc-C-CCCCCEEEEECCEEeCChhHHH--HHHhcCCCCeEEEEEE
Q 001276 297 TGLLVVDSVVPGGPAHL-R-LEPGDVLVRVNGEVITQFLKLE--TLLDDGVDKNIELLIE 352 (1109)
Q Consensus 297 ~G~lVv~~V~~~spA~~-g-L~~GD~Il~VnG~~v~~~~~l~--~~l~~~~g~~v~l~v~ 352 (1109)
--++|| .|..++||++ | ++.||.|++|||..|..-..+. .++.... +.|++++.
T Consensus 30 PClYiV-QvFD~tPAa~dG~i~~GDEi~avNg~svKGktKveVAkmIQ~~~-~eV~IhyN 87 (429)
T KOG3651|consen 30 PCLYIV-QVFDKTPAAKDGRIRCGDEIVAVNGISVKGKTKVEVAKMIQVSL-NEVKIHYN 87 (429)
T ss_pred CeEEEE-EeccCCchhccCccccCCeeEEecceeecCccHHHHHHHHHHhc-cceEEEeh
Confidence 355665 9999999999 5 9999999999999998765544 4444433 35666653
No 116
>KOG0606 consensus Microtubule-associated serine/threonine kinase and related proteins [Signal transduction mechanisms; General function prediction only]
Probab=86.89 E-value=0.9 Score=57.98 Aligned_cols=51 Identities=29% Similarity=0.378 Sum_probs=44.3
Q ss_pred EEEEecCCChhhhcCCCCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEEE
Q 001276 1011 YVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRT 1063 (1109)
Q Consensus 1011 ~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~~ 1063 (1109)
.|..|..||||..+||+++|.|++|||+++..+ .++.+.+.+ .|..+.+++
T Consensus 661 ~v~sv~egsPA~~agls~~DlIthvnge~v~gl~H~ev~~Lll~--~gn~v~~~t 713 (1205)
T KOG0606|consen 661 SVGSVEEGSPAFEAGLSAGDLITHVNGEPVHGLVHTEVMELLLK--SGNKVTLRT 713 (1205)
T ss_pred eeeeecCCCCccccCCCccceeEeccCcccchhhHHHHHHHHHh--cCCeeEEEe
Confidence 689999999999999999999999999999987 577777775 477777774
No 117
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=86.63 E-value=1.9 Score=50.55 Aligned_cols=56 Identities=30% Similarity=0.509 Sum_probs=48.4
Q ss_pred EecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCe---EEEEEEE-CCEEEE
Q 001276 304 SVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKN---IELLIER-GGISMT 359 (1109)
Q Consensus 304 ~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~---v~l~v~R-~g~~~~ 359 (1109)
.+..+++|.. +|++||.++++|++++.+|.++...+....+.. +.+.+.| ++..+.
T Consensus 135 ~v~~~s~a~~a~l~~Gd~iv~~~~~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ 195 (375)
T COG0750 135 EVAPKSAAALAGLRPGDRIVAVDGEKVASWDDVRRLLVAAAGDVFNLLTILVIRLDGEAHA 195 (375)
T ss_pred ecCCCCHHHHcCCCCCCEEEeECCEEccCHHHHHHHHHhccCCcccceEEEEEeccceeee
Confidence 6889999999 999999999999999999999998887666665 7888889 666543
No 118
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=86.53 E-value=1.1 Score=48.04 Aligned_cols=54 Identities=20% Similarity=0.408 Sum_probs=46.6
Q ss_pred cEEEEEecCCChhhhcCC-CCCCeEEEECCeeC--CCHHHHHHHHHhCCCCceEEEE
Q 001276 1009 GVYVARWCHGSPVHRYGL-YALQWIVEINGKRT--PDLEAFVNVTKEIEHGEFVRVR 1062 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~GL-~~gD~I~~VNg~~v--~~l~~f~~~l~~~~~~~~v~l~ 1062 (1109)
|++|++..+|+-|+--|| ..+|.|++|||.+| +++|+....+-+...|-.|+++
T Consensus 195 GIFISRlVpGGLAeSTGLLaVnDEVlEVNGIEVaGKTLDQVTDMMvANshNLIiTVk 251 (358)
T KOG3606|consen 195 GIFISRLVPGGLAESTGLLAVNDEVLEVNGIEVAGKTLDQVTDMMVANSHNLIITVK 251 (358)
T ss_pred ceEEEeecCCccccccceeeecceeEEEcCEEeccccHHHHHHHHhhcccceEEEec
Confidence 899999999999999987 78999999999887 5889999999886666666554
No 119
>PF11874 DUF3394: Domain of unknown function (DUF3394); InterPro: IPR021814 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with PF06808 from PFAM.
Probab=86.39 E-value=2.5 Score=43.85 Aligned_cols=83 Identities=19% Similarity=0.272 Sum_probs=54.4
Q ss_pred hhHHHHHHHhccCCCCCCCeEEEEEEe---CCEEE--EEEEeeeecCCCCcceEEeecCccccCCchhhhhccCCCCCCC
Q 001276 934 FHDIENACQALDKDGEDNGKLDITIFR---QGREI--ELQVGTDVRDGNGTTRVINWCGCIVQDPHPAVRALGFLPEEGH 1008 (1109)
Q Consensus 934 ~~dl~~~l~~~~~g~~~~~~v~l~V~R---~g~~~--~l~v~l~~~~~~~t~~~~~~~G~~~~~p~~~~r~~~~lp~~~~ 1008 (1109)
..++...+.....| +.+.++|.+ .|+.. ++.+++.+.. ....| +.-+|+.+.+ ++.
T Consensus 62 ~~~~~~~~~~~~~g----~~lrl~V~G~~~~G~~~~k~v~lpl~~~~-~g~eR-L~~~GL~l~~-------------e~~ 122 (183)
T PF11874_consen 62 PSELVQVAEQLPPG----SSLRLRVEGPDFEGDPVTKTVLLPLGDGA-DGEER-LEAAGLTLME-------------EGG 122 (183)
T ss_pred HHHHHHHHhcCCCC----CEEEEEEEccCCCCCceEEEEEEEcCCCC-CHHHH-HHhCCCEEEe-------------eCC
Confidence 44566666555555 889999987 35544 4445544332 12222 3344665533 123
Q ss_pred cEEEEEecCCChhhhcCCCCCCeEEEE
Q 001276 1009 GVYVARWCHGSPVHRYGLYALQWIVEI 1035 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~GL~~gD~I~~V 1035 (1109)
.+.|..+..||||+++|+..+..|++|
T Consensus 123 ~~~Vd~v~fgS~A~~~g~d~d~~I~~v 149 (183)
T PF11874_consen 123 KVIVDEVEFGSPAEKAGIDFDWEITEV 149 (183)
T ss_pred EEEEEecCCCCHHHHcCCCCCcEEEEE
Confidence 689999999999999999999999887
No 120
>KOG1892 consensus Actin filament-binding protein Afadin [Cytoskeleton]
Probab=86.37 E-value=0.43 Score=59.04 Aligned_cols=65 Identities=20% Similarity=0.313 Sum_probs=49.0
Q ss_pred CCCccceEEEEeecCCCHHhhh--ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCE
Q 001276 895 DPVRRQVLRVKGCLAGSKAENM--LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGR 963 (1109)
Q Consensus 895 ~~~~~~~~~V~~V~~~spA~~a--L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~ 963 (1109)
..++.-|++|..|.+|++|+.- |+.||.+|+|||+..-...+-+.+-.+.+.| ..|.+.|...|.
T Consensus 955 aGq~klGIYvKsVV~GgaAd~DGRL~aGDQLLsVdG~SLiGisQErAA~lmtrtg----~vV~leVaKqgA 1021 (1629)
T KOG1892|consen 955 AGQRKLGIYVKSVVEGGAADHDGRLEAGDQLLSVDGHSLIGISQERAARLMTRTG----NVVHLEVAKQGA 1021 (1629)
T ss_pred CCccccceEEEEeccCCccccccccccCceeeeecCcccccccHHHHHHHHhccC----CeEEEehhhhhh
Confidence 4456678999999999999854 9999999999999987766544333233443 778888876554
No 121
>KOG3627 consensus Trypsin [Amino acid transport and metabolism]
Probab=86.05 E-value=17 Score=39.79 Aligned_cols=147 Identities=17% Similarity=0.135 Sum_probs=72.7
Q ss_pred EEEEEEEeCCCcEEEeCccccCCCC-eEEEEEec---------CC---eEEEE-EEEEEcC-------C-CcEEEEEEcC
Q 001276 69 YATGFVVDKRRGIILTNRHVVKPGP-VVAEAMFV---------NR---EEIPV-YPIYRDP-------V-HDFGFFRYDP 126 (1109)
Q Consensus 69 ~GSGfvV~~~~G~IlTn~HVv~~~~-~~~~v~~~---------~~---~~~~a-~vv~~d~-------~-~DlAlLk~~~ 126 (1109)
.+.|.+|++ .+|||++|++.... ....|.+. ++ ..... +++ .++ . .|||+|+++.
