Query 001280
Match_columns 1108
No_of_seqs 781 out of 5604
Neff 7.6
Searched_HMMs 46136
Date Thu Mar 28 20:38:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001280.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001280hhsearch_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 1E-155 2E-160 1306.2 74.7 918 17-1100 33-953 (955)
2 PRK10139 serine endoprotease; 100.0 2.9E-52 6.4E-57 491.0 46.9 375 36-453 40-445 (455)
3 TIGR02037 degP_htrA_DO peripla 100.0 4.4E-52 9.6E-57 491.5 46.8 382 37-454 2-420 (428)
4 PRK10942 serine endoprotease; 100.0 4.2E-50 9.2E-55 474.9 47.3 375 36-453 38-463 (473)
5 PRK10139 serine endoprotease; 100.0 3.4E-50 7.5E-55 473.5 46.3 388 619-1074 44-454 (455)
6 KOG1421 Predicted signaling-as 100.0 1.5E-50 3.2E-55 456.8 37.5 443 619-1106 56-504 (955)
7 TIGR02037 degP_htrA_DO peripla 100.0 6.2E-50 1.3E-54 473.3 44.8 395 620-1073 6-427 (428)
8 PRK10942 serine endoprotease; 100.0 2E-48 4.3E-53 460.7 43.8 360 648-1074 110-472 (473)
9 TIGR02038 protease_degS peripl 100.0 8.5E-44 1.8E-48 408.2 36.6 299 32-366 41-349 (351)
10 PRK10898 serine endoprotease; 100.0 4.3E-43 9.4E-48 401.8 37.7 300 32-367 41-351 (353)
11 TIGR02038 protease_degS peripl 100.0 5.5E-39 1.2E-43 368.5 35.9 298 619-973 49-349 (351)
12 PRK10898 serine endoprotease; 100.0 2.1E-38 4.6E-43 363.2 34.2 300 619-974 49-351 (353)
13 COG0265 DegQ Trypsin-like seri 100.0 5.7E-33 1.2E-37 320.4 32.6 293 36-365 33-340 (347)
14 COG0265 DegQ Trypsin-like seri 100.0 1.8E-28 4E-33 283.0 30.4 293 620-972 38-340 (347)
15 KOG1320 Serine protease [Postt 99.9 2.6E-22 5.7E-27 229.6 23.3 314 33-362 125-464 (473)
16 KOG1320 Serine protease [Postt 99.8 1.7E-18 3.6E-23 198.6 21.7 309 620-972 133-468 (473)
17 KOG3209 WW domain-containing p 99.7 4.9E-16 1.1E-20 178.4 28.8 177 257-456 349-566 (984)
18 PRK10779 zinc metallopeptidase 99.7 2E-16 4.2E-21 188.3 19.7 157 902-1077 129-289 (449)
19 PF12812 PDZ_1: PDZ-like domai 99.6 4.8E-15 1E-19 131.1 7.6 77 368-444 1-78 (78)
20 TIGR00054 RIP metalloprotease 99.6 4.4E-14 9.5E-19 166.6 17.9 144 899-1078 128-272 (420)
21 PRK10779 zinc metallopeptidase 99.5 2E-13 4.4E-18 162.6 17.2 141 302-454 130-278 (449)
22 PF13365 Trypsin_2: Trypsin-li 99.5 2.4E-13 5.1E-18 131.8 12.3 110 70-216 1-120 (120)
23 TIGR00054 RIP metalloprotease 99.4 3.5E-12 7.6E-17 150.5 13.8 129 297-454 128-260 (420)
24 PF13180 PDZ_2: PDZ domain; PD 99.2 1.1E-10 2.4E-15 105.6 10.9 78 261-362 1-80 (82)
25 PF12812 PDZ_1: PDZ-like domai 99.1 1.2E-10 2.5E-15 103.4 8.2 76 976-1055 2-78 (78)
26 PF13180 PDZ_2: PDZ domain; PD 99.1 3.6E-10 7.7E-15 102.4 11.1 69 1007-1076 14-82 (82)
27 PF13365 Trypsin_2: Trypsin-li 99.0 9.1E-10 2E-14 106.6 10.6 55 651-709 1-65 (120)
28 cd00987 PDZ_serine_protease PD 99.0 4.7E-09 1E-13 96.5 11.7 87 261-361 1-89 (90)
29 cd00987 PDZ_serine_protease PD 99.0 5E-09 1.1E-13 96.4 11.2 88 984-1073 2-89 (90)
30 cd00991 PDZ_archaeal_metallopr 98.9 1.8E-08 3.9E-13 90.5 10.8 68 1007-1075 10-77 (79)
31 cd00986 PDZ_LON_protease PDZ d 98.8 2.9E-08 6.2E-13 89.2 10.2 70 296-366 7-78 (79)
32 cd00991 PDZ_archaeal_metallopr 98.8 4.6E-08 9.9E-13 87.9 10.4 68 898-969 9-77 (79)
33 cd00986 PDZ_LON_protease PDZ d 98.7 8.1E-08 1.7E-12 86.2 10.7 69 1007-1077 8-76 (79)
34 cd00989 PDZ_metalloprotease PD 98.7 1.1E-07 2.3E-12 85.2 10.6 66 1008-1075 13-78 (79)
35 PF00089 Trypsin: Trypsin; In 98.7 3.2E-07 6.9E-12 98.4 15.8 177 46-238 12-219 (220)
36 cd00990 PDZ_glycyl_aminopeptid 98.6 1.8E-07 3.9E-12 84.1 9.9 63 297-362 12-75 (80)
37 TIGR01713 typeII_sec_gspC gene 98.6 3.6E-07 7.8E-12 100.5 14.2 97 233-362 159-257 (259)
38 cd00988 PDZ_CTP_protease PDZ d 98.6 2.9E-07 6.4E-12 83.7 9.9 66 296-362 12-81 (85)
39 cd00989 PDZ_metalloprotease PD 98.6 2.5E-07 5.3E-12 82.9 9.1 63 300-362 14-77 (79)
40 TIGR01713 typeII_sec_gspC gene 98.5 1.4E-06 3.1E-11 95.8 15.8 101 831-970 158-259 (259)
41 cd00988 PDZ_CTP_protease PDZ d 98.5 4.5E-07 9.7E-12 82.5 9.6 68 1007-1076 13-83 (85)
42 KOG3580 Tight junction protein 98.5 4.7E-07 1E-11 103.5 11.1 55 1008-1062 430-486 (1027)
43 cd00990 PDZ_glycyl_aminopeptid 98.5 6.6E-07 1.4E-11 80.4 9.7 66 1008-1077 13-78 (80)
44 cd00190 Tryp_SPc Trypsin-like 98.4 3.9E-06 8.4E-11 90.7 15.5 164 46-221 12-208 (232)
45 cd00136 PDZ PDZ domain, also c 98.3 2.4E-06 5.2E-11 74.6 8.2 53 298-351 14-69 (70)
46 cd00136 PDZ PDZ domain, also c 98.3 3E-06 6.4E-11 74.0 7.8 53 1008-1061 14-68 (70)
47 smart00020 Tryp_SPc Trypsin-li 98.2 2.6E-05 5.7E-10 84.3 16.7 164 46-221 13-208 (229)
48 KOG3580 Tight junction protein 98.2 1.1E-05 2.3E-10 92.8 12.2 159 295-456 217-491 (1027)
49 KOG3209 WW domain-containing p 98.2 1.3E-05 2.9E-10 94.0 12.8 138 297-440 674-825 (984)
50 COG3591 V8-like Glu-specific e 98.1 5.4E-05 1.2E-09 81.7 14.7 178 47-242 38-249 (251)
51 PF00863 Peptidase_C4: Peptida 98.0 0.00012 2.5E-09 78.5 15.6 165 44-233 15-185 (235)
52 PF14685 Tricorn_PDZ: Tricorn 98.0 4.1E-05 8.8E-10 69.6 9.8 65 297-361 11-87 (88)
53 smart00228 PDZ Domain present 98.0 3.1E-05 6.8E-10 69.9 8.7 58 297-355 26-85 (85)
54 PF00595 PDZ: PDZ domain (Also 97.9 2.8E-05 6.1E-10 70.0 7.7 54 297-352 25-81 (81)
55 PF00595 PDZ: PDZ domain (Also 97.9 2.8E-05 6.1E-10 70.0 7.5 53 1007-1061 25-79 (81)
56 TIGR02860 spore_IV_B stage IV 97.9 7E-05 1.5E-09 86.3 12.4 68 1007-1076 105-180 (402)
57 KOG3834 Golgi reassembly stack 97.9 0.00012 2.6E-09 82.6 13.1 164 898-1080 14-183 (462)
58 smart00228 PDZ Domain present 97.9 3.7E-05 7.9E-10 69.5 7.6 60 1007-1067 26-85 (85)
59 cd00992 PDZ_signaling PDZ doma 97.9 4.2E-05 9.2E-10 68.8 8.0 52 1008-1061 27-80 (82)
60 PLN00049 carboxyl-terminal pro 97.9 6.7E-05 1.5E-09 88.2 11.4 76 1008-1085 103-180 (389)
61 TIGR03279 cyano_FeS_chp putati 97.9 2.8E-05 6.2E-10 90.0 8.0 63 1011-1077 2-64 (433)
62 TIGR00225 prc C-terminal pepti 97.8 4.3E-05 9.2E-10 88.2 8.5 65 297-362 62-129 (334)
63 TIGR00225 prc C-terminal pepti 97.8 9.9E-05 2.1E-09 85.2 11.1 77 1008-1086 63-143 (334)
64 TIGR02860 spore_IV_B stage IV 97.7 9.1E-05 2E-09 85.4 9.4 67 296-362 104-178 (402)
65 PLN00049 carboxyl-terminal pro 97.7 0.00012 2.5E-09 86.2 9.6 64 298-362 103-169 (389)
66 cd00992 PDZ_signaling PDZ doma 97.7 0.00012 2.7E-09 65.7 7.3 53 297-351 26-81 (82)
67 PF04495 GRASP55_65: GRASP55/6 97.7 0.00019 4E-09 71.3 8.9 73 1007-1080 43-117 (138)
68 TIGR03279 cyano_FeS_chp putati 97.7 0.00012 2.6E-09 84.9 8.6 61 903-971 2-64 (433)
69 PF00089 Trypsin: Trypsin; In 97.6 0.0018 4E-08 69.1 16.6 169 648-838 24-220 (220)
70 COG0793 Prc Periplasmic protea 97.5 0.00026 5.7E-09 83.2 9.6 78 1008-1087 113-194 (406)
71 PF14685 Tricorn_PDZ: Tricorn 97.3 0.0015 3.3E-08 59.4 9.9 64 899-967 12-87 (88)
72 COG0793 Prc Periplasmic protea 97.3 0.00082 1.8E-08 79.1 9.2 65 297-362 112-181 (406)
73 KOG3553 Tax interaction protei 97.2 0.00028 6.1E-09 63.5 3.5 57 1007-1067 59-117 (124)
74 PRK09681 putative type II secr 97.2 0.0011 2.4E-08 72.8 8.4 62 905-970 210-275 (276)
75 COG3480 SdrC Predicted secrete 97.1 0.0015 3.2E-08 71.6 8.4 70 1007-1077 130-199 (342)
76 PF04495 GRASP55_65: GRASP55/6 97.1 0.0011 2.4E-08 65.8 6.9 83 260-362 25-111 (138)
77 cd00190 Tryp_SPc Trypsin-like 97.1 0.0079 1.7E-07 64.7 14.0 94 647-747 23-133 (232)
78 PRK09681 putative type II secr 97.1 0.0018 3.9E-08 71.2 8.7 66 296-362 203-273 (276)
79 KOG3605 Beta amyloid precursor 97.0 0.0013 2.8E-08 77.3 7.5 114 305-440 680-802 (829)
80 PRK11186 carboxy-terminal prot 97.0 0.0022 4.7E-08 79.5 9.6 69 1008-1078 256-335 (667)
81 COG3480 SdrC Predicted secrete 97.0 0.0025 5.5E-08 69.8 8.8 71 899-973 130-201 (342)
82 PF00863 Peptidase_C4: Peptida 96.9 0.011 2.3E-07 63.7 13.1 178 621-841 13-196 (235)
83 KOG3605 Beta amyloid precursor 96.9 0.0014 3.1E-08 77.0 6.7 120 903-1051 677-802 (829)
84 smart00020 Tryp_SPc Trypsin-li 96.9 0.013 2.8E-07 63.2 13.5 93 647-747 24-133 (229)
85 KOG3834 Golgi reassembly stack 96.9 0.012 2.7E-07 66.8 13.3 161 297-474 15-185 (462)
86 KOG3129 26S proteasome regulat 96.8 0.0037 8E-08 64.4 7.7 69 1008-1078 140-211 (231)
87 KOG3129 26S proteasome regulat 96.8 0.004 8.6E-08 64.2 7.6 71 297-367 138-213 (231)
88 PRK11186 carboxy-terminal prot 96.7 0.0037 8.1E-08 77.4 8.8 63 300-362 257-331 (667)
89 COG3975 Predicted protease wit 96.6 0.0029 6.3E-08 73.8 6.3 80 263-362 439-520 (558)
90 COG3031 PulC Type II secretory 96.6 0.0045 9.7E-08 65.0 6.9 66 900-969 208-274 (275)
91 PF10459 Peptidase_S46: Peptid 96.2 0.013 2.8E-07 73.0 8.8 42 117-158 200-252 (698)
92 COG3975 Predicted protease wit 95.9 0.014 3E-07 68.3 6.4 77 982-1080 450-526 (558)
93 COG3031 PulC Type II secretory 95.8 0.018 3.9E-07 60.6 6.3 60 303-362 212-273 (275)
94 PF05579 Peptidase_S32: Equine 95.6 0.084 1.8E-06 56.8 10.4 117 66-221 110-229 (297)
95 PF05580 Peptidase_S55: SpoIVB 95.4 0.18 3.9E-06 53.2 11.9 168 66-236 18-216 (218)
96 KOG3553 Tax interaction protei 95.3 0.022 4.8E-07 51.6 4.3 46 395-440 56-105 (124)
97 COG3591 V8-like Glu-specific e 94.8 0.46 1E-05 51.8 13.3 170 649-841 64-249 (251)
98 KOG3550 Receptor targeting pro 94.7 0.079 1.7E-06 51.7 6.3 53 297-351 115-171 (207)
99 PF02122 Peptidase_S39: Peptid 94.6 0.0098 2.1E-07 62.8 0.1 144 66-232 28-181 (203)
100 PF10459 Peptidase_S46: Peptid 94.4 0.04 8.7E-07 68.7 4.7 55 190-244 623-688 (698)
101 KOG3542 cAMP-regulated guanine 94.1 0.037 8.1E-07 65.4 3.5 55 1006-1061 561-615 (1283)
102 KOG3532 Predicted protein kina 93.9 0.13 2.9E-06 61.2 7.2 57 296-353 396-453 (1051)
103 KOG3552 FERM domain protein FR 93.5 0.072 1.6E-06 65.5 4.5 53 300-353 77-131 (1298)
104 PF00548 Peptidase_C3: 3C cyst 93.4 1 2.2E-05 46.8 12.2 139 66-220 23-170 (172)
105 KOG3532 Predicted protein kina 93.3 0.17 3.6E-06 60.5 6.8 46 899-944 398-444 (1051)
106 PF00949 Peptidase_S7: Peptida 93.3 0.055 1.2E-06 53.1 2.5 31 191-221 88-118 (132)
107 PF08192 Peptidase_S64: Peptid 92.5 0.51 1.1E-05 57.2 9.4 121 114-242 540-688 (695)
108 KOG3571 Dishevelled 3 and rela 91.8 0.45 9.7E-06 55.4 7.5 63 982-1052 260-325 (626)
109 KOG3550 Receptor targeting pro 91.7 0.38 8.2E-06 47.1 5.9 52 1008-1061 116-170 (207)
110 KOG1892 Actin filament-binding 89.7 0.4 8.7E-06 59.3 5.0 61 295-356 958-1021(1629)
111 PF03761 DUF316: Domain of unk 89.7 8.8 0.00019 43.1 15.8 106 115-236 159-272 (282)
112 KOG3542 cAMP-regulated guanine 89.2 0.32 7E-06 57.9 3.7 53 398-451 562-616 (1283)
113 KOG3627 Trypsin [Amino acid tr 89.2 8.8 0.00019 42.2 15.1 147 69-222 39-229 (256)
114 PF11874 DUF3394: Domain of un 88.4 1.9 4.1E-05 44.8 8.2 83 933-1034 62-149 (183)
115 KOG3552 FERM domain protein FR 88.2 0.57 1.2E-05 58.1 4.9 56 899-960 75-132 (1298)
116 COG0750 Predicted membrane-ass 87.1 1.6 3.6E-05 51.1 8.0 54 304-357 135-193 (375)
117 KOG2921 Intramembrane metallop 86.5 0.92 2E-05 51.5 4.9 46 1006-1051 219-265 (484)
118 KOG3606 Cell polarity protein 86.0 1.3 2.7E-05 47.9 5.4 54 1008-1061 195-251 (358)
119 COG0750 Predicted membrane-ass 85.6 2.8 6E-05 49.2 8.9 58 1010-1069 132-193 (375)
120 KOG0606 Microtubule-associated 85.3 1.2 2.6E-05 57.0 5.6 51 1010-1062 661-713 (1205)
121 KOG1892 Actin filament-binding 85.2 1 2.2E-05 56.0 4.8 67 892-962 953-1021(1629)
122 PF00548 Peptidase_C3: 3C cyst 84.7 13 0.00029 38.6 12.3 151 622-808 9-169 (172)
123 KOG3606 Cell polarity protein 83.7 2.7 5.8E-05 45.4 6.6 60 295-356 192-255 (358)
124 KOG0609 Calcium/calmodulin-dep 83.2 2 4.2E-05 51.1 5.9 74 1008-1083 147-226 (542)
125 KOG3651 Protein kinase C, alph 82.4 2.4 5.3E-05 46.3 5.7 54 297-352 30-87 (429)
126 PF00944 Peptidase_S3: Alphavi 82.3 1.2 2.5E-05 43.2 3.0 32 191-222 97-128 (158)
127 KOG3551 Syntrophins (type beta 80.8 1.4 3E-05 49.9 3.3 55 296-351 109-166 (506)
128 KOG3571 Dishevelled 3 and rela 77.3 3.3 7.2E-05 48.5 5.1 70 398-483 277-351 (626)
129 PF08192 Peptidase_S64: Peptid 75.4 26 0.00055 43.3 11.9 125 698-841 540-688 (695)
130 KOG3551 Syntrophins (type beta 75.2 2.8 6E-05 47.6 3.6 51 1009-1061 112-165 (506)
131 KOG3549 Syntrophins (type gamm 73.9 4.2 9E-05 45.4 4.5 53 300-352 82-137 (505)
132 PF03510 Peptidase_C24: 2C end 72.1 10 0.00022 35.8 6.0 52 72-135 3-54 (105)
133 KOG2921 Intramembrane metallop 71.6 5.5 0.00012 45.5 4.9 46 295-341 218-265 (484)
134 KOG3651 Protein kinase C, alph 71.4 9.1 0.0002 42.1 6.3 57 896-958 27-87 (429)
135 PF01732 DUF31: Putative pepti 69.5 2.9 6.2E-05 49.2 2.4 30 190-219 345-374 (374)
136 KOG0609 Calcium/calmodulin-dep 69.4 8.6 0.00019 45.9 6.1 52 300-352 148-203 (542)
137 KOG0606 Microtubule-associated 63.4 10 0.00022 49.0 5.4 48 302-350 662-712 (1205)
138 PF11874 DUF3394: Domain of un 60.1 44 0.00095 35.0 8.5 80 332-424 62-150 (183)
139 KOG3938 RGS-GAIP interacting p 59.0 24 0.00052 38.4 6.4 56 1009-1064 151-209 (334)
140 KOG3549 Syntrophins (type gamm 56.7 14 0.0003 41.5 4.4 54 901-958 82-137 (505)
141 PF02907 Peptidase_S29: Hepati 55.2 7.9 0.00017 37.8 2.0 113 71-219 15-127 (148)
142 COG5233 GRH1 Peripheral Golgi 50.4 35 0.00076 38.1 6.1 68 1015-1082 195-265 (417)
143 PF00949 Peptidase_S7: Peptida 50.3 12 0.00027 36.9 2.6 28 780-808 89-116 (132)
144 PF12381 Peptidase_C3G: Tungro 46.6 27 0.00058 37.1 4.4 56 188-243 168-229 (231)
145 PF05416 Peptidase_C37: Southa 45.1 73 0.0016 37.2 7.8 136 68-221 379-527 (535)
146 COG0298 HypC Hydrogenase matur 44.5 37 0.00081 30.3 4.2 48 689-744 4-52 (82)
147 PF00947 Pico_P2A: Picornaviru 34.5 44 0.00096 32.6 3.5 33 188-221 78-110 (127)
148 KOG4407 Predicted Rho GTPase-a 33.9 28 0.0006 45.7 2.6 87 303-443 101-192 (1973)
149 cd01735 LSm12_N LSm12 belongs 31.5 1.1E+02 0.0023 26.2 4.9 32 678-710 8-39 (61)
150 KOG3938 RGS-GAIP interacting p 30.7 41 0.00088 36.7 2.8 55 900-958 150-208 (334)
151 KOG1738 Membrane-associated gu 27.9 34 0.00074 41.8 2.0 37 297-333 224-262 (638)
152 KOG4371 Membrane-associated pr 27.0 1.5E+02 0.0032 38.7 7.0 115 314-431 1186-1306(1332)
153 PF00944 Peptidase_S3: Alphavi 26.7 87 0.0019 30.8 4.0 23 790-812 107-129 (158)
154 PF01455 HupF_HypC: HupF/HypC 26.2 1.3E+02 0.0029 26.2 4.8 44 689-741 4-47 (68)
155 cd01726 LSm6 The eukaryotic Sm 26.1 1E+02 0.0022 26.6 4.0 31 677-708 11-41 (67)
156 cd00600 Sm_like The eukaryotic 25.3 1.3E+02 0.0027 25.2 4.5 31 677-708 7-37 (63)
157 cd01732 LSm5 The eukaryotic Sm 25.1 1.2E+02 0.0025 27.1 4.3 30 677-707 14-43 (76)
158 cd01717 Sm_B The eukaryotic Sm 23.4 1.2E+02 0.0025 27.2 4.1 31 677-708 11-41 (79)
159 PF09342 DUF1986: Domain of un 23.3 6.7E+02 0.015 27.6 10.2 90 66-157 26-131 (267)
160 cd01722 Sm_F The eukaryotic Sm 22.9 1.2E+02 0.0027 26.2 4.0 31 677-708 12-42 (68)
161 cd06168 LSm9 The eukaryotic Sm 22.7 1.5E+02 0.0032 26.4 4.5 31 677-708 11-41 (75)
162 KOG4371 Membrane-associated pr 22.4 1.2E+02 0.0025 39.6 5.0 117 916-1042 1187-1306(1332)
163 cd01730 LSm3 The eukaryotic Sm 22.4 1.1E+02 0.0025 27.5 3.8 29 677-706 12-40 (82)
164 cd01719 Sm_G The eukaryotic Sm 22.0 1.5E+02 0.0032 26.1 4.4 57 677-742 11-67 (72)
165 KOG1738 Membrane-associated gu 21.8 1E+02 0.0022 37.9 4.3 46 899-945 225-272 (638)
166 cd01729 LSm7 The eukaryotic Sm 21.5 1.5E+02 0.0032 26.7 4.4 31 677-708 13-43 (81)
167 PRK00737 small nuclear ribonuc 21.2 1.5E+02 0.0032 26.0 4.2 31 677-708 15-45 (72)
168 cd01731 archaeal_Sm1 The archa 21.1 1.5E+02 0.0033 25.5 4.2 31 677-708 11-41 (68)
169 cd01728 LSm1 The eukaryotic Sm 21.0 1.7E+02 0.0036 26.0 4.4 60 677-742 13-72 (74)
170 PF02122 Peptidase_S39: Peptid 20.9 6.7E+02 0.015 26.9 9.8 133 651-809 30-166 (203)
171 PF15436 PGBA_N: Plasminogen-b 20.8 6.1E+02 0.013 27.5 9.4 66 85-152 22-88 (218)
172 PF05579 Peptidase_S32: Equine 20.0 2.4E+02 0.0053 31.2 6.3 19 790-808 209-227 (297)
No 1
>KOG1421 consensus Predicted signaling-associated protein (contains a PDZ domain) [General function prediction only]
Probab=100.00 E-value=1e-155 Score=1306.18 Aligned_cols=918 Identities=46% Similarity=0.717 Sum_probs=857.5
Q ss_pred cccccccCCCCCccCccCchhHHHHHHHhCCceEEEEEeeeeccCCCCCCccEEEEEEEeCCCcEEEEcccccCCCCeEE
Q 001280 17 KEDMCMEVDPPLRENVATADDWRKALNKVVPAVVVLRTTACRAFDTEAAGASYATGFVVDKRRGIILTNRHVVKPGPVVA 96 (1108)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sVV~I~~~~~~~~d~~~~~~~~GSGfvV~~~~G~ILTn~HVV~~~~~~~ 96 (1108)
+++++.+..|+.....+...+|+..+..+.+|||+|++.....||++.++.+.||||+|++..|||||||||+.+++...
T Consensus 33 ~~el~~e~~p~~~~s~~~~e~w~~~ia~VvksvVsI~~S~v~~fdtesag~~~atgfvvd~~~gyiLtnrhvv~pgP~va 112 (955)
T KOG1421|consen 33 KEELVIEPDPPLNESLATSEDWRNTIANVVKSVVSIRFSAVRAFDTESAGESEATGFVVDKKLGYILTNRHVVAPGPFVA 112 (955)
T ss_pred hcccccccCCCCCcccchhhhhhhhhhhhcccEEEEEehheeecccccccccceeEEEEecccceEEEeccccCCCCcee
Confidence 44466666666666677778999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCeEEeEEEEEEcCCCceEEEEECCCCcccccccCCCCCCcccCCCCEEEEEecCCCCCCeEEEEEEEEecCCCC
Q 001280 97 EAMFVNREEIPVYPIYRDPVHDFGFFRYDPSAIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAP 176 (1108)
Q Consensus 97 ~v~~~d~~~~~a~vv~~d~~~DlAlLk~d~~~~~~~~~~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~is~~~~~~~ 176 (1108)
.+.|.|.++++..++|+||.|||+|++++|+.+.+..+..+.++++..++|.+++++||+++++.++..|.+++++|++|
T Consensus 113 ~avf~n~ee~ei~pvyrDpVhdfGf~r~dps~ir~s~vt~i~lap~~akvgseirvvgNDagEklsIlagflSrldr~ap 192 (955)
T KOG1421|consen 113 SAVFDNHEEIEIYPVYRDPVHDFGFFRYDPSTIRFSIVTEICLAPELAKVGSEIRVVGNDAGEKLSILAGFLSRLDRNAP 192 (955)
T ss_pred EEEecccccCCcccccCCchhhcceeecChhhcceeeeeccccCccccccCCceEEecCCccceEEeehhhhhhccCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCcccccceEEEEeeecCCCCCCCceecccCcEEEEeecccCCCCcccccChHHHHHHHHHHHhcCCccccccccc
Q 001280 177 HYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSSSASAFFLPLERVVRALRFLQERRDCNIHNWEAV 256 (1108)
Q Consensus 177 ~~~~~~~~~~~~~~i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~~~~~falPi~~i~~~l~~l~~~~~~~~~~~~~~ 256 (1108)
.|++..|++||++|+|..+..++|+||+||+|.+|++|++++++...++.+|+||+++++|+|.++|+++
T Consensus 193 dyg~~~yndfnTfy~QaasstsggssgspVv~i~gyAVAl~agg~~ssas~ffLpLdrV~RaL~clq~n~---------- 262 (955)
T KOG1421|consen 193 DYGEDTYNDFNTFYIQAASSTSGGSSGSPVVDIPGYAVALNAGGSISSASDFFLPLDRVVRALRCLQNNT---------- 262 (955)
T ss_pred cccccccccccceeeeehhcCCCCCCCCceecccceEEeeecCCcccccccceeeccchhhhhhhhhcCC----------
Confidence 9999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccCCCccCeEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCCccccCCCCCCEEEEECCEEeCChhHHH
Q 001280 257 SIPRGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHLRLEPGDVLVRVNGEVITQFLKLE 336 (1108)
Q Consensus 257 ~v~rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~gL~~GD~Il~VnG~~v~~~~~l~ 336 (1108)
+++||+|+++|.++.++|||+|||+.|||+.+|.++| ..+|||||+.|+++|||++.|++||++++||+..+.+|..+.
T Consensus 263 PItRGtLqvefl~k~~de~rrlGL~sE~eqv~r~k~P-~~tgmLvV~~vL~~gpa~k~Le~GDillavN~t~l~df~~l~ 341 (955)
T KOG1421|consen 263 PITRGTLQVEFLHKLFDECRRLGLSSEWEQVVRTKFP-ERTGMLVVETVLPEGPAEKKLEPGDILLAVNSTCLNDFEALE 341 (955)
T ss_pred CcccceEEEEEehhhhHHHHhcCCcHHHHHHHHhcCc-ccceeEEEEEeccCCchhhccCCCcEEEEEcceehHHHHHHH
Confidence 8999999999999999999999999999999999999 799999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCeEEEEEEECCEEEEEEE-cccccccCCCcccccCCeEEccCCHHHhhccCcCCCeEEEECCCChhHHcCCC
Q 001280 337 TLLDDGVDKNIELLIERGGISMTVNL-VQDLHSITPDYFLEVSGAVIHPLSYQQARNFRFPCGLVYVAEPGYMLFRAGVP 415 (1108)
Q Consensus 337 ~~l~~~~g~~v~l~V~R~g~~~~~~v-~~~~~~~~~~~~~~~~G~~~~~l~~q~~~~~~~~~~gv~v~~~~~~a~~aGl~ 415 (1108)
.+|++.+|+.++|+|+|+|+++++++ ++++|.++|+||++|||++||+++||++|.|.+|++|+||+++++.++..+-.