T Consensus 39 ~Cggsli~~--~~vltaaHC~~~~~~~~~~V~~G~~~~~~~~~~~~~~~~~~v~~~i-~H~~y~~~~~~~nDiall~l~~ 115 (256)
T KOG3627|consen 39 LCGGSLISP--RWVLTAAHCVKGASASLYTVRLGEHDINLSVSEGEEQLVGDVEKII-VHPNYNPRTLENNDIALLRLSE 115 (256)
T ss_pred eeeeEEeeC--CEEEEChhhCCCCCCcceEEEECccccccccccCchhhhceeeEEE-ECCCCCCCCCCCCCEEEEEECC
Confidence 566767764 49999999999531 03333332 11 11111 222 332 2 7999999986
Q ss_pred CC-cccccccCCCCC--Cc--cCCCCCEEEEEecCCCC----C--CeEEEEEEEEecC--CCCCCCCC-CccccceeeEE
Q 001276 127 SA-IQFLNYDEIPLA--PE--AACVGLEIRVVGNDSGE----K--VSILAGTLARLDR--DAPHYKKD-GYNDFNTFYMQ 192 (1109)
Q Consensus 127 ~~-~~~~~l~~l~l~--~~--~~~~G~~V~~iG~p~g~----~--~si~~G~vs~~~~--~~~~~~~~-~~~~~~~~~iq 192 (1109)
.- +. -.+.++.|. .. ....+....+.|+.... . ..+....+..+.. -...+... ...+ ..+-
T Consensus 116 ~v~~~-~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~~~L~~~~v~i~~~~~C~~~~~~~~~~~~---~~~C 191 (256)
T KOG3627|consen 116 PVTFS-SHIQPICLPSSADPYFPPGGTTCLVSGWGRTESGGGPLPDTLQEVDVPIISNSECRRAYGGLGTITD---TMLC 191 (256)
T ss_pred CcccC-CcccccCCCCCcccCCCCCCCEEEEEeCCCcCCCCCCCCceeEEEEEeEcChhHhcccccCccccCC---CEEe
Confidence 42 21 123344443 22 23445888888864321 1 1122122222221 11111110 0001 1122
Q ss_pred Ee-----eccCCCCCCCceecCC---CcEEEEeccccC
Q 001276 193 AA-----SGTKGGSSGSPVIDWQ---GRAVALNAGSKS 222 (1109)
Q Consensus 193 ~~-----a~~~~G~SGgPv~n~~---G~vVGi~~~~~~ 222 (1109)
+. ..+-.|.|||||+-.+ ..++||.+.+..
T Consensus 192 a~~~~~~~~~C~GDSGGPLv~~~~~~~~~~GivS~G~~ 229 (256)
T KOG3627|consen 192 AGGPEGGKDACQGDSGGPLVCEDNGRWVLVGIVSWGSG 229 (256)
T ss_pred eCccCCCCccccCCCCCeEEEeeCCcEEEEEEEEecCC
Confidence 21 2235599999998654 699999988754
No 122
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=84.56 E-value=3.3 Score=48.60 Aligned_cols=58 Identities=17% Similarity=0.252 Sum_probs=48.8
Q ss_pred EEEEecCCChhhhcCCCCCCeEEEECCeeCCCHHHHHHHHHhCCCCce---EEEEEEEe-CCeE
Q 001276 1011 YVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEF---VRVRTVHL-NGKP 1070 (1109)
Q Consensus 1011 ~V~~v~~gSPA~~~GL~~gD~I~~VNg~~v~~l~~f~~~l~~~~~~~~---v~l~~v~r-dg~~ 1070 (1109)
++..+..+|+|..+|+++||.|+++|++++.++++....+.... +.. +.+. +.| ++..
T Consensus 132 ~~~~v~~~s~a~~a~l~~Gd~iv~~~~~~i~~~~~~~~~~~~~~-~~~~~~~~i~-~~~~~~~~ 193 (375)
T COG0750 132 VVGEVAPKSAAALAGLRPGDRIVAVDGEKVASWDDVRRLLVAAA-GDVFNLLTIL-VIRLDGEA 193 (375)
T ss_pred eeeecCCCCHHHHcCCCCCCEEEeECCEEccCHHHHHHHHHhcc-CCcccceEEE-EEecccee
Confidence 35578999999999999999999999999999999999988865 444 6777 555 7776
No 123
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=84.46 E-value=1.3 Score=50.16 Aligned_cols=46 Identities=22% Similarity=0.278 Sum_probs=42.3
Q ss_pred CCcEEEEEecCCChhhhc-CCCCCCeEEEECCeeCCCHHHHHHHHHh
Q 001276 1007 GHGVYVARWCHGSPVHRY-GLYALQWIVEINGKRTPDLEAFVNVTKE 1052 (1109)
Q Consensus 1007 ~~gV~V~~v~~gSPA~~~-GL~~gD~I~~VNg~~v~~l~~f~~~l~~ 1052 (1109)
+.+|.|++|...||+..+ ||.+||.|+++||-||.+.+++.+-++.
T Consensus 219 g~gV~Vtev~~~Spl~gprGL~vgdvitsldgcpV~~v~dW~ecl~t 265 (484)
T KOG2921|consen 219 GEGVTVTEVPSVSPLFGPRGLSVGDVITSLDGCPVHKVSDWLECLAT 265 (484)
T ss_pred CceEEEEeccccCCCcCcccCCccceEEecCCcccCCHHHHHHHHHh
Confidence 468999999999998866 9999999999999999999999998877
No 124
>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=83.70 E-value=0.93 Score=43.76 Aligned_cols=33 Identities=33% Similarity=0.545 Sum_probs=26.6
Q ss_pred eEEEeeccCCCCCCCceecCCCcEEEEeccccC
Q 001276 190 YMQAASGTKGGSSGSPVIDWQGRAVALNAGSKS 222 (1109)
Q Consensus 190 ~iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~ 222 (1109)
|..-...-.+|.||-|++|-.|+||||+.++.+
T Consensus 96 ftip~g~g~~GDSGRpi~DNsGrVVaIVLGG~n 128 (158)
T PF00944_consen 96 FTIPTGVGKPGDSGRPIFDNSGRVVAIVLGGAN 128 (158)
T ss_dssp EEEETTS-STTSTTEEEESTTSBEEEEEEEEEE
T ss_pred EEeccCCCCCCCCCCccCcCCCCEEEEEecCCC
Confidence 344456678999999999999999999988754
No 125
>KOG0609 consensus Calcium/calmodulin-dependent serine protein kinase/membrane-associated guanylate kinase [Signal transduction mechanisms]
Probab=83.20 E-value=2 Score=51.01 Aligned_cols=74 Identities=23% Similarity=0.315 Sum_probs=57.9
Q ss_pred cEEEEEecCCChhhhcCC-CCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEEEEEeC---CeEEEEEEeeCCccC
Q 001276 1009 GVYVARWCHGSPVHRYGL-YALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVHLN---GKPRVLTLKQDLHYW 1082 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~GL-~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~~v~rd---g~~~~i~lk~~~~y~ 1082 (1109)
.++|.++..|+-+++-|+ +.||.|.+|||..+.+. +++.+.+++.. ..++++++--- .....+-++.-.+|+
T Consensus 147 ~~~vARI~~GG~~~r~glL~~GD~i~EvNGi~v~~~~~~e~q~~l~~~~--G~itfkiiP~~~~~~~~~~~~vra~FdYd 224 (542)
T KOG0609|consen 147 KVVVARIMHGGMADRQGLLHVGDEILEVNGISVANKSPEELQELLRNSR--GSITFKIIPSYRPPPQQQVVFVRALFDYD 224 (542)
T ss_pred ccEEeeeccCCcchhccceeeccchheecCeecccCCHHHHHHHHHhCC--CcEEEEEcccccCCCceeeeeehhhcCcC
Confidence 469999999999999986 88999999999998765 89999999864 44777744321 233357788888888
Q ss_pred cc
Q 001276 1083 PT 1084 (1109)
Q Consensus 1083 pt 1084 (1109)
|-
T Consensus 225 P~ 226 (542)
T KOG0609|consen 225 PK 226 (542)
T ss_pred cc
Confidence 85
No 126
>KOG3551 consensus Syntrophins (type beta) [Extracellular structures]
Probab=82.70 E-value=0.88 Score=51.26 Aligned_cols=52 Identities=23% Similarity=0.305 Sum_probs=41.1
Q ss_pred EEEEEecCCCcccc--CCCCCCEEEEECCEEeCChhHHHHHH-hcCCCCeEEEEE
Q 001276 300 LVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFLKLETLL-DDGVDKNIELLI 351 (1109)
Q Consensus 300 lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~~l~~~l-~~~~g~~v~l~v 351 (1109)
++|+.+.+|=.|++ -|-.||.|++|||+.+.+..+-+..- .+..|+.|.++|
T Consensus 112 IlISKIFkGlAADQt~aL~~gDaIlSVNG~dL~~AtHdeAVqaLKraGkeV~lev 166 (506)
T KOG3551|consen 112 ILISKIFKGLAADQTGALFLGDAILSVNGEDLRDATHDEAVQALKRAGKEVLLEV 166 (506)
T ss_pred eehhHhccccccccccceeeccEEEEecchhhhhcchHHHHHHHHhhCceeeeee
Confidence 44589999999999 59999999999999999887666443 456788766554
No 127
>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=82.55 E-value=20 Score=37.22 Aligned_cols=151 Identities=14% Similarity=0.143 Sum_probs=79.7
Q ss_pred ccccccEEEEEEEcCcccccCCcccceeeEEEEEEEeeCCceEEEEeCceecCCCCcEEEEeecCCeEE--eEEEEEeeC
Q 001276 623 SVIEPTLVMFEVHVPPSCMIDGVHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEI--PGEVVFLHP 700 (1109)
Q Consensus 623 ~~~~~SvV~V~~~~~~~~~~dg~~~~~~~GsG~VId~~~~~G~IlTn~~~V~~~~~di~V~~~d~~~~~--~a~vv~~dp 700 (1109)
+.+++-++.|++ . ...+.++++-|. +.+.|.++| ......+.+. ++.+ ...+.-.+.