T Consensus 342 ~iLDegvgk~l~LtI~Rggqelel~vtvqdlh~itp~R~levcGav~hdlsyq~ar~y~lP~~GvyVa~~~gsf~~~~~~ 421 (955)
T KOG1421|consen 342 QILDEGVGKNLELTIQRGGQELELTVTVQDLHGITPDRFLEVCGAVFHDLSYQLARLYALPVEGVYVASPGGSFRHRGPR 421 (955)
T ss_pred HHHhhccCceEEEEEEeCCEEEEEEEEeccccCCCCceEEEEcceEecCCCHHHHhhcccccCcEEEccCCCCccccCCc
Confidence 99999999999999999999999999 99999999999999999999999999999999999999999986555544433
Q ss_pred CCCEEEEeCCeecCCHHHHHHHHHhcCCCCeEEEEEeeecccccceEEEEEEecCCCCCCCeeEEecCCCCCceecccCC
Q 001280 416 RHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYSSYTDRHRRKSVLVTIDRHEWYAPPQIYTRNDSSGLWSANPAIL 495 (1108)
Q Consensus 416 ~Gd~I~~Vng~~v~~l~~~~~~i~~~~~~~~v~l~~~~~~~~~~~~~~~l~idR~~~~~~~~~~~r~d~~g~W~~~~~~~ 495 (1108)
-|++|.+|||+++++|++|+++++++++|+||+++|++++|+|+++..+++||| ||||++++++|||++|+||++.+.+
T Consensus 422 y~~ii~~vanK~tPdLdaFidvlk~L~dg~rV~vry~hl~dkh~p~v~~v~iDr-Hwy~p~~~~trndetglWdrk~L~~ 500 (955)
T KOG1421|consen 422 YGQIIDSVANKPTPDLDAFIDVLKELPDGARVPVRYHHLTDKHSPRVTTVTIDR-HWYWPFREYTRNDETGLWDRKNLKD 500 (955)
T ss_pred ceEEEEeecCCcCCCHHHHHHHHHhccCCCeeeEEEEEecCCCCceEEEEEEec-cccccceeeeeCCCcccccccccCC
Confidence 499999999999999999999999999999999999999999999999999999 9999999999999999999999999
Q ss_pred CCCCCCCCCCCCCccCcccccccccccccccccccccCccccccCccccchhcccccccccccCCCcccccccceeeccc
Q 001280 496 SEVLMPSSGINGGVQGVASQTVSICGELVHMEHMHQRNNQELTDGVTSMETACEHASAESISRGESDNGRKKRRVEENIS 575 (1108)
Q Consensus 496 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~ 575 (1108)
|.| +.+.+|.+.+.. +
T Consensus 501 pqP--------------a~~~kP~s~~ip------------------~-------------------------------- 516 (955)
T KOG1421|consen 501 PQP--------------AISIKPASVSIP------------------S-------------------------------- 516 (955)
T ss_pred CCc--------------ccccCCccccCC------------------C--------------------------------
Confidence 887 345666554422 0
Q ss_pred cCCccccCCCCCCCCccccccccccccCCCCCCCCCcccCccccccccccccEEEEEEEcCcccccCCcccceeeEEEEE
Q 001280 576 ADGVVADCSPHESGDARLEDSSTMENAGSRDYFGAPAATTNASFAESVIEPTLVMFEVHVPPSCMIDGVHSQHFFGTGVI 655 (1108)
Q Consensus 576 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~S~V~V~~~~~~~~~~dg~~~~~~~GsG~i 655 (1108)
++ ..++..+.+..++|.|.+.+| ..+||..+....|||+|
T Consensus 517 -----------------i~---------------------~~~~~~~~i~~~~~~v~~~~~--~~l~g~s~~i~kgt~~i 556 (955)
T KOG1421|consen 517 -----------------IG---------------------VNNFPSADISNCLVDVEPMMP--VNLDGVSSDIYKGTALI 556 (955)
T ss_pred -----------------cC---------------------cCCcchhHHhhhhhhheecee--eccccchhhhhcCceEE
Confidence 11 012234568899999999999 59999999889999999
Q ss_pred EEeeCCceEEEEeCceecCCCceEEEEeecCCeEEeEEEEEeeCCCcEEEEEECCCCCCcccccceeccccCCCccCCCC
Q 001280 656 IYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGEVVFLHPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRG 735 (1108)
Q Consensus 656 Id~~~~~G~IlTnr~~V~~~~~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G 735 (1108)
++ .++||++++|.+|+.+++|++|++++ +..++|.+.|+||.+|+|++||||++.-. ++|.+.. +++|
T Consensus 557 ~d--~~~g~~vvsr~~vp~d~~d~~vt~~d-S~~i~a~~~fL~~t~n~a~~kydp~~~~~--------~kl~~~~-v~~g 624 (955)
T KOG1421|consen 557 MD--TSKGLGVVSRSVVPSDAKDQRVTEAD-SDGIPANVSFLHPTENVASFKYDPALEVQ--------LKLTDTT-VLRG 624 (955)
T ss_pred EE--ccCCceeEecccCCchhhceEEeecc-cccccceeeEecCccceeEeccChhHhhh--------hccceee-EecC
Confidence 99 47999999999999999999999998 99999999999999999999999986644 8898776 9999
Q ss_pred CEEEEEeeCCCCCceeeeeeEeccccccccCCCCCCccccccceEEEEecccCCCC-CceEEcCCeeEEEEEeecccccc
Q 001280 736 DSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRAMNMEVIELDTDFGSTF-SGVLTDEHGRVQAIWGSFSTQVK 814 (1108)
Q Consensus 736 ~~V~~vG~p~~~~~~~~~~~Vt~~~~~~~i~~~~~~~y~~~~~~~I~~d~~ig~~s-GGpL~d~~G~VvGi~~~~~~~~~ 814 (1108)
|++.+.|+..+.+.++++++|++++ ..++++...||||++|+++|.++++++..| .|.|.|.||+|+|+|.++.++.
T Consensus 625 D~~~f~g~~~~~r~ltaktsv~dvs-~~~~ps~~~pr~r~~n~e~Is~~~nlsT~c~sg~ltdddg~vvalwl~~~ge~- 702 (955)
T KOG1421|consen 625 DECTFEGFTEDLRALTAKTSVTDVS-VVIIPSSVMPRFRATNLEVISFMDNLSTSCLSGRLTDDDGEVVALWLSVVGED- 702 (955)
T ss_pred CceeEecccccchhhcccceeeeeE-EEEecCCCCcceeecceEEEEEeccccccccceEEECCCCeEEEEEeeeeccc-
Confidence 9999999999999999999999987 788999999999999999999999998767 9999999999999999988873
Q ss_pred ccCCCCCcceeEecccHHHHHHHHHHHHcCCCCCcccccCcccCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcC
Q 001280 815 FGCSSSEDHQFVRGIPIYTISRVLDKIISGASGPSLLINGVKRPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKD 894 (1108)
Q Consensus 815 ~~~~~~~~~~~~~aipi~~i~~vl~~l~~~~~~~~~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~ 894 (1108)
.++.+..|.+|+.+.+++++|++|+.|.+ +..+++|+||..|+.++||.+|+|.||+-+++...
T Consensus 703 ---~~~kd~~y~~gl~~~~~l~vl~rlk~g~~-------------~rp~i~~vef~~i~laqar~lglp~e~imk~e~es 766 (955)
T KOG1421|consen 703 ---VGGKDYTYKYGLSMSYILPVLERLKLGPS-------------ARPTIAGVEFSHITLAQARTLGLPSEFIMKSEEES 766 (955)
T ss_pred ---cCCceeEEEeccchHHHHHHHHHHhcCCC-------------CCceeeccceeeEEeehhhccCCCHHHHhhhhhcC
Confidence 45788899999999999999999999953 34579999999999999999999999999999999
Q ss_pred CCccceEEEEeecCCCHHhHhccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeecccC
Q 001280 895 PVRRQVLRVKGCLAGSKAENMLEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRD 974 (1108)
Q Consensus 895 ~~~~~~~~V~~V~~~s~A~~aL~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~~~~~ 974 (1108)
..++|+++|++|.+..+ +.|..||+|+++|||.|+.++||.. + ..++++|+|+|.++++++|+-+..
T Consensus 767 ~~~~ql~~ishv~~~~~--kil~~gdiilsvngk~itr~~dl~d-~----------~eid~~ilrdg~~~~ikipt~p~~ 833 (955)
T KOG1421|consen 767 TIPRQLYVISHVRPLLH--KILGVGDIILSVNGKMITRLSDLHD-F----------EEIDAVILRDGIEMEIKIPTYPEY 833 (955)
T ss_pred CCcceEEEEEeeccCcc--cccccccEEEEecCeEEeeehhhhh-h----------hhhheeeeecCcEEEEEecccccc
Confidence 99999999999987654 3399999999999999999999986 3 358899999999999999998765
Q ss_pred CCCCcceeeeccccccCCchhhhhc-CCCCCCCCeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCC
Q 001280 975 GNGTTRVINWCGCIVQDPHPAVRAL-GFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIE 1053 (1108)
Q Consensus 975 ~~~t~~~~~~~G~~~~~p~~~vr~~-~~lp~~~~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~ 1053 (1108)
+++|++.|.|+++|.||++++++ ..+|. ||||+.+..||||.+ +|.+..||++|||..++++|+|..+++++|
T Consensus 834 --et~r~vi~~gailq~ph~av~~q~edlp~---gvyvt~rg~gspalq-~l~aa~fitavng~~t~~lddf~~~~~~ip 907 (955)
T KOG1421|consen 834 --ETSRAVIWMGAILQPPHSAVFEQVEDLPE---GVYVTSRGYGSPALQ-MLRAAHFITAVNGHDTNTLDDFYHMLLEIP 907 (955)
T ss_pred --ccceEEEEEeccccCchHHHHHHHhccCC---ceEEeecccCChhHh-hcchheeEEEecccccCcHHHHHHHHhhCC
Confidence 89999999999999999999985 88998 999999999999999 999999999999999999999999999999
Q ss_pred CCceEEEEEEEeCCeEEEEEEEeCCccCcceEEEEcCCCCCeEEEEe
Q 001280 1054 HGEFVRVRTVHLNGKPRVLTLKQDLHYWPTWELIFDPDTALWRRKSV 1100 (1108)
Q Consensus 1054 ~~~~v~l~~v~rdg~~~~~~lk~d~~y~pt~el~~~~~~~~W~~~~~ 1100 (1108)
+|.||+++.++|+|.|..+++|+|+|||||.+|.+|..+. |+.++.
T Consensus 908 dnsyv~v~~mtfd~vp~~~s~k~n~hyfpt~~l~rd~~~~-wi~kev 953 (955)
T KOG1421|consen 908 DNSYVQVKQMTFDGVPSIVSVKPNPHYFPTCILERDSNGR-WITKEV 953 (955)
T ss_pred CCceEEEEEeccCCCceEEEeccCCccCceeEEEecccCc-eeeeec
Confidence 9999999999999999999999999999999999998554 977664
No 2
>PRK10139 serine endoprotease; Provisional
Probab=100.00 E-value=2.9e-52 Score=491.03 Aligned_cols=375 Identities=19% Similarity=0.314 Sum_probs=308.0
Q ss_pred hhHHHHHHHhCCceEEEEEeeeec------------cCC------CCCCccEEEEEEEeCCCcEEEEcccccCCCCeEEE
Q 001280 36 DDWRKALNKVVPAVVVLRTTACRA------------FDT------EAAGASYATGFVVDKRRGIILTNRHVVKPGPVVAE 97 (1108)
Q Consensus 36 ~~~~~~~~~~~~sVV~I~~~~~~~------------~d~------~~~~~~~GSGfvV~~~~G~ILTn~HVV~~~~~~~~ 97 (1108)
.+|..+++++.||||+|.+..... |.. .....+.||||+|++++||||||+|||. +...+.
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 479999999999999999864321 111 1123578999999865799999999999 567899
Q ss_pred EEecCCeEEeEEEEEEcCCCceEEEEECC-CCcccccccCCCCCCcccCCCCEEEEEecCCCCCCeEEEEEEEEecCCCC
Q 001280 98 AMFVNREEIPVYPIYRDPVHDFGFFRYDP-SAIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAP 176 (1108)
Q Consensus 98 v~~~d~~~~~a~vv~~d~~~DlAlLk~d~-~~~~~~~~~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~is~~~~~~~ 176 (1108)
|+|.|+++++|++++.|+.+||||||++. ..++++.+++ +..+++||+|+++|||+|...+++.|+||++.|...
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 5666666665 788999999999999999999999999999988632
Q ss_pred CCCCCCcccccceEEEEeeecCCCCCCCceecccCcEEEEeecccCC----CCcccccChHHHHHHHHHHHhcCCccccc
Q 001280 177 HYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSS----SASAFFLPLERVVRALRFLQERRDCNIHN 252 (1108)
Q Consensus 177 ~~~~~~~~~~~~~~i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~----~~~~falPi~~i~~~l~~l~~~~~~~~~~ 252 (1108)
.. .++. .|||+|+++++|||||||||.+|+||||+++.... .+.+|+||++.+++++++|.+++
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 21 1233 46999999999999999999999999999875432 57899999999999999999988
Q ss_pred ccccccCCCccCeEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCC
Q 001280 253 WEAVSIPRGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQ 331 (1108)
Q Consensus 253 ~~~~~v~rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~ 331 (1108)
.+.|||||+.++.++.+.++.|||+ ...|++| ..|.++|||++ ||++||+|++|||++|.+
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 7899999999999999999999997 5679887 69999999999 999999999999999999
Q ss_pred hhHHHHHHhc-CCCCeEEEEEEECCEEEEEEE-cccccccCCCcc---cccCCeEEccCCHHHhhccCcCCCeEEEE--C
Q 001280 332 FLKLETLLDD-GVDKNIELLIERGGISMTVNL-VQDLHSITPDYF---LEVSGAVIHPLSYQQARNFRFPCGLVYVA--E 404 (1108)
Q Consensus 332 ~~~l~~~l~~-~~g~~v~l~V~R~g~~~~~~v-~~~~~~~~~~~~---~~~~G~~~~~l~~q~~~~~~~~~~gv~v~--~ 404 (1108)
|.++...+.. .+|+++.++|.|+|+.+++++ +........... ..+.|+.+.+. ..+. ...|++|. .
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 9999988854 789999999999999999888 754332111111 12334444431 1111 12578887 4
Q ss_pred CCChhHHcCCCCCCEEEEeCCeecCCHHHHHHHHHhcCCCCeEEEEEee
Q 001280 405 PGYMLFRAGVPRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYSS 453 (1108)
Q Consensus 405 ~~~~a~~aGl~~Gd~I~~Vng~~v~~l~~~~~~i~~~~~~~~v~l~~~~ 453 (1108)
++++|+++||++||+|++|||+++.+|++|.+++++.+ +.+.|++.|
T Consensus 399 ~~spA~~aGL~~GD~I~~Ing~~v~~~~~~~~~l~~~~--~~v~l~v~R 445 (455)
T PRK10139 399 KGSPAAQAGLQKDDVIIGVNRDRVNSIAEMRKVLAAKP--AIIALQIVR 445 (455)
T ss_pred CCChHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhCC--CeEEEEEEE
Confidence 89999999999999999999999999999999998843 345554443
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=4.4e-52 Score=491.53 Aligned_cols=382 Identities=25% Similarity=0.376 Sum_probs=330.4
Q ss_pred hHHHHHHHhCCceEEEEEeeee---------------ccCC----------CCCCccEEEEEEEeCCCcEEEEcccccCC
Q 001280 37 DWRKALNKVVPAVVVLRTTACR---------------AFDT----------EAAGASYATGFVVDKRRGIILTNRHVVKP 91 (1108)
Q Consensus 37 ~~~~~~~~~~~sVV~I~~~~~~---------------~~d~----------~~~~~~~GSGfvV~~~~G~ILTn~HVV~~ 91 (1108)
++.++++++.||||.|.+.... .|.. .....+.||||+|++ +||||||+||+.
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 4788999999999999986421 1111 112457899999997 699999999999
Q ss_pred CCeEEEEEecCCeEEeEEEEEEcCCCceEEEEECCC-CcccccccCCCCCCcccCCCCEEEEEecCCCCCCeEEEEEEEE
Q 001280 92 GPVVAEAMFVNREEIPVYPIYRDPVHDFGFFRYDPS-AIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLAR 170 (1108)
Q Consensus 92 ~~~~~~v~~~d~~~~~a~vv~~d~~~DlAlLk~d~~-~~~~~~~~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~is~ 170 (1108)
+...+.|++.|++.++|++++.|+.+||||||++.. .++++.+++ +..+++|++|+++|||++...+++.|+|++
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 577899999999999999999999999999999865 566666654 678999999999999999999999999999
Q ss_pred ecCCCCCCCCCCcccccceEEEEeeecCCCCCCCceecccCcEEEEeecccCC----CCcccccChHHHHHHHHHHHhcC
Q 001280 171 LDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSS----SASAFFLPLERVVRALRFLQERR 246 (1108)
Q Consensus 171 ~~~~~~~~~~~~~~~~~~~~i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~----~~~~falPi~~i~~~l~~l~~~~ 246 (1108)
..+... ....|.+ +||+++++++|+|||||||.+|+||||+++.... .+.+|+||++.+++++++|++++
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 987632 1223333 6999999999999999999999999999775432 46899999999999999999998
Q ss_pred CcccccccccccCCCccCeEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEEC
Q 001280 247 DCNIHNWEAVSIPRGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVN 325 (1108)
Q Consensus 247 ~~~~~~~~~~~v~rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~Vn 325 (1108)
.+.|+|||+.++.++.+.++.|||+ ...|++| ..|.++|||++ ||++||+|++||
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 7899999999999999999999998 5678887 69999999999 999999999999
Q ss_pred CEEeCChhHHHHHHh-cCCCCeEEEEEEECCEEEEEEE-cccccccCCCcccccCCeEEccCCHHHhhccCcCC--CeEE
Q 001280 326 GEVITQFLKLETLLD-DGVDKNIELLIERGGISMTVNL-VQDLHSITPDYFLEVSGAVIHPLSYQQARNFRFPC--GLVY 401 (1108)
Q Consensus 326 G~~v~~~~~l~~~l~-~~~g~~v~l~V~R~g~~~~~~v-~~~~~~~~~~~~~~~~G~~~~~l~~q~~~~~~~~~--~gv~ 401 (1108)
|++|.++.++..++. ..+|++++++|.|+|+.+++++ +..++...+.+...+.|+.++++++...+.++++. .|++
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 999999999998885 4788999999999999999999 87766544456677899999999998888888874 6899
Q ss_pred EE--CCCChhHHcCCCCCCEEEEeCCeecCCHHHHHHHHHhcCCCCeEEEEEeee
Q 001280 402 VA--EPGYMLFRAGVPRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYSSY 454 (1108)
Q Consensus 402 v~--~~~~~a~~aGl~~Gd~I~~Vng~~v~~l~~~~~~i~~~~~~~~v~l~~~~~ 454 (1108)
|. .++|+|+++||++||+|++|||+++.++++|.+++++.+.++.+.|++.|-
T Consensus 366 V~~V~~~SpA~~aGL~~GDvI~~Ing~~V~s~~d~~~~l~~~~~g~~v~l~v~R~ 420 (428)
T TIGR02037 366 VTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLDRAKKGGRVALLILRG 420 (428)
T ss_pred EEEeCCCCHHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhcCCCCEEEEEEEEC
Confidence 98 589999999999999999999999999999999999877777777776653
No 4
>PRK10942 serine endoprotease; Provisional
Probab=100.00 E-value=4.2e-50 Score=474.91 Aligned_cols=375 Identities=20% Similarity=0.327 Sum_probs=307.0
Q ss_pred hhHHHHHHHhCCceEEEEEeeee-------------ccCC----------------------------CCCCccEEEEEE
Q 001280 36 DDWRKALNKVVPAVVVLRTTACR-------------AFDT----------------------------EAAGASYATGFV 74 (1108)
Q Consensus 36 ~~~~~~~~~~~~sVV~I~~~~~~-------------~~d~----------------------------~~~~~~~GSGfv 74 (1108)
.++.++++++.||||+|.+.... .|.. .....+.||||+
T Consensus 38 ~~~~~~~~~~~pavv~i~~~~~~~~~~~~~~~~~~~ff~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GSG~i 117 (473)
T PRK10942 38 PSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRQFQQFFGDNSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVI 117 (473)
T ss_pred ccHHHHHHHhCCceEEEEEEEeccccCCCCChhHHHhhcccccccccccccccccccccccccccccccccccceEEEEE
Confidence 46999999999999999876521 0110 001246899999
Q ss_pred EeCCCcEEEEcccccCCCCeEEEEEecCCeEEeEEEEEEcCCCceEEEEEC-CCCcccccccCCCCCCcccCCCCEEEEE
Q 001280 75 VDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYPIYRDPVHDFGFFRYD-PSAIQFLNYDEIPLAPEAACVGLEIRVV 153 (1108)
Q Consensus 75 V~~~~G~ILTn~HVV~~~~~~~~v~~~d~~~~~a~vv~~d~~~DlAlLk~d-~~~~~~~~~~~l~l~~~~~~~G~~V~~i 153 (1108)
|++++||||||+|||. +.+.+.|+|.|+++++|++++.|+.+||||||++ +..++++.+++ +..+++|++|+++
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 5678999999999999999999999999999996 45566666665 7789999999999
Q ss_pred ecCCCCCCeEEEEEEEEecCCCCCCCCCCcccccceEEEEeeecCCCCCCCceecccCcEEEEeecccCC----CCcccc
Q 001280 154 GNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSS----SASAFF 229 (1108)
Q Consensus 154 G~p~g~~~si~~G~is~~~~~~~~~~~~~~~~~~~~~i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~----~~~~fa 229 (1108)
|||+|...+++.|+|+++.+... ....|. .|||+|+++++|||||||+|.+|+||||+++.... .+.+|+
T Consensus 193 G~P~g~~~tvt~GiVs~~~r~~~--~~~~~~----~~iqtda~i~~GnSGGpL~n~~GeviGI~t~~~~~~g~~~g~gfa 266 (473)
T PRK10942 193 GNPYGLGETVTSGIVSALGRSGL--NVENYE----NFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFA 266 (473)
T ss_pred cCCCCCCcceeEEEEEEeecccC--Cccccc----ceEEeccccCCCCCcCccCCCCCeEEEEEEEEEcCCCCcccEEEE
Confidence 99999999999999999987522 112333 35999999999999999999999999999876432 468999
Q ss_pred cChHHHHHHHHHHHhcCCcccccccccccCCCccCeEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCC
Q 001280 230 LPLERVVRALRFLQERRDCNIHNWEAVSIPRGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGG 309 (1108)
Q Consensus 230 lPi~~i~~~l~~l~~~~~~~~~~~~~~~v~rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~s 309 (1108)
||++.+++++++|++++ .+.|||||+.++.++.+.++.|||+ ...|++| ..|.++|
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 99999999999999988 7999999999999999999999997 5689888 6999999
Q ss_pred cccc-CCCCCCEEEEECCEEeCChhHHHHHHh-cCCCCeEEEEEEECCEEEEEEE-cccccccCCCcccccCCeEEccCC
Q 001280 310 PAHL-RLEPGDVLVRVNGEVITQFLKLETLLD-DGVDKNIELLIERGGISMTVNL-VQDLHSITPDYFLEVSGAVIHPLS 386 (1108)
Q Consensus 310 pA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~-~~~g~~v~l~V~R~g~~~~~~v-~~~~~~~~~~~~~~~~G~~~~~l~ 386 (1108)
||++ ||++||+|++|||++|.+|.++...+. ..+|+++.++|.|+|+.+++.+ +.............+.|+....++
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 4788999999999999999888 655322111122223443333332
Q ss_pred HHHhhccCcCCCeEEEE--CCCChhHHcCCCCCCEEEEeCCeecCCHHHHHHHHHhcCCCCeEEEEEee
Q 001280 387 YQQARNFRFPCGLVYVA--EPGYMLFRAGVPRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYSS 453 (1108)
Q Consensus 387 ~q~~~~~~~~~~gv~v~--~~~~~a~~aGl~~Gd~I~~Vng~~v~~l~~~~~~i~~~~~~~~v~l~~~~ 453 (1108)
... ...|++|. .++++|.++||++||+|++|||++|.++++|.+++++.+ +.+.|+++|
T Consensus 403 ~~~------~~~gvvV~~V~~~S~A~~aGL~~GDvIv~VNg~~V~s~~dl~~~l~~~~--~~v~l~V~R 463 (473)
T PRK10942 403 NKG------GDKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAELRKILDSKP--SVLALNIQR 463 (473)
T ss_pred ccc------CCCCeEEEEeCCCChHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhCC--CeEEEEEEE
Confidence 210 11478887 489999999999999999999999999999999999833 455555554
No 5
>PRK10139 serine endoprotease; Provisional
Probab=100.00 E-value=3.4e-50 Score=473.49 Aligned_cols=388 Identities=19% Similarity=0.263 Sum_probs=308.6
Q ss_pred cccccccccEEEEEEEcCccc----------ccCC-c-----ccceeeEEEEEEEeeCCceEEEEeCceecCCCceEEEE
Q 001280 619 FAESVIEPTLVMFEVHVPPSC----------MIDG-V-----HSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLS 682 (1108)
Q Consensus 619 ~~~~~~~~S~V~V~~~~~~~~----------~~dg-~-----~~~~~~GsG~iId~~~~~G~IlTnr~~V~~~~~~i~V~ 682 (1108)
...+++.||||.|.+...... .+.. . ......||||||+ .++|||||| +||+.++.+|.|+
T Consensus 44 ~~~~~~~pavV~i~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~GSG~ii~--~~~g~IlTn-~HVv~~a~~i~V~ 120 (455)
T PRK10139 44 PMLEKVLPAVVSVRVEGTASQGQKIPEEFKKFFGDDLPDQPAQPFEGLGSGVIID--AAKGYVLTN-NHVINQAQKISIQ 120 (455)
T ss_pred HHHHHhCCcEEEEEEEEeecccccCchhHHHhccccCCccccccccceEEEEEEE--CCCCEEEeC-hHHhCCCCEEEEE
Confidence 378899999999987532110 1110 0 1224689999998 247999999 5677888999999
Q ss_pred eecCCeEEeEEEEEeeCCCcEEEEEEC-CCCCCcccccceeccccCCCccCCCCCEEEEEeeCCCCCceeeeeeEecccc
Q 001280 683 FAAFPIEIPGEVVFLHPVHNFALIAYD-PSSLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCA 761 (1108)
Q Consensus 683 ~~~~~~~~~a~vv~~dp~~dlAilk~d-~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~vG~p~~~~~~~~~~~Vt~~~~ 761 (1108)
+.| +++++|++++.|+.+||||||++ +..+++ ++|+++..+++||+|++||||+++.. ++|
T Consensus 121 ~~d-g~~~~a~vvg~D~~~DlAvlkv~~~~~l~~--------~~lg~s~~~~~G~~V~aiG~P~g~~~-----tvt---- 182 (455)
T PRK10139 121 LND-GREFDAKLIGSDDQSDIALLQIQNPSKLTQ--------IAIADSDKLRVGDFAVAVGNPFGLGQ-----TAT---- 182 (455)
T ss_pred ECC-CCEEEEEEEEEcCCCCEEEEEecCCCCCce--------eEecCccccCCCCEEEEEecCCCCCC-----ceE----
Confidence 998 99999999999999999999997 445665 89999888999999999999999865 444
Q ss_pred ccccCCCCCCccc-cccceEEEEecccCC-CCCceEEcCCeeEEEEEeeccccccccCCCCCcceeEecccHHHHHHHHH
Q 001280 762 ALNISSADCPRYR-AMNMEVIELDTDFGS-TFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLD 839 (1108)
Q Consensus 762 ~~~i~~~~~~~y~-~~~~~~I~~d~~ig~-~sGGpL~d~~G~VvGi~~~~~~~~~~~~~~~~~~~~~~aipi~~i~~vl~ 839 (1108)
.|++++..+..+. ..+..+||+|+++++ ||||||+|.+|+||||+++.... +....++.|+||++.++++++
T Consensus 183 ~GivS~~~r~~~~~~~~~~~iqtda~in~GnSGGpl~n~~G~vIGi~~~~~~~------~~~~~gigfaIP~~~~~~v~~ 256 (455)
T PRK10139 183 SGIISALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAP------GGGSVGIGFAIPSNMARTLAQ 256 (455)
T ss_pred EEEEccccccccCCCCcceEEEECCccCCCCCcceEECCCCeEEEEEEEEEcC------CCCccceEEEEEhHHHHHHHH
Confidence 5555554432211 113479999999965 79999999999999999985433 122344558999999999999
Q ss_pred HHHcCCCCCcccccCcccCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCHHhHh-ccC
Q 001280 840 KIISGASGPSLLINGVKRPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSKAENM-LEQ 918 (1108)
Q Consensus 840 ~l~~~~~~~~~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~s~A~~a-L~~ 918 (1108)
+|+++++ +.|+ |||+.++.++...++.+|++.. .+++|..|.++|||+++ |++
T Consensus 257 ~l~~~g~--------v~r~-----~LGv~~~~l~~~~~~~lgl~~~-------------~Gv~V~~V~~~SpA~~AGL~~ 310 (455)
T PRK10139 257 QLIDFGE--------IKRG-----LLGIKGTEMSADIAKAFNLDVQ-------------RGAFVSEVLPNSGSAKAGVKA 310 (455)
T ss_pred HHhhcCc--------cccc-----ceeEEEEECCHHHHHhcCCCCC-------------CceEEEEECCCChHHHCCCCC
Confidence 9999886 7788 9999999999888888887643 67889999999999999 999
Q ss_pred CCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeecccCCCCCcce---eeeccccccCCchh
Q 001280 919 GDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGNGTTRV---INWCGCIVQDPHPA 995 (1108)
Q Consensus 919 GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~~~~~~~~t~~~---~~~~G~~~~~p~~~ 995 (1108)
||+|++|||++|.+|.++...+....++ +++.++|.|+|+++++++++........... ..+.|+.++..
T Consensus 311 GDvIl~InG~~V~s~~dl~~~l~~~~~g----~~v~l~V~R~G~~~~l~v~~~~~~~~~~~~~~~~~~~~g~~l~~~--- 383 (455)
T PRK10139 311 GDIITSLNGKPLNSFAELRSRIATTEPG----TKVKLGLLRNGKPLEVEVTLDTSTSSSASAEMITPALQGATLSDG--- 383 (455)
T ss_pred CCEEEEECCEECCCHHHHHHHHHhcCCC----CEEEEEEEECCEEEEEEEEECCCCCcccccccccccccccEeccc---
Confidence 9999999999999999999988665665 7899999999999999998754432211111 11345444431
Q ss_pred hhhcCCCCCCCCeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEeCCeEEEEEE
Q 001280 996 VRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTL 1074 (1108)
Q Consensus 996 vr~~~~lp~~~~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~~l 1074 (1108)
+ ++....|++|..|.++|||+++||++||+|++|||+++.+|++|.+.+++.+ +.+.|. +.|+|+.+.+.+
T Consensus 384 --~---~~~~~~Gv~V~~V~~~spA~~aGL~~GD~I~~Ing~~v~~~~~~~~~l~~~~--~~v~l~-v~R~g~~~~~~~ 454 (455)
T PRK10139 384 --Q---LKDGTKGIKIDEVVKGSPAAQAGLQKDDVIIGVNRDRVNSIAEMRKVLAAKP--AIIALQ-IVRGNESIYLLL 454 (455)
T ss_pred --c---cccCCCceEEEEeCCCChHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhCC--CeEEEE-EEECCEEEEEEe
Confidence 1 1112248999999999999999999999999999999999999999999843 678888 899999888776
No 6
>KOG1421 consensus Predicted signaling-associated protein (contains a PDZ domain) [General function prediction only]
Probab=100.00 E-value=1.5e-50 Score=456.85 Aligned_cols=443 Identities=29% Similarity=0.422 Sum_probs=386.1
Q ss_pred cccccccccEEEEEEEcCcccccCCcccceeeEEEEEEEeeCCceEEEEeCceecCCCceEEEEeecCCeEEeEEEEEee
Q 001280 619 FAESVIEPTLVMFEVHVPPSCMIDGVHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGEVVFLH 698 (1108)
Q Consensus 619 ~~~~~~~~S~V~V~~~~~~~~~~dg~~~~~~~GsG~iId~~~~~G~IlTnr~~V~~~~~~i~V~~~~~~~~~~a~vv~~d 698 (1108)
..++.+.+|+|.|+.... ..+|...+..+.|+|||+| +..||||||||+|..+..--.+.|.+ -.+++--.++.|
T Consensus 56 ~~ia~VvksvVsI~~S~v--~~fdtesag~~~atgfvvd--~~~gyiLtnrhvv~pgP~va~avf~n-~ee~ei~pvyrD 130 (955)
T KOG1421|consen 56 NTIANVVKSVVSIRFSAV--RAFDTESAGESEATGFVVD--KKLGYILTNRHVVAPGPFVASAVFDN-HEEIEIYPVYRD 130 (955)
T ss_pred hhhhhhcccEEEEEehhe--eecccccccccceeEEEEe--cccceEEEeccccCCCCceeEEEecc-cccCCcccccCC
Confidence 377889999999988776 4778888889999999999 57999999999999999888899998 788888889999
Q ss_pred CCCcEEEEEECCCCCCcccccceeccccCCCccCCCCCEEEEEeeCCCCCceeeeeeEeccccccccCCC--CCCccccc
Q 001280 699 PVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSA--DCPRYRAM 776 (1108)
Q Consensus 699 p~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~vG~p~~~~~~~~~~~Vt~~~~~~~i~~~--~~~~y~~~ 776 (1108)
|.|||.+++|||+.+.. ..|+.+.++++. .+.|-++..+||..+--+..-.+.++ +..-... .-..|...
T Consensus 131 pVhdfGf~r~dps~ir~---s~vt~i~lap~~-akvgseirvvgNDagEklsIlagflS----rldr~apdyg~~~yndf 202 (955)
T KOG1421|consen 131 PVHDFGFFRYDPSTIRF---SIVTEICLAPEL-AKVGSEIRVVGNDAGEKLSILAGFLS----RLDRNAPDYGEDTYNDF 202 (955)
T ss_pred chhhcceeecChhhcce---eeeeccccCccc-cccCCceEEecCCccceEEeehhhhh----hccCCCccccccccccc
Confidence 99999999999998875 788888998876 79999999999987663322222222 2221111 12234446
Q ss_pred cceEEEEeccc-CCCCCceEEcCCeeEEEEEeeccccccccCCCCCcceeEecccHHHHHHHHHHHHcCCCCCcccccCc
Q 001280 777 NMEVIELDTDF-GSTFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLDKIISGASGPSLLINGV 855 (1108)
Q Consensus 777 ~~~~I~~d~~i-g~~sGGpL~d~~G~VvGi~~~~~~~~~~~~~~~~~~~~~~aipi~~i~~vl~~l~~~~~~~~~~~~~v 855 (1108)
|..++|.-+.- |+.||.|++|..|..|+++.... ...... |.+|++.+.+.|.-|+++.. +
T Consensus 203 nTfy~QaasstsggssgspVv~i~gyAVAl~agg~--------~ssas~--ffLpLdrV~RaL~clq~n~P--------I 264 (955)
T KOG1421|consen 203 NTFYIQAASSTSGGSSGSPVVDIPGYAVALNAGGS--------ISSASD--FFLPLDRVVRALRCLQNNTP--------I 264 (955)
T ss_pred cceeeeehhcCCCCCCCCceecccceEEeeecCCc--------cccccc--ceeeccchhhhhhhhhcCCC--------c
Confidence 78888888766 44679999999999999976432 234455 55999999999999998864 7
Q ss_pred ccCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCHHhHhccCCCEEEEECCEEcCChhH
Q 001280 856 KRPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSKAENMLEQGDMMLAINKQPVTCFHD 935 (1108)
Q Consensus 856 ~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~s~A~~aL~~GDiIlsVnG~~V~~~~d 935 (1108)
.|+ +|.++|.....+++|.+||+.||++.+..++|.+++.++|..|.+++||++.|++||++++||+.-+.++..
T Consensus 265 tRG-----tLqvefl~k~~de~rrlGL~sE~eqv~r~k~P~~tgmLvV~~vL~~gpa~k~Le~GDillavN~t~l~df~~ 339 (955)
T KOG1421|consen 265 TRG-----TLQVEFLHKLFDECRRLGLSSEWEQVVRTKFPERTGMLVVETVLPEGPAEKKLEPGDILLAVNSTCLNDFEA 339 (955)
T ss_pred ccc-----eEEEEEehhhhHHHHhcCCcHHHHHHHHhcCcccceeEEEEEeccCCchhhccCCCcEEEEEcceehHHHHH
Confidence 888 999999999999999999999999999999999999999999999999999999999999999888887777
Q ss_pred HHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeecccCCCCCcceeeeccccccCCchhhhhcCCCCCCCCeEEEEEec
Q 001280 936 IENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGNGTTRVINWCGCIVQDPHPAVRALGFLPEEGHGVYVARWC 1015 (1108)
Q Consensus 936 l~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~~~~~~~~t~~~~~~~G~~~~~p~~~vr~~~~lp~~~~gV~V~~v~ 1015 (1108)
+...+ ..| .++.+.++|+|+|++.++++++..+.+..+.|++.|||+.++.|++++++++++|- +|+||++..
T Consensus 340 l~~iL---Deg--vgk~l~LtI~Rggqelel~vtvqdlh~itp~R~levcGav~hdlsyq~ar~y~lP~--~GvyVa~~~ 412 (955)
T KOG1421|consen 340 LEQIL---DEG--VGKNLELTIQRGGQELELTVTVQDLHGITPDRFLEVCGAVFHDLSYQLARLYALPV--EGVYVASPG 412 (955)
T ss_pred HHHHH---hhc--cCceEEEEEEeCCEEEEEEEEeccccCCCCceEEEEcceEecCCCHHHHhhccccc--CcEEEccCC
Confidence 76666 333 45889999999999999999999999999999999999999999999999988986 499999999
Q ss_pred CCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEeC--CeEEEEEEEeCCc-cCcceEEEEcCCC
Q 001280 1016 HGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLN--GKPRVLTLKQDLH-YWPTWELIFDPDT 1092 (1108)
Q Consensus 1016 ~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~rd--g~~~~~~lk~d~~-y~pt~el~~~~~~ 1092 (1108)
||++++++++ +.||.+||++++++|++|+++++++++|++|+++++..+ +++++++++.|.| |||+|++.||+++
T Consensus 413 -gsf~~~~~~y-~~ii~~vanK~tPdLdaFidvlk~L~dg~rV~vry~hl~dkh~p~v~~v~iDrHwy~p~~~~trndet 490 (955)
T KOG1421|consen 413 -GSFRHRGPRY-GQIIDSVANKPTPDLDAFIDVLKELPDGARVPVRYHHLTDKHSPRVTTVTIDRHWYWPFREYTRNDET 490 (955)
T ss_pred -CCccccCCcc-eEEEEeecCCcCCCHHHHHHHHHhccCCCeeeEEEEEecCCCCceEEEEEEeccccccceeeeeCCCc
Confidence 9999999999 999999999999999999999999999999999999998 7899999999999 9999999999999
Q ss_pred CCeEEEEecccCCC
Q 001280 1093 ALWRRKSVKALNSS 1106 (1108)
Q Consensus 1093 ~~W~~~~~~~~~~~ 1106 (1108)
+.|++...+.+||.
T Consensus 491 glWdrk~L~~pqPa 504 (955)
T KOG1421|consen 491 GLWDRKNLKDPQPA 504 (955)
T ss_pred ccccccccCCCCcc
Confidence 99999999999885
No 7
>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=473.27 Aligned_cols=395 Identities=24% Similarity=0.329 Sum_probs=326.2
Q ss_pred ccccccccEEEEEEEcCccc-------------ccCC----c------ccceeeEEEEEEEeeCCceEEEEeCceecCCC
Q 001280 620 AESVIEPTLVMFEVHVPPSC-------------MIDG----V------HSQHFFGTGVIIYHSQSMGLVVVDKNTVAISA 676 (1108)
Q Consensus 620 ~~~~~~~S~V~V~~~~~~~~-------------~~dg----~------~~~~~~GsG~iId~~~~~G~IlTnr~~V~~~~ 676 (1108)
+++++.||||.|.+...... .+.. . ......||||||+ ..|||||| +||+.++
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 1134689999999 56999999 5677889
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEEEECCC-CCCcccccceeccccCCCccCCCCCEEEEEeeCCCCCceeeeee
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAYDPS-SLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSI 755 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~d~~-~l~~~~~~~v~~~~l~~~~~l~~G~~V~~vG~p~~~~~~~~~~~ 755 (1108)
+++.|++++ +..++|++++.|+.+||||||++.. .+++ ++|+++..+++||+|+++|||++.......+.
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 9999999999999999999999864 4554 89998888999999999999999865544555
Q ss_pred EeccccccccCCCCCCcc-ccccceEEEEecccCC-CCCceEEcCCeeEEEEEeeccccccccCCCCCcceeEecccHHH
Q 001280 756 VTNPCAALNISSADCPRY-RAMNMEVIELDTDFGS-TFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYT 833 (1108)
Q Consensus 756 Vt~~~~~~~i~~~~~~~y-~~~~~~~I~~d~~ig~-~sGGpL~d~~G~VvGi~~~~~~~~~~~~~~~~~~~~~~aipi~~ 833 (1108)
|+ +..+... ......+||+|+++++ ||||||+|.+|+|+|||++.... +....++.||||++.
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 54 2222110 0112368999999955 79999999999999999885433 122345668999999
Q ss_pred HHHHHHHHHcCCCCCcccccCcccCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCHHh
Q 001280 834 ISRVLDKIISGASGPSLLINGVKRPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSKAE 913 (1108)
Q Consensus 834 i~~vl~~l~~~~~~~~~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~s~A~ 913 (1108)
+++++++|+++++ +.|+ |||+.++.++...++.+|++.. .+++|.+|.++|||+
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 9999999999976 6677 9999999999999999998754 678899999999999
Q ss_pred Hh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeecccCCCCCcceeeeccccccCC
Q 001280 914 NM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGNGTTRVINWCGCIVQDP 992 (1108)
Q Consensus 914 ~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~~~~~~~~t~~~~~~~G~~~~~p 992 (1108)
++ |++||+|++|||++|.++.++..++.....+ +.+.++|.|+|+.+++++++...++....+...|+|+.++.+
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 9999999999999999999999998766665 889999999999999999987665444455667899999999
Q ss_pred chhhhhcCCCCCCCCeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEeCCeEEEE
Q 001280 993 HPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVL 1072 (1108)
Q Consensus 993 ~~~vr~~~~lp~~~~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~ 1072 (1108)
+...++...++....|++|++|.++|||+++||++||+|++|||+++.++++|.+++++.+.++.++|. +.|+|+.+.+
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 888877555654345999999999999999999999999999999999999999999987779999999 8999998766
Q ss_pred E
Q 001280 1073 T 1073 (1108)
Q Consensus 1073 ~ 1073 (1108)
.
T Consensus 427 ~ 427 (428)
T TIGR02037 427 T 427 (428)
T ss_pred E
Confidence 4
No 8
>PRK10942 serine endoprotease; Provisional
Probab=100.00 E-value=2e-48 Score=460.68 Aligned_cols=360 Identities=19% Similarity=0.273 Sum_probs=292.4
Q ss_pred eeeEEEEEEEeeCCceEEEEeCceecCCCceEEEEeecCCeEEeEEEEEeeCCCcEEEEEEC-CCCCCcccccceecccc
Q 001280 648 HFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGEVVFLHPVHNFALIAYD-PSSLGVAGASVVRAAEL 726 (1108)
Q Consensus 648 ~~~GsG~iId~~~~~G~IlTnr~~V~~~~~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~d-~~~l~~~~~~~v~~~~l 726 (1108)
.+.||||||+ .++|||||| +||+.++++|.|+|+| +++++|+|++.|+.+||||||++ +..+++ ++|
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 4689999998 346999999 5567888999999998 99999999999999999999995 555665 899
Q ss_pred CCCccCCCCCEEEEEeeCCCCCceeeeeeEeccccccccCCCCCCccccccceEEEEecccCC-CCCceEEcCCeeEEEE
Q 001280 727 LPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRAMNMEVIELDTDFGS-TFSGVLTDEHGRVQAI 805 (1108)
Q Consensus 727 ~~~~~l~~G~~V~~vG~p~~~~~~~~~~~Vt~~~~~~~i~~~~~~~y~~~~~~~I~~d~~ig~-~sGGpL~d~~G~VvGi 805 (1108)
+++..+++||+|++||+|+++..+...+.|+... ........| ..+||+|+++++ ||||||+|.+|+||||
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 9988899999999999999986544445554211 111111233 368999999965 7999999999999999
Q ss_pred EeeccccccccCCCCCcceeEecccHHHHHHHHHHHHcCCCCCcccccCcccCCCceeeeeeEEEEcChHhHHHcCCCHH
Q 001280 806 WGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLDKIISGASGPSLLINGVKRPMPLVRILEVELYPTLLSKARSFGLSDD 885 (1108)
Q Consensus 806 ~~~~~~~~~~~~~~~~~~~~~~aipi~~i~~vl~~l~~~~~~~~~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~ 885 (1108)
|+++... +....++.|+||++.+++++++|+++++ +.|+ |||+.++.++...++.+|++..
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 1223456689999999999999999886 7787 9999999999888888888654
Q ss_pred HHHHHHhcCCCccceEEEEeecCCCHHhHh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEE
Q 001280 886 WVQALVKKDPVRRQVLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREI 964 (1108)
Q Consensus 886 wi~~~~~~~~~~~~~~~V~~V~~~s~A~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~ 964 (1108)
++++|..|.++|||+++ |++||+|++|||++|.+++++..++.....+ +++.++|.|+|+.+
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 EEEEeecccCCCCCcceeeeccccccCCchhhhhcCCCCCCCCeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHH
Q 001280 965 ELQVGTDVRDGNGTTRVINWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEA 1044 (1108)
Q Consensus 965 ~v~v~~~~~~~~~t~~~~~~~G~~~~~p~~~vr~~~~lp~~~~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~ 1044 (1108)
++.+++.........+...++|+........ ....|++|++|.++|||+++||++||+|++|||++|.++++
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--------GGDKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAE 445 (473)
T ss_pred EEEEEeCcCcccccccccccccceeeecccc--------cCCCCeEEEEeCCCChHHHcCCCCCCEEEEECCEEcCCHHH
Confidence 9999886643222222233455443322210 01138999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCCceEEEEEEEeCCeEEEEEE
Q 001280 1045 FVNVTKEIEHGEFVRVRTVHLNGKPRVLTL 1074 (1108)
Q Consensus 1045 f~~~v~~~~~~~~v~l~~v~rdg~~~~~~l 1074 (1108)
|.+++++. ++.+.|+ +.|+|..+.+.+
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 3678888 899999888765
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=8.5e-44 Score=408.20 Aligned_cols=299 Identities=19% Similarity=0.297 Sum_probs=257.1
Q ss_pred ccCchhHHHHHHHhCCceEEEEEeeeec-cCCCCCCccEEEEEEEeCCCcEEEEcccccCCCCeEEEEEecCCeEEeEEE
Q 001280 32 VATADDWRKALNKVVPAVVVLRTTACRA-FDTEAAGASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYP 110 (1108)
Q Consensus 32 ~~~~~~~~~~~~~~~~sVV~I~~~~~~~-~d~~~~~~~~GSGfvV~~~~G~ILTn~HVV~~~~~~~~v~~~d~~~~~a~v 110 (1108)
.+.+..+.++++++.||||.|....... ........+.||||+|++ +||||||+|||. +...+.++|.|++.++|++
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 111223467899999997 899999999999 5678999999999999999
Q ss_pred EEEcCCCceEEEEECCCCcccccccCCCCCCcccCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCcccccceE
Q 001280 111 IYRDPVHDFGFFRYDPSAIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFY 190 (1108)
Q Consensus 111 v~~d~~~DlAlLk~d~~~~~~~~~~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~is~~~~~~~~~~~~~~~~~~~~~ 190 (1108)
+++|+.+||||||++...++++++.. +..+++||+|+++|||++...+++.|+|+++.+... ...++ ..+
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 99999999999999987766666654 678999999999999999999999999999988642 11122 346
Q ss_pred EEEeeecCCCCCCCceecccCcEEEEeecccC------CCCcccccChHHHHHHHHHHHhcCCcccccccccccCCCccC
Q 001280 191 MQAASGTKGGSSGSPVIDWQGRAVALNAGSKS------SSASAFFLPLERVVRALRFLQERRDCNIHNWEAVSIPRGTLQ 264 (1108)
Q Consensus 191 i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~------~~~~~falPi~~i~~~l~~l~~~~~~~~~~~~~~~v~rg~lg 264 (1108)
||+|+++++|||||||+|.+|+||||+++... ..+.+|+||++.+++++++|++++ .+.|+|||
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 99999999999999999999999999976432 147899999999999999999888 78899999
Q ss_pred eEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhc-C
Q 001280 265 VTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDD-G 342 (1108)
Q Consensus 265 ~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~-~ 342 (1108)
+.++.+....++.||++ ...|++| ..|.++|||++ ||++||+|++|||++|.++.++...+.. .
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 99999999999999997 4578887 69999999999 9999999999999999999999988854 7
Q ss_pred CCCeEEEEEEECCEEEEEEE-cccc
Q 001280 343 VDKNIELLIERGGISMTVNL-VQDL 366 (1108)
Q Consensus 343 ~g~~v~l~V~R~g~~~~~~v-~~~~ 366 (1108)
+|+++.++|.|+|+.+++.+ +..+
T Consensus 325 ~g~~v~l~v~R~g~~~~~~v~l~~~ 349 (351)
T TIGR02038 325 PGSKVMVTVLRQGKQLELPVTIDEK 349 (351)
T ss_pred CCCEEEEEEEECCEEEEEEEEecCC
Confidence 89999999999999999888 6543
No 10
>PRK10898 serine endoprotease; Provisional
Probab=100.00 E-value=4.3e-43 Score=401.81 Aligned_cols=300 Identities=18% Similarity=0.291 Sum_probs=255.6
Q ss_pred ccCchhHHHHHHHhCCceEEEEEeeeeccC-CCCCCccEEEEEEEeCCCcEEEEcccccCCCCeEEEEEecCCeEEeEEE
Q 001280 32 VATADDWRKALNKVVPAVVVLRTTACRAFD-TEAAGASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYP 110 (1108)
Q Consensus 32 ~~~~~~~~~~~~~~~~sVV~I~~~~~~~~d-~~~~~~~~GSGfvV~~~~G~ILTn~HVV~~~~~~~~v~~~d~~~~~a~v 110 (1108)
......+.++++++.||||.|.......+. ......+.||||+|++ +||||||+|||. +...+.|++.|++.++|++
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 2233457899999997 799999999999 5678999999999999999
Q ss_pred EEEcCCCceEEEEECCCCcccccccCCCCCCcccCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCcccccceE
Q 001280 111 IYRDPVHDFGFFRYDPSAIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFY 190 (1108)
Q Consensus 111 v~~d~~~DlAlLk~d~~~~~~~~~~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~is~~~~~~~~~~~~~~~~~~~~~ 190 (1108)
+++|+.+||||||++...++++++.+ +..+++|++|+++|||++...+++.|+|++..+.... ..++ ..+
T Consensus 119 v~~d~~~DlAvl~v~~~~l~~~~l~~----~~~~~~G~~V~aiG~P~g~~~~~t~Giis~~~r~~~~--~~~~----~~~ 188 (353)
T PRK10898 119 VGSDSLTDLAVLKINATNLPVIPINP----KRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLS--PTGR----QNF 188 (353)
T ss_pred EEEcCCCCEEEEEEcCCCCCeeeccC----cCcCCCCCEEEEEeCCCCcCCCcceeEEEeccccccC--Cccc----cce
Confidence 99999999999999987777666664 5678999999999999999999999999998875321 1122 236
Q ss_pred EEEeeecCCCCCCCceecccCcEEEEeecccCC-------CCcccccChHHHHHHHHHHHhcCCcccccccccccCCCcc
Q 001280 191 MQAASGTKGGSSGSPVIDWQGRAVALNAGSKSS-------SASAFFLPLERVVRALRFLQERRDCNIHNWEAVSIPRGTL 263 (1108)
Q Consensus 191 i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~-------~~~~falPi~~i~~~l~~l~~~~~~~~~~~~~~~v~rg~l 263 (1108)
||+|+++++|||||||+|.+|+||||+++.... .+.+|+||++.+++++++|.+++ .+.|+||
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 999999999999999999999999999764321 46899999999999999998888 7899999
Q ss_pred CeEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHh-c
Q 001280 264 QVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLD-D 341 (1108)
Q Consensus 264 g~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~-~ 341 (1108)
|+..+.++...+..+|++ ...|++| ..|.++|||++ ||++||+|++|||++|.++.++...+. .
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 999998877666667765 4578888 69999999999 999999999999999999999988875 4
Q ss_pred CCCCeEEEEEEECCEEEEEEE-ccccc
Q 001280 342 GVDKNIELLIERGGISMTVNL-VQDLH 367 (1108)
Q Consensus 342 ~~g~~v~l~V~R~g~~~~~~v-~~~~~ 367 (1108)
.+|+++.++|.|+|+.+++.+ +..++
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 789999999999999999888 76554
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=5.5e-39 Score=368.49 Aligned_cols=298 Identities=19% Similarity=0.248 Sum_probs=241.1
Q ss_pred cccccccccEEEEEEEcCcccccCCcccceeeEEEEEEEeeCCceEEEEeCceecCCCceEEEEeecCCeEEeEEEEEee
Q 001280 619 FAESVIEPTLVMFEVHVPPSCMIDGVHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGEVVFLH 698 (1108)
Q Consensus 619 ~~~~~~~~S~V~V~~~~~~~~~~dg~~~~~~~GsG~iId~~~~~G~IlTnr~~V~~~~~~i~V~~~~~~~~~~a~vv~~d 698 (1108)
..++++.||+|.|.+...... ........+.||||||+ ++||||||+| |+.++..+.|+|.+ +..++|++++.|
T Consensus 49 ~~~~~~~psVV~I~~~~~~~~-~~~~~~~~~~GSG~vi~---~~G~IlTn~H-VV~~~~~i~V~~~d-g~~~~a~vv~~d 122 (351)
T TIGR02038 49 KAVRRAAPAVVNIYNRSISQN-SLNQLSIQGLGSGVIMS---KEGYILTNYH-VIKKADQIVVALQD-GRKFEAELVGSD 122 (351)
T ss_pred HHHHhcCCcEEEEEeEecccc-ccccccccceEEEEEEe---CCeEEEeccc-EeCCCCEEEEEECC-CCEEEEEEEEec
Confidence 378899999999987654211 11112234679999999 6899999955 55778889999998 999999999999
Q ss_pred CCCcEEEEEECCCCCCcccccceeccccCCCccCCCCCEEEEEeeCCCCCceeeeeeEeccccccccCCCCCCcccc-cc
Q 001280 699 PVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRA-MN 777 (1108)
Q Consensus 699 p~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~vG~p~~~~~~~~~~~Vt~~~~~~~i~~~~~~~y~~-~~ 777 (1108)
+.+||||||++...+++ ++|+++..+++||+|+++|||+++..+...+.|+ ...+..+.. ..
T Consensus 123 ~~~DlAvlkv~~~~~~~--------~~l~~s~~~~~G~~V~aiG~P~~~~~s~t~GiIs---------~~~r~~~~~~~~ 185 (351)
T TIGR02038 123 PLTDLAVLKIEGDNLPT--------IPVNLDRPPHVGDVVLAIGNPYNLGQTITQGIIS---------ATGRNGLSSVGR 185 (351)
T ss_pred CCCCEEEEEecCCCCce--------EeccCcCccCCCCEEEEEeCCCCCCCcEEEEEEE---------eccCcccCCCCc
Confidence 99999999998877765 7888877899999999999999986644444444 332221111 12
Q ss_pred ceEEEEecccCC-CCCceEEcCCeeEEEEEeeccccccccCCCCCcceeEecccHHHHHHHHHHHHcCCCCCcccccCcc
Q 001280 778 MEVIELDTDFGS-TFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLDKIISGASGPSLLINGVK 856 (1108)
Q Consensus 778 ~~~I~~d~~ig~-~sGGpL~d~~G~VvGi~~~~~~~~~~~~~~~~~~~~~~aipi~~i~~vl~~l~~~~~~~~~~~~~v~ 856 (1108)
.++||+|+++++ ||||||+|.+|+|||||++.... + ......+++|+||++.+++++++|+++++ +.
T Consensus 186 ~~~iqtda~i~~GnSGGpl~n~~G~vIGI~~~~~~~---~-~~~~~~g~~faIP~~~~~~vl~~l~~~g~--------~~ 253 (351)
T TIGR02038 186 QNFIQTDAAINAGNSGGALINTNGELVGINTASFQK---G-GDEGGEGINFAIPIKLAHKIMGKIIRDGR--------VI 253 (351)
T ss_pred ceEEEECCccCCCCCcceEECCCCeEEEEEeeeecc---c-CCCCccceEEEecHHHHHHHHHHHhhcCc--------cc
Confidence 478999999966 79999999999999999874332 0 11223456689999999999999998876 56
Q ss_pred cCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCHHhHh-ccCCCEEEEECCEEcCChhH
Q 001280 857 RPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHD 935 (1108)
Q Consensus 857 r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~s~A~~a-L~~GDiIlsVnG~~V~~~~d 935 (1108)
|+ |||+.++++....++.+|++.. ++++|.+|.++|||+++ |++||+|++|||++|.++.+
T Consensus 254 r~-----~lGv~~~~~~~~~~~~lgl~~~-------------~Gv~V~~V~~~spA~~aGL~~GDvI~~Ing~~V~s~~d 315 (351)
T TIGR02038 254 RG-----YIGVSGEDINSVVAQGLGLPDL-------------RGIVITGVDPNGPAARAGILVRDVILKYDGKDVIGAEE 315 (351)
T ss_pred ce-----EeeeEEEECCHHHHHhcCCCcc-------------ccceEeecCCCChHHHCCCCCCCEEEEECCEEcCCHHH
Confidence 66 9999999999888888998744 67889999999999999 99999999999999999999
Q ss_pred HHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeeccc
Q 001280 936 IENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVR 973 (1108)
Q Consensus 936 l~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~~~~ 973 (1108)
+...+.....+ +++.++|.|+|+.+++.+++.+.