T Consensus 9 ~~~~~N~~~v~~--~---------~g~~t~l~~gi~----~~~~lvp~H----~~~~~~i~i~--g~~~~~~d~~~lv~~ 67 (172)
T PF00548_consen 9 SLIKKNVVPVTT--G---------KGEFTMLALGIY----DRYFLVPTH----EEPEDTIYID--GVEYKVDDSVVLVDR 67 (172)
T ss_dssp HHHHHHEEEEEE--T---------TEEEEEEEEEEE----BTEEEEEGG----GGGCSEEEET--TEEEEEEEEEEEEET
T ss_pred HHHhccEEEEEe--C---------CceEEEecceEe----eeEEEEECc----CCCcEEEEEC--CEEEEeeeeEEEecC
Confidence 345566666655 2 566789988898 568888877 2222334443 4443 224444555
Q ss_pred C---CcEEEEEECCC-CCCcccccceeceecCCCccCCCCCeEEEEeeCCCCcceeeeeeEeccccccccCCCCCCcccc
Q 001276 701 V---HNFALIAYDPS-SLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRA 776 (1109)
Q Consensus 701 ~---~dlAilk~d~~-~l~~~~~~~v~~~~l~~~~~l~~G~~V~~iG~p~~~~~~~~~~~vt~i~~~~~i~~~~~~~y~~ 776 (1109)
. .|+++++++.. .+. .-.+-+. +.. -...+.+.++=.+...+.....+.|+. .+.+.....+.
T Consensus 68 ~~~~~Dl~~v~l~~~~kfr----DIrk~~~--~~~-~~~~~~~l~v~~~~~~~~~~~v~~v~~---~~~i~~~g~~~--- 134 (172)
T PF00548_consen 68 DGVDTDLTLVKLPRNPKFR----DIRKFFP--ESI-PEYPECVLLVNSTKFPRMIVEVGFVTN---FGFINLSGTTT--- 134 (172)
T ss_dssp TSSEEEEEEEEEESSS-B------GGGGSB--SSG-GTEEEEEEEEESSSSTCEEEEEEEEEE---EEEEEETTEEE---
T ss_pred CCcceeEEEEEccCCcccC----chhhhhc--ccc-ccCCCcEEEEECCCCccEEEEEEEEee---cCccccCCCEe---
Confidence 4 59999999542 221 1111122 221 144556666655544444434444442 22221111111
Q ss_pred cceeEEEEeccc-CCCCCceEEcC---CeeEEEEEee
Q 001276 777 MNMEVIELDTDF-GSTFSGVLTDE---HGRVQAIWGS 809 (1109)
Q Consensus 777 ~~~~~I~~d~~i-g~~sGGpL~d~---~G~VvGi~~~ 809 (1109)
...+.-+++- ...|||+|+.. .++++||..+
T Consensus 135 --~~~~~Y~~~t~~G~CG~~l~~~~~~~~~i~GiHva 169 (172)
T PF00548_consen 135 --PRSLKYKAPTKPGMCGSPLVSRIGGQGKIIGIHVA 169 (172)
T ss_dssp --EEEEEEESEEETTGTTEEEEESCGGTTEEEEEEEE
T ss_pred --eEEEEEccCCCCCccCCeEEEeeccCccEEEEEec
Confidence 1234444433 33599999863 4799999876
No 128
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=81.41 E-value=2.1 Score=46.07 Aligned_cols=46 Identities=15% Similarity=0.325 Sum_probs=40.7
Q ss_pred CeEEEEc--CCChhHHcC-CCCCCEEEEcCCeec--CCHHHHHHHHHhcCC
Q 001276 399 GLVYVAE--PGYMLFRAG-VPRHAIIKKFAGEEI--SRLEDLISVLSKLSR 444 (1109)
Q Consensus 399 ~gv~v~~--pg~~a~~aG-l~~GD~I~~Vng~~v--~~l~~~~~~i~~~~~ 444 (1109)
.|+||+. ||+.|+..| |...|.|++|||.++ .++++..+.|-++..
T Consensus 194 pGIFISRlVpGGLAeSTGLLaVnDEVlEVNGIEVaGKTLDQVTDMMvANsh 244 (358)
T KOG3606|consen 194 PGIFISRLVPGGLAESTGLLAVNDEVLEVNGIEVAGKTLDQVTDMMVANSH 244 (358)
T ss_pred CceEEEeecCCccccccceeeecceeEEEcCEEeccccHHHHHHHHhhccc
Confidence 5899995 999999999 678999999999998 689999999998653
No 129
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=77.09 E-value=3.4 Score=47.03 Aligned_cols=46 Identities=22% Similarity=0.258 Sum_probs=40.0
Q ss_pred CCCceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChhHHHHHHhc
Q 001276 295 GETGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFLKLETLLDD 341 (1109)
Q Consensus 295 ~~~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~~l~~~l~~ 341 (1109)
...|+.| ..|...||+.. ||++||+|.++||-+|.+..+..+.++.
T Consensus 218 ~g~gV~V-tev~~~Spl~gprGL~vgdvitsldgcpV~~v~dW~ecl~t 265 (484)
T KOG2921|consen 218 HGEGVTV-TEVPSVSPLFGPRGLSVGDVITSLDGCPVHKVSDWLECLAT 265 (484)
T ss_pred cCceEEE-EeccccCCCcCcccCCccceEEecCCcccCCHHHHHHHHHh
Confidence 4567777 69999999998 9999999999999999998888877754
No 130
>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=76.16 E-value=19 Score=44.22 Aligned_cols=125 Identities=17% Similarity=0.196 Sum_probs=69.2
Q ss_pred eCCCcEEEEEECCCC-----CCcccc--cceeceecCC------CccCCCCCeEEEEeeCCCCcceeeeeeEeccccccc
Q 001276 699 HPVHNFALIAYDPSS-----LGVAGA--SVVRAAELLP------EPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALN 765 (1109)
Q Consensus 699 dp~~dlAilk~d~~~-----l~~~~~--~~v~~~~l~~------~~~l~~G~~V~~iG~p~~~~~~~~~~~vt~i~~~~~ 765 (1109)
....|+||||++... +..... .+=.++.+.+ -..+..|..|+=+|..-++. .|.+.++. -..
T Consensus 540 ~~LsD~AIIkV~~~~~~~N~LGddi~f~~~dP~l~f~NlyV~~~~~~~~~G~~VfK~GrTTgyT----~G~lNg~k-lvy 614 (695)
T PF08192_consen 540 KRLSDWAIIKVNKERKCQNYLGDDIQFNEPDPTLMFQNLYVREVVSNLVPGMEVFKVGRTTGYT----TGILNGIK-LVY 614 (695)
T ss_pred ccccceEEEEeCCCceecCCCCccccccCCCccccccccchhhhhhccCCCCeEEEecccCCcc----ceEecceE-EEE
Confidence 456799999998653 221000 0111122322 12467899999999888874 66666543 111
Q ss_pred cCCCCCCcccccceeEEEEe---ccc--CCCCCceEEcCCee------EEEEEeeccccccccCCCCCCceeEecccHHH
Q 001276 766 ISSADCPRYRAMNMEVIELD---TDF--GSTFSGVLTDEHGR------VQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYT 834 (1109)
Q Consensus 766 i~~~~~~~y~~~~~~~I~~d---~~i--g~~sGGpL~d~~G~------VvGi~~~~~~~~~~g~~~~~~~~~~~aipi~~ 834 (1109)
....... ..+++-.. ..+ ++-||..+++.-+. |+||..+|-++ -.+|.+-.|+..
T Consensus 615 w~dG~i~-----s~efvV~s~~~~~Fa~~GDSGS~VLtk~~d~~~gLgvvGMlhsydge---------~kqfglftPi~~ 680 (695)
T PF08192_consen 615 WADGKIQ-----SSEFVVSSDNNPAFASGGDSGSWVLTKLEDNNKGLGVVGMLHSYDGE---------QKQFGLFTPINE 680 (695)
T ss_pred ecCCCeE-----EEEEEEecCCCccccCCCCcccEEEecccccccCceeeEEeeecCCc---------cceeeccCcHHH
Confidence 1111111 12333222 123 22467777786555 99999988654 345555578777
Q ss_pred HHHHHHHH
Q 001276 835 ISRVLDKI 842 (1109)
Q Consensus 835 i~~~l~~l 842 (1109)
|+.-|+++
T Consensus 681 il~rl~~v 688 (695)
T PF08192_consen 681 ILDRLEEV 688 (695)
T ss_pred HHHHHHHh
Confidence 77665554
No 131
>KOG0609 consensus Calcium/calmodulin-dependent serine protein kinase/membrane-associated guanylate kinase [Signal transduction mechanisms]
Probab=74.99 E-value=5.5 Score=47.43 Aligned_cols=53 Identities=30% Similarity=0.417 Sum_probs=41.4
Q ss_pred eEEEEEecCCCcccc-C-CCCCCEEEEECCEEeCC--hhHHHHHHhcCCCCeEEEEEE
Q 001276 299 LLVVDSVVPGGPAHL-R-LEPGDVLVRVNGEVITQ--FLKLETLLDDGVDKNIELLIE 352 (1109)
Q Consensus 299 ~lVv~~V~~~spA~~-g-L~~GD~Il~VnG~~v~~--~~~l~~~l~~~~g~~v~l~v~ 352 (1109)
-++|..+..|+.+++ | |+.||.|+.|||..+.+ ..++..+|...-| .+++.+.
T Consensus 147 ~~~vARI~~GG~~~r~glL~~GD~i~EvNGi~v~~~~~~e~q~~l~~~~G-~itfkii 203 (542)
T KOG0609|consen 147 KVVVARIMHGGMADRQGLLHVGDEILEVNGISVANKSPEELQELLRNSRG-SITFKII 203 (542)
T ss_pred ccEEeeeccCCcchhccceeeccchheecCeecccCCHHHHHHHHHhCCC-cEEEEEc
Confidence 344579999999999 6 99999999999999986 4677788866544 5666553
No 132
>KOG3549 consensus Syntrophins (type gamma) [Extracellular structures]
Probab=73.62 E-value=3.8 Score=45.69 Aligned_cols=53 Identities=21% Similarity=0.324 Sum_probs=41.6
Q ss_pred EEEEEecCCCcccc-C-CCCCCEEEEECCEEeCChhHHHH-HHhcCCCCeEEEEEE
Q 001276 300 LVVDSVVPGGPAHL-R-LEPGDVLVRVNGEVITQFLKLET-LLDDGVDKNIELLIE 352 (1109)
Q Consensus 300 lVv~~V~~~spA~~-g-L~~GD~Il~VnG~~v~~~~~l~~-~l~~~~g~~v~l~v~ 352 (1109)
+||+.+..+..|+. | |=.||-|+.|||..|+...+-+. .+..+.|+.|+|+|.