T Consensus 316 l~~~l~~~~~g----~~v~l~v~R~g~~~~~~v~l~~~ 349 (351)
T TIGR02038 316 LMDRIAETRPG----SKVMVTVLRQGKQLELPVTIDEK 349 (351)
T ss_pred HHHHHHhcCCC----CEEEEEEEECCEEEEEEEEecCC
Confidence 99988766665 78999999999999999887643
No 12
>PRK10898 serine endoprotease; Provisional
Probab=100.00 E-value=2.1e-38 Score=363.17 Aligned_cols=300 Identities=16% Similarity=0.220 Sum_probs=238.3
Q ss_pred cccccccccEEEEEEEcCcccccCCcccceeeEEEEEEEeeCCceEEEEeCceecCCCceEEEEeecCCeEEeEEEEEee
Q 001280 619 FAESVIEPTLVMFEVHVPPSCMIDGVHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGEVVFLH 698 (1108)
Q Consensus 619 ~~~~~~~~S~V~V~~~~~~~~~~dg~~~~~~~GsG~iId~~~~~G~IlTnr~~V~~~~~~i~V~~~~~~~~~~a~vv~~d 698 (1108)
..++++.||+|.|.+.... ..........+.||||||+ ++||||||+ ||+.++.++.|++.| +..++|++++.|
T Consensus 49 ~~~~~~~psvV~v~~~~~~-~~~~~~~~~~~~GSGfvi~---~~G~IlTn~-HVv~~a~~i~V~~~d-g~~~~a~vv~~d 122 (353)
T PRK10898 49 QAVRRAAPAVVNVYNRSLN-STSHNQLEIRTLGSGVIMD---QRGYILTNK-HVINDADQIIVALQD-GRVFEALLVGSD 122 (353)
T ss_pred HHHHHhCCcEEEEEeEecc-ccCcccccccceeeEEEEe---CCeEEEecc-cEeCCCCEEEEEeCC-CCEEEEEEEEEc
Confidence 3788999999999887652 1111222334789999999 689999995 566688899999998 999999999999
Q ss_pred CCCcEEEEEECCCCCCcccccceeccccCCCccCCCCCEEEEEeeCCCCCceeeeeeEeccccccccCCCCCCccc-ccc
Q 001280 699 PVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYR-AMN 777 (1108)
Q Consensus 699 p~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~vG~p~~~~~~~~~~~Vt~~~~~~~i~~~~~~~y~-~~~ 777 (1108)
+.+||||||++...++. ++|+++..+++||+|+++|||++.......+.|+ +..+..+. ...
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 99999999999877765 8888887799999999999999876544444444 33221111 112
Q ss_pred ceEEEEecccCC-CCCceEEcCCeeEEEEEeeccccccccCCCCCcceeEecccHHHHHHHHHHHHcCCCCCcccccCcc
Q 001280 778 MEVIELDTDFGS-TFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLDKIISGASGPSLLINGVK 856 (1108)
Q Consensus 778 ~~~I~~d~~ig~-~sGGpL~d~~G~VvGi~~~~~~~~~~~~~~~~~~~~~~aipi~~i~~vl~~l~~~~~~~~~~~~~v~ 856 (1108)
.++||+|+++++ ||||||+|.+|+|+||+++..... + ......++.|+||++.+++++++|+++++ +.
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 378999999966 799999999999999998754330 0 01112356689999999999999998876 66
Q ss_pred cCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCHHhHh-ccCCCEEEEECCEEcCChhH
Q 001280 857 RPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHD 935 (1108)
Q Consensus 857 r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~s~A~~a-L~~GDiIlsVnG~~V~~~~d 935 (1108)
|+ |||+..+.+....+..++++.. ++++|.+|.++|||+++ |++||+|++|||++|.++.+
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 9999999887665555554332 78899999999999999 99999999999999999999
Q ss_pred HHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeecccC
Q 001280 936 IENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRD 974 (1108)
Q Consensus 936 l~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~~~~~ 974 (1108)
+...+.....+ +.+.++|.|+|+.+++.+++.+.+
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 99888666665 789999999999999999886543
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=5.7e-33 Score=320.42 Aligned_cols=293 Identities=24% Similarity=0.421 Sum_probs=253.7
Q ss_pred hhHHHHHHHhCCceEEEEEeeeecc----CCCC--C-CccEEEEEEEeCCCcEEEEcccccCCCCeEEEEEecCCeEEeE
Q 001280 36 DDWRKALNKVVPAVVVLRTTACRAF----DTEA--A-GASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPV 108 (1108)
Q Consensus 36 ~~~~~~~~~~~~sVV~I~~~~~~~~----d~~~--~-~~~~GSGfvV~~~~G~ILTn~HVV~~~~~~~~v~~~d~~~~~a 108 (1108)
..+...++++.|+||.+........ .... . ..+.||||++++ +|||+||.||+.. ...+.+.+.|++++++
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 6899999999999999998754321 1111 1 148899999996 8999999999995 8889999999999999
Q ss_pred EEEEEcCCCceEEEEECCCC-cccccccCCCCCCcccCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCccccc
Q 001280 109 YPIYRDPVHDFGFFRYDPSA-IQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFN 187 (1108)
Q Consensus 109 ~vv~~d~~~DlAlLk~d~~~-~~~~~~~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~is~~~~~~~~~~~~~~~~~~ 187 (1108)
++++.|+..|+|+||++... ++++.++. +..+++|++++++|+|+|...+++.|+++.+.|. .+....+ .
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 99999999999999999754 66666666 7788999999999999999999999999999997 2222111 2
Q ss_pred ceEEEEeeecCCCCCCCceecccCcEEEEeecccCCC----CcccccChHHHHHHHHHHHhcCCcccccccccccCCCcc
Q 001280 188 TFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSSS----ASAFFLPLERVVRALRFLQERRDCNIHNWEAVSIPRGTL 263 (1108)
Q Consensus 188 ~~~i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~~----~~~falPi~~i~~~l~~l~~~~~~~~~~~~~~~v~rg~l 263 (1108)
..+||+|+++++|+||||++|.+|++|||++...... +.+|++|++.+++++.++...+ ++.|+++
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 3469999999999999999999999999998877553 4899999999999999999866 7899999
Q ss_pred CeEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHH-hc
Q 001280 264 QVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLL-DD 341 (1108)
Q Consensus 264 g~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l-~~ 341 (1108)
|+.+..+..+.+ +|++ ...|++| ..|.+++||++ |++.||+|+++||+++.+..++...+ ..
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 999998888777 8876 5788777 79999999999 99999999999999999999999888 45
Q ss_pred CCCCeEEEEEEECCEEEEEEE-ccc
Q 001280 342 GVDKNIELLIERGGISMTVNL-VQD 365 (1108)
Q Consensus 342 ~~g~~v~l~V~R~g~~~~~~v-~~~ 365 (1108)
.+|+.+.+.+.|+|+.+++.+ +.+
T Consensus 316 ~~g~~v~~~~~r~g~~~~~~v~l~~ 340 (347)
T COG0265 316 RPGDEVALKLLRGGKERELAVTLGD 340 (347)
T ss_pred CCCCEEEEEEEECCEEEEEEEEecC
Confidence 789999999999999999999 766
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=1.8e-28 Score=282.98 Aligned_cols=293 Identities=27% Similarity=0.356 Sum_probs=238.2
Q ss_pred ccccccccEEEEEEEcCccc--ccCC---cccceeeEEEEEEEeeCCceEEEEeCceecCCCceEEEEeecCCeEEeEEE
Q 001280 620 AESVIEPTLVMFEVHVPPSC--MIDG---VHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGEV 694 (1108)
Q Consensus 620 ~~~~~~~S~V~V~~~~~~~~--~~dg---~~~~~~~GsG~iId~~~~~G~IlTnr~~V~~~~~~i~V~~~~~~~~~~a~v 694 (1108)
..+++.|++|.+........ .+.. .......||||+++ ..|||+|| +||+.++..+.+++.| ++.++|++
T Consensus 38 ~~~~~~~~vV~~~~~~~~~~~~~~~~~~~~~~~~~~gSg~i~~---~~g~ivTn-~hVi~~a~~i~v~l~d-g~~~~a~~ 112 (347)
T COG0265 38 AVEKVAPAVVSIATGLTAKLRSFFPSDPPLRSAEGLGSGFIIS---SDGYIVTN-NHVIAGAEEITVTLAD-GREVPAKL 112 (347)
T ss_pred HHHhcCCcEEEEEeeeeecchhcccCCcccccccccccEEEEc---CCeEEEec-ceecCCcceEEEEeCC-CCEEEEEE
Confidence 77888999999987654211 0011 01115889999999 79999999 5566669999999987 99999999
Q ss_pred EEeeCCCcEEEEEECCCC-CCcccccceeccccCCCccCCCCCEEEEEeeCCCCCceeeeeeEeccccccccCCCCCCcc
Q 001280 695 VFLHPVHNFALIAYDPSS-LGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRY 773 (1108)
Q Consensus 695 v~~dp~~dlAilk~d~~~-l~~~~~~~v~~~~l~~~~~l~~G~~V~~vG~p~~~~~~~~~~~Vt~~~~~~~i~~~~~~~y 773 (1108)
++.|+.+|+|++|++... ++. +.|+++..++.||+++++|+|+++. .+|+ .|+++...+..+
T Consensus 113 vg~d~~~dlavlki~~~~~~~~--------~~~~~s~~l~vg~~v~aiGnp~g~~-----~tvt----~Givs~~~r~~v 175 (347)
T COG0265 113 VGKDPISDLAVLKIDGAGGLPV--------IALGDSDKLRVGDVVVAIGNPFGLG-----QTVT----SGIVSALGRTGV 175 (347)
T ss_pred EecCCccCEEEEEeccCCCCce--------eeccCCCCcccCCEEEEecCCCCcc-----ccee----ccEEeccccccc
Confidence 999999999999998754 655 7999999999999999999999964 4565 666666555311
Q ss_pred c--cccceEEEEecccCC-CCCceEEcCCeeEEEEEeeccccccccCCCCCcceeEecccHHHHHHHHHHHHcCCCCCcc
Q 001280 774 R--AMNMEVIELDTDFGS-TFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLDKIISGASGPSL 850 (1108)
Q Consensus 774 ~--~~~~~~I~~d~~ig~-~sGGpL~d~~G~VvGi~~~~~~~~~~~~~~~~~~~~~~aipi~~i~~vl~~l~~~~~~~~~ 850 (1108)
. .....+||+|+++++ +|||||+|.+|+++||++...... + +..+.+ |+||++.+++++.++...++
T Consensus 176 ~~~~~~~~~IqtdAain~gnsGgpl~n~~g~~iGint~~~~~~--~--~~~gig--faiP~~~~~~v~~~l~~~G~---- 245 (347)
T COG0265 176 GSAGGYVNFIQTDAAINPGNSGGPLVNIDGEVVGINTAIIAPS--G--GSSGIG--FAIPVNLVAPVLDELISKGK---- 245 (347)
T ss_pred cCcccccchhhcccccCCCCCCCceEcCCCcEEEEEEEEecCC--C--CcceeE--EEecHHHHHHHHHHHHHcCC----
Confidence 1 125689999999976 899999999999999998855441 1 123444 88999999999999998555
Q ss_pred cccCcccCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCCHHhHh-ccCCCEEEEECCEE
Q 001280 851 LINGVKRPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGSKAENM-LEQGDMMLAINKQP 929 (1108)
Q Consensus 851 ~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~s~A~~a-L~~GDiIlsVnG~~ 929 (1108)
+.|+ ++|+.+.++....+ +|++.. .|.+|..|.+++||+++ ++.||+|+++||++
T Consensus 246 ----v~~~-----~lgv~~~~~~~~~~--~g~~~~-------------~G~~V~~v~~~spa~~agi~~Gdii~~vng~~ 301 (347)
T COG0265 246 ----VVRG-----YLGVIGEPLTADIA--LGLPVA-------------AGAVVLGVLPGSPAAKAGIKAGDIITAVNGKP 301 (347)
T ss_pred ----cccc-----ccceEEEEcccccc--cCCCCC-------------CceEEEecCCCChHHHcCCCCCCEEEEECCEE
Confidence 7788 89999998887666 665533 66889999999999999 99999999999999
Q ss_pred cCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeecc
Q 001280 930 VTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDV 972 (1108)
Q Consensus 930 V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~~~ 972 (1108)
+.+..++...+....+| ..+.+++.|+|+++++.+++..
T Consensus 302 v~~~~~l~~~v~~~~~g----~~v~~~~~r~g~~~~~~v~l~~ 340 (347)
T COG0265 302 VASLSDLVAAVASNRPG----DEVALKLLRGGKERELAVTLGD 340 (347)
T ss_pred ccCHHHHHHHHhccCCC----CEEEEEEEECCEEEEEEEEecC
Confidence 99999999999777765 8999999999999999999876
No 15
>KOG1320 consensus Serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=2.6e-22 Score=229.59 Aligned_cols=314 Identities=19% Similarity=0.249 Sum_probs=237.0
Q ss_pred cCchhHHHHHHHhCCceEEEEEee----eeccCCCCCCccEEEEEEEeCCCcEEEEcccccCCCCe----------EEEE
Q 001280 33 ATADDWRKALNKVVPAVVVLRTTA----CRAFDTEAAGASYATGFVVDKRRGIILTNRHVVKPGPV----------VAEA 98 (1108)
Q Consensus 33 ~~~~~~~~~~~~~~~sVV~I~~~~----~~~~d~~~~~~~~GSGfvV~~~~G~ILTn~HVV~~~~~----------~~~v 98 (1108)
...+..+...++...|+|.|.... ..+|....-....||||||+. +|+++||+||+..... .+.+
T Consensus 125 k~~~~v~~~~~~cd~Avv~Ie~~~f~~~~~~~e~~~ip~l~~S~~Vv~g-d~i~VTnghV~~~~~~~y~~~~~~l~~vqi 203 (473)
T KOG1320|consen 125 KYKAFVAAVFEECDLAVVYIESEEFWKGMNPFELGDIPSLNGSGFVVGG-DGIIVTNGHVVRVEPRIYAHSSTVLLRVQI 203 (473)
T ss_pred hhhhhHHHhhhcccceEEEEeeccccCCCcccccCCCcccCccEEEEcC-CcEEEEeeEEEEEEeccccCCCcceeeEEE
Confidence 335678889999999999999642 223555666778899999997 8999999999986433 3666
Q ss_pred EecCC--eEEeEEEEEEcCCCceEEEEECCCC--cccccccCCCCCCcccCCCCEEEEEecCCCCCCeEEEEEEEEecCC
Q 001280 99 MFVNR--EEIPVYPIYRDPVHDFGFFRYDPSA--IQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRD 174 (1108)
Q Consensus 99 ~~~d~--~~~~a~vv~~d~~~DlAlLk~d~~~--~~~~~~~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~is~~~~~ 174 (1108)
..+++ ..+.+.+.+.|+..|+|+++++..+ ++.+++.. ...++.|+++..+|+|++.....+.|+++...|.
T Consensus 204 ~aa~~~~~s~ep~i~g~d~~~gvA~l~ik~~~~i~~~i~~~~----~~~~~~G~~~~a~~~~f~~~nt~t~g~vs~~~R~ 279 (473)
T KOG1320|consen 204 DAAIGPGNSGEPVIVGVDKVAGVAFLKIKTPENILYVIPLGV----SSHFRTGVEVSAIGNGFGLLNTLTQGMVSGQLRK 279 (473)
T ss_pred EEeecCCccCCCeEEccccccceEEEEEecCCcccceeecce----eeeecccceeeccccCceeeeeeeeccccccccc
Confidence 66666 8899999999999999999996432 34444443 7889999999999999999999999999999997
Q ss_pred CCCCCCCCcccccceEEEEeeecCCCCCCCceecccCcEEEEeecccCC----CCcccccChHHHHHHHHHHHhcCCccc
Q 001280 175 APHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSS----SASAFFLPLERVVRALRFLQERRDCNI 250 (1108)
Q Consensus 175 ~~~~~~~~~~~~~~~~i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~----~~~~falPi~~i~~~l~~l~~~~~~~~ 250 (1108)
....+.. ......+|+|+++.++.|+||+|++|.||++||++++.... .+.+|++|.+.++.++.+.-+.+- ..
T Consensus 280 ~~~lg~~-~g~~i~~~~qtd~ai~~~nsg~~ll~~DG~~IgVn~~~~~ri~~~~~iSf~~p~d~vl~~v~r~~e~~~-~l 357 (473)
T KOG1320|consen 280 SFKLGLE-TGVLISKINQTDAAINPGNSGGPLLNLDGEVIGVNTRKVTRIGFSHGISFKIPIDTVLVIVLRLGEFQI-SL 357 (473)
T ss_pred ccccCcc-cceeeeeecccchhhhcccCCCcEEEecCcEeeeeeeeeEEeeccccceeccCchHhhhhhhhhhhhce-ee
Confidence 6554333 22335568999999999999999999999999999876653 688999999999998876532220 00
Q ss_pred ccccccccCCCccCeEEEEcChhHHH-hcCCChhHHHhhhcCCCCCC-CceEEEEEecCCCcccc-CCCCCCEEEEECCE
Q 001280 251 HNWEAVSIPRGTLQVTFVHKGFDETR-RLGLQSATEQMVRHASPPGE-TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGE 327 (1108)
Q Consensus 251 ~~~~~~~v~rg~lg~~~~~~~~~~~r-~lGl~~~~~~~~~~~~~~~~-~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~ 327 (1108)
.+.......+.++|.....+.....- .++.+ ..+|+.. .++++ ..|.|++++.. ++++||+|++|||+
T Consensus 358 r~~~~~~p~~~~~g~~s~~i~~g~vf~~~~~~--------~~~~~~~~q~v~i-s~Vlp~~~~~~~~~~~g~~V~~vng~ 428 (473)
T KOG1320|consen 358 RPVKPLVPVHQYIGLPSYYIFAGLVFVPLTKS--------YIFPSGVVQLVLV-SQVLPGSINGGYGLKPGDQVVKVNGK 428 (473)
T ss_pred ccccCcccccccCCceeEEEecceEEeecCCC--------ccccccceeEEEE-EEeccCCCcccccccCCCEEEEECCE
Confidence 01111123345666664443322221 13333 1234333 35555 79999999999 99999999999999
Q ss_pred EeCChhHHHHHHhc-CCCCeEEEEEEECCEEEEEEE
Q 001280 328 VITQFLKLETLLDD-GVDKNIELLIERGGISMTVNL 362 (1108)
Q Consensus 328 ~v~~~~~l~~~l~~-~~g~~v~l~V~R~g~~~~~~v 362 (1108)
+|.+..++..++.. ..+++|.+...|+-+..++.+
T Consensus 429 ~V~n~~~l~~~i~~~~~~~~v~vl~~~~~e~~tl~I 464 (473)
T KOG1320|consen 429 PVKNLKHLYELIEECSTEDKVAVLDRRSAEDATLEI 464 (473)
T ss_pred EeechHHHHHHHHhcCcCceEEEEEecCccceeEEe
Confidence 99999999999954 666889999889988888887
No 16
>KOG1320 consensus Serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.80 E-value=1.7e-18 Score=198.57 Aligned_cols=309 Identities=17% Similarity=0.163 Sum_probs=219.4
Q ss_pred ccccccccEEEEEE---EcCcccccCCcccceeeEEEEEEEeeCCceEEEEeCceecCCCc----------eEEEEeecC
Q 001280 620 AESVIEPTLVMFEV---HVPPSCMIDGVHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISAS----------DVMLSFAAF 686 (1108)
Q Consensus 620 ~~~~~~~S~V~V~~---~~~~~~~~dg~~~~~~~GsG~iId~~~~~G~IlTnr~~V~~~~~----------~i~V~~~~~ 686 (1108)
..++...++|.|+. +-.. .++.+..-....|||||++ .+|+++||.|++..... .|.|+.++
T Consensus 133 ~~~~cd~Avv~Ie~~~f~~~~-~~~e~~~ip~l~~S~~Vv~---gd~i~VTnghV~~~~~~~y~~~~~~l~~vqi~aa~- 207 (473)
T KOG1320|consen 133 VFEECDLAVVYIESEEFWKGM-NPFELGDIPSLNGSGFVVG---GDGIIVTNGHVVRVEPRIYAHSSTVLLRVQIDAAI- 207 (473)
T ss_pred hhhcccceEEEEeeccccCCC-cccccCCCcccCccEEEEc---CCcEEEEeeEEEEEEeccccCCCcceeeEEEEEee-
Confidence 34455677888875 2221 2366666777899999999 79999999777664433 48888887
Q ss_pred C--eEEeEEEEEeeCCCcEEEEEECCC--CCCcccccceeccccCCCccCCCCCEEEEEeeCCCCCceeeeeeEeccccc
Q 001280 687 P--IEIPGEVVFLHPVHNFALIAYDPS--SLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAA 762 (1108)
Q Consensus 687 ~--~~~~a~vv~~dp~~dlAilk~d~~--~l~~~~~~~v~~~~l~~~~~l~~G~~V~~vG~p~~~~~~~~~~~Vt~~~~~ 762 (1108)
+ ...++.+++.|+..|+|+++++.. .++. ++++-+..++.|+++.++|.|+++. .+++ .
T Consensus 208 ~~~~s~ep~i~g~d~~~gvA~l~ik~~~~i~~~--------i~~~~~~~~~~G~~~~a~~~~f~~~-----nt~t----~ 270 (473)
T KOG1320|consen 208 GPGNSGEPVIVGVDKVAGVAFLKIKTPENILYV--------IPLGVSSHFRTGVEVSAIGNGFGLL-----NTLT----Q 270 (473)
T ss_pred cCCccCCCeEEccccccceEEEEEecCCcccce--------eecceeeeecccceeeccccCceee-----eeee----e
Confidence 6 899999999999999999999533 2332 6676666799999999999999884 4555 6
Q ss_pred cccCCCCCCccc------cccceEEEEecccCC-CCCceEEcCCeeEEEEEeeccccccccCCCCCcceeEecccHHHHH
Q 001280 763 LNISSADCPRYR------AMNMEVIELDTDFGS-TFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTIS 835 (1108)
Q Consensus 763 ~~i~~~~~~~y~------~~~~~~I~~d~~ig~-~sGGpL~d~~G~VvGi~~~~~~~~~~~~~~~~~~~~~~aipi~~i~ 835 (1108)
|.++...+..|. -...+++|+|++++. ++||||+|.||++||+++..... ..-.....|++|.+.++
T Consensus 271 g~vs~~~R~~~~lg~~~g~~i~~~~qtd~ai~~~nsg~~ll~~DG~~IgVn~~~~~r------i~~~~~iSf~~p~d~vl 344 (473)
T KOG1320|consen 271 GMVSGQLRKSFKLGLETGVLISKINQTDAAINPGNSGGPLLNLDGEVIGVNTRKVTR------IGFSHGISFKIPIDTVL 344 (473)
T ss_pred cccccccccccccCcccceeeeeecccchhhhcccCCCcEEEecCcEeeeeeeeeEE------eeccccceeccCchHhh
Confidence 666666554443 244689999999965 79999999999999988773321 11223334889999999
Q ss_pred HHHHHHHcCCCCCcccccCcccCCCceeeeeeEEEEcChHhHH-HcCCCHHHHHHHHhcCC-CccceEEEEeecCCCHHh
Q 001280 836 RVLDKIISGASGPSLLINGVKRPMPLVRILEVELYPTLLSKAR-SFGLSDDWVQALVKKDP-VRRQVLRVKGCLAGSKAE 913 (1108)
Q Consensus 836 ~vl~~l~~~~~~~~~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~-~~Gl~~~wi~~~~~~~~-~~~~~~~V~~V~~~s~A~ 913 (1108)
.++.+....... -..+++..|.-+|+|...+.+.....- -.+.+.. ++ ...|+++|..|.+++++.
T Consensus 345 ~~v~r~~e~~~~----lr~~~~~~p~~~~~g~~s~~i~~g~vf~~~~~~~~--------~~~~~~q~v~is~Vlp~~~~~ 412 (473)
T KOG1320|consen 345 VIVLRLGEFQIS----LRPVKPLVPVHQYIGLPSYYIFAGLVFVPLTKSYI--------FPSGVVQLVLVSQVLPGSING 412 (473)
T ss_pred hhhhhhhhhcee----eccccCcccccccCCceeEEEecceEEeecCCCcc--------ccccceeEEEEEEeccCCCcc
Confidence 988887433210 001222233445666655544322211 1111111 11 234789999999999999
Q ss_pred Hh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeecc
Q 001280 914 NM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDV 972 (1108)
Q Consensus 914 ~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~~~ 972 (1108)
.. +++||+|++|||++|.+..++..++.....+ +++.+...|..|..++.+....
T Consensus 413 ~~~~~~g~~V~~vng~~V~n~~~l~~~i~~~~~~----~~v~vl~~~~~e~~tl~Il~~~ 468 (473)
T KOG1320|consen 413 GYGLKPGDQVVKVNGKPVKNLKHLYELIEECSTE----DKVAVLDRRSAEDATLEILPEH 468 (473)
T ss_pred cccccCCCEEEEECCEEeechHHHHHHHHhcCcC----ceEEEEEecCccceeEEecccc
Confidence 99 9999999999999999999999998654443 6788888888888888876543
No 17
>KOG3209 consensus WW domain-containing protein [General function prediction only]
Probab=99.75 E-value=4.9e-16 Score=178.44 Aligned_cols=177 Identities=21% Similarity=0.296 Sum_probs=110.6
Q ss_pred ccCCCccCeEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChhH
Q 001280 257 SIPRGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFLK 334 (1108)
Q Consensus 257 ~v~rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~~ 334 (1108)
.+.+|+.|+.|..+.-+.. ...-.|-|..|+.++||++ .|+.||+|+.|||+.+-...+
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 5567778887776543221 2344677799999999999 699999999999999987665
Q ss_pred HH--HHHh-cCCCCeEEEEEEECCE-----EE-----EEEEcccccccCCCcccccCCeEE------------ccCCHHH
Q 001280 335 LE--TLLD-DGVDKNIELLIERGGI-----SM-----TVNLVQDLHSITPDYFLEVSGAVI------------HPLSYQQ 389 (1108)
Q Consensus 335 l~--~~l~-~~~g~~v~l~V~R~g~-----~~-----~~~v~~~~~~~~~~~~~~~~G~~~------------~~l~~q~ 389 (1108)
.+ .++. -.+|..|.|++.|+=+ +. .+-|+..|+...+ .-.|.-+ ++-++..
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 54 4443 4679999999999521 11 1111222321111 1111111 0000000
Q ss_pred --------hhccCcC----CCeEEEECCCChhHHcCCCCCCEEEEeCCeecCCHH--HHHHHHHhcCCCCeEEEEEeeec
Q 001280 390 --------ARNFRFP----CGLVYVAEPGYMLFRAGVPRHAIIKKFAGEEISRLE--DLISVLSKLSRGARVPIEYSSYT 455 (1108)
Q Consensus 390 --------~~~~~~~----~~gv~v~~~~~~a~~aGl~~Gd~I~~Vng~~v~~l~--~~~~~i~~~~~~~~v~l~~~~~~ 455 (1108)
..-|++. ..|.-+...-.+-+.-||..||+|+.+|++.+.+|. +++++++..|.|.++.|.++|..
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 012222222234455689999999999999998876 88999999999999998888765
Q ss_pred c
Q 001280 456 D 456 (1108)
Q Consensus 456 ~ 456 (1108)
.
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=99.71 E-value=2e-16 Score=188.31 Aligned_cols=157 Identities=20% Similarity=0.217 Sum_probs=127.8
Q ss_pred EEEeecCCCHHhHh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeecccCCCC---
Q 001280 902 RVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGNG--- 977 (1108)
Q Consensus 902 ~V~~V~~~s~A~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~~~~~~~~--- 977 (1108)
+|..|.++|||++| ||+||+|++|||++|.+|+++...+....++ ++++++|.|+|+.+++++++...+...
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 9999999999999999999999988666665 789999999999988888875442111
Q ss_pred CcceeeeccccccCCchhhhhcCCCCCCCCeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCce
Q 001280 978 TTRVINWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEF 1057 (1108)
Q Consensus 978 t~~~~~~~G~~~~~p~~~vr~~~~lp~~~~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~ 1057 (1108)
+.......|+....+. .+++|++|.++|||+++||++||.|++|||+++.+|+++.+.++.. .++.
T Consensus 205 ~~~~~~~lGl~~~~~~-------------~~~vV~~V~~~SpA~~AGL~~GDvIl~Ing~~V~s~~dl~~~l~~~-~~~~ 270 (449)
T PRK10779 205 KQDPVSSLGIRPRGPQ-------------IEPVLAEVQPNSAASKAGLQAGDRIVKVDGQPLTQWQTFVTLVRDN-PGKP 270 (449)
T ss_pred ccchhhcccccccCCC-------------cCcEEEeeCCCCHHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhC-CCCE
Confidence 1111122333221111 1468999999999999999999999999999999999999999984 4788
Q ss_pred EEEEEEEeCCeEEEEEEEeC
Q 001280 1058 VRVRTVHLNGKPRVLTLKQD 1077 (1108)
Q Consensus 1058 v~l~~v~rdg~~~~~~lk~d 1077 (1108)
+.++ +.|+|+.+.++++++
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
>PF12812 PDZ_1: PDZ-like domain
Probab=99.57 E-value=4.8e-15 Score=131.13 Aligned_cols=77 Identities=45% Similarity=0.699 Sum_probs=71.7
Q ss_pred ccCCCcccccCCeEEccCCHHHhhccCcCCCeEEEECCCChhHHcC-CCCCCEEEEeCCeecCCHHHHHHHHHhcCCC
Q 001280 368 SITPDYFLEVSGAVIHPLSYQQARNFRFPCGLVYVAEPGYMLFRAG-VPRHAIIKKFAGEEISRLEDLISVLSKLSRG 444 (1108)
Q Consensus 368 ~~~~~~~~~~~G~~~~~l~~q~~~~~~~~~~gv~v~~~~~~a~~aG-l~~Gd~I~~Vng~~v~~l~~~~~~i~~~~~~ 444 (1108)
+++|+|+++|+|++||+|+||++|+|+++++|+|++.++++...++ +.+|++|++|||+||+||++|+++|+++||+
T Consensus 1 ~itp~r~v~~~Ga~f~~Ls~q~aR~~~~~~~gv~v~~~~g~~~~~~~i~~g~iI~~Vn~kpt~~Ld~f~~vvk~ipd~ 78 (78)
T PF12812_consen 1 AITPSRFVEVCGAVFHDLSYQQARQYGIPVGGVYVAVSGGSLAFAGGISKGFIITSVNGKPTPDLDDFIKVVKKIPDN 78 (78)
T ss_pred CccCCEEEEEcCeecccCCHHHHHHhCCCCCEEEEEecCCChhhhCCCCCCeEEEeECCcCCcCHHHHHHHHHhCCCC
Confidence 4789999999999999999999999999999999998766666666 9999999999999999999999999999983
No 20
>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=99.57 E-value=4.4e-14 Score=166.57 Aligned_cols=144 Identities=22% Similarity=0.322 Sum_probs=119.5
Q ss_pred ceEEEEeecCCCHHhHh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeecccCCCC
Q 001280 899 QVLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGNG 977 (1108)
Q Consensus 899 ~~~~V~~V~~~s~A~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~~~~~~~~ 977 (1108)
.+.+|.+|.++|||+++ |++||+|+++||+++.++.++...+.... +++.+++.|+++..++.+++.
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 357899999888766544322
Q ss_pred CcceeeeccccccCCchhhhhcCCCCCCCCeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCce
Q 001280 978 TTRVINWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEF 1057 (1108)
Q Consensus 978 t~~~~~~~G~~~~~p~~~vr~~~~lp~~~~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~ 1057 (1108)
+....|. .+++|.+|.++|||+++||++||.|++|||+++.+++++.+.+++.+ ++.
T Consensus 196 ---------~~~~~~~-------------~g~vV~~V~~~SpA~~aGL~~GD~Iv~Vng~~V~s~~dl~~~l~~~~-~~~ 252 (420)
T TIGR00054 196 ---------LIPRGPK-------------IEPVLSDVTPNSPAEKAGLKEGDYIQSINGEKLRSWTDFVSAVKENP-GKS 252 (420)
T ss_pred ---------ceecCCC-------------cCcEEEEECCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHHHhCC-CCc
Confidence 1111111 25689999999999999999999999999999999999999999854 778
Q ss_pred EEEEEEEeCCeEEEEEEEeCC
Q 001280 1058 VRVRTVHLNGKPRVLTLKQDL 1078 (1108)
Q Consensus 1058 v~l~~v~rdg~~~~~~lk~d~ 1078 (1108)
+.++ +.|+|+.+.++++++.
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 8999999999998864
No 21
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=99.51 E-value=2e-13 Score=162.57 Aligned_cols=141 Identities=18% Similarity=0.241 Sum_probs=107.8
Q ss_pred EEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHH-hcCCCCeEEEEEEECCEEEEEEE-ccccccc-CC--Cccc
Q 001280 302 VDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLL-DDGVDKNIELLIERGGISMTVNL-VQDLHSI-TP--DYFL 375 (1108)
Q Consensus 302 v~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l-~~~~g~~v~l~V~R~g~~~~~~v-~~~~~~~-~~--~~~~ 375 (1108)
|..|.++|||++ |||+||+|++|||++|.+|.++...+ ....|++++++|.|+|+.++.++ +...+.. .+ ....
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 379999999999 99999999999999999999999877 45677899999999999888777 5322111 01 1111
Q ss_pred ccCCeEEccCCHHHhhccCcCCCeEEEE--CCCChhHHcCCCCCCEEEEeCCeecCCHHHHHHHHHhcCCCCeEEEEEee
Q 001280 376 EVSGAVIHPLSYQQARNFRFPCGLVYVA--EPGYMLFRAGVPRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYSS 453 (1108)
Q Consensus 376 ~~~G~~~~~l~~q~~~~~~~~~~gv~v~--~~~~~a~~aGl~~Gd~I~~Vng~~v~~l~~~~~~i~~~~~~~~v~l~~~~ 453 (1108)
...| +.++.++ .++.|. .++|+|++|||++||+|++|||+++.+|+++.+.++.. .++.+.+++.|
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---------IEPVLAEVQPNSAASKAGLQAGDRIVKVDGQPLTQWQTFVTLVRDN-PGKPLALEIER 277 (449)
T ss_pred hccc--ccccCCC---------cCcEEEeeCCCCHHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhC-CCCEEEEEEEE
Confidence 1223 2222221 124555 58999999999999999999999999999999999884 45677777766
Q ss_pred e
Q 001280 454 Y 454 (1108)
Q Consensus 454 ~ 454 (1108)
-
T Consensus 278 ~ 278 (449)
T PRK10779 278 Q 278 (449)
T ss_pred C
Confidence 4
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=99.48 E-value=2.4e-13 Score=131.81 Aligned_cols=110 Identities=35% Similarity=0.597 Sum_probs=74.9
Q ss_pred EEEEEEeCCCcEEEEcccccCC-------CCeEEEEEecCCeEEe--EEEEEEcCC-CceEEEEECCCCcccccccCCCC
Q 001280 70 ATGFVVDKRRGIILTNRHVVKP-------GPVVAEAMFVNREEIP--VYPIYRDPV-HDFGFFRYDPSAIQFLNYDEIPL 139 (1108)
Q Consensus 70 GSGfvV~~~~G~ILTn~HVV~~-------~~~~~~v~~~d~~~~~--a~vv~~d~~-~DlAlLk~d~~~~~~~~~~~l~l 139 (1108)
||||+|++ +|+||||+||+.. ....+.+.+.++..+. +++++.|+. +|+|||+++.. .
T Consensus 1 GTGf~i~~-~g~ilT~~Hvv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~All~v~~~-----~------ 68 (120)
T PF13365_consen 1 GTGFLIGP-DGYILTAAHVVEDWNDGKQPDNSSVEVVFPDGRRVPPVAEVVYFDPDDYDLALLKVDPW-----T------ 68 (120)
T ss_dssp EEEEEEET-TTEEEEEHHHHTCCTT--G-TCSEEEEEETTSCEEETEEEEEEEETT-TTEEEEEESCE-----E------
T ss_pred CEEEEEcC-CceEEEchhheecccccccCCCCEEEEEecCCCEEeeeEEEEEECCccccEEEEEEecc-----c------
Confidence 79999997 7899999999995 3456888888888888 999999999 99999999800 0
Q ss_pred CCcccCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCcccccceEEEEeeecCCCCCCCceecccCcEEEE
Q 001280 140 APEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVAL 216 (1108)
Q Consensus 140 ~~~~~~~G~~V~~iG~p~g~~~si~~G~is~~~~~~~~~~~~~~~~~~~~~i~~~a~~~~G~SGgPv~n~~G~vVGi 216 (1108)
..+..... .+........ ........++ +++.+.+|+|||||||.+|+||||
T Consensus 69 -----~~~~~~~~------------~~~~~~~~~~-------~~~~~~~~~~-~~~~~~~G~SGgpv~~~~G~vvGi 120 (120)
T PF13365_consen 69 -----GVGGGVRV------------PGSTSGVSPT-------STNDNRMLYI-TDADTRPGSSGGPVFDSDGRVVGI 120 (120)
T ss_dssp -----EEEEEEEE------------EEEEEEEEEE-------EEEETEEEEE-ESSS-STTTTTSEEEETTSEEEEE
T ss_pred -----ceeeeeEe------------eeeccccccc-------cCcccceeEe-eecccCCCcEeHhEECCCCEEEeC
Confidence 00000000 0000011000 0000011124 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=99.36 E-value=3.5e-12 Score=150.49 Aligned_cols=129 Identities=19% Similarity=0.248 Sum_probs=103.6
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEECCEEEEEEE-cccccccCCCcc
Q 001280 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIERGGISMTVNL-VQDLHSITPDYF 374 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~V~R~g~~~~~~v-~~~~~~~~~~~~ 374 (1108)
.|.+| ..|.++|||++ ||++||+|+++||+++.++.++...+.... .++.+++.|+|+..++.+ +.
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 56677 79999999999 999999999999999999999998875544 688999999888766544 22
Q ss_pred cccCCeEEccCCHHHhhccCcCCCeEEEE--CCCChhHHcCCCCCCEEEEeCCeecCCHHHHHHHHHhcCCCCeEEEEEe
Q 001280 375 LEVSGAVIHPLSYQQARNFRFPCGLVYVA--EPGYMLFRAGVPRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEYS 452 (1108)
Q Consensus 375 ~~~~G~~~~~l~~q~~~~~~~~~~gv~v~--~~~~~a~~aGl~~Gd~I~~Vng~~v~~l~~~~~~i~~~~~~~~v~l~~~ 452 (1108)
+.+..+ ..++.|. .++|+|++|||++||+|++|||+++.+|+++.+.+++.+ ++.+.+++.
T Consensus 196 -------~~~~~~---------~~g~vV~~V~~~SpA~~aGL~~GD~Iv~Vng~~V~s~~dl~~~l~~~~-~~~v~l~v~ 258 (420)
T TIGR00054 196 -------LIPRGP---------KIEPVLSDVTPNSPAEKAGLKEGDYIQSINGEKLRSWTDFVSAVKENP-GKSMDIKVE 258 (420)
T ss_pred -------ceecCC---------CcCcEEEEECCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHHHhCC-CCceEEEEE
Confidence 111111 0234555 589999999999999999999999999999999999854 566777776
Q ss_pred ee
Q 001280 453 SY 454 (1108)
Q Consensus 453 ~~ 454 (1108)
|-
T Consensus 259 R~ 260 (420)
T TIGR00054 259 RN 260 (420)
T ss_pred EC
Confidence 63
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=99.20 E-value=1.1e-10 Score=105.64 Aligned_cols=78 Identities=32% Similarity=0.553 Sum_probs=66.9
Q ss_pred CccCeEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHH
Q 001280 261 GTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLL 339 (1108)
Q Consensus 261 g~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l 339 (1108)
|+||+.+.... ...|++| ..|.++|||++ ||++||+|++|||++|.++.++..++
T Consensus 1 ~~lGv~~~~~~-----------------------~~~g~~V-~~V~~~spA~~aGl~~GD~I~~ing~~v~~~~~~~~~l 56 (82)
T PF13180_consen 1 GGLGVTVQNLS-----------------------DTGGVVV-VSVIPGSPAAKAGLQPGDIILAINGKPVNSSEDLVNIL 56 (82)
T ss_dssp -E-SEEEEECS-----------------------CSSSEEE-EEESTTSHHHHTTS-TTEEEEEETTEESSSHHHHHHHH
T ss_pred CEECeEEEEcc-----------------------CCCeEEE-EEeCCCCcHHHCCCCCCcEEEEECCEEcCCHHHHHHHH
Confidence 57899988642 2368888 58999999999 99999999999999999999999888
Q ss_pred -hcCCCCeEEEEEEECCEEEEEEE
Q 001280 340 -DDGVDKNIELLIERGGISMTVNL 362 (1108)
Q Consensus 340 -~~~~g~~v~l~V~R~g~~~~~~v 362 (1108)
...+|++++|+|.|+|+.+++++
T Consensus 57 ~~~~~g~~v~l~v~R~g~~~~~~v 80 (82)
T PF13180_consen 57 SKGKPGDTVTLTVLRDGEELTVEV 80 (82)
T ss_dssp HCSSTTSEEEEEEEETTEEEEEEE
T ss_pred HhCCCCCEEEEEEEECCEEEEEEE
Confidence 56899999999999999999887
No 25
>PF12812 PDZ_1: PDZ-like domain
Probab=99.15 E-value=1.2e-10 Score=103.36 Aligned_cols=76 Identities=30% Similarity=0.484 Sum_probs=66.2
Q ss_pred CCCcceeeeccccccC-CchhhhhcCCCCCCCCeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCC
Q 001280 976 NGTTRVINWCGCIVQD-PHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEH 1054 (1108)
Q Consensus 976 ~~t~~~~~~~G~~~~~-p~~~vr~~~~lp~~~~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~ 1054 (1108)
..++|++.|+|+.+++ +++.+|++. ++. ++++.+...|+++.++|+.+|-+|++|||+||+|+|+|+++++++||
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 777888865 343 35555778999999999999999999999999999999999999997
Q ss_pred C
Q 001280 1055 G 1055 (1108)
Q Consensus 1055 ~ 1055 (1108)
+
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=99.13 E-value=3.6e-10 Score=102.35 Aligned_cols=69 Identities=29% Similarity=0.377 Sum_probs=64.1
Q ss_pred CeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEeCCeEEEEEEEe
Q 001280 1007 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQ 1076 (1108)
Q Consensus 1007 ~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~~lk~ 1076 (1108)
.|++|.++.++|||+++||++||.|++|||+++.++++|...+...+.|+.++|+ +.|+|+.+.++++.
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=99.05 E-value=9.1e-10 Score=106.60 Aligned_cols=55 Identities=31% Similarity=0.512 Sum_probs=47.5
Q ss_pred EEEEEEEeeCCceEEEEeCceecC-------CCceEEEEeecCCeEEe--EEEEEeeCC-CcEEEEEEC
Q 001280 651 GTGVIIYHSQSMGLVVVDKNTVAI-------SASDVMLSFAAFPIEIP--GEVVFLHPV-HNFALIAYD 709 (1108)
Q Consensus 651 GsG~iId~~~~~G~IlTnr~~V~~-------~~~~i~V~~~~~~~~~~--a~vv~~dp~-~dlAilk~d 709 (1108)
||||+|+ ++|||||++|++.. ....+.+.+.+ +...+ |++++.|+. +|+|||+++
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 67799999776653 45678888887 77788 999999999 999999998
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=98.98 E-value=4.7e-09 Score=96.52 Aligned_cols=87 Identities=37% Similarity=0.540 Sum_probs=73.0
Q ss_pred CccCeEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHH
Q 001280 261 GTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLL 339 (1108)
Q Consensus 261 g~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l 339 (1108)
+++|+.++.......++++++ ...|++| ..|.+++||++ ||++||+|++|||+.+.++.++..++
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 478999999887666666654 4567665 79999999998 99999999999999999999999888
Q ss_pred hc-CCCCeEEEEEEECCEEEEEE
Q 001280 340 DD-GVDKNIELLIERGGISMTVN 361 (1108)
Q Consensus 340 ~~-~~g~~v~l~V~R~g~~~~~~ 361 (1108)
.. ..++.+.+++.|+|+..++.
T Consensus 67 ~~~~~~~~i~l~v~r~g~~~~~~ 89 (90)
T cd00987 67 AELKPGDKVTLTVLRGGKELTVT 89 (90)
T ss_pred HhcCCCCEEEEEEEECCEEEEee
Confidence 55 45889999999999876654
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=98.96 E-value=5e-09 Score=96.37 Aligned_cols=88 Identities=31% Similarity=0.411 Sum_probs=74.6
Q ss_pred eccccccCCchhhhhcCCCCCCCCeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEE
Q 001280 984 WCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTV 1063 (1108)
Q Consensus 984 ~~G~~~~~p~~~vr~~~~lp~~~~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v 1063 (1108)
|+|+.++..+...+....+ ....|++|..+.++|||+++||++||.|++|||+++.+++++.+.+.....++.+.+. +
T Consensus 2 ~~G~~~~~~~~~~~~~~~~-~~~~g~~V~~v~~~s~a~~~gl~~GD~I~~Ing~~i~~~~~~~~~l~~~~~~~~i~l~-v 79 (90)
T cd00987 2 WLGVTVQDLTPDLAEELGL-KDTKGVLVASVDPGSPAAKAGLKPGDVILAVNGKPVKSVADLRRALAELKPGDKVTLT-V 79 (90)
T ss_pred ccceEEeECCHHHHHHcCC-CCCCEEEEEEECCCCHHHHcCCCcCCEEEEECCEECCCHHHHHHHHHhcCCCCEEEEE-E
Confidence 7899999988766653222 2345999999999999999999999999999999999999999999987668899999 6
Q ss_pred EeCCeEEEEE
Q 001280 1064 HLNGKPRVLT 1073 (1108)
Q Consensus 1064 ~rdg~~~~~~ 1073 (1108)
.|+|+.+.++
T Consensus 80 ~r~g~~~~~~ 89 (90)
T cd00987 80 LRGGKELTVT 89 (90)
T ss_pred EECCEEEEee
Confidence 8999876654
No 30
>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=98.86 E-value=1.8e-08 Score=90.51 Aligned_cols=68 Identities=26% Similarity=0.268 Sum_probs=62.2
Q ss_pred CeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEeCCeEEEEEEE
Q 001280 1007 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLK 1075 (1108)
Q Consensus 1007 ~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~~lk 1075 (1108)
.|++|.++.++|||+++||++||.|++|||+++.+|++|...+.....++.+.+. +.|+|+...+++.
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 7899998877764
No 31
>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=98.81 E-value=2.9e-08 Score=89.15 Aligned_cols=70 Identities=24% Similarity=0.412 Sum_probs=62.0
Q ss_pred CCceEEEEEecCCCccccCCCCCCEEEEECCEEeCChhHHHHHHhc-CCCCeEEEEEEECCEEEEEEE-cccc
Q 001280 296 ETGLLVVDSVVPGGPAHLRLEPGDVLVRVNGEVITQFLKLETLLDD-GVDKNIELLIERGGISMTVNL-VQDL 366 (1108)
Q Consensus 296 ~~G~lVv~~V~~~spA~~gL~~GD~Il~VnG~~v~~~~~l~~~l~~-~~g~~v~l~V~R~g~~~~~~v-~~~~ 366 (1108)
..|++| ..|.++|||+.+|++||+|++|||+++.+|.++..++.. ..|+.+.+++.|+|+..++++ +..+
T Consensus 7 ~~Gv~V-~~V~~~s~A~~gL~~GD~I~~Ing~~v~~~~~~~~~l~~~~~~~~v~l~v~r~g~~~~~~v~l~~~ 78 (79)
T cd00986 7 YHGVYV-TSVVEGMPAAGKLKAGDHIIAVDGKPFKEAEELIDYIQSKKEGDTVKLKVKREEKELPEDLILKTF 78 (79)
T ss_pred ecCEEE-EEECCCCchhhCCCCCCEEEEECCEECCCHHHHHHHHHhCCCCCEEEEEEEECCEEEEEEEEEecc
Confidence 357776 699999999889999999999999999999999988864 778899999999999999888 6654
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=98.77 E-value=4.6e-08 Score=87.87 Aligned_cols=68 Identities=24% Similarity=0.381 Sum_probs=60.1
Q ss_pred cceEEEEeecCCCHHhHh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEe
Q 001280 898 RQVLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVG 969 (1108)
Q Consensus 898 ~~~~~V~~V~~~s~A~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~ 969 (1108)
.++++|.+|.++|||+++ |++||+|++|||+++.+|.++...+....++ +.+.+++.|+|+.++++++
T Consensus 9 ~~Gv~V~~V~~~spa~~aGL~~GDiI~~Ing~~v~~~~d~~~~l~~~~~g----~~v~l~v~r~g~~~~~~~~ 77 (79)
T cd00991 9 VAGVVIVGVIVGSPAENAVLHTGDVIYSINGTPITTLEDFMEALKPTKPG----EVITVTVLPSTTKLTNVST 77 (79)
T ss_pred CCcEEEEEECCCChHHhcCCCCCCEEEEECCEEcCCHHHHHHHHhcCCCC----CEEEEEEEECCEEEEEEEE
Confidence 467889999999999999 9999999999999999999999888655455 7899999999998887764
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=98.73 E-value=8.1e-08 Score=86.24 Aligned_cols=69 Identities=26% Similarity=0.398 Sum_probs=62.4
Q ss_pred CeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEeCCeEEEEEEEeC
Q 001280 1007 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQD 1077 (1108)
Q Consensus 1007 ~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~~lk~d 1077 (1108)
.|++|..+.++|||++ ||++||.|++|||+++.++++|...++..+.++.+.|. +.|+|+...+++++.
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 89999999999999999999999999976668899999 789999988887763
No 34
>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=98.70 E-value=1.1e-07 Score=85.21 Aligned_cols=66 Identities=30% Similarity=0.421 Sum_probs=59.1
Q ss_pred eEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEeCCeEEEEEEE
Q 001280 1008 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLK 1075 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~~lk 1075 (1108)
.++|..+.++|||+++||++||.|++|||+++.+++++...++... ++.+.+. +.|+|+...++++
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 3689999999999999999999999999999999999999998864 7788998 6889988777764
No 35
>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=98.69 E-value=3.2e-07 Score=98.39 Aligned_cols=177 Identities=21% Similarity=0.262 Sum_probs=109.1
Q ss_pred CCceEEEEEeeeeccCCCCCCccEEEEEEEeCCCcEEEEcccccCCCCeEEEEEec-------CC--eEEeEEEEEEcC-
Q 001280 46 VPAVVVLRTTACRAFDTEAAGASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFV-------NR--EEIPVYPIYRDP- 115 (1108)
Q Consensus 46 ~~sVV~I~~~~~~~~d~~~~~~~~GSGfvV~~~~G~ILTn~HVV~~~~~~~~v~~~-------d~--~~~~a~vv~~d~- 115 (1108)
.|.+|.|.... ....|+|++|+++ +|||++||+.. ...+.+.+. ++ ..+...-++.++
T Consensus 12 ~p~~v~i~~~~---------~~~~C~G~li~~~--~vLTaahC~~~-~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~h~~ 79 (220)
T PF00089_consen 12 FPWVVSIRYSN---------GRFFCTGTLISPR--WVLTAAHCVDG-ASDIKVRLGTYSIRNSDGSEQTIKVSKIIIHPK 79 (220)
T ss_dssp STTEEEEEETT---------TEEEEEEEEEETT--EEEEEGGGHTS-GGSEEEEESESBTTSTTTTSEEEEEEEEEEETT
T ss_pred CCeEEEEeeCC---------CCeeEeEEecccc--ccccccccccc-ccccccccccccccccccccccccccccccccc
Confidence 36677777742 1678999999964 99999999996 333444322 22 456665555543
Q ss_pred ------CCceEEEEECCCCcccccccCCCCCC--cccCCCCEEEEEecCCCCC----CeEEEEEEEEecCC-C-CCCCCC
Q 001280 116 ------VHDFGFFRYDPSAIQFLNYDEIPLAP--EAACVGLEIRVVGNDSGEK----VSILAGTLARLDRD-A-PHYKKD 181 (1108)
Q Consensus 116 ------~~DlAlLk~d~~~~~~~~~~~l~l~~--~~~~~G~~V~~iG~p~g~~----~si~~G~is~~~~~-~-~~~~~~ 181 (1108)
.+|+|||+++..-.....+.++.+.. ..++.|+.+.++|++.... ..+....+....+. . ..+...
T Consensus 80 ~~~~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~ 159 (220)
T PF00089_consen 80 YDPSTYDNDIALLKLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNGYSSNLQSVTVPVVSRKTCRSSYNDN 159 (220)
T ss_dssp SBTTTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTTSBTSBEEEEEEEEEEHHHHHHHTTTT
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 47999999986521111233333333 4458999999999987533 23444444433321 0 001111
Q ss_pred CcccccceEEEEee----ecCCCCCCCceecccCcEEEEeecccCCC---CcccccChHHHHHH
Q 001280 182 GYNDFNTFYMQAAS----GTKGGSSGSPVIDWQGRAVALNAGSKSSS---ASAFFLPLERVVRA 238 (1108)
Q Consensus 182 ~~~~~~~~~i~~~a----~~~~G~SGgPv~n~~G~vVGi~~~~~~~~---~~~falPi~~i~~~ 238 (1108)
....++.+.. ....|+|||||+..++.++||.+.+..-. ...++.++...++.
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 77889999999998889999998874332 23667777665543
No 36
>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=98.64 E-value=1.8e-07 Score=84.09 Aligned_cols=63 Identities=27% Similarity=0.178 Sum_probs=52.4
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEECCEEEEEEE
Q 001280 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIERGGISMTVNL 362 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~V~R~g~~~~~~v 362 (1108)
.|++| ..|.++|||++ ||++||+|++|||+++.+|.++... ...++.+.+++.|+|+..++.+
T Consensus 12 ~~~~V-~~V~~~s~a~~aGl~~GD~I~~Ing~~v~~~~~~l~~--~~~~~~v~l~v~r~g~~~~~~v 75 (80)
T cd00990 12 GLGKV-TFVRDDSPADKAGLVAGDELVAVNGWRVDALQDRLKE--YQAGDPVELTVFRDDRLIEVPL 75 (80)
T ss_pred CcEEE-EEECCCChHHHhCCCCCCEEEEECCEEhHHHHHHHHh--cCCCCEEEEEEEECCEEEEEEE
Confidence 45555 79999999999 9999999999999999986654222 2467899999999999888777
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=98.63 E-value=3.6e-07 Score=100.52 Aligned_cols=97 Identities=18% Similarity=0.128 Sum_probs=80.6
Q ss_pred HHHHHHHHHHHhcCCcccccccccccCCCccCeEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCCccc
Q 001280 233 ERVVRALRFLQERRDCNIHNWEAVSIPRGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAH 312 (1108)
Q Consensus 233 ~~i~~~l~~l~~~~~~~~~~~~~~~v~rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~ 312 (1108)
..++++++++.+.+ .+-++++|+.-.... | ...|++| ..+.+++||+
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 45677888888776 677888888764321 1 2468777 6999999999
Q ss_pred c-CCCCCCEEEEECCEEeCChhHHHHHHhc-CCCCeEEEEEEECCEEEEEEE
Q 001280 313 L-RLEPGDVLVRVNGEVITQFLKLETLLDD-GVDKNIELLIERGGISMTVNL 362 (1108)
Q Consensus 313 ~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~-~~g~~v~l~V~R~g~~~~~~v 362 (1108)
+ ||++||+|++|||+++.++.++..++.. ..+++++|+|+|+|+.+++.+
T Consensus 206 ~aGLr~GDvIv~ING~~i~~~~~~~~~l~~~~~~~~v~l~V~R~G~~~~i~v 257 (259)
T TIGR01713 206 KSGLQDGDIAVALNGLDLRDPEQAFQALQMLREETNLTLTVERDGQREDIYV 257 (259)
T ss_pred HcCCCCCCEEEEECCEEcCCHHHHHHHHHhcCCCCeEEEEEEECCEEEEEEE
Confidence 9 9999999999999999999999998865 677899999999999888776
No 38
>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=98.58 E-value=2.9e-07 Score=83.68 Aligned_cols=66 Identities=32% Similarity=0.630 Sum_probs=57.2
Q ss_pred CCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCCh--hHHHHHHhcCCCCeEEEEEEEC-CEEEEEEE
Q 001280 296 ETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQF--LKLETLLDDGVDKNIELLIERG-GISMTVNL 362 (1108)
Q Consensus 296 ~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g~~v~l~V~R~-g~~~~~~v 362 (1108)
..+++| ..|.+++||++ ||++||+|++|||+.+.+| .++..++....|+.+.+++.|+ |+..++++
T Consensus 12 ~~~~~V-~~v~~~s~a~~~gl~~GD~I~~vng~~i~~~~~~~~~~~l~~~~~~~i~l~v~r~~~~~~~~~~ 81 (85)
T cd00988 12 DGGLVI-TSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGKAGTKVRLTLKRGDGEPREVTL 81 (85)
T ss_pred CCeEEE-EEecCCCCHHHcCCCCCCEEEEECCEEcCCCCHHHHHHHhcCCCCCEEEEEEEcCCCCEEEEEE
Confidence 355555 79999999999 9999999999999999999 8888888666788999999998 88777665
No 39
>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=98.58 E-value=2.5e-07 Score=82.88 Aligned_cols=63 Identities=33% Similarity=0.588 Sum_probs=55.3
Q ss_pred EEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEECCEEEEEEE
Q 001280 300 LVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIERGGISMTVNL 362 (1108)
Q Consensus 300 lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~V~R~g~~~~~~v 362 (1108)
++|..|.+++||++ ||++||+|++|||+++.++.++...+....++.+.+++.|+|+..++.+
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 34479999999998 9999999999999999999999988866567899999999998766654
No 40
>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=98.55 E-value=1.4e-06 Score=95.82 Aligned_cols=101 Identities=17% Similarity=0.168 Sum_probs=81.7
Q ss_pred HHHHHHHHHHHHcCCCCCcccccCcccCCCceeeeeeEEEEcChHhHHHcCCCHHHHHHHHhcCCCccceEEEEeecCCC
Q 001280 831 IYTISRVLDKIISGASGPSLLINGVKRPMPLVRILEVELYPTLLSKARSFGLSDDWVQALVKKDPVRRQVLRVKGCLAGS 910 (1108)
Q Consensus 831 i~~i~~vl~~l~~~~~~~~~~~~~v~r~~p~~~~Lgv~~~~i~~~~a~~~Gl~~~wi~~~~~~~~~~~~~~~V~~V~~~s 910 (1108)
...+.+++++|.+.++ +-|. |+|+...... ....|++|..+.+++
T Consensus 158 ~~~~~~v~~~l~~~g~--------~~~~-----~lgi~p~~~~----------------------g~~~G~~v~~v~~~s 202 (259)
T TIGR01713 158 IVVSRRIIEELTKDPQ--------KMFD-----YIRLSPVMKN----------------------DKLEGYRLNPGKDPS 202 (259)
T ss_pred hhhHHHHHHHHHHCHH--------hhhh-----eEeEEEEEeC----------------------CceeEEEEEecCCCC
Confidence 3457788899887754 4444 7777654321 123689999999999
Q ss_pred HHhHh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEee
Q 001280 911 KAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGT 970 (1108)
Q Consensus 911 ~A~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~ 970 (1108)
+|+++ |++||+|++|||++++++.++..++..+..+ +.+.++|.|+|+.+++.+.+
T Consensus 203 ~a~~aGLr~GDvIv~ING~~i~~~~~~~~~l~~~~~~----~~v~l~V~R~G~~~~i~v~~ 259 (259)
T TIGR01713 203 LFYKSGLQDGDIAVALNGLDLRDPEQAFQALQMLREE----TNLTLTVERDGQREDIYVRF 259 (259)
T ss_pred HHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhcCCC----CeEEEEEEECCEEEEEEEEC
Confidence 99999 9999999999999999999999999777665 78999999999998888753
No 41
>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=98.53 E-value=4.5e-07 Score=82.47 Aligned_cols=68 Identities=31% Similarity=0.482 Sum_probs=61.0
Q ss_pred CeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCH--HHHHHHHHcCCCCceEEEEEEEeC-CeEEEEEEEe
Q 001280 1007 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVHLN-GKPRVLTLKQ 1076 (1108)
Q Consensus 1007 ~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~v~~~~~~~~v~l~~v~rd-g~~~~~~lk~ 1076 (1108)
.+++|..+.++|||+++||++||.|++|||+++.++ +++...++..+ ++.+.|. +.|+ |+.+.+++++
T Consensus 13 ~~~~V~~v~~~s~a~~~gl~~GD~I~~vng~~i~~~~~~~~~~~l~~~~-~~~i~l~-v~r~~~~~~~~~~~~ 83 (85)
T cd00988 13 GGLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGKA-GTKVRLT-LKRGDGEPREVTLTR 83 (85)
T ss_pred CeEEEEEecCCCCHHHcCCCCCCEEEEECCEEcCCCCHHHHHHHhcCCC-CCEEEEE-EEcCCCCEEEEEEEE
Confidence 378999999999999999999999999999999999 99999998744 8889998 6788 8888888875
No 42
>KOG3580 consensus Tight junction proteins [Signal transduction mechanisms]
Probab=98.51 E-value=4.7e-07 Score=103.52 Aligned_cols=55 Identities=31% Similarity=0.384 Sum_probs=51.8
Q ss_pred eEEEEEecCCChhhhcCCCCCCEEEEECCeecCCH--HHHHHHHHcCCCCceEEEEE
Q 001280 1008 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRT 1062 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~v~~~~~~~~v~l~~ 1062 (1108)
|++|+.|..||||++.||+.||.|+.||.++..++ ++.+..+-.+|+|+.++|..