T Consensus 82 vviSkI~kdQaAd~tG~LFvGDAilqvNGi~v~~c~HeevV~iLRNAGdeVtlTV~ 137 (505)
T KOG3549|consen 82 VVISKIYKDQAADITGQLFVGDAILQVNGIYVTACPHEEVVNILRNAGDEVTLTVK 137 (505)
T ss_pred EEeehhhhhhhhhhcCceEeeeeeEEeccEEeecCChHHHHHHHHhcCCEEEEEeH
Confidence 56689999999998 6 88999999999999987654332 224567888888874
No 133
>KOG3551 consensus Syntrophins (type beta) [Extracellular structures]
Probab=72.78 E-value=3.5 Score=46.65 Aligned_cols=52 Identities=21% Similarity=0.346 Sum_probs=45.0
Q ss_pred cEEEEEecCCChhhhcC-CCCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEE
Q 001276 1009 GVYVARWCHGSPVHRYG-LYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVR 1062 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~G-L~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~ 1062 (1109)
.++|+.+.+|-.|+|.+ |..||.|++|||....+. |+.++++|. .|+.|.|.
T Consensus 111 PIlISKIFkGlAADQt~aL~~gDaIlSVNG~dL~~AtHdeAVqaLKr--aGkeV~le 165 (506)
T KOG3551|consen 111 PILISKIFKGLAADQTGALFLGDAILSVNGEDLRDATHDEAVQALKR--AGKEVLLE 165 (506)
T ss_pred ceehhHhccccccccccceeeccEEEEecchhhhhcchHHHHHHHHh--hCceeeee
Confidence 45899999999999874 799999999999988765 889999997 58888777
No 134
>PF11874 DUF3394: Domain of unknown function (DUF3394); InterPro: IPR021814 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with PF06808 from PFAM.
Probab=71.07 E-value=22 Score=37.03 Aligned_cols=79 Identities=24% Similarity=0.208 Sum_probs=51.8
Q ss_pred hHHHHHHhc-CCCCeEEEEEEE---CCEEE--EEEEEeecCCCCCCCccccccceEEecCCHHHhhccCCCCCeEEEEc-
Q 001276 333 LKLETLLDD-GVDKNIELLIER---GGISM--TVNLVVQDLHSITPDYFLEVSGAVIHPLSYQQARNFRFPCGLVYVAE- 405 (1109)
Q Consensus 333 ~~l~~~l~~-~~g~~v~l~v~R---~g~~~--~~~v~l~~~~~~~~~~~~~~~G~~~~~l~~~~~~~~~~~~~gv~v~~- 405 (1109)
.++.+.+.. ..|+.+.++|.+ .|+.. ++.+++.+.. +...-+.-.|+.+.+.. +.+.|.+
T Consensus 63 ~~~~~~~~~~~~g~~lrl~V~G~~~~G~~~~k~v~lpl~~~~--~g~eRL~~~GL~l~~e~-----------~~~~Vd~v 129 (183)
T PF11874_consen 63 SELVQVAEQLPPGSSLRLRVEGPDFEGDPVTKTVLLPLGDGA--DGEERLEAAGLTLMEEG-----------GKVIVDEV 129 (183)
T ss_pred HHHHHHHhcCCCCCEEEEEEEccCCCCCceEEEEEEEcCCCC--CHHHHHHhCCCEEEeeC-----------CEEEEEec
Confidence 456666644 678999999988 35544 4445554332 33333445577665421 3456664
Q ss_pred -CCChhHHcCCCCCCEEEEc
Q 001276 406 -PGYMLFRAGVPRHAIIKKF 424 (1109)
Q Consensus 406 -pg~~a~~aGl~~GD~I~~V 424 (1109)
.||+|+++|+.-++.|++|
T Consensus 130 ~fgS~A~~~g~d~d~~I~~v 149 (183)
T PF11874_consen 130 EFGSPAEKAGIDFDWEITEV 149 (183)
T ss_pred CCCCHHHHcCCCCCcEEEEE
Confidence 7999999999999988876
No 135
>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=70.33 E-value=10 Score=41.06 Aligned_cols=51 Identities=20% Similarity=0.264 Sum_probs=42.9
Q ss_pred cCCChhHHcC-CCCCCEEEEcCCeecCCH--HHHHHHHHhcCCCCeEeEEEEee
Q 001276 405 EPGYMLFRAG-VPRHAIIKKFAGEEISRL--EDLISVLSKLSRGARVPIEYSSY 455 (1109)
Q Consensus 405 ~pg~~a~~aG-l~~GD~I~~Vng~~v~~l--~~~~~~i~~~~~g~~v~l~~~~~ 455 (1109)
.+||-.++-- +.+||.|.+|||+.+-.+ .+..+.++.++.|+..+|+....
T Consensus 157 kegsvidri~~i~VGd~IEaiNge~ivG~RHYeVArmLKel~rge~ftlrLieP 210 (334)
T KOG3938|consen 157 KEGSVIDRIEAICVGDHIEAINGESIVGKRHYEVARMLKELPRGETFTLRLIEP 210 (334)
T ss_pred cCCchhhhhhheeHHhHHHhhcCccccchhHHHHHHHHHhcccCCeeEEEeecc
Confidence 4777776654 789999999999999887 68899999999999998887654
No 136
>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=68.21 E-value=3.3 Score=48.66 Aligned_cols=29 Identities=31% Similarity=0.416 Sum_probs=24.1
Q ss_pred EEEeeccCCCCCCCceecCCCcEEEEecc
Q 001276 191 MQAASGTKGGSSGSPVIDWQGRAVALNAG 219 (1109)
Q Consensus 191 iq~~a~~~~G~SGgPv~n~~G~vVGi~~~ 219 (1109)
+.-.....+|+||+.|+|.+|++|||..+
T Consensus 346 ~~~~~~l~gGaSGS~V~n~~~~lvGIy~g 374 (374)
T PF01732_consen 346 LIDNYSLGGGASGSMVINQNNELVGIYFG 374 (374)
T ss_pred cccccCCCCCCCcCeEECCCCCEEEEeCC
Confidence 33455778999999999999999999753
No 137
>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=67.58 E-value=18 Score=34.02 Aligned_cols=52 Identities=10% Similarity=0.096 Sum_probs=32.7
Q ss_pred EEEEeCCCcEEEeCccccCCCCeEEEEEecCCeEEEEEEEEEcCCCcEEEEEEcCCCccccccc
Q 001276 72 GFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYPIYRDPVHDFGFFRYDPSAIQFLNYD 135 (1109)
Q Consensus 72 GfvV~~~~G~IlTn~HVv~~~~~~~~v~~~~~~~~~a~vv~~d~~~DlAlLk~~~~~~~~~~l~ 135 (1109)
++-|. +|..+|+.||.+.... + ++.++ + -....-|+++++.....++.++++
T Consensus 3 avHIG--nG~~vt~tHva~~~~~-v-----~g~~f--~--~~~~~ge~~~v~~~~~~~p~~~ig 54 (105)
T PF03510_consen 3 AVHIG--NGRYVTVTHVAKSSDS-V-----DGQPF--K--IVKTDGELCWVQSPLVHLPAAQIG 54 (105)
T ss_pred eEEeC--CCEEEEEEEEeccCce-E-----cCcCc--E--EEEeccCEEEEECCCCCCCeeEec
Confidence 45565 7999999999984321 1 12222 2 233455999999987666655554
No 138
>KOG3651 consensus Protein kinase C, alpha binding protein [Signal transduction mechanisms]
Probab=65.75 E-value=14 Score=40.58 Aligned_cols=56 Identities=16% Similarity=0.137 Sum_probs=41.2
Q ss_pred ccceEEEEeecCCCHHhhh--ccCCCEEEEECCEEcCCh--hHHHHHHHhccCCCCCCCeEEEEEE
Q 001276 898 RRQVLRVKGCLAGSKAENM--LEQGDMMLAINKQPVTCF--HDIENACQALDKDGEDNGKLDITIF 959 (1109)
Q Consensus 898 ~~~~~~V~~V~~~spA~~a--L~~GDiIlsVnG~~V~~~--~dl~~~l~~~~~g~~~~~~v~l~V~ 959 (1109)
....++|..|-.++||++- ++.||.|++|||..|..- .++..+++... +.|.+++-
T Consensus 28 yCPClYiVQvFD~tPAa~dG~i~~GDEi~avNg~svKGktKveVAkmIQ~~~------~eV~IhyN 87 (429)
T KOG3651|consen 28 YCPCLYIVQVFDKTPAAKDGRIRCGDEIVAVNGISVKGKTKVEVAKMIQVSL------NEVKIHYN 87 (429)
T ss_pred cCCeEEEEEeccCCchhccCccccCCeeEEecceeecCccHHHHHHHHHHhc------cceEEEeh
Confidence 3467888899999999965 999999999999999753 44555664322 34566553
No 139
>KOG0606 consensus Microtubule-associated serine/threonine kinase and related proteins [Signal transduction mechanisms; General function prediction only]
Probab=64.31 E-value=9.4 Score=49.31 Aligned_cols=49 Identities=33% Similarity=0.481 Sum_probs=36.5
Q ss_pred eEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhH--HHHHHhcCCCCeEEE
Q 001276 299 LLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLK--LETLLDDGVDKNIEL 349 (1109)
Q Consensus 299 ~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~--l~~~l~~~~g~~v~l 349 (1109)
-+| ..|.++|||.. |+++||.|+.+||+++....+ +.++|.. .|..+.+
T Consensus 660 h~v-~sv~egsPA~~agls~~DlIthvnge~v~gl~H~ev~~Lll~-~gn~v~~ 711 (1205)
T KOG0606|consen 660 HSV-GSVEEGSPAFEAGLSAGDLITHVNGEPVHGLVHTEVMELLLK-SGNKVTL 711 (1205)
T ss_pred eee-eeecCCCCccccCCCccceeEeccCcccchhhHHHHHHHHHh-cCCeeEE