T Consensus 430 GIFVaGvqegspA~~eGlqEGDQIL~VN~vdF~nl~REeAVlfLL~lPkGEevtila 486 (1027)
T KOG3580|consen 430 GIFVAGVQEGSPAEQEGLQEGDQILKVNTVDFRNLVREEAVLFLLELPKGEEVTILA 486 (1027)
T ss_pred eEEEeecccCCchhhccccccceeEEeccccchhhhHHHHHHHHhcCCCCcEEeehh
Confidence 89999999999999999999999999999999999 78888888999999999863
No 43
>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=98.50 E-value=6.6e-07 Score=80.36 Aligned_cols=66 Identities=26% Similarity=0.239 Sum_probs=56.3
Q ss_pred eEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEeCCeEEEEEEEeC
Q 001280 1008 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQD 1077 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~~lk~d 1077 (1108)
+++|+.+.++|||+++||++||.|++|||+++.+|.++. +....++.+.+. +.|+|+.+.+++++.
T Consensus 13 ~~~V~~V~~~s~a~~aGl~~GD~I~~Ing~~v~~~~~~l---~~~~~~~~v~l~-v~r~g~~~~~~v~~~ 78 (80)
T cd00990 13 LGKVTFVRDDSPADKAGLVAGDELVAVNGWRVDALQDRL---KEYQAGDPVELT-VFRDDRLIEVPLTLA 78 (80)
T ss_pred cEEEEEECCCChHHHhCCCCCCEEEEECCEEhHHHHHHH---HhcCCCCEEEEE-EEECCEEEEEEEEec
Confidence 689999999999999999999999999999999866554 443357789998 789999988888764
No 44
>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=98.43 E-value=3.9e-06 Score=90.66 Aligned_cols=164 Identities=19% Similarity=0.223 Sum_probs=94.2
Q ss_pred CCceEEEEEeeeeccCCCCCCccEEEEEEEeCCCcEEEEcccccCCC-CeEEEEEec---------CCeEEeEEEEEEcC
Q 001280 46 VPAVVVLRTTACRAFDTEAAGASYATGFVVDKRRGIILTNRHVVKPG-PVVAEAMFV---------NREEIPVYPIYRDP 115 (1108)
Q Consensus 46 ~~sVV~I~~~~~~~~d~~~~~~~~GSGfvV~~~~G~ILTn~HVV~~~-~~~~~v~~~---------d~~~~~a~vv~~d~ 115 (1108)
.|-+|.|.... ....++|.+|+++ +|||+|||+... .....+.+. ....+.++-+..+|
T Consensus 12 ~Pw~v~i~~~~---------~~~~C~GtlIs~~--~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp 80 (232)
T cd00190 12 FPWQVSLQYTG---------GRHFCGGSLISPR--WVLTAAHCVYSSAPSNYTVRLGSHDLSSNEGGGQVIKVKKVIVHP 80 (232)
T ss_pred CCCEEEEEccC---------CcEEEEEEEeeCC--EEEECHHhcCCCCCccEEEEeCcccccCCCCceEEEEEEEEEECC
Confidence 46677776531 4578999999964 999999999853 123444433 13345555566664
Q ss_pred -------CCceEEEEECCCCcccccccCCCCCCc--ccCCCCEEEEEecCCCCCC-----eEEEEEEEEecCC--CCCCC
Q 001280 116 -------VHDFGFFRYDPSAIQFLNYDEIPLAPE--AACVGLEIRVVGNDSGEKV-----SILAGTLARLDRD--APHYK 179 (1108)
Q Consensus 116 -------~~DlAlLk~d~~~~~~~~~~~l~l~~~--~~~~G~~V~~iG~p~g~~~-----si~~G~is~~~~~--~~~~~ 179 (1108)
.+|+|||+++..--....+.++.|... .+..|+.+.+.|+...... ......+..+.+. ...+.
T Consensus 81 ~y~~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~ 160 (232)
T cd00190 81 NYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEGGPLPDVLQEVNVPIVSNAECKRAYS 160 (232)
T ss_pred CCCCCCCcCCEEEEEECCcccCCCcccceECCCccccCCCCCEEEEEeCCcCCCCCCCCceeeEEEeeeECHHHhhhhcc
Confidence 479999999743211112445555444 6788999999998754331 1222222222210 00010
Q ss_pred C-CCcccccceEEEE---eeecCCCCCCCceeccc---CcEEEEeeccc
Q 001280 180 K-DGYNDFNTFYMQA---ASGTKGGSSGSPVIDWQ---GRAVALNAGSK 221 (1108)
Q Consensus 180 ~-~~~~~~~~~~i~~---~a~~~~G~SGgPv~n~~---G~vVGi~~~~~ 221 (1108)
. ..... +...... ....-.|.|||||+... +.++||.+.+.
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 0001111 23355699999999765 89999998764
No 45
>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=98.30 E-value=2.4e-06 Score=74.55 Aligned_cols=53 Identities=36% Similarity=0.619 Sum_probs=47.6
Q ss_pred ceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCCh--hHHHHHHhcCCCCeEEEEE
Q 001280 298 GLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQF--LKLETLLDDGVDKNIELLI 351 (1108)
Q Consensus 298 G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g~~v~l~V 351 (1108)
|++| ..|.+++||+. ||++||+|++|||+++.++ .++..++....|+.++|+|
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 6665 79999999999 9999999999999999999 8888888777788888876
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=98.26 E-value=3e-06 Score=73.96 Aligned_cols=53 Identities=36% Similarity=0.441 Sum_probs=50.1
Q ss_pred eEEEEEecCCChhhhcCCCCCCEEEEECCeecCCH--HHHHHHHHcCCCCceEEEE
Q 001280 1008 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVR 1061 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~v~~~~~~~~v~l~ 1061 (1108)
+++|..+.++|||+++||++||.|++|||+++.++ +++.+.++..+ ++.++|+
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 99999999866 8888887
No 47
>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=98.25 E-value=2.6e-05 Score=84.32 Aligned_cols=164 Identities=16% Similarity=0.183 Sum_probs=94.3
Q ss_pred CCceEEEEEeeeeccCCCCCCccEEEEEEEeCCCcEEEEcccccCCCC-eEEEEEecCC--------eEEeEEEEEEcC-
Q 001280 46 VPAVVVLRTTACRAFDTEAAGASYATGFVVDKRRGIILTNRHVVKPGP-VVAEAMFVNR--------EEIPVYPIYRDP- 115 (1108)
Q Consensus 46 ~~sVV~I~~~~~~~~d~~~~~~~~GSGfvV~~~~G~ILTn~HVV~~~~-~~~~v~~~d~--------~~~~a~vv~~d~- 115 (1108)
.|-+|.|.... ....++|.+|++ .+|||++||+.... ..+.+.+... ..+.+.-+..+|
T Consensus 13 ~Pw~~~i~~~~---------~~~~C~GtlIs~--~~VLTaahC~~~~~~~~~~v~~g~~~~~~~~~~~~~~v~~~~~~p~ 81 (229)
T smart00020 13 FPWQVSLQYRG---------GRHFCGGSLISP--RWVLTAAHCVYGSDPSNIRVRLGSHDLSSGEEGQVIKVSKVIIHPN 81 (229)
T ss_pred CCcEEEEEEcC---------CCcEEEEEEecC--CEEEECHHHcCCCCCcceEEEeCcccCCCCCCceEEeeEEEEECCC
Confidence 35566665421 367899999995 49999999999542 3556665432 345555555443
Q ss_pred ------CCceEEEEECCCC-cccccccCCCCCC--cccCCCCEEEEEecCCCCC------CeEEEEEEEEecCC--CCCC
Q 001280 116 ------VHDFGFFRYDPSA-IQFLNYDEIPLAP--EAACVGLEIRVVGNDSGEK------VSILAGTLARLDRD--APHY 178 (1108)
Q Consensus 116 ------~~DlAlLk~d~~~-~~~~~~~~l~l~~--~~~~~G~~V~~iG~p~g~~------~si~~G~is~~~~~--~~~~ 178 (1108)
.+|+|||+++..- +.. .+.++.|.. ..+..++.+.+.|++.... .......+..+.+. ...+
T Consensus 82 ~~~~~~~~DiAll~L~~~i~~~~-~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~ 160 (229)
T smart00020 82 YNPSTYDNDIALLKLKSPVTLSD-NVRPICLPSSNYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNVPIVSNATCRRAY 160 (229)
T ss_pred CCCCCCcCCEEEEEECcccCCCC-ceeeccCCCcccccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEEEEeCHHHhhhhh
Confidence 5799999997531 111 234444443 3677899999999876542 11222222222220 0001
Q ss_pred CCC-CcccccceEEE--EeeecCCCCCCCceecccC--cEEEEeeccc
Q 001280 179 KKD-GYNDFNTFYMQ--AASGTKGGSSGSPVIDWQG--RAVALNAGSK 221 (1108)
Q Consensus 179 ~~~-~~~~~~~~~i~--~~a~~~~G~SGgPv~n~~G--~vVGi~~~~~ 221 (1108)
... ........... .....-+|+||||++...+ .++||.+.+.
T Consensus 161 ~~~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~~~~~l~Gi~s~g~ 208 (229)
T smart00020 161 SGGGAITDNMLCAGGLEGGKDACQGDSGGPLVCNDGRWVLVGIVSWGS 208 (229)
T ss_pred ccccccCCCcEeecCCCCCCcccCCCCCCeeEEECCCEEEEEEEEECC
Confidence 000 01110000001 1244567999999997654 8999998764
No 48
>KOG3580 consensus Tight junction proteins [Signal transduction mechanisms]
Probab=98.19 E-value=1.1e-05 Score=92.81 Aligned_cols=159 Identities=22% Similarity=0.333 Sum_probs=109.1
Q ss_pred CCCceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCCh--hHHHHHHhcCCCCeEEEEEEECCEEEEEEE--ccccc-
Q 001280 295 GETGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQF--LKLETLLDDGVDKNIELLIERGGISMTVNL--VQDLH- 367 (1108)
Q Consensus 295 ~~~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g~~v~l~V~R~g~~~~~~v--~~~~~- 367 (1108)
-...++| ..+...+.|++ +|++||+||+|||....++ .+.+.++..+- .++.|.|+|+....-+.| +.+-.
T Consensus 217 LgSqIFv-Keit~~gLAardgnlqEGDiiLkINGtvteNmSLtDar~LIEkS~-GKL~lvVlRD~~qtLiNiP~l~d~dS 294 (1027)
T KOG3580|consen 217 LGSQIFV-KEITRTGLAARDGNLQEGDIILKINGTVTENMSLTDARKLIEKSR-GKLQLVVLRDSQQTLINIPSLNDSDS 294 (1027)
T ss_pred ccchhhh-hhhcccchhhccCCcccccEEEEECcEeeccccchhHHHHHHhcc-CceEEEEEecCCceeeecCCCccccc
Confidence 3456676 78888999988 8999999999999988775 44555554443 468999999877766666 43200
Q ss_pred ------cc--------------------------------------CCCcccccCCe-----------------------
Q 001280 368 ------SI--------------------------------------TPDYFLEVSGA----------------------- 380 (1108)
Q Consensus 368 ------~~--------------------------------------~~~~~~~~~G~----------------------- 380 (1108)
.+ ++.| +...|+
T Consensus 295 e~~disEi~tms~rs~spp~rrs~~~s~d~~s~s~h~p~~Ps~r~~~~~R-~s~~gat~tPvks~~d~~~~~V~e~t~e~ 373 (1027)
T KOG3580|consen 295 EIEDISEIETMSDRSFSPPERRSQYSSYDYHSSSEHLPERPSSREDTPSR-LSRMGATPTPVKSTGDIAGTVVPETTKEP 373 (1027)
T ss_pred cccchhhhhccccccCCCchhhhhccCccccCchhcCCCCCCccccchhh-cccCCCCCCCccCccccCCccccccccCc
Confidence 00 0000 011111
Q ss_pred ----------------EEccCCHHHhhccCcC----------------------CCeEEEE--CCCChhHHcCCCCCCEE
Q 001280 381 ----------------VIHPLSYQQARNFRFP----------------------CGLVYVA--EPGYMLFRAGVPRHAII 420 (1108)
Q Consensus 381 ----------------~~~~l~~q~~~~~~~~----------------------~~gv~v~--~~~~~a~~aGl~~Gd~I 420 (1108)
+|..++++....|+.. .-|+||+ ..|+||+.-||+.||.|
T Consensus 374 ~~~q~p~lP~pk~~~~~~~~pS~~~m~~ygysP~tk~VrF~KGdSvGLRLAGGNDVGIFVaGvqegspA~~eGlqEGDQI 453 (1027)
T KOG3580|consen 374 RYQQEPPLPQPKAAPRTFLRPSPEDMAIYGYSPNTKMVRFKKGDSVGLRLAGGNDVGIFVAGVQEGSPAEQEGLQEGDQI 453 (1027)
T ss_pred ccccCCCCCCcccCcceeeecCHHHHHHhcCCCCceeEEeecCCeeeeEeccCCceeEEEeecccCCchhhcccccccee
Confidence 1222233333333321 1378998 58999999999999999
Q ss_pred EEeCCeecCCHH--HHHHHHHhcCCCCeEEEEEeeecc
Q 001280 421 KKFAGEEISRLE--DLISVLSKLSRGARVPIEYSSYTD 456 (1108)
Q Consensus 421 ~~Vng~~v~~l~--~~~~~i~~~~~~~~v~l~~~~~~~ 456 (1108)
++||.++..|+- +.+..|-.+|+|..|+|...+-.|
T Consensus 454 L~VN~vdF~nl~REeAVlfLL~lPkGEevtilaQ~k~D 491 (1027)
T KOG3580|consen 454 LKVNTVDFRNLVREEAVLFLLELPKGEEVTILAQSKAD 491 (1027)
T ss_pred EEeccccchhhhHHHHHHHHhcCCCCcEEeehhhhhhH
Confidence 999999999985 778888899999999997655433
No 49
>KOG3209 consensus WW domain-containing protein [General function prediction only]
Probab=98.17 E-value=1.3e-05 Score=93.99 Aligned_cols=138 Identities=21% Similarity=0.242 Sum_probs=84.5
Q ss_pred CceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChhH--HHHHHh-cCCCCeEEEEEEECCEEEEEEE--ccccccc
Q 001280 297 TGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFLK--LETLLD-DGVDKNIELLIERGGISMTVNL--VQDLHSI 369 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~~--l~~~l~-~~~g~~v~l~V~R~g~~~~~~v--~~~~~~~ 369 (1108)
+-++| +.|.+.+.|++ -|++||.|+.|||.+|..-.+ +..++. ..-+..|.|+|.|.-..-...- ..+....
T Consensus 674 qpi~i-G~Iv~lGaAe~DGRL~~gDElv~iDG~pV~GksH~~vv~Lm~~AArnghV~LtVRRkv~~~~~~rsp~~s~~~~ 752 (984)
T KOG3209|consen 674 QPIYI-GAIVPLGAAEEDGRLREGDELVCIDGIPVEGKSHSEVVDLMEAAARNGHVNLTVRRKVRTGPARRSPRNSAAPS 752 (984)
T ss_pred CeeEE-eeeeecccccccCcccCCCeEEEecCeeccCccHHHHHHHHHHHHhcCceEEEEeeeeeeccccCCcccccCCC
Confidence 44555 89999999999 599999999999999976544 334442 3445679999987311000000 0111112
Q ss_pred CCCccc----ccCCeEEccCCHHHhhccCcCCCeEEEECCCChhHHcC-CCCCCEEEEeCCeecCCHH--HHHHHHHh
Q 001280 370 TPDYFL----EVSGAVIHPLSYQQARNFRFPCGLVYVAEPGYMLFRAG-VPRHAIIKKFAGEEISRLE--DLISVLSK 440 (1108)
Q Consensus 370 ~~~~~~----~~~G~~~~~l~~q~~~~~~~~~~gv~v~~~~~~a~~aG-l~~Gd~I~~Vng~~v~~l~--~~~~~i~~ 440 (1108)
.+.+.+ +--|+.|.-++-+-. +..|+=-.-+||||.+-| |+.||+|++|||+.|-++. +.++.||.
T Consensus 753 ~~yDV~lhR~ENeGFGFVi~sS~~k-----p~sgiGrIieGSPAdRCgkLkVGDrilAVNG~sI~~lsHadiv~LIKd 825 (984)
T KOG3209|consen 753 GPYDVVLHRKENEGFGFVIMSSQNK-----PESGIGRIIEGSPADRCGKLKVGDRILAVNGQSILNLSHADIVSLIKD 825 (984)
T ss_pred CCeeeEEecccCCceeEEEEecccC-----CCCCccccccCChhHhhccccccceEEEecCeeeeccCchhHHHHHHh
Confidence 222211 122333322222111 112211113789999887 9999999999999998886 77888887
No 50
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=98.10 E-value=5.4e-05 Score=81.68 Aligned_cols=178 Identities=14% Similarity=0.116 Sum_probs=100.2
Q ss_pred CceEEEEEeeeeccCCC-----CCCccEEEEEEEeCCCcEEEEcccccCCCCe-EEEE-Eec-----CCe---EEeEEEE
Q 001280 47 PAVVVLRTTACRAFDTE-----AAGASYATGFVVDKRRGIILTNRHVVKPGPV-VAEA-MFV-----NRE---EIPVYPI 111 (1108)
Q Consensus 47 ~sVV~I~~~~~~~~d~~-----~~~~~~GSGfvV~~~~G~ILTn~HVV~~~~~-~~~v-~~~-----d~~---~~~a~vv 111 (1108)
..+..|.-....+|..- ..+...+++|+|.++ .+||++||+-.... +..+ .+. ++. .+.....
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 44555554444443321 123334466999976 99999999985432 1111 111 111 1222222
Q ss_pred EEcC----CCceEEEEECCCCc----cccc---ccCCCCCCcccCCCCEEEEEecCCCCCCe----EEEEEEEEecCCCC
Q 001280 112 YRDP----VHDFGFFRYDPSAI----QFLN---YDEIPLAPEAACVGLEIRVVGNDSGEKVS----ILAGTLARLDRDAP 176 (1108)
Q Consensus 112 ~~d~----~~DlAlLk~d~~~~----~~~~---~~~l~l~~~~~~~G~~V~~iG~p~g~~~s----i~~G~is~~~~~~~ 176 (1108)
...+ +.|.+...+.+..+ ++.. +...++ ....+.++.+.++|||.+.... ...+.+.....
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 2222 34555555543221 1111 111122 4567899999999999876522 33444443322
Q ss_pred CCCCCCcccccceEEEEeeecCCCCCCCceecccCcEEEEeecccCCC---Ccccc-cChHHHHHHHHHH
Q 001280 177 HYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSSS---ASAFF-LPLERVVRALRFL 242 (1108)
Q Consensus 177 ~~~~~~~~~~~~~~i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~~---~~~fa-lPi~~i~~~l~~l 242 (1108)
.+++.++.+.+|+||+||++.+.+++|+++.+.... ..+++ .-...++++++++
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 248999999999999999999999999998765431 22333 3345666666543
No 51
>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=98.03 E-value=0.00012 Score=78.49 Aligned_cols=165 Identities=19% Similarity=0.235 Sum_probs=91.6
Q ss_pred HhCCceEEEEEeeeeccCCCCCCccEEEEEEEeCCCcEEEEcccccCCCCeEEEEEecCCeEEeEE-----EEEEcCCCc
Q 001280 44 KVVPAVVVLRTTACRAFDTEAAGASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVY-----PIYRDPVHD 118 (1108)
Q Consensus 44 ~~~~sVV~I~~~~~~~~d~~~~~~~~GSGfvV~~~~G~ILTn~HVV~~~~~~~~v~~~d~~~~~a~-----vv~~d~~~D 118 (1108)
-+...|+.|.... ......--||.... +|+||+|....+...+.+...-|. |... -+..=+..|
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 11223345666664 999999999877677777766653 3222 244456799
Q ss_pred eEEEEECCCCcccccccCCCCCCcccCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCcccccceEEEEeeecC
Q 001280 119 FGFFRYDPSAIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAASGTK 198 (1108)
Q Consensus 119 lAlLk~d~~~~~~~~~~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~is~~~~~~~~~~~~~~~~~~~~~i~~~a~~~ 198 (1108)
+.++|+. +++|+.+- .+.-..++.|++|..||..+..+...+ .+|.-....|. . +..+...-.++.
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 9999995 44443221 222456899999999998665443211 12222111111 1 222578888889
Q ss_pred CCCCCCceec-ccCcEEEEeecccCCCCcccccChH
Q 001280 199 GGSSGSPVID-WQGRAVALNAGSKSSSASAFFLPLE 233 (1108)
Q Consensus 199 ~G~SGgPv~n-~~G~vVGi~~~~~~~~~~~falPi~ 233 (1108)
.|+-|+|+++ .||++|||++........+|+.|+.
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 52
>PF14685 Tricorn_PDZ: Tricorn protease PDZ domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A.
Probab=98.00 E-value=4.1e-05 Score=69.56 Aligned_cols=65 Identities=25% Similarity=0.355 Sum_probs=47.9
Q ss_pred CceEEEEEecCC--------Ccccc-C--CCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEECC-EEEEEE
Q 001280 297 TGLLVVDSVVPG--------GPAHL-R--LEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIERGG-ISMTVN 361 (1108)
Q Consensus 297 ~G~lVv~~V~~~--------spA~~-g--L~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~V~R~g-~~~~~~ 361 (1108)
.|.+.|.+|.++ ||..+ | +++||+|++|||+++..-.++..+|....|++|.|+|.+.+ +.+++.
T Consensus 11 ~~~y~I~~I~~gd~~~~~~~sPL~~pGv~v~~GD~I~aInG~~v~~~~~~~~lL~~~agk~V~Ltv~~~~~~~R~v~ 87 (88)
T PF14685_consen 11 NGGYRIARIYPGDPWNPNARSPLAQPGVDVREGDYILAINGQPVTADANPYRLLEGKAGKQVLLTVNRKPGGARTVV 87 (88)
T ss_dssp TTEEEEEEE-BS-TTSSS-B-GGGGGS----TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEEE-STT-EEEEE
T ss_pred CCEEEEEEEeCCCCCCccccCCccCCCCCCCCCCEEEEECCEECCCCCCHHHHhcccCCCEEEEEEecCCCCceEEE
Confidence 566777899875 78778 6 55999999999999999999999999999999999999965 455543
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=97.97 E-value=3.1e-05 Score=69.91 Aligned_cols=58 Identities=38% Similarity=0.615 Sum_probs=48.0
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHh-cCCCCeEEEEEEECC
Q 001280 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLD-DGVDKNIELLIERGG 355 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~-~~~g~~v~l~V~R~g 355 (1108)
.|++| ..|.+++||++ ||++||+|++|||+.+.++.+...... ...+..+.+++.|++
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 56666 79999999999 999999999999999999877665542 334568999998864
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=2.8e-05 Score=70.03 Aligned_cols=54 Identities=33% Similarity=0.612 Sum_probs=43.6
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHH--HHhcCCCCeEEEEEE
Q 001280 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLET--LLDDGVDKNIELLIE 352 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~--~l~~~~g~~v~l~V~ 352 (1108)
.+++| ..|.++|||+. ||+.||+|++|||+.+.++...+. ++... ++.|+|+|+
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 57777 79999999999 999999999999999998866553 34444 348888774
No 55
>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=97.93 E-value=2.8e-05 Score=70.03 Aligned_cols=53 Identities=32% Similarity=0.494 Sum_probs=46.5
Q ss_pred CeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCH--HHHHHHHHcCCCCceEEEE
Q 001280 1007 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVR 1061 (1108)
Q Consensus 1007 ~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~v~~~~~~~~v~l~ 1061 (1108)
.++||+++.++|||+++||++||.|++|||+++.++ ++..+.++..+ ..++|+
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 389999999999999999999999999999999977 77788888754 367776
No 56
>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=97.93 E-value=7e-05 Score=86.31 Aligned_cols=68 Identities=24% Similarity=0.385 Sum_probs=59.8
Q ss_pred CeEEEEEec--------CCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEeCCeEEEEEEEe
Q 001280 1007 HGVYVARWC--------HGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQ 1076 (1108)
Q Consensus 1007 ~gV~V~~v~--------~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~~lk~ 1076 (1108)
.||+|.... .+|||+++||++||.|++|||+++.++++|.+.+++.. ++.+.|+ +.|+|+...+++++
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 478776542 36999999999999999999999999999999999876 8889999 78999999888874
No 57
>KOG3834 consensus Golgi reassembly stacking protein GRASP65, contains PDZ domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.89 E-value=0.00012 Score=82.64 Aligned_cols=164 Identities=16% Similarity=0.101 Sum_probs=109.2
Q ss_pred cceEEEEeecCCCHHhHh-ccC-CCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCC--EEEEEEEeeccc
Q 001280 898 RQVLRVKGCLAGSKAENM-LEQ-GDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQG--REIELQVGTDVR 973 (1108)
Q Consensus 898 ~~~~~V~~V~~~s~A~~a-L~~-GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g--~~~~v~v~~~~~ 973 (1108)
..++.|-+|..+|+|.++ |.+ =|-|++|||+.+..-.|...++..... ++|+++|+... ....+.|+....
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 356778899999999999 666 789999999999987766555522222 55999998532 222333332221
Q ss_pred CCCCCcceeeeccccccCCchhhhhcCCCCCCCCeEEEEEecCCChhhhcCCC-CCCEEEEECCeecCCHHHHHHHHHcC
Q 001280 974 DGNGTTRVINWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLY-ALQWIVEINGKRTPDLEAFVNVTKEI 1052 (1108)
Q Consensus 974 ~~~~t~~~~~~~G~~~~~p~~~vr~~~~lp~~~~gV~V~~v~~gSpA~~~GL~-~gD~I~~VNg~~v~~l~~f~~~v~~~ 1052 (1108)
. ... ++|+.++-=... .+. ..--=|-+|.++|||+.+||. -+|.|+.+-..-..+.+||...|..+
T Consensus 89 w---ggq---llGvsvrFcsf~------~A~-~~vwHvl~V~p~SPaalAgl~~~~DYivG~~~~~~~~~eDl~~lIesh 155 (462)
T KOG3834|consen 89 W---GGQ---LLGVSVRFCSFD------GAV-ESVWHVLSVEPNSPAALAGLRPYTDYIVGIWDAVMHEEEDLFTLIESH 155 (462)
T ss_pred c---ccc---ccceEEEeccCc------cch-hheeeeeecCCCCHHHhcccccccceEecchhhhccchHHHHHHHHhc
Confidence 1 111 233333211100 000 001126789999999999998 88999999555567778899999886
Q ss_pred CCCceEEEEEEEeC-CeEEEEEEEeCCcc
Q 001280 1053 EHGEFVRVRTVHLN-GKPRVLTLKQDLHY 1080 (1108)
Q Consensus 1053 ~~~~~v~l~~v~rd-g~~~~~~lk~d~~y 1080 (1108)
. ++.++|-+.+-| ...+.+++++|.+|
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 888988754444 45889999999885
No 58
>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=97.89 E-value=3.7e-05 Score=69.48 Aligned_cols=60 Identities=30% Similarity=0.349 Sum_probs=47.2
Q ss_pred CeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEeCC
Q 001280 1007 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNG 1067 (1108)
Q Consensus 1007 ~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~rdg 1067 (1108)
.+++|..+.++|||+++||++||.|++|||+++.++.+..........+..++|. +.|++
T Consensus 26 ~~~~i~~v~~~s~a~~~gl~~GD~I~~In~~~v~~~~~~~~~~~~~~~~~~~~l~-i~r~~ 85 (85)
T smart00228 26 GGVVVSSVVPGSPAAKAGLKVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLT-VLRGG 85 (85)
T ss_pred CCEEEEEECCCCHHHHcCCCCCCEEEEECCEECCCCCHHHHHHHHHhCCCeEEEE-EEeCC
Confidence 3899999999999999999999999999999999875544444332335578887 55543
No 59
>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=4.2e-05 Score=68.76 Aligned_cols=52 Identities=31% Similarity=0.412 Sum_probs=46.6
Q ss_pred eEEEEEecCCChhhhcCCCCCCEEEEECCeecC--CHHHHHHHHHcCCCCceEEEE
Q 001280 1008 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTP--DLEAFVNVTKEIEHGEFVRVR 1061 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~--~l~~f~~~v~~~~~~~~v~l~ 1061 (1108)
+++|..+.++|||+++||++||.|++|||+++. +++++.+.++... + .++|.