Confidence 344 78999999988 999999999999999987654 3344443 3455444
No 140
>KOG3549 consensus Syntrophins (type gamma) [Extracellular structures]
Probab=63.33 E-value=6.1 Score=44.09 Aligned_cols=68 Identities=22% Similarity=0.338 Sum_probs=52.6
Q ss_pred cEEEEEecCCChhhhcCC-CCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEEEEEeCCeEEEEEEeeC
Q 001276 1009 GVYVARWCHGSPVHRYGL-YALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQD 1078 (1109)
Q Consensus 1009 gV~V~~v~~gSPA~~~GL-~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~~v~rdg~~~~i~lk~~ 1078 (1109)
.|+|+.+..+-.|+.-|+ -.||-|+.|||.-|..- ++.+.++++ .|+.|+|++-.....|-++.+..+
T Consensus 81 PvviSkI~kdQaAd~tG~LFvGDAilqvNGi~v~~c~HeevV~iLRN--AGdeVtlTV~~lr~ApaFLklpL~ 151 (505)
T KOG3549|consen 81 PVVISKIYKDQAADITGQLFVGDAILQVNGIYVTACPHEEVVNILRN--AGDEVTLTVKHLRAAPAFLKLPLT 151 (505)
T ss_pred cEEeehhhhhhhhhhcCceEeeeeeEEeccEEeecCChHHHHHHHHh--cCCEEEEEeHhhhcCcHHhcCccC
Confidence 368999999999999885 89999999999988754 899999997 588999884333344444444443
No 141
>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=58.08 E-value=18 Score=41.84 Aligned_cols=137 Identities=23% Similarity=0.332 Sum_probs=68.5
Q ss_pred cEEEEEEEeCCCcEEEeCccccCCCCeEEEEEecCCeEEEEEEEEEcCCCcEEEEEEcCCCcccccccCCCCCCccCCCC
Q 001276 68 SYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYPIYRDPVHDFGFFRYDPSAIQFLNYDEIPLAPEAACVG 147 (1109)
Q Consensus 68 ~~GSGfvV~~~~G~IlTn~HVv~~~~~~~~v~~~~~~~~~a~vv~~d~~~DlAlLk~~~~~~~~~~l~~l~l~~~~~~~G 147 (1109)
+.|-||.|+++ +.+|+-||++.+...+.= .+..-+..+..-+|+-++|..+ +.+ ++.-+-|. +....|
T Consensus 379 GsGWGfWVS~~--lfITttHViP~g~~E~FG-------v~i~~i~vh~sGeF~~~rFpk~-iRP-DvtgmiLE-eGapEG 446 (535)
T PF05416_consen 379 GSGWGFWVSPT--LFITTTHVIPPGAKEAFG-------VPISQIQVHKSGEFCRFRFPKP-IRP-DVTGMILE-EGAPEG 446 (535)
T ss_dssp TTEEEEESSSS--EEEEEGGGS-STTSEETT-------EECGGEEEEEETTEEEEEESS--SST-TS---EE--SS--TT
T ss_pred CCceeeeecce--EEEEeeeecCCcchhhhC-------CChhHeEEeeccceEEEecCCC-CCC-Cccceeec-cCCCCc
Confidence 66889999975 999999999976543221 1112245566678888888532 211 12111111 223345
Q ss_pred CEEEE-EecCCCCC--CeEEEEEEEEecCCCCCCCCCCccccceeeEEE-------eeccCCCCCCCceecCCCc---EE
Q 001276 148 LEIRV-VGNDSGEK--VSILAGTLARLDRDAPHYKKDGYNDFNTFYMQA-------ASGTKGGSSGSPVIDWQGR---AV 214 (1109)
Q Consensus 148 ~~V~~-iG~p~g~~--~si~~G~vs~~~~~~~~~~~~~~~~~~~~~iq~-------~a~~~~G~SGgPv~n~~G~---vV 214 (1109)
.-..+ |=.|.|+- +.+..|...+..-.- ....-.+.++.+ |-.+.||.-|.|-+=..|+ |+
T Consensus 447 tV~siLiKR~sGEllpLAvRMgt~AsmkIqg------r~v~GQ~GMLLTGaNAK~mDLGT~PGDCGcPYvyKrgNd~VV~ 520 (535)
T PF05416_consen 447 TVCSILIKRPSGELLPLAVRMGTHASMKIQG------RTVHGQMGMLLTGANAKGMDLGTIPGDCGCPYVYKRGNDWVVI 520 (535)
T ss_dssp -EEEEEEE-TTSBEEEEEEEEEEEEEEEETT------EEEEEEEEEETTSTT-SSTTTS--TTGTT-EEEEEETTEEEEE
T ss_pred eEEEEEEEcCCccchhhhhhhccceeEEEcc------eeecceeeeeeecCCccccccCCCCCCCCCceeeecCCcEEEE
Confidence 44433 45777754 455556555432110 000001112222 3346789999999876665 89
Q ss_pred EEeccccC
Q 001276 215 ALNAGSKS 222 (1109)
Q Consensus 215 Gi~~~~~~ 222 (1109)
|++++...
T Consensus 521 GVH~AAtr 528 (535)
T PF05416_consen 521 GVHAAATR 528 (535)
T ss_dssp EEEEEE-S
T ss_pred EEEehhcc
Confidence 99876443
No 142
>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=55.06 E-value=8.3 Score=37.61 Aligned_cols=114 Identities=19% Similarity=0.216 Sum_probs=58.0
Q ss_pred EEEEEeCCCcEEEeCccccCCCCeEEEEEecCCeEEEEEEEEEcCCCcEEEEEEcCCCcccccccCCCCCCccCCCCCEE
Q 001276 71 TGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYPIYRDPVHDFGFFRYDPSAIQFLNYDEIPLAPEAACVGLEI 150 (1109)
Q Consensus 71 SGfvV~~~~G~IlTn~HVv~~~~~~~~v~~~~~~~~~a~vv~~d~~~DlAlLk~~~~~~~~~~l~~l~l~~~~~~~G~~V 150 (1109)
-|+.| +|.+-|.+|--... .+--..| +....|.+...|+..-...+..- .+.+..-.+ ..+
T Consensus 15 mgt~v---nGV~wT~~HGagsr----tlAgp~G---pv~q~~~s~~~Dlv~~p~P~Ga~---SL~pCtCg~------~dl 75 (148)
T PF02907_consen 15 MGTCV---NGVMWTVYHGAGSR----TLAGPKG---PVNQMYTSVDDDLVGWPAPPGAR---SLTPCTCGS------SDL 75 (148)
T ss_dssp EEEEE---TTEEEEEHHHHTTS----EEEBTTS---EB-ESEEETTTTEEEEE-STTB-----BBB-SSSS------SEE
T ss_pred ehhEE---ccEEEEEEecCCcc----cccCCCC---cceEeEEcCCCCCcccccccccc---cCCccccCC------ccE
Confidence 46677 58999999976631 1111222 33456888889998887765321 122211111 346
Q ss_pred EEEecCCCCCCeEEEEEEEEecCCCCCCCCCCccccceeeEEEeeccCCCCCCCceecCCCcEEEEeccc
Q 001276 151 RVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGS 220 (1109)
Q Consensus 151 ~~iG~p~g~~~si~~G~vs~~~~~~~~~~~~~~~~~~~~~iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~ 220 (1109)
++|-+.... ..+ .+.+. .+.. -..-.-.+...|+||||++=.+|.+|||..+.
T Consensus 76 ylVtr~~~v----~p~--rr~gd--------~~~~---L~sp~pis~lkGSSGgPiLC~~GH~vG~f~aa 128 (148)
T PF02907_consen 76 YLVTRDADV----IPV--RRRGD--------SRAS---LLSPRPISDLKGSSGGPILCPSGHAVGMFRAA 128 (148)
T ss_dssp EEE-TTS-E----EEE--EEEST--------TEEE---EEEEEEHHHHTT-TT-EEEETTSEEEEEEEEE
T ss_pred EEEeccCcE----eee--EEcCC--------CceE---ecCCceeEEEecCCCCcccCCCCCEEEEEEEE
Confidence 666554332 111 11111 0000 00111223457999999999999999997543
No 143
>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=52.07 E-value=18 Score=38.26 Aligned_cols=57 Identities=19% Similarity=0.339 Sum_probs=45.2
Q ss_pred eeeEEEeeccCCCCCCCceec----CCCcEEEEeccccCCCCCccccch--HHHHHHHHHHHh
Q 001276 188 TFYMQAASGTKGGSSGSPVID----WQGRAVALNAGSKSSSASAFFLPL--ERVVRALRFLQE 244 (1109)
Q Consensus 188 ~~~iq~~a~~~~G~SGgPv~n----~~G~vVGi~~~~~~~~~~~falP~--~~i~~~l~~l~~ 244 (1109)
...++..++...|+-|||++- .--+++||+.++..+.+.+||-++ +.++++++.|.+
T Consensus 168 r~gleY~~~t~~GdCGs~i~~~~t~~~RKIvGiHVAG~~~~~~gYAe~itQEDL~~A~~~l~~ 230 (231)
T PF12381_consen 168 RQGLEYQMPTMNGDCGSPIVRNNTQMVRKIVGIHVAGSANHAMGYAESITQEDLMRAINKLEK 230 (231)
T ss_pred eeeeeEECCCcCCCccceeeEcchhhhhhhheeeecccccccceehhhhhHHHHHHHHHhhcC
Confidence 345677889999999999873 236899999999888889999555 688888877753
No 144
>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=51.57 E-value=13 Score=40.18 Aligned_cols=56 Identities=23% Similarity=0.353 Sum_probs=47.3
Q ss_pred EEEEEecCCChhhhc-CCCCCCeEEEECCeeCCCH--HHHHHHHHhCCCCceEEEEEEE
Q 001276 1010 VYVARWCHGSPVHRY-GLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVH 1065 (1109)
Q Consensus 1010 V~V~~v~~gSPA~~~-GL~~gD~I~~VNg~~v~~l--~~f~~~l~~~~~~~~v~l~~v~ 1065 (1109)
-+|..+.+||--.+. -+..||.|-+|||+.+-.+ .+..+.|++++.++.++|+++.
T Consensus 151 AFIKrIkegsvidri~~i~VGd~IEaiNge~ivG~RHYeVArmLKel~rge~ftlrLie 209 (334)
T KOG3938|consen 151 AFIKRIKEGSVIDRIEAICVGDHIEAINGESIVGKRHYEVARMLKELPRGETFTLRLIE 209 (334)
T ss_pred eeeEeecCCchhhhhhheeHHhHHHhhcCccccchhHHHHHHHHHhcccCCeeEEEeec
Confidence 378888888877765 4689999999999999887 5778999999999999998654
No 145
>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=49.38 E-value=14 Score=36.51 Aligned_cols=27 Identities=26% Similarity=0.537 Sum_probs=17.7
Q ss_pred EEEecccCCCCCceEEcCCeeEEEEEee
Q 001276 782 IELDTDFGSTFSGVLTDEHGRVQAIWGS 809 (1109)
Q Consensus 782 I~~d~~ig~~sGGpL~d~~G~VvGi~~~ 809 (1109)
+.+|-.-|+ ||.|++|.+|+|+||-..
T Consensus 90 ~~~d~~~Gs-SGSpi~n~~g~ivGlYg~ 116 (132)
T PF00949_consen 90 IDLDFPKGS-SGSPIFNQNGEIVGLYGN 116 (132)
T ss_dssp E---S-TTG-TT-EEEETTSCEEEEEEE
T ss_pred eecccCCCC-CCCceEcCCCcEEEEEcc
Confidence 344433355 899999999999999655
No 146
>COG5233 GRH1 Peripheral Golgi membrane protein [Intracellular trafficking and secretion]
Probab=47.78 E-value=35 Score=38.00 Aligned_cols=68 Identities=13% Similarity=0.018 Sum_probs=46.4
Q ss_pred cCCChhhhcCCCC-CCeEE-EECCeeCCCHHHHHHHHHhCCCCceEEEEEEE-eCCeEEEEEEeeCCccCc
Q 001276 1016 CHGSPVHRYGLYA-LQWIV-EINGKRTPDLEAFVNVTKEIEHGEFVRVRTVH-LNGKPRVLTLKQDLHYWP 1083 (1109)
Q Consensus 1016 ~~gSPA~~~GL~~-gD~I~-~VNg~~v~~l~~f~~~l~~~~~~~~v~l~~v~-rdg~~~~i~lk~~~~y~p 1083 (1109)
.+++|++.++|.| -|+|. .=+|++..--+-..+-+..++-+-..+|.+.. .+...+.+|+..+.|+=|
T Consensus 195 I~d~p~a~a~l~PdEdyi~gs~dg~~~~~ge~~l~Dv~es~~n~pl~Ly~yn~i~d~~R~~T~~~~~h~g~ 265 (417)
T COG5233 195 IQDKPPAYALLSPDEDYIDGSSDGQPLEIGELDLEDVNESPVNLPLSLYYYNPIDDQERAKTERDGVHKGI 265 (417)
T ss_pred cCCCchhhcccCCcccccccCCCcccccchhhHHHHHhhcccCCceEEEEEecccccccceeeccCccccC
Confidence 6889999999977 45665 46788886555555555555667767776332 466778888887777644
No 147
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=37.97 E-value=57 Score=29.06 Aligned_cols=48 Identities=27% Similarity=0.498 Sum_probs=32.6
Q ss_pred EEeEEEEEeeCCCcEEEEEECCCCCCcccccceeceecCCCccCCCCCeEEE-EeeC
Q 001276 690 EIPGEVVFLHPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYL-VGLS 745 (1109)
Q Consensus 690 ~~~a~vv~~dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~-iG~p 745 (1109)
-+|++|+..+...++|++.+-.- . ..|. +.|-++ .++.||.|++ +||.
T Consensus 4 aiPgqI~~I~~~~~~A~Vd~gGv--k----reV~-l~Lv~~-~v~~GdyVLVHvGfA 52 (82)
T COG0298 4 AIPGQIVEIDDNNHLAIVDVGGV--K----REVN-LDLVGE-EVKVGDYVLVHVGFA 52 (82)
T ss_pred ccccEEEEEeCCCceEEEEeccE--e----EEEE-eeeecC-ccccCCEEEEEeeEE
Confidence 36899999999888999988542 1 0111 233333 3799999998 6654
No 148
>KOG4371 consensus Membrane-associated protein tyrosine phosphatase PTP-BAS and related proteins, contain FERM domain [Signal transduction mechanisms]
Probab=34.74 E-value=78 Score=40.91 Aligned_cols=116 Identities=15% Similarity=0.119 Sum_probs=60.0
Q ss_pred CCCCCCEEEEECCEEeCChhHHHHHH-hcCCCCeEEEEEEECCEEEEEEEEeecCCCCCCCccccccceEEecCCHHHh-
Q 001276 314 RLEPGDVLVRVNGEVITQFLKLETLL-DDGVDKNIELLIERGGISMTVNLVVQDLHSITPDYFLEVSGAVIHPLSYQQA- 391 (1109)
Q Consensus 314 gL~~GD~Il~VnG~~v~~~~~l~~~l-~~~~g~~v~l~v~R~g~~~~~~v~l~~~~~~~~~~~~~~~G~~~~~l~~~~~- 391 (1109)
.|..||.++.+||..+.--.+....- ....|+.|.|-|+|..-.. ....+.. ....+..+.---+.+.+...+..
T Consensus 1186 d~~~g~~l~~~n~i~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~-~d~~~~s--~~~~~~~l~~~~~~~~p~~~~~~~ 1262 (1332)
T KOG4371|consen 1186 DIRVGDVLLYVNGIAVEGKVHQEVVAMLRGGGDRVVLGVQRPPPAY-SDQHHAS--STSASAPLISVMLLKKPMATLGLS 1262 (1332)
T ss_pred CcchhhhhhhccceeeechhhHHHHHHHhccCceEEEEeecCCccc-ccchhhh--hhcccchhhhheeeeccccccccc
Confidence 79999999999998776544433322 3456788999999854321 1111100 00000111111111222111000
Q ss_pred hccCCCCCeEEEEc--CCChhHH-cCCCCCCEEEEcCCeecCCH
Q 001276 392 RNFRFPCGLVYVAE--PGYMLFR-AGVPRHAIIKKFAGEEISRL 432 (1109)
Q Consensus 392 ~~~~~~~~gv~v~~--pg~~a~~-aGl~~GD~I~~Vng~~v~~l 432 (1109)
-.-..+.+|+|+.. .++.|.. ..+++||.+...+|+++.-.
T Consensus 1263 ~~~~~~s~~~~~~~~~~~~~a~~~~~~r~g~~~~~~~~~~~~~~ 1306 (1332)
T KOG4371|consen 1263 LAKRTMSDGIFIRNIAQDSAASSEGTLRVGDRLVSLDGEPVDGF 1306 (1332)
T ss_pred ccccCcCCceeeecccccccccccccccccceeeccCCccCCCC
Confidence 00011236777663 2222222 24999999999999998665
No 149
>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=31.81 E-value=99 Score=26.30 Aligned_cols=32 Identities=16% Similarity=0.162 Sum_probs=26.6
Q ss_pred cEEEEeecCCeEEeEEEEEeeCCCcEEEEEECC
Q 001276 679 DVMLSFAAFPIEIPGEVVFLHPVHNFALIAYDP 711 (1109)
Q Consensus 679 di~V~~~d~~~~~~a~vv~~dp~~dlAilk~d~ 711 (1109)
.+.++... |.+++|+|+.+|+...+.|||-..
T Consensus 8 ~V~~kTc~-g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 8 QVSCRTCF-EQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred EEEEEecC-CceEEEEEEEecCCCcEEEEECcc
Confidence 35566665 889999999999999999998544
No 150
>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=31.20 E-value=56 Score=31.86 Aligned_cols=34 Identities=6% Similarity=0.054 Sum_probs=25.7
Q ss_pred ceeeEEEeeccCCCCCCCceecCCCcEEEEecccc
Q 001276 187 NTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSK 221 (1109)
Q Consensus 187 ~~~~iq~~a~~~~G~SGgPv~n~~G~vVGi~~~~~ 221 (1109)
...++....+..||.-||+|+=.. -||||.+++.
T Consensus 77 Q~~~l~g~Gp~~PGdCGg~L~C~H-GViGi~Tagg 110 (127)
T PF00947_consen 77 QYNLLIGEGPAEPGDCGGILRCKH-GVIGIVTAGG 110 (127)
T ss_dssp EECEEEEE-SSSTT-TCSEEEETT-CEEEEEEEEE
T ss_pred ecCceeecccCCCCCCCceeEeCC-CeEEEEEeCC
Confidence 345678888999999999999544 4999998864
No 151
>KOG4407 consensus Predicted Rho GTPase-activating protein [General function prediction only]
Probab=29.39 E-value=36 Score=44.65 Aligned_cols=86 Identities=7% Similarity=0.059 Sum_probs=60.3
Q ss_pred EEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEECCEEEEEEEEeecCCCCCCCccccccce
Q 001276 303 DSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIERGGISMTVNLVVQDLHSITPDYFLEVSGA 381 (1109)
Q Consensus 303 ~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~v~R~g~~~~~~v~l~~~~~~~~~~~~~~~G~ 381 (1109)
..+..++|+.. |+..||.|+.|||..+.+-..+--.+..+.