T Consensus 27 ~~~V~~v~~~s~a~~~gl~~GD~I~~ing~~i~~~~~~~~~~~l~~~~-~-~v~l~ 80 (82)
T cd00992 27 GIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHEEAVELLKNSG-D-EVTLT 80 (82)
T ss_pred CeEEEEECCCChHHhCCCCCCCEEEEECCEEcCccCHHHHHHHHHhCC-C-eEEEE
Confidence 789999999999999999999999999999999 9999999999743 2 55554
No 60
>PLN00049 carboxyl-terminal processing protease; Provisional
Probab=97.87 E-value=6.7e-05 Score=88.15 Aligned_cols=76 Identities=21% Similarity=0.273 Sum_probs=63.6
Q ss_pred eEEEEEecCCChhhhcCCCCCCEEEEECCeecCCH--HHHHHHHHcCCCCceEEEEEEEeCCeEEEEEEEeCCccCcceE
Q 001280 1008 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQDLHYWPTWE 1085 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~~lk~d~~y~pt~e 1085 (1108)
+++|..+.++|||+++||++||+|++|||+++.++ +++...++. +.++.+.|+ +.|+|..+.++|+...-..+++.
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 78999999999999999999999999999999864 777888865 458899998 78999988888876544444443
No 61
>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=89.99 Aligned_cols=63 Identities=21% Similarity=0.312 Sum_probs=54.8
Q ss_pred EEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEeCCeEEEEEEEeC
Q 001280 1011 VARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQD 1077 (1108)
Q Consensus 1011 V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~~lk~d 1077 (1108)
|..|.++|||+++||++||.|++|||+++++|.++...+. ++.+.|++..|+|+.+.+.+.++
T Consensus 2 I~~V~pgSpAe~AGLe~GD~IlsING~~V~Dw~D~~~~l~----~e~l~L~V~~rdGe~~~l~Ie~~ 64 (433)
T TIGR03279 2 ISAVLPGSIAEELGFEPGDALVSINGVAPRDLIDYQFLCA----DEELELEVLDANGESHQIEIEKD 64 (433)
T ss_pred cCCcCCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHhc----CCcEEEEEEcCCCeEEEEEEecC
Confidence 5678999999999999999999999999999999888874 35688884358999999988875
No 62
>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=97.82 E-value=4.3e-05 Score=88.21 Aligned_cols=65 Identities=23% Similarity=0.434 Sum_probs=54.6
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCCh--hHHHHHHhcCCCCeEEEEEEECCEEEEEEE
Q 001280 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQF--LKLETLLDDGVDKNIELLIERGGISMTVNL 362 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g~~v~l~V~R~g~~~~~~v 362 (1108)
.+++| ..|.++|||++ ||+.||+|++|||+++.+| .++..++....|..+.++|.|+|+..++++
T Consensus 62 ~~~~V-~~V~~~spA~~aGL~~GD~I~~Ing~~v~~~~~~~~~~~l~~~~g~~v~l~v~R~g~~~~~~v 129 (334)
T TIGR00225 62 GEIVI-VSPFEGSPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALIRGKKGTKVSLEILRAGKSKPLTF 129 (334)
T ss_pred CEEEE-EEeCCCChHHHcCCCCCCEEEEECCEECCCCCHHHHHHhccCCCCCEEEEEEEeCCCCceEEE
Confidence 35555 79999999999 9999999999999999987 456566666678999999999987766666
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=9.9e-05 Score=85.19 Aligned_cols=77 Identities=26% Similarity=0.365 Sum_probs=61.3
Q ss_pred eEEEEEecCCChhhhcCCCCCCEEEEECCeecCCH--HHHHHHHHcCCCCceEEEEEEEeCCeEEEE--EEEeCCccCcc
Q 001280 1008 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVHLNGKPRVL--TLKQDLHYWPT 1083 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~--~lk~d~~y~pt 1083 (1108)
+++|..|.++|||+++||++||+|++|||+++.+| +++...++. +.++.+.|+ +.|+|+...+ ++.....+.|+
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 68999999999999999999999999999999986 577777766 348899999 7888765444 45544445555
Q ss_pred eEE
Q 001280 1084 WEL 1086 (1108)
Q Consensus 1084 ~el 1086 (1108)
...
T Consensus 141 v~~ 143 (334)
T TIGR00225 141 VKA 143 (334)
T ss_pred eEE
Confidence 554
No 64
>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=97.74 E-value=9.1e-05 Score=85.36 Aligned_cols=67 Identities=28% Similarity=0.468 Sum_probs=57.8
Q ss_pred CCceEEEEEec-------CCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEECCEEEEEEE
Q 001280 296 ETGLLVVDSVV-------PGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIERGGISMTVNL 362 (1108)
Q Consensus 296 ~~G~lVv~~V~-------~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~V~R~g~~~~~~v 362 (1108)
..|+|||..-. .++||++ ||++||+|++|||++|.+|.++..++....++.+.++|.|+|+..++.+
T Consensus 104 t~GVlVvg~~~v~~~~g~~~SPAa~AGLq~GDiIvsING~~V~s~~DL~~iL~~~~g~~V~LtV~R~Ge~~tv~V 178 (402)
T TIGR02860 104 TKGVLVVGFSDIETEKGKIHSPGEEAGIQIGDRILKINGEKIKNMDDLANLINKAGGEKLTLTIERGGKIIETVI 178 (402)
T ss_pred cCEEEEEEEEcccccCCCCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHHHhCCCCeEEEEEEECCEEEEEEE
Confidence 48999975321 2589999 9999999999999999999999999977668899999999998877766
No 65
>PLN00049 carboxyl-terminal processing protease; Provisional
Probab=97.69 E-value=0.00012 Score=86.19 Aligned_cols=64 Identities=31% Similarity=0.553 Sum_probs=54.8
Q ss_pred ceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCCh--hHHHHHHhcCCCCeEEEEEEECCEEEEEEE
Q 001280 298 GLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQF--LKLETLLDDGVDKNIELLIERGGISMTVNL 362 (1108)
Q Consensus 298 G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g~~v~l~V~R~g~~~~~~v 362 (1108)
|++| ..|.++|||++ ||++||+|++|||++|.++ .++..++....|+.+.|+|.|+|+..++++
T Consensus 103 g~~V-~~V~~~SPA~~aGl~~GD~Iv~InG~~v~~~~~~~~~~~l~g~~g~~v~ltv~r~g~~~~~~l 169 (389)
T PLN00049 103 GLVV-VAPAPGGPAARAGIRPGDVILAIDGTSTEGLSLYEAADRLQGPEGSSVELTLRRGPETRLVTL 169 (389)
T ss_pred cEEE-EEeCCCChHHHcCCCCCCEEEEECCEECCCCCHHHHHHHHhcCCCCEEEEEEEECCEEEEEEE
Confidence 6665 69999999999 9999999999999999865 566666666678899999999998777766
No 66
>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=97.67 E-value=0.00012 Score=65.73 Aligned_cols=53 Identities=34% Similarity=0.577 Sum_probs=43.9
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeC--ChhHHHHHHhcCCCCeEEEEE
Q 001280 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVIT--QFLKLETLLDDGVDKNIELLI 351 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~--~~~~l~~~l~~~~g~~v~l~V 351 (1108)
.|++| ..|.+++||++ ||++||+|++|||+++. ++.++..++....+ .+.+++
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 56666 79999999999 99999999999999999 88888888765433 566654
No 67
>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=97.66 E-value=0.00019 Score=71.30 Aligned_cols=73 Identities=19% Similarity=0.309 Sum_probs=53.4
Q ss_pred CeEEEEEecCCChhhhcCCCC-CCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEe-CCeEEEEEEEeCCcc
Q 001280 1007 HGVYVARWCHGSPVHRYGLYA-LQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHL-NGKPRVLTLKQDLHY 1080 (1108)
Q Consensus 1007 ~gV~V~~v~~gSpA~~~GL~~-gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~r-dg~~~~~~lk~d~~y 1080 (1108)
.+.-|.+|.++|||+++||++ .|+|+.+|+....+.++|.+.++... ++.+.|.+.+- ....+.+++.|+.++
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 367799999999999999998 69999999999999999999999965 88999984332 345778888886543
No 68
>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=97.65 E-value=0.00012 Score=84.92 Aligned_cols=61 Identities=25% Similarity=0.517 Sum_probs=52.7
Q ss_pred EEeecCCCHHhHh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEE-eCCEEEEEEEeec
Q 001280 903 VKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIF-RQGREIELQVGTD 971 (1108)
Q Consensus 903 V~~V~~~s~A~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~-R~g~~~~v~v~~~ 971 (1108)
|..|.++|+|+++ |++||+|++|||++|.+|.|+...+. ++.+.++|. |+|+..++.+...
T Consensus 2 I~~V~pgSpAe~AGLe~GD~IlsING~~V~Dw~D~~~~l~--------~e~l~L~V~~rdGe~~~l~Ie~~ 64 (433)
T TIGR03279 2 ISAVLPGSIAEELGFEPGDALVSINGVAPRDLIDYQFLCA--------DEELELEVLDANGESHQIEIEKD 64 (433)
T ss_pred cCCcCCCCHHHHcCCCCCCEEEEECCEECCCHHHHHHHhc--------CCcEEEEEEcCCCeEEEEEEecC
Confidence 6788999999999 99999999999999999999887772 256889997 8998888877654
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=97.60 E-value=0.0018 Score=69.14 Aligned_cols=169 Identities=20% Similarity=0.218 Sum_probs=96.3
Q ss_pred eeeEEEEEEEeeCCceEEEEeCceecCCCceEEEEeec------CC--eEEeEEEEEeeC-------CCcEEEEEECCC-
Q 001280 648 HFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAA------FP--IEIPGEVVFLHP-------VHNFALIAYDPS- 711 (1108)
Q Consensus 648 ~~~GsG~iId~~~~~G~IlTnr~~V~~~~~~i~V~~~~------~~--~~~~a~vv~~dp-------~~dlAilk~d~~- 711 (1108)
...++|++|. +-+|||.+|.+.. ..++.+.+.. .+ ..+..+-+..|| .+|+|||+++..
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 5599999887766 4455554332 02 234444444553 469999999776
Q ss_pred CCCcccccceeccccCC-CccCCCCCEEEEEeeCCCCCce----eeeeeEeccccccccCCCCCCc-ccc-ccceEEEEe
Q 001280 712 SLGVAGASVVRAAELLP-EPALRRGDSVYLVGLSRSLQAT----SRKSIVTNPCAALNISSADCPR-YRA-MNMEVIELD 784 (1108)
Q Consensus 712 ~l~~~~~~~v~~~~l~~-~~~l~~G~~V~~vG~p~~~~~~----~~~~~Vt~~~~~~~i~~~~~~~-y~~-~~~~~I~~d 784 (1108)
.+. ..+.++.+.. ...++.|+.+.++|++...... .....+. .++...... |.. .....+...
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 2336899999999998753221 1111121 011100001 111 122344444
Q ss_pred c----cc-CCCCCceEEcCCeeEEEEEeeccccccccCCCCCcceeEecccHHHHHHHH
Q 001280 785 T----DF-GSTFSGVLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVL 838 (1108)
Q Consensus 785 ~----~i-g~~sGGpL~d~~G~VvGi~~~~~~~~~~~~~~~~~~~~~~aipi~~i~~vl 838 (1108)
. .. ...|||||+..++.|+||.+....- ...+. ..+..++...+++|
T Consensus 169 ~~~~~~~~~g~sG~pl~~~~~~lvGI~s~~~~c------~~~~~-~~v~~~v~~~~~WI 220 (220)
T PF00089_consen 169 SSGSGDACQGDSGGPLICNNNYLVGIVSFGENC------GSPNY-PGVYTRVSSYLDWI 220 (220)
T ss_dssp TTSSSBGGTTTTTSEEEETTEEEEEEEEEESSS------SBTTS-EEEEEEGGGGHHHH
T ss_pred ccccccccccccccccccceeeecceeeecCCC------CCCCc-CEEEEEHHHhhccC
Confidence 3 22 2358999999999999998764111 11111 23447777666654
No 70
>COG0793 Prc Periplasmic protease [Cell envelope biogenesis, outer membrane]
Probab=97.54 E-value=0.00026 Score=83.17 Aligned_cols=78 Identities=24% Similarity=0.318 Sum_probs=66.1
Q ss_pred eEEEEEecCCChhhhcCCCCCCEEEEECCeecCCH--HHHHHHHHcCCCCceEEEEEEEeC--CeEEEEEEEeCCccCcc
Q 001280 1008 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVHLN--GKPRVLTLKQDLHYWPT 1083 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~v~~~~~~~~v~l~~v~rd--g~~~~~~lk~d~~y~pt 1083 (1108)
++.|.+..+||||+++|+++||.|+.|||+++.+. ++.++.++. +.|+.|+|+ +.|. ++++.++++-+.-.-++
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 77899999999999999999999999999999988 668888887 459999999 7785 67899988887666555
Q ss_pred eEEE
Q 001280 1084 WELI 1087 (1108)
Q Consensus 1084 ~el~ 1087 (1108)
..++
T Consensus 191 v~~~ 194 (406)
T COG0793 191 VAAK 194 (406)
T ss_pred eeee
Confidence 5543
No 71
>PF14685 Tricorn_PDZ: Tricorn protease PDZ domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A.
Probab=97.35 E-value=0.0015 Score=59.43 Aligned_cols=64 Identities=23% Similarity=0.239 Sum_probs=43.2
Q ss_pred ceEEEEeecCC--------CHHhHh---ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCC-EEEEE
Q 001280 899 QVLRVKGCLAG--------SKAENM---LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQG-REIEL 966 (1108)
Q Consensus 899 ~~~~V~~V~~~--------s~A~~a---L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g-~~~~v 966 (1108)
+++.|.++.++ ||..+. +++||+|++|||++++.-.++..++. .+.| ..+.|+|.+.+ +..++
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 67888888764 777765 77999999999999999999988883 3443 78999999865 45554
Q ss_pred E
Q 001280 967 Q 967 (1108)
Q Consensus 967 ~ 967 (1108)
.
T Consensus 87 ~ 87 (88)
T PF14685_consen 87 V 87 (88)
T ss_dssp E
T ss_pred E
Confidence 4
No 72
>COG0793 Prc Periplasmic protease [Cell envelope biogenesis, outer membrane]
Probab=97.26 E-value=0.00082 Score=79.06 Aligned_cols=65 Identities=29% Similarity=0.511 Sum_probs=52.6
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChh--HHHHHHhcCCCCeEEEEEEEC--CEEEEEEE
Q 001280 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFL--KLETLLDDGVDKNIELLIERG--GISMTVNL 362 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~--~l~~~l~~~~g~~v~l~V~R~--g~~~~~~v 362 (1108)
.++.| .++.+++||++ ||++||+|++|||+++.... +....+....|.+|+|+|.|. ++..++++
T Consensus 112 ~~~~V-~s~~~~~PA~kagi~~GD~I~~IdG~~~~~~~~~~av~~irG~~Gt~V~L~i~r~~~~k~~~v~l 181 (406)
T COG0793 112 GGVKV-VSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTILRAGGGKPFTVTL 181 (406)
T ss_pred CCcEE-EecCCCChHHHcCCCCCCEEEEECCEEccCCCHHHHHHHhCCCCCCeEEEEEEEcCCCceeEEEE
Confidence 44455 59999999999 99999999999999998874 455566778899999999997 44555554
No 73
>KOG3553 consensus Tax interaction protein TIP1 [Cell wall/membrane/envelope biogenesis]
Probab=97.21 E-value=0.00028 Score=63.49 Aligned_cols=57 Identities=28% Similarity=0.394 Sum_probs=43.1
Q ss_pred CeEEEEEecCCChhhhcCCCCCCEEEEECCeecC--CHHHHHHHHHcCCCCceEEEEEEEeCC
Q 001280 1007 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTP--DLEAFVNVTKEIEHGEFVRVRTVHLNG 1067 (1108)
Q Consensus 1007 ~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~--~l~~f~~~v~~~~~~~~v~l~~v~rdg 1067 (1108)
.|+||++|.+||||+.+||+.+|.|+.|||.... +-+..++.+++ ++-+++. |.|.+
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 33566666654 4444443 44444
No 74
>PRK09681 putative type II secretion protein GspC; Provisional
Probab=97.17 E-value=0.0011 Score=72.83 Aligned_cols=62 Identities=18% Similarity=0.345 Sum_probs=51.9
Q ss_pred eecCCC---HHhHh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEee
Q 001280 905 GCLAGS---KAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGT 970 (1108)
Q Consensus 905 ~V~~~s---~A~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~ 970 (1108)
++.|+. ...++ ||+||++++|||..+++.++...+++.+... ..++++|+|+|+.+++.+.+
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 344553 34466 9999999999999999999988888777765 88999999999999998765
No 75
>COG3480 SdrC Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms]
Probab=97.11 E-value=0.0015 Score=71.58 Aligned_cols=70 Identities=21% Similarity=0.312 Sum_probs=61.9
Q ss_pred CeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEEEEEeCCeEEEEEEEeC
Q 001280 1007 HGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQD 1077 (1108)
Q Consensus 1007 ~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~~lk~d 1077 (1108)
.|||+..+..+|||..- |++||.|++|||+++.+.++|...++..+.|+.|+|.+-..++.+...+++.-
T Consensus 130 ~gvyv~~v~~~~~~~gk-l~~gD~i~avdg~~f~s~~e~i~~v~~~k~Gd~VtI~~~r~~~~~~~~~~tl~ 199 (342)
T COG3480 130 AGVYVLSVIDNSPFKGK-LEAGDTIIAVDGEPFTSSDELIDYVSSKKPGDEVTIDYERHNETPEIVTITLI 199 (342)
T ss_pred eeEEEEEccCCcchhce-eccCCeEEeeCCeecCCHHHHHHHHhccCCCCeEEEEEEeccCCCceEEEEEE
Confidence 59999999999999864 99999999999999999999999999999999999995445888877766553
No 76
>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=97.11 E-value=0.0011 Score=65.85 Aligned_cols=83 Identities=24% Similarity=0.395 Sum_probs=59.0
Q ss_pred CCccCeEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCC-CCEEEEECCEEeCChhHHHH
Q 001280 260 RGTLQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEP-GDVLVRVNGEVITQFLKLET 337 (1108)
Q Consensus 260 rg~lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~-GD~Il~VnG~~v~~~~~l~~ 337 (1108)
.|-||+.++.-.+..+ ...+.-| -+|.|+|||++ ||++ .|-|+.+|+..+.+.++|..
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 3778888776544333 3456666 49999999999 9999 69999999999999999999
Q ss_pred HHhcCCCCeEEEEEEEC--CEEEEEEE
Q 001280 338 LLDDGVDKNIELLIERG--GISMTVNL 362 (1108)
Q Consensus 338 ~l~~~~g~~v~l~V~R~--g~~~~~~v 362 (1108)
.+..+.++.+.|.|... ...++++|
T Consensus 85 ~v~~~~~~~l~L~Vyns~~~~vR~V~i 111 (138)
T PF04495_consen 85 LVEANENKPLQLYVYNSKTDSVREVTI 111 (138)
T ss_dssp HHHHTTTS-EEEEEEETTTTCEEEEEE
T ss_pred HHHHcCCCcEEEEEEECCCCeEEEEEE
Confidence 99888999999999874 34455555
No 77
>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=97.07 E-value=0.0079 Score=64.73 Aligned_cols=94 Identities=21% Similarity=0.230 Sum_probs=62.4
Q ss_pred ceeeEEEEEEEeeCCceEEEEeCceecCC-CceEEEEeecC--------CeEEeEEEEEeeC-------CCcEEEEEECC
Q 001280 647 QHFFGTGVIIYHSQSMGLVVVDKNTVAIS-ASDVMLSFAAF--------PIEIPGEVVFLHP-------VHNFALIAYDP 710 (1108)
Q Consensus 647 ~~~~GsG~iId~~~~~G~IlTnr~~V~~~-~~~i~V~~~~~--------~~~~~a~vv~~dp-------~~dlAilk~d~ 710 (1108)
....++|.+|+ +.+|||.+|.+... ...+.|.+... ...+..+-+..|| .+|+|||+++.
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 34689999999 67999998887654 23455554321 2234455566675 47999999975
Q ss_pred CCCCcccccceeccccCCCc-cCCCCCEEEEEeeCCCC
Q 001280 711 SSLGVAGASVVRAAELLPEP-ALRRGDSVYLVGLSRSL 747 (1108)
Q Consensus 711 ~~l~~~~~~~v~~~~l~~~~-~l~~G~~V~~vG~p~~~ 747 (1108)
..-.. ..+.++.|.... .+..|+.+.++|+....
T Consensus 99 ~~~~~---~~v~picl~~~~~~~~~~~~~~~~G~g~~~ 133 (232)
T cd00190 99 PVTLS---DNVRPICLPSSGYNLPAGTTCTVSGWGRTS 133 (232)
T ss_pred cccCC---CcccceECCCccccCCCCCEEEEEeCCcCC
Confidence 42211 245666765542 47889999999986543
No 78
>PRK09681 putative type II secretion protein GspC; Provisional
Probab=97.07 E-value=0.0018 Score=71.19 Aligned_cols=66 Identities=21% Similarity=0.351 Sum_probs=52.7
Q ss_pred CCceEEEEEecCCCcc---cc-CCCCCCEEEEECCEEeCChhHHHHHHhc-CCCCeEEEEEEECCEEEEEEE
Q 001280 296 ETGLLVVDSVVPGGPA---HL-RLEPGDVLVRVNGEVITQFLKLETLLDD-GVDKNIELLIERGGISMTVNL 362 (1108)
Q Consensus 296 ~~G~lVv~~V~~~spA---~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~-~~g~~v~l~V~R~g~~~~~~v 362 (1108)
+.| ++==.+.|+..+ .+ |||+||++++|||..+++..+..+++.. +....++|+|+|+|+..++.+
T Consensus 203 ~~G-l~GYrl~Pgkd~~lF~~~GLq~GDva~sING~dL~D~~qa~~l~~~L~~~tei~ltVeRdGq~~~i~i 273 (276)
T PRK09681 203 KEG-IVGYAVKPGADRSLFDASGFKEGDIAIALNQQDFTDPRAMIALMRQLPSMDSIQLTVLRKGARHDISI 273 (276)
T ss_pred eCC-ceEEEECCCCcHHHHHHcCCCCCCEEEEeCCeeCCCHHHHHHHHHHhccCCeEEEEEEECCEEEEEEE
Confidence 345 432355676544 34 9999999999999999999998888854 666789999999999998877
No 79
>KOG3605 consensus Beta amyloid precursor-binding protein [General function prediction only]
Probab=97.03 E-value=0.0013 Score=77.33 Aligned_cols=114 Identities=20% Similarity=0.296 Sum_probs=75.3
Q ss_pred ecCCCcccc--CCCCCCEEEEECCEEeCCh--hHHHHHHhc-CCCCeEEEEEEECCEEEEEEEcccccccCCCcccccCC
Q 001280 305 VVPGGPAHL--RLEPGDVLVRVNGEVITQF--LKLETLLDD-GVDKNIELLIERGGISMTVNLVQDLHSITPDYFLEVSG 379 (1108)
Q Consensus 305 V~~~spA~~--gL~~GD~Il~VnG~~v~~~--~~l~~~l~~-~~g~~v~l~V~R~g~~~~~~v~~~~~~~~~~~~~~~~G 379 (1108)
...++||++ .|-.||.|++|||..+-.+ ...+.++.. +....|+++|.+=--..++.| .+
T Consensus 680 mm~~GpAarsgkLnIGDQiiaING~SLVGLPLstcQs~Ik~~KnQT~VkltiV~cpPV~~V~I--~R------------- 744 (829)
T KOG3605|consen 680 MMHGGPAARSGKLNIGDQIMSINGTSLVGLPLSTCQSIIKGLKNQTAVKLNIVSCPPVTTVLI--RR------------- 744 (829)
T ss_pred cccCChhhhcCCccccceeEeecCceeccccHHHHHHHHhcccccceEEEEEecCCCceEEEe--ec-------------
Confidence 456899999 7999999999999987664 445566644 333457887766333333333 00
Q ss_pred eEEccCCHHHhhccCcCC-CeEEEE-CCCChhHHcCCCCCCEEEEeCCeecCC--HHHHHHHHHh
Q 001280 380 AVIHPLSYQQARNFRFPC-GLVYVA-EPGYMLFRAGVPRHAIIKKFAGEEISR--LEDLISVLSK 440 (1108)
Q Consensus 380 ~~~~~l~~q~~~~~~~~~-~gv~v~-~~~~~a~~aGl~~Gd~I~~Vng~~v~~--l~~~~~~i~~ 440 (1108)
+.....+||.+ .||+.+ ..|+-|++.|++.|-+|++|||+.|-- .+-.++.|..
T Consensus 745 -------Pd~kyQLGFSVQNGiICSLlRGGIAERGGVRVGHRIIEINgQSVVA~pHekIV~lLs~ 802 (829)
T KOG3605|consen 745 -------PDLRYQLGFSVQNGIICSLLRGGIAERGGVRVGHRIIEINGQSVVATPHEKIVQLLSN 802 (829)
T ss_pred -------ccchhhccceeeCcEeehhhcccchhccCceeeeeEEEECCceEEeccHHHHHHHHHH
Confidence 11111233333 477776 489999999999999999999999832 2344455544
No 80
>PRK11186 carboxy-terminal protease; Provisional
Probab=97.00 E-value=0.0022 Score=79.48 Aligned_cols=69 Identities=28% Similarity=0.364 Sum_probs=56.0
Q ss_pred eEEEEEecCCChhhhc-CCCCCCEEEEEC--CeecCC-----HHHHHHHHHcCCCCceEEEEEEEe---CCeEEEEEEEe
Q 001280 1008 GVYVARWCHGSPVHRY-GLYALQWIVEIN--GKRTPD-----LEAFVNVTKEIEHGEFVRVRTVHL---NGKPRVLTLKQ 1076 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~-GL~~gD~I~~VN--g~~v~~-----l~~f~~~v~~~~~~~~v~l~~v~r---dg~~~~~~lk~ 1076 (1108)
+++|.++.+||||+++ ||++||+|++|| |+++.+ +++.++.++. +.|+.|+|+ +.| ++.++.++|.-
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 6789999999999998 999999999999 555433 4688888887 569999999 666 45778787765
Q ss_pred CC
Q 001280 1077 DL 1078 (1108)
Q Consensus 1077 d~ 1078 (1108)
+.
T Consensus 334 ~~ 335 (667)
T PRK11186 334 DK 335 (667)
T ss_pred ee
Confidence 53
No 81
>COG3480 SdrC Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms]
Probab=96.98 E-value=0.0025 Score=69.84 Aligned_cols=71 Identities=15% Similarity=0.192 Sum_probs=62.8
Q ss_pred ceEEEEeecCCCHHhHhccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEe-CCEEEEEEEeeccc
Q 001280 899 QVLRVKGCLAGSKAENMLEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFR-QGREIELQVGTDVR 973 (1108)
Q Consensus 899 ~~~~V~~V~~~s~A~~aL~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R-~g~~~~v~v~~~~~ 973 (1108)
.|++|..+..++++...|+.||.|++|||+++.+..++..++...++| +++++++.| ++++..+++++...
T Consensus 130 ~gvyv~~v~~~~~~~gkl~~gD~i~avdg~~f~s~~e~i~~v~~~k~G----d~VtI~~~r~~~~~~~~~~tl~~~ 201 (342)
T COG3480 130 AGVYVLSVIDNSPFKGKLEAGDTIIAVDGEPFTSSDELIDYVSSKKPG----DEVTIDYERHNETPEIVTITLIKN 201 (342)
T ss_pred eeEEEEEccCCcchhceeccCCeEEeeCCeecCCHHHHHHHHhccCCC----CeEEEEEEeccCCCceEEEEEEee
Confidence 466788888899999889999999999999999999999999888887 999999997 78777777777666
No 82
>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=96.95 E-value=0.011 Score=63.72 Aligned_cols=178 Identities=11% Similarity=0.076 Sum_probs=88.0
Q ss_pred cccccccEEEEEEEcCcccccCCcccceeeEEEEEEEeeCCceEEEEeCceecCCCceEEEEeecCCeEEeEE---E--E
Q 001280 621 ESVIEPTLVMFEVHVPPSCMIDGVHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIPGE---V--V 695 (1108)
Q Consensus 621 ~~~~~~S~V~V~~~~~~~~~~dg~~~~~~~GsG~iId~~~~~G~IlTnr~~V~~~~~~i~V~~~~~~~~~~a~---v--v 695 (1108)
..-+...++.++.... .....=.|+... .+||||+|........+.|+... |.- ... - +
T Consensus 13 yn~Ia~~ic~l~n~s~---------~~~~~l~gigyG-----~~iItn~HLf~~nng~L~i~s~h-G~f-~v~nt~~lkv 76 (235)
T PF00863_consen 13 YNPIASNICRLTNESD---------GGTRSLYGIGYG-----SYIITNAHLFKRNNGELTIKSQH-GEF-TVPNTTQLKV 76 (235)
T ss_dssp -HHHHTTEEEEEEEET---------TEEEEEEEEEET-----TEEEEEGGGGSSTTCEEEEEETT-EEE-EECEGGGSEE
T ss_pred cchhhheEEEEEEEeC---------CCeEEEEEEeEC-----CEEEEChhhhccCCCeEEEEeCc-eEE-EcCCccccce
Confidence 3446677888865443 122334455554 49999988887887888887774 432 111 1 2
Q ss_pred EeeCCCcEEEEEECCCCCCcccccceeccccCCCccCCCCCEEEEEeeCCCCCceeeeeeEeccccccccCCCCCCcccc
Q 001280 696 FLHPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRA 775 (1108)
Q Consensus 696 ~~dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~vG~p~~~~~~~~~~~Vt~~~~~~~i~~~~~~~y~~ 775 (1108)
.-=+..|+.|+|... ++|+ --+-++|. ..+.||.|..||..+..... .++||+.+ -+.+......+
T Consensus 77 ~~i~~~DiviirmPk-DfpP----f~~kl~FR---~P~~~e~v~mVg~~fq~k~~--~s~vSesS--~i~p~~~~~fW-- 142 (235)
T PF00863_consen 77 HPIEGRDIVIIRMPK-DFPP----FPQKLKFR---APKEGERVCMVGSNFQEKSI--SSTVSESS--WIYPEENSHFW-- 142 (235)
T ss_dssp EE-TCSSEEEEE--T-TS--------S---B-------TT-EEEEEEEECSSCCC--EEEEEEEE--EEEEETTTTEE--
T ss_pred EEeCCccEEEEeCCc-ccCC----cchhhhcc---CCCCCCEEEEEEEEEEcCCe--eEEECCce--EEeecCCCCee--
Confidence 222467999999744 3432 00113443 25899999999987644321 33343211 11111111111
Q ss_pred ccceEEEEecccCCCCCceEEcCC-eeEEEEEeeccccccccCCCCCcceeEecccHHHHHHHHHHH
Q 001280 776 MNMEVIELDTDFGSTFSGVLTDEH-GRVQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYTISRVLDKI 841 (1108)
Q Consensus 776 ~~~~~I~~d~~ig~~sGGpL~d~~-G~VvGi~~~~~~~~~~~~~~~~~~~~~~aipi~~i~~vl~~l 841 (1108)
.-.+++.-|. ||+||++.. |.+|||.+.... .....|+-++|-+.+..+++..