T Consensus 101 ~Q~~s~~~~~nsG~~s~~~v~~itG~e~~~~TS~~~~~vk~~-------------------------------------- 142 (1973)
T KOG4407|consen 101 PQEASSAAGSNSGSSSSVGVAGITGLEPTSPTSLPPYQVKAM-------------------------------------- 142 (1973)
T ss_pred chhcccCcccccCcccccceeeecccccCCCccccHHHHhhh--------------------------------------
Confidence 45566788888 999999999999998876543322221110
Q ss_pred EEecCCHHHhhccCCCCCeEEEE--cCCChhHHcCCCCCCEEEEcCCeecCCH--HHHHHHHHhcC
Q 001276 382 VIHPLSYQQARNFRFPCGLVYVA--EPGYMLFRAGVPRHAIIKKFAGEEISRL--EDLISVLSKLS 443 (1109)
Q Consensus 382 ~~~~l~~~~~~~~~~~~~gv~v~--~pg~~a~~aGl~~GD~I~~Vng~~v~~l--~~~~~~i~~~~ 443 (1109)
.-+|+. .+.+++--+.|+-||.++.||++++..+ .+.+..++..+
T Consensus 143 -----------------eT~~~~eV~~n~~~~~a~LQ~~~~V~~v~~q~~A~i~~s~~~S~~~qt~ 191 (1973)
T KOG4407|consen 143 -----------------ETIFIKEVQANGPAHYANLQTGDRVLMVNNQPIAGIAYSTIVSMIKQTP 191 (1973)
T ss_pred -----------------hhhhhhhhccCChhHHHhhhccceeEEeecCcccchhhhhhhhhhccCC
Confidence 011222 3678888889999999999999999988 35555555544
No 152
>KOG1738 consensus Membrane-associated guanylate kinase-interacting protein/connector enhancer of KSR-like [Nucleotide transport and metabolism]
Probab=28.94 E-value=32 Score=42.02 Aligned_cols=37 Identities=19% Similarity=0.427 Sum_probs=32.8
Q ss_pred CceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChh
Q 001276 297 TGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFL 333 (1109)
Q Consensus 297 ~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~ 333 (1109)
.|.-++..+.+++||+. .|..||.++.||+..+..|+
T Consensus 224 dg~h~~s~~~e~Spad~~~kI~dgdEv~qiN~qtvVgwq 262 (638)
T KOG1738|consen 224 DGPHVTSKIFEQSPADYRQKILDGDEVLQINEQTVVGWQ 262 (638)
T ss_pred CCceeccccccCChHHHhhcccCccceeeecccccccch
Confidence 56666788999999999 79999999999999998884
No 153
>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=26.15 E-value=97 Score=26.64 Aligned_cols=30 Identities=20% Similarity=0.262 Sum_probs=26.7
Q ss_pred cEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001276 679 DVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 709 (1109)
Q Consensus 679 di~V~~~d~~~~~~a~vv~~dp~~dlAilk~ 709 (1109)
.+.|.+.+ ++.+.|++.++|+..|+.+=..
T Consensus 12 ~V~V~Lk~-g~~~~G~L~~~D~~mNlvL~~~ 41 (67)
T cd01726 12 PVVVKLNS-GVDYRGILACLDGYMNIALEQT 41 (67)
T ss_pred eEEEEECC-CCEEEEEEEEEccceeeEEeeE
Confidence 58899998 9999999999999999987554
No 154
>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=25.42 E-value=1.2e+02 Score=25.28 Aligned_cols=31 Identities=16% Similarity=0.144 Sum_probs=27.0
Q ss_pred CcEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001276 678 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 709 (1109)
Q Consensus 678 ~di~V~~~d~~~~~~a~vv~~dp~~dlAilk~ 709 (1109)
..+.|.+.+ ++.+.|.+.+.|...|+.+-..
T Consensus 7 ~~V~V~l~~-g~~~~G~L~~~D~~~Ni~L~~~ 37 (63)
T cd00600 7 KTVRVELKD-GRVLEGVLVAFDKYMNLVLDDV 37 (63)
T ss_pred CEEEEEECC-CcEEEEEEEEECCCCCEEECCE
Confidence 358899998 9999999999999999987654
No 155
>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=25.26 E-value=1.1e+02 Score=27.17 Aligned_cols=30 Identities=17% Similarity=0.203 Sum_probs=26.3
Q ss_pred CcEEEEeecCCeEEeEEEEEeeCCCcEEEEE
Q 001276 678 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIA 708 (1109)
Q Consensus 678 ~di~V~~~d~~~~~~a~vv~~dp~~dlAilk 708 (1109)
..+.|.+.+ ++.+.|+++++|...|+.+=.
T Consensus 14 ~~V~V~l~~-gr~~~G~L~g~D~~mNlvL~d 43 (76)
T cd01732 14 SRIWIVMKS-DKEFVGTLLGFDDYVNMVLED 43 (76)
T ss_pred CEEEEEECC-CeEEEEEEEEeccceEEEEcc
Confidence 458899998 999999999999999998643
No 156
>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=25.17 E-value=1.5e+02 Score=25.68 Aligned_cols=44 Identities=25% Similarity=0.369 Sum_probs=29.1
Q ss_pred EEeEEEEEeeCCCcEEEEEECCCCCCcccccceeceecCCCccCCCCCeEEEE
Q 001276 690 EIPGEVVFLHPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLV 742 (1109)
Q Consensus 690 ~~~a~vv~~dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~i 742 (1109)
-+|++|+..+...+.|++.+....-. +.+.=-+++++||+|++-
T Consensus 4 ~iP~~Vv~v~~~~~~A~v~~~G~~~~---------V~~~lv~~v~~Gd~VLVH 47 (68)
T PF01455_consen 4 AIPGRVVEVDEDGGMAVVDFGGVRRE---------VSLALVPDVKVGDYVLVH 47 (68)
T ss_dssp CEEEEEEEEETTTTEEEEEETTEEEE---------EEGTTCTSB-TT-EEEEE
T ss_pred cccEEEEEEeCCCCEEEEEcCCcEEE---------EEEEEeCCCCCCCEEEEe
Confidence 37999999998899999988753211 222222237999999984
No 157
>PF14275 DUF4362: Domain of unknown function (DUF4362)
Probab=25.07 E-value=2e+02 Score=26.94 Aligned_cols=53 Identities=21% Similarity=0.228 Sum_probs=40.0
Q ss_pred CCCCEEEEcCCeecCCHHHHHHHHHhcCCCCeEeEEEEeecccccceEEEEEEec
Q 001276 416 PRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYSSYTDRHRRKSVLVTIDR 470 (1109)
Q Consensus 416 ~~GD~I~~Vng~~v~~l~~~~~~i~~~~~g~~v~l~~~~~~~~~~~~~~~l~i~R 470 (1109)
+.||+|.+ +-.+.|++.|-+.+.....++.=.+++.+++....+-...|..+.
T Consensus 1 ~~~DVi~~--~~~i~Nl~kl~~Fi~nv~~~k~d~IrIv~yT~EGdPI~~~L~~~G 53 (98)
T PF14275_consen 1 KNNDVINK--HGEIENLDKLDQFIENVEQGKPDKIRIVQYTIEGDPIFQDLEYDG 53 (98)
T ss_pred CCCCEEEe--CCeEEeHHHHHHHHHHHhcCCCCEEEEEEecCCCCCEEEEEEECC
Confidence 46899988 444889988888888888888888999999876655444444444
No 158
>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=24.48 E-value=1.9e+02 Score=24.65 Aligned_cols=32 Identities=3% Similarity=-0.106 Sum_probs=28.1
Q ss_pred EEEEEecCCeEEEEEEEEEcCCCcEEEEEEcC
Q 001276 95 VAEAMFVNREEIPVYPIYRDPVHDFGFFRYDP 126 (1109)
Q Consensus 95 ~~~v~~~~~~~~~a~vv~~d~~~DlAlLk~~~ 126 (1109)
.+.++...|++++++++.+|....+.+|+-..
T Consensus 8 ~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 8 QVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred EEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 46677788999999999999999999998654
No 159
>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=24.23 E-value=1e+02 Score=30.25 Aligned_cols=23 Identities=26% Similarity=0.174 Sum_probs=19.6
Q ss_pred CCCceEEcCCeeEEEEEeecccc
Q 001276 791 TFSGVLTDEHGRVQAIWGSFSTQ 813 (1109)
Q Consensus 791 ~sGGpL~d~~G~VvGi~~~~~~~ 813 (1109)
.||=|++|..|+||||.+...++
T Consensus 107 DSGRpi~DNsGrVVaIVLGG~ne 129 (158)
T PF00944_consen 107 DSGRPIFDNSGRVVAIVLGGANE 129 (158)
T ss_dssp STTEEEESTTSBEEEEEEEEEEE
T ss_pred CCCCccCcCCCCEEEEEecCCCC
Confidence 58999999999999998875444
No 160
>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=23.75 E-value=1.3e+02 Score=26.64 Aligned_cols=29 Identities=10% Similarity=0.068 Sum_probs=25.8
Q ss_pred cEEEEeecCCeEEeEEEEEeeCCCcEEEEE
Q 001276 679 DVMLSFAAFPIEIPGEVVFLHPVHNFALIA 708 (1109)
Q Consensus 679 di~V~~~d~~~~~~a~vv~~dp~~dlAilk 708 (1109)
.+.|++.| |+.+.|++.++|...|+.+=.