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 999999975 999999886432 3445677677766666555444
No 83
>KOG3605 consensus Beta amyloid precursor-binding protein [General function prediction only]
Probab=96.93 E-value=0.0014 Score=77.02 Aligned_cols=120 Identities=19% Similarity=0.299 Sum_probs=78.0
Q ss_pred EEeecCCCHHhHh--ccCCCEEEEECCEEcCCh--hHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeecccCCCCC
Q 001280 903 VKGCLAGSKAENM--LEQGDMMLAINKQPVTCF--HDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGNGT 978 (1108)
Q Consensus 903 V~~V~~~s~A~~a--L~~GDiIlsVnG~~V~~~--~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~~~~~~~~t 978 (1108)
|.....++||++. |.-||.|++|||...-.+ +.-..+++..+. ...|+|+|++=--..++.|.-
T Consensus 677 iAnmm~~GpAarsgkLnIGDQiiaING~SLVGLPLstcQs~Ik~~Kn----QT~VkltiV~cpPV~~V~I~R-------- 744 (829)
T KOG3605|consen 677 IANMMHGGPAARSGKLNIGDQIMSINGTSLVGLPLSTCQSIIKGLKN----QTAVKLNIVSCPPVTTVLIRR-------- 744 (829)
T ss_pred HHhcccCChhhhcCCccccceeEeecCceeccccHHHHHHHHhcccc----cceEEEEEecCCCceEEEeec--------
Confidence 4456678999977 999999999999877653 233344433333 256888888643333333321
Q ss_pred cceeeeccccccCCchhhhhcCCCCCCCCeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCH--HHHHHHHHc
Q 001280 979 TRVINWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKE 1051 (1108)
Q Consensus 979 ~~~~~~~G~~~~~p~~~vr~~~~lp~~~~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~v~~ 1051 (1108)
.+...-+||.+| +|| |.+...|+-|++-|++.|-+|++|||+.|--- +-.+++|..
T Consensus 745 Pd~kyQLGFSVQ----------------NGi-ICSLlRGGIAERGGVRVGHRIIEINgQSVVA~pHekIV~lLs~ 802 (829)
T KOG3605|consen 745 PDLRYQLGFSVQ----------------NGI-ICSLLRGGIAERGGVRVGHRIIEINGQSVVATPHEKIVQLLSN 802 (829)
T ss_pred ccchhhccceee----------------CcE-eehhhcccchhccCceeeeeEEEECCceEEeccHHHHHHHHHH
Confidence 111122444443 266 45578999999999999999999999986432 445555554
No 84
>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=96.89 E-value=0.013 Score=63.23 Aligned_cols=93 Identities=22% Similarity=0.275 Sum_probs=63.9
Q ss_pred ceeeEEEEEEEeeCCceEEEEeCceecCCC-ceEEEEeecCC-------eEEeEEEEEeeC-------CCcEEEEEECCC
Q 001280 647 QHFFGTGVIIYHSQSMGLVVVDKNTVAISA-SDVMLSFAAFP-------IEIPGEVVFLHP-------VHNFALIAYDPS 711 (1108)
Q Consensus 647 ~~~~GsG~iId~~~~~G~IlTnr~~V~~~~-~~i~V~~~~~~-------~~~~a~vv~~dp-------~~dlAilk~d~~ 711 (1108)
....++|.+|+ +.+|||.+|.+.... ..+.|.+.... ......-+..|| .+|+|||+++..
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 35689999999 779999988877653 46677776422 334444455554 579999999654
Q ss_pred -CCCcccccceeccccCCC-ccCCCCCEEEEEeeCCCC
Q 001280 712 -SLGVAGASVVRAAELLPE-PALRRGDSVYLVGLSRSL 747 (1108)
Q Consensus 712 -~l~~~~~~~v~~~~l~~~-~~l~~G~~V~~vG~p~~~ 747 (1108)
.+. ..++++.|... ..+..|+.+.+.|+....
T Consensus 100 i~~~----~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~ 133 (229)
T smart00020 100 VTLS----DNVRPICLPSSNYNVPAGTTCTVSGWGRTS 133 (229)
T ss_pred cCCC----CceeeccCCCcccccCCCCEEEEEeCCCCC
Confidence 222 24566666553 236789999999987654
No 85
>KOG3834 consensus Golgi reassembly stacking protein GRASP65, contains PDZ domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.88 E-value=0.012 Score=66.83 Aligned_cols=161 Identities=20% Similarity=0.216 Sum_probs=101.9
Q ss_pred CceEEEEEecCCCcccc-CCCC-CCEEEEECCEEeCChhHHH-HHHhcCCCCeEEEEEEECC--EEEEEEE-cccccccC
Q 001280 297 TGLLVVDSVVPGGPAHL-RLEP-GDVLVRVNGEVITQFLKLE-TLLDDGVDKNIELLIERGG--ISMTVNL-VQDLHSIT 370 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~-GD~Il~VnG~~v~~~~~l~-~~l~~~~g~~v~l~V~R~g--~~~~~~v-~~~~~~~~ 370 (1108)
.|.-| .+|..+|||++ ||++ -|-|++|||..+..-.+.. +.|+.++-+ |+++|.--. +.+.+.| ..+..
T Consensus 15 eg~hv-lkVqedSpa~~aglepffdFIvSI~g~rL~~dnd~Lk~llk~~sek-Vkltv~n~kt~~~R~v~I~ps~~w--- 89 (462)
T KOG3834|consen 15 EGYHV-LKVQEDSPAHKAGLEPFFDFIVSINGIRLNKDNDTLKALLKANSEK-VKLTVYNSKTQEVRIVEIVPSNNW--- 89 (462)
T ss_pred eeEEE-EEeecCChHHhcCcchhhhhhheeCcccccCchHHHHHHHHhcccc-eEEEEEecccceeEEEEecccccc---
Confidence 44444 69999999999 9988 5889999999998765554 445554444 999987532 2333333 11110
Q ss_pred CCcccccCCeEEccCCHHHhhccCcCCCe---EEEECCCChhHHcCCC-CCCEEEEeCCeecCCHHHHHHHHHhcCCCCe
Q 001280 371 PDYFLEVSGAVIHPLSYQQARNFRFPCGL---VYVAEPGYMLFRAGVP-RHAIIKKFAGEEISRLEDLISVLSKLSRGAR 446 (1108)
Q Consensus 371 ~~~~~~~~G~~~~~l~~q~~~~~~~~~~g---v~v~~~~~~a~~aGl~-~Gd~I~~Vng~~v~~l~~~~~~i~~~~~~~~ 446 (1108)
.. .+.|..+...+- ..++.- ++-..+.++|++|||. -+|.|+-+-+.-...-+||...|... .++.
T Consensus 90 --gg-qllGvsvrFcsf------~~A~~~vwHvl~V~p~SPaalAgl~~~~DYivG~~~~~~~~~eDl~~lIesh-e~kp 159 (462)
T KOG3834|consen 90 --GG-QLLGVSVRFCSF------DGAVESVWHVLSVEPNSPAALAGLRPYTDYIVGIWDAVMHEEEDLFTLIESH-EGKP 159 (462)
T ss_pred --cc-cccceEEEeccC------ccchhheeeeeecCCCCHHHhcccccccceEecchhhhccchHHHHHHHHhc-cCCC
Confidence 00 134444332221 111221 3333689999999999 57999999555556677888888874 4677
Q ss_pred EEEEEeeecccccceEEEEEEecCCCCC
Q 001280 447 VPIEYSSYTDRHRRKSVLVTIDRHEWYA 474 (1108)
Q Consensus 447 v~l~~~~~~~~~~~~~~~l~idR~~~~~ 474 (1108)
+.+-+...+. ...+.+.|+-++ .|-.
T Consensus 160 LklyVYN~D~-d~~ReVti~pn~-awGg 185 (462)
T KOG3834|consen 160 LKLYVYNHDT-DSCREVTITPNS-AWGG 185 (462)
T ss_pred cceeEeecCC-CccceEEeeccc-cccc
Confidence 8877776654 344556666666 6653
No 86
>KOG3129 consensus 26S proteasome regulatory complex, subunit PSMD9 [Posttranslational modification, protein turnover, chaperones]
Probab=96.80 E-value=0.0037 Score=64.43 Aligned_cols=69 Identities=23% Similarity=0.267 Sum_probs=56.4
Q ss_pred eEEEEEecCCChhhhcCCCCCCEEEEECCeecCC---HHHHHHHHHcCCCCceEEEEEEEeCCeEEEEEEEeCC
Q 001280 1008 GVYVARWCHGSPVHRYGLYALQWIVEINGKRTPD---LEAFVNVTKEIEHGEFVRVRTVHLNGKPRVLTLKQDL 1078 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~---l~~f~~~v~~~~~~~~v~l~~v~rdg~~~~~~lk~d~ 1078 (1108)
-++|++|.++|||+.+||+.||.|+++.....-+ +.....+++.. .++.+.++ +.|.|+...++|.|..
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 4689999999999999999999999976665554 45555566664 48899999 8999999999998843
No 87
>KOG3129 consensus 26S proteasome regulatory complex, subunit PSMD9 [Posttranslational modification, protein turnover, chaperones]
Probab=96.76 E-value=0.004 Score=64.22 Aligned_cols=71 Identities=28% Similarity=0.455 Sum_probs=58.9
Q ss_pred CceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHH---HHhcCCCCeEEEEEEECCEEEEEEE-ccccc
Q 001280 297 TGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLET---LLDDGVDKNIELLIERGGISMTVNL-VQDLH 367 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~---~l~~~~g~~v~l~V~R~g~~~~~~v-~~~~~ 367 (1108)
..+.+|..|.|+|||+. ||+.||.|+++....--+|..|.. ....+.++.+.++|.|.|+...+.+ ...|.
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~ 213 (231)
T KOG3129|consen 138 RPFAVVDSVVPGSPADEAGLCVGDEILKFGNVHSGNFLPLQNIAAVVQSNEDQIVSVTVIREGQKVVLSLTPKKWQ 213 (231)
T ss_pred cceEEEeecCCCChhhhhCcccCceEEEecccccccchhHHHHHHHHHhccCcceeEEEecCCCEEEEEeCccccc
Confidence 44677899999999999 999999999999888878776653 3466788899999999999988887 54443
No 88
>PRK11186 carboxy-terminal protease; Provisional
Probab=96.75 E-value=0.0037 Score=77.43 Aligned_cols=63 Identities=30% Similarity=0.451 Sum_probs=48.2
Q ss_pred EEEEEecCCCcccc--CCCCCCEEEEEC--CEEeCC---h--hHHHHHHhcCCCCeEEEEEEEC---CEEEEEEE
Q 001280 300 LVVDSVVPGGPAHL--RLEPGDVLVRVN--GEVITQ---F--LKLETLLDDGVDKNIELLIERG---GISMTVNL 362 (1108)
Q Consensus 300 lVv~~V~~~spA~~--gL~~GD~Il~Vn--G~~v~~---~--~~l~~~l~~~~g~~v~l~V~R~---g~~~~~~v 362 (1108)
++|..|.|+|||++ ||++||+|++|| |+++.+ | .++..++....|.+|.|+|.|+ ++..++++
T Consensus 257 ~~V~~vipGsPA~ka~gLk~GD~IlaVn~~g~~~~dv~g~~~~~vv~lirG~~Gt~V~LtV~r~~~~~~~~~vtl 331 (667)
T PRK11186 257 TVINSLVAGGPAAKSKKLSVGDKIVGVGQDGKPIVDVIGWRLDDVVALIKGPKGSKVRLEILPAGKGTKTRIVTL 331 (667)
T ss_pred EEEEEccCCChHHHhCCCCCCCEEEEECCCCCcccccccCCHHHHHHHhcCCCCCEEEEEEEeCCCCCceEEEEE
Confidence 44469999999998 899999999999 554432 2 4666777777899999999994 45555555
No 89
>COG3975 Predicted protease with the C-terminal PDZ domain [General function prediction only]
Probab=96.63 E-value=0.0029 Score=73.80 Aligned_cols=80 Identities=33% Similarity=0.449 Sum_probs=63.7
Q ss_pred cCeEEEEcChhHHHhcCCChhHHHhhhcCCCCCCCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHH-h
Q 001280 263 LQVTFVHKGFDETRRLGLQSATEQMVRHASPPGETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLL-D 340 (1108)
Q Consensus 263 lg~~~~~~~~~~~r~lGl~~~~~~~~~~~~~~~~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l-~ 340 (1108)
.|+.+..++.+ .-.||+.-. .+.|-.++..|.++|||++ ||.+||.|++|||. ...+ +
T Consensus 439 ~gL~~~~~~~~-~~~LGl~v~-----------~~~g~~~i~~V~~~gPA~~AGl~~Gd~ivai~G~--------s~~l~~ 498 (558)
T COG3975 439 FGLTFTPKPRE-AYYLGLKVK-----------SEGGHEKITFVFPGGPAYKAGLSPGDKIVAINGI--------SDQLDR 498 (558)
T ss_pred cceEEEecCCC-CcccceEec-----------ccCCeeEEEecCCCChhHhccCCCccEEEEEcCc--------cccccc
Confidence 67777777654 445777521 4566666789999999999 99999999999999 2233 4
Q ss_pred cCCCCeEEEEEEECCEEEEEEE
Q 001280 341 DGVDKNIELLIERGGISMTVNL 362 (1108)
Q Consensus 341 ~~~g~~v~l~V~R~g~~~~~~v 362 (1108)
..+++.|++++.|.|..+++.+
T Consensus 499 ~~~~d~i~v~~~~~~~L~e~~v 520 (558)
T COG3975 499 YKVNDKIQVHVFREGRLREFLV 520 (558)
T ss_pred cccccceEEEEccCCceEEeec
Confidence 5788999999999999999887
No 90
>COG3031 PulC Type II secretory pathway, component PulC [Intracellular trafficking and secretion]
Probab=96.61 E-value=0.0045 Score=65.04 Aligned_cols=66 Identities=27% Similarity=0.334 Sum_probs=55.1
Q ss_pred eEEEEeecCCCHHhHh-ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEe
Q 001280 900 VLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVG 969 (1108)
Q Consensus 900 ~~~V~~V~~~s~A~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~ 969 (1108)
|+.+.-...++..++. ||.||+-+++|+..+++.+++..+++.+..- ..++++|.|+|+..++.|.
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 3444444456777777 9999999999999999999999999887765 7899999999999988764
No 91
>PF10459 Peptidase_S46: Peptidase S46; InterPro: IPR019500 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents S46 peptidases, where dipeptidyl-peptidase 7 (DPP-7) is the best-characterised member of this family. It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains.
Probab=96.19 E-value=0.013 Score=73.03 Aligned_cols=42 Identities=19% Similarity=0.270 Sum_probs=34.1
Q ss_pred CceEEEEECCC-----------CcccccccCCCCCCcccCCCCEEEEEecCCC
Q 001280 117 HDFGFFRYDPS-----------AIQFLNYDEIPLAPEAACVGLEIRVVGNDSG 158 (1108)
Q Consensus 117 ~DlAlLk~d~~-----------~~~~~~~~~l~l~~~~~~~G~~V~~iG~p~g 158 (1108)
-||+|+|+=.. +.|+-+-.-++++.+.++.||.|+++|||..
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 5666666678888999999999999999944
No 92
>COG3975 Predicted protease with the C-terminal PDZ domain [General function prediction only]
Probab=95.85 E-value=0.014 Score=68.32 Aligned_cols=77 Identities=22% Similarity=0.235 Sum_probs=59.9
Q ss_pred eeeccccccCCchhhhhcCCCCCCCCeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEE
Q 001280 982 INWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVR 1061 (1108)
Q Consensus 982 ~~~~G~~~~~p~~~vr~~~~lp~~~~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~ 1061 (1108)
-.|+|+.+..- .++..|+.|.++|||++|||.+||.|++|||. .+.+...+.|..+.+.
T Consensus 450 ~~~LGl~v~~~-------------~g~~~i~~V~~~gPA~~AGl~~Gd~ivai~G~--------s~~l~~~~~~d~i~v~ 508 (558)
T COG3975 450 AYYLGLKVKSE-------------GGHEKITFVFPGGPAYKAGLSPGDKIVAINGI--------SDQLDRYKVNDKIQVH 508 (558)
T ss_pred CcccceEeccc-------------CCeeEEEecCCCChhHhccCCCccEEEEEcCc--------cccccccccccceEEE
Confidence 35777776432 23678999999999999999999999999999 2233444568889998
Q ss_pred EEEeCCeEEEEEEEeCCcc
Q 001280 1062 TVHLNGKPRVLTLKQDLHY 1080 (1108)
Q Consensus 1062 ~v~rdg~~~~~~lk~d~~y 1080 (1108)
+.+.|+.+.+.++..-.+
T Consensus 509 -~~~~~~L~e~~v~~~~~~ 526 (558)
T COG3975 509 -VFREGRLREFLVKLGGDP 526 (558)
T ss_pred -EccCCceEEeecccCCCc
Confidence 788888888888876554
No 93
>COG3031 PulC Type II secretory pathway, component PulC [Intracellular trafficking and secretion]
Probab=95.79 E-value=0.018 Score=60.64 Aligned_cols=60 Identities=22% Similarity=0.217 Sum_probs=49.1
Q ss_pred EEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhc-CCCCeEEEEEEECCEEEEEEE
Q 001280 303 DSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDD-GVDKNIELLIERGGISMTVNL 362 (1108)
Q Consensus 303 ~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~-~~g~~v~l~V~R~g~~~~~~v 362 (1108)
+-..+++..+. |||.||+.++||+..+++-.++..+|.. ..-..+.++|.|+|+...+.+
T Consensus 212 ~pgkd~slF~~sglq~GDIavaiNnldltdp~~m~~llq~l~~m~s~qlTv~R~G~rhdInV 273 (275)
T COG3031 212 EPGKDGSLFYKSGLQRGDIAVAINNLDLTDPEDMFRLLQMLRNMPSLQLTVIRRGKRHDINV 273 (275)
T ss_pred cCCCCcchhhhhcCCCcceEEEecCcccCCHHHHHHHHHhhhcCcceEEEEEecCccceeee
Confidence 34444555667 9999999999999999999999988843 555789999999999887765
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=95.59 E-value=0.084 Score=56.85 Aligned_cols=117 Identities=21% Similarity=0.225 Sum_probs=58.6
Q ss_pred CccEEEEEEEeCC-CcEEEEcccccCCCCeEEEEEecCCeEEeEEEEEEcCCCceEEEEECCC--CcccccccCCCCCCc
Q 001280 66 GASYATGFVVDKR-RGIILTNRHVVKPGPVVAEAMFVNREEIPVYPIYRDPVHDFGFFRYDPS--AIQFLNYDEIPLAPE 142 (1108)
Q Consensus 66 ~~~~GSGfvV~~~-~G~ILTn~HVV~~~~~~~~v~~~d~~~~~a~vv~~d~~~DlAlLk~d~~--~~~~~~~~~l~l~~~ 142 (1108)
+++.|||=++.-+ +-.|+|+.||+..+ ..++... +... ..-+...-|||.-.++.- ..|.+++.+
T Consensus 110 Gss~Gsggvft~~~~~vvvTAtHVlg~~--~a~v~~~-g~~~---~~tF~~~GDfA~~~~~~~~G~~P~~k~a~------ 177 (297)
T PF05579_consen 110 GSSVGSGGVFTIGGNTVVVTATHVLGGN--TARVSGV-GTRR---MLTFKKNGDFAEADITNWPGAAPKYKFAQ------ 177 (297)
T ss_dssp SSSEEEEEEEECTTEEEEEEEHHHCBTT--EEEEEET-TEEE---EEEEEEETTEEEEEETTS-S---B--B-T------
T ss_pred eecccccceEEECCeEEEEEEEEEcCCC--eEEEEec-ceEE---EEEEeccCcEEEEECCCCCCCCCceeecC------
Confidence 3456666666531 33999999999943 3444432 2222 233445569999999431 223222221
Q ss_pred ccCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCcccccceEEEEeeecCCCCCCCceecccCcEEEEeeccc
Q 001280 143 AACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSK 221 (1108)
Q Consensus 143 ~~~~G~~V~~iG~p~g~~~si~~G~is~~~~~~~~~~~~~~~~~~~~~i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~ 221 (1108)
-..|---+. . ..-+..|.|..- ..=+-+.+|.||+||+..+|.+||++++..
T Consensus 178 -~~~GrAyW~---t---~tGvE~G~ig~~--------------------~~~~fT~~GDSGSPVVt~dg~liGVHTGSn 229 (297)
T PF05579_consen 178 -NYTGRAYWL---T---STGVEPGFIGGG--------------------GAVCFTGPGDSGSPVVTEDGDLIGVHTGSN 229 (297)
T ss_dssp -T-SEEEEEE---E---TTEEEEEEEETT--------------------EEEESS-GGCTT-EEEETTC-EEEEEEEEE
T ss_pred -CcccceEEE---c---ccCcccceecCc--------------------eEEEEcCCCCCCCccCcCCCCEEEEEecCC
Confidence 011111110 0 011223332110 111335689999999999999999998854
No 95
>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=95.38 E-value=0.18 Score=53.16 Aligned_cols=168 Identities=15% Similarity=0.090 Sum_probs=87.2
Q ss_pred CccEEEEEEEeCCCcEEEEcccccCCCCeEEEEEecCCeEEeEEEEEEcCC----------------CceEEEEEC----
Q 001280 66 GASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYPIYRDPV----------------HDFGFFRYD---- 125 (1108)
Q Consensus 66 ~~~~GSGfvV~~~~G~ILTn~HVV~~~~~~~~v~~~d~~~~~a~vv~~d~~----------------~DlAlLk~d---- 125 (1108)
..+.||=-+++++++..--=.|.+.+......+.+.+|+.+++++....+. .-++-+.-+
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 456677778887667777777888865545566777888888877655322 112222221
Q ss_pred ------CCC-cccccccCCCCC-CcccCCCCEEEEEecCCCCCC-eEEEEEEEEecCC-CCCCCCCCcccccceEEEEee
Q 001280 126 ------PSA-IQFLNYDEIPLA-PEAACVGLEIRVVGNDSGEKV-SILAGTLARLDRD-APHYKKDGYNDFNTFYMQAAS 195 (1108)
Q Consensus 126 ------~~~-~~~~~~~~l~l~-~~~~~~G~~V~~iG~p~g~~~-si~~G~is~~~~~-~~~~~~~~~~~~~~~~i~~~a 195 (1108)
... .....-.++|++ .+.++.|..-+.--. .|... .... .|..+.++ .+.....-..-....++....
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 IYGTLDQDDISNPSYNEPIPVAPKQEVKPGPAYILTVI-DGTKIEEFDI-EIEKVLPQSSPSGKGMVIKVTDPRLLEKTG 175 (218)
T ss_pred eeEEeccccccccccCceeEEEEHHHceEccEEEEEEE-cCCeEEEeEE-EEEEEccCCCCCCCcEEEEECCcchhhhhC
Confidence 110 111122233333 456777764322111 12211 1111 12222222 111111000000112334444
Q ss_pred ecCCCCCCCceecccCcEEEEeecccCC-CCcccccChHHHH
Q 001280 196 GTKGGSSGSPVIDWQGRAVALNAGSKSS-SASAFFLPLERVV 236 (1108)
Q Consensus 196 ~~~~G~SGgPv~n~~G~vVGi~~~~~~~-~~~~falPi~~i~ 236 (1108)
-+-.|+||+|++ .+|++||=++....+ ...+|.++++..+
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 699999998766543 5778888876543
No 96
>KOG3553 consensus Tax interaction protein TIP1 [Cell wall/membrane/envelope biogenesis]
Probab=95.32 E-value=0.022 Score=51.60 Aligned_cols=46 Identities=20% Similarity=0.250 Sum_probs=37.2
Q ss_pred cCCCeEEEE--CCCChhHHcCCCCCCEEEEeCCeec--CCHHHHHHHHHh
Q 001280 395 FPCGLVYVA--EPGYMLFRAGVPRHAIIKKFAGEEI--SRLEDLISVLSK 440 (1108)
Q Consensus 395 ~~~~gv~v~--~~~~~a~~aGl~~Gd~I~~Vng~~v--~~l~~~~~~i~~ 440 (1108)
-+..|+||. +.||||+.|||+.+|.|+.|||-.. -+-+..++.|++
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 345799999 5899999999999999999999655 455566666666
No 97
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=94.76 E-value=0.46 Score=51.84 Aligned_cols=170 Identities=11% Similarity=-0.008 Sum_probs=85.3
Q ss_pred eeEEEEEEEeeCCceEEEEeCceecCCC---ceEEEEee-c--CCe---EEeEEEEEeeC----CCcEEEEEECCCCCC-
Q 001280 649 FFGTGVIIYHSQSMGLVVVDKNTVAISA---SDVMLSFA-A--FPI---EIPGEVVFLHP----VHNFALIAYDPSSLG- 714 (1108)
Q Consensus 649 ~~GsG~iId~~~~~G~IlTnr~~V~~~~---~~i~V~~~-~--~~~---~~~a~vv~~dp----~~dlAilk~d~~~l~- 714 (1108)
...++|+|. +-.|||+.|++-... .++.+... . ++. .+.....+..+ ..|.+...+.+..+.
T Consensus 64 ~~~~~~lI~----pntvLTa~Hc~~s~~~G~~~~~~~p~g~~~~~~~~~~~~~~~~~~~~g~~~~~d~~~~~v~~~~~~~ 139 (251)
T COG3591 64 LCTAATLIG----PNTVLTAGHCIYSPDYGEDDIAAAPPGVNSDGGPFYGITKIEIRVYPGELYKEDGASYDVGEAALES 139 (251)
T ss_pred ceeeEEEEc----CceEEEeeeEEecCCCChhhhhhcCCcccCCCCCCCceeeEEEEecCCceeccCCceeeccHHHhcc
Confidence 345669999 779999988765333 22222210 0 010 12222222222 346666666544332
Q ss_pred -cccccceeccccCCCccCCCCCEEEEEeeCCCCCceeeeeeEeccccccccCCCCCCccccccceEEEEecccCCCCCc
Q 001280 715 -VAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRAMNMEVIELDTDFGSTFSG 793 (1108)
Q Consensus 715 -~~~~~~v~~~~l~~~~~l~~G~~V~~vG~p~~~~~~~~~~~Vt~~~~~~~i~~~~~~~y~~~~~~~I~~d~~ig~~sGG 793 (1108)
.....-+....+......+.+|.+-.+|||.+.......-.- .+-+ .... ...-..++|+-.|+ ||-
T Consensus 140 g~~~~~~~~~~~~~~~~~~~~~d~i~v~GYP~dk~~~~~~~e~-----t~~v-----~~~~-~~~l~y~~dT~pG~-SGS 207 (251)
T COG3591 140 GINIGDVVNYLKRNTASEAKANDRITVIGYPGDKPNIGTMWES-----TGKV-----NSIK-GNKLFYDADTLPGS-SGS 207 (251)
T ss_pred CCCccccccccccccccccccCceeEEEeccCCCCcceeEeee-----ccee-----EEEe-cceEEEEecccCCC-CCC
Confidence 100111221233334457999999999999876421100001 1111 0111 11223455554465 999
Q ss_pred eEEcCCeeEEEEEeeccccccccCCCCCcceeEec-ccHHHHHHHHHHH
Q 001280 794 VLTDEHGRVQAIWGSFSTQVKFGCSSSEDHQFVRG-IPIYTISRVLDKI 841 (1108)
Q Consensus 794 pL~d~~G~VvGi~~~~~~~~~~~~~~~~~~~~~~a-ipi~~i~~vl~~l 841 (1108)
|+++.+.+|+|++...... .++..|+++ .-...++++|.++
T Consensus 208 pv~~~~~~vigv~~~g~~~-------~~~~~~n~~vr~t~~~~~~I~~~ 249 (251)
T COG3591 208 PVLISKDEVIGVHYNGPGA-------NGGSLANNAVRLTPEILNFIQQN 249 (251)
T ss_pred ceEecCceEEEEEecCCCc-------ccccccCcceEecHHHHHHHHHh
Confidence 9999999999998875443 111223222 2345666666654
No 98
>KOG3550 consensus Receptor targeting protein Lin-7 [Extracellular structures]
Probab=94.66 E-value=0.079 Score=51.67 Aligned_cols=53 Identities=28% Similarity=0.503 Sum_probs=40.2
Q ss_pred CceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChhHH--HHHHhcCCCCeEEEEE
Q 001280 297 TGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFLKL--ETLLDDGVDKNIELLI 351 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~~l--~~~l~~~~g~~v~l~V 351 (1108)
..+++ +++.|++.|+. ||+-||.+++|||..|..-.+- .++|....| +|++.|
T Consensus 115 spiyi-sriipggvadrhgglkrgdqllsvngvsvege~hekavellkaa~g-svklvv 171 (207)
T KOG3550|consen 115 SPIYI-SRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKAAVG-SVKLVV 171 (207)
T ss_pred CceEE-EeecCCccccccCcccccceeEeecceeecchhhHHHHHHHHHhcC-cEEEEE