T Consensus 12 ~v~V~l~d-gR~~~G~l~~~D~~~NivL~~ 40 (75)
T cd06168 12 TMRIHMTD-GRTLVGVFLCTDRDCNIILGS 40 (75)
T ss_pred eEEEEEcC-CeEEEEEEEEEcCCCcEEecC
Confidence 58899998 999999999999999997643
No 161
>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=23.51 E-value=1.1e+02 Score=27.25 Aligned_cols=29 Identities=10% Similarity=0.182 Sum_probs=25.6
Q ss_pred cEEEEeecCCeEEeEEEEEeeCCCcEEEEE
Q 001276 679 DVMLSFAAFPIEIPGEVVFLHPVHNFALIA 708 (1109)
Q Consensus 679 di~V~~~d~~~~~~a~vv~~dp~~dlAilk 708 (1109)
.+.|++.+ ++.+.|.+.++|...|+.|=.
T Consensus 12 ~V~V~l~d-gR~~~G~L~~~D~~~NlVL~~ 40 (79)
T cd01717 12 RLRVTLQD-GRQFVGQFLAFDKHMNLVLSD 40 (79)
T ss_pred EEEEEECC-CcEEEEEEEEEcCccCEEcCC
Confidence 47899998 999999999999999997643
No 162
>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=23.18 E-value=1.2e+02 Score=26.19 Aligned_cols=30 Identities=20% Similarity=0.268 Sum_probs=26.7
Q ss_pred cEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001276 679 DVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 709 (1109)
Q Consensus 679 di~V~~~d~~~~~~a~vv~~dp~~dlAilk~ 709 (1109)
.+.|.+.+ |+.+.|+++++|...|+.+=..
T Consensus 13 ~V~V~Lk~-g~~~~G~L~~~D~~mNi~L~~~ 42 (68)
T cd01722 13 PVIVKLKW-GMEYKGTLVSVDSYMNLQLANT 42 (68)
T ss_pred EEEEEECC-CcEEEEEEEEECCCEEEEEeeE
Confidence 58899998 9999999999999999987544
No 163
>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=22.54 E-value=1.1e+02 Score=27.55 Aligned_cols=29 Identities=17% Similarity=0.165 Sum_probs=25.8
Q ss_pred CcEEEEeecCCeEEeEEEEEeeCCCcEEEE
Q 001276 678 SDVMLSFAAFPIEIPGEVVFLHPVHNFALI 707 (1109)
Q Consensus 678 ~di~V~~~d~~~~~~a~vv~~dp~~dlAil 707 (1109)
..|.|.+.+ ++.+.|++.++|.+.|+.+=
T Consensus 12 k~V~V~l~~-gr~~~G~L~~fD~~mNlvL~ 40 (82)
T cd01730 12 ERVYVKLRG-DRELRGRLHAYDQHLNMILG 40 (82)
T ss_pred CEEEEEECC-CCEEEEEEEEEccceEEecc
Confidence 358899998 99999999999999999763
No 164
>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=21.79 E-value=1.5e+02 Score=26.04 Aligned_cols=56 Identities=14% Similarity=0.153 Sum_probs=37.6
Q ss_pred cEEEEeecCCeEEeEEEEEeeCCCcEEEEEECCCCCCcccccceeceecCCCccCCCCCeEEEEe
Q 001276 679 DVMLSFAAFPIEIPGEVVFLHPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLVG 743 (1109)
Q Consensus 679 di~V~~~d~~~~~~a~vv~~dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~iG 743 (1109)
.+.|.+.+ ++.+.|++.++|...|+.+=...... . .....+++.- +-+|+.|..|+
T Consensus 12 ~V~V~L~~-g~~~~G~L~~~D~~mNlvL~~~~E~~-~-----~~~~~~lg~v--~IRG~~I~~i~ 67 (72)
T cd01719 12 KLSLKLNG-NRKVSGILRGFDPFMNLVLDDAVEVN-S-----GGEKNNIGMV--VIRGNSIVMLE 67 (72)
T ss_pred eEEEEECC-CeEEEEEEEEEcccccEEeccEEEEc-c-----CCceeEeceE--EECCCEEEEEE
Confidence 47889998 99999999999999999874431100 0 0011344432 57788888776
No 165
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=21.62 E-value=1.4e+02 Score=26.12 Aligned_cols=30 Identities=20% Similarity=0.139 Sum_probs=26.9
Q ss_pred cEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001276 679 DVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 709 (1109)
Q Consensus 679 di~V~~~d~~~~~~a~vv~~dp~~dlAilk~ 709 (1109)
.|.|.+.+ |+.+.|++.++|+..|+.+=..
T Consensus 16 ~V~V~lk~-g~~~~G~L~~~D~~mNlvL~d~ 45 (72)
T PRK00737 16 PVLVRLKG-GREFRGELQGYDIHMNLVLDNA 45 (72)
T ss_pred EEEEEECC-CCEEEEEEEEEcccceeEEeeE
Confidence 48899998 9999999999999999987665
No 166
>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=21.60 E-value=1.4e+02 Score=25.68 Aligned_cols=31 Identities=16% Similarity=0.191 Sum_probs=27.5
Q ss_pred CcEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001276 678 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 709 (1109)
Q Consensus 678 ~di~V~~~d~~~~~~a~vv~~dp~~dlAilk~ 709 (1109)
..|.|.+.+ ++.+.|++.++|...|+.+-..
T Consensus 11 ~~V~V~l~~-g~~~~G~L~~~D~~mNlvL~~~ 41 (68)
T cd01731 11 KPVLVKLKG-GKEVRGRLKSYDQHMNLVLEDA 41 (68)
T ss_pred CEEEEEECC-CCEEEEEEEEECCcceEEEeeE
Confidence 358899998 9999999999999999988765
No 167
>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=21.32 E-value=1.6e+02 Score=26.12 Aligned_cols=60 Identities=15% Similarity=0.078 Sum_probs=38.2
Q ss_pred CcEEEEeecCCeEEeEEEEEeeCCCcEEEEEECCCCCCcccccceeceecCCCccCCCCCeEEEEe
Q 001276 678 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLVG 743 (1109)
Q Consensus 678 ~di~V~~~d~~~~~~a~vv~~dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~iG 743 (1109)
..+.|.+.+ ++.+.|.+.++|+..|+.+=......... .......++. -+-+|+.|..+|
T Consensus 13 k~v~V~l~~-gr~~~G~L~~fD~~~NlvL~d~~E~~~~~---~~~~~~~lG~--~viRG~~V~~ig 72 (74)
T cd01728 13 KKVVVLLRD-GRKLIGILRSFDQFANLVLQDTVERIYVG---DKYGDIPRGI--FIIRGENVVLLG 72 (74)
T ss_pred CEEEEEEcC-CeEEEEEEEEECCcccEEecceEEEEecC---CccceeEeeE--EEEECCEEEEEE
Confidence 358899998 99999999999999999774331100000 0000122332 267788888887
No 168
>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=21.09 E-value=1.5e+02 Score=26.68 Aligned_cols=30 Identities=17% Similarity=0.210 Sum_probs=26.1
Q ss_pred CcEEEEeecCCeEEeEEEEEeeCCCcEEEEE
Q 001276 678 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIA 708 (1109)
Q Consensus 678 ~di~V~~~d~~~~~~a~vv~~dp~~dlAilk 708 (1109)
..+.|.+.+ ++.+.+++.++|...|+.+=.
T Consensus 13 k~V~V~l~~-gr~~~G~L~~~D~~mNlvL~~ 42 (81)
T cd01729 13 KKIRVKFQG-GREVTGILKGYDQLLNLVLDD 42 (81)
T ss_pred CeEEEEECC-CcEEEEEEEEEcCcccEEecC
Confidence 358899998 999999999999999997743
No 169
>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=20.86 E-value=2.2e+02 Score=31.52 Aligned_cols=19 Identities=11% Similarity=0.183 Sum_probs=15.3
Q ss_pred CCCceEEcCCeeEEEEEee
Q 001276 791 TFSGVLTDEHGRVQAIWGS 809 (1109)
Q Consensus 791 ~sGGpL~d~~G~VvGi~~~ 809 (1109)
.||.|++..+|.++|+.+.
T Consensus 209 DSGSPVVt~dg~liGVHTG 227 (297)
T PF05579_consen 209 DSGSPVVTEDGDLIGVHTG 227 (297)
T ss_dssp CTT-EEEETTC-EEEEEEE
T ss_pred CCCCccCcCCCCEEEEEec
Confidence 4899999999999999876
No 170
>KOG1738 consensus Membrane-associated guanylate kinase-interacting protein/connector enhancer of KSR-like [Nucleotide transport and metabolism]
Probab=20.15 E-value=1.2e+02 Score=37.41 Aligned_cols=45 Identities=22% Similarity=0.268 Sum_probs=35.6
Q ss_pred ceEEEEeecCCCHHhhh--ccCCCEEEEECCEEcCChhHHHHHHHhcc
Q 001276 900 QVLRVKGCLAGSKAENM--LEQGDMMLAINKQPVTCFHDIENACQALD 945 (1109)
Q Consensus 900 ~~~~V~~V~~~spA~~a--L~~GDiIlsVnG~~V~~~~dl~~~l~~~~ 945 (1109)
+..+|..+-++|||... |..||.|+.||++.|-.| ++..++..+.
T Consensus 225 g~h~~s~~~e~Spad~~~kI~dgdEv~qiN~qtvVgw-qlk~vV~sL~ 271 (638)
T KOG1738|consen 225 GPHVTSKIFEQSPADYRQKILDGDEVLQINEQTVVGW-QLKVVVSSLR 271 (638)
T ss_pred CceeccccccCChHHHhhcccCccceeeecccccccc-hhHhHHhhcc
Confidence 33456778889999966 999999999999999888 5666665444
Done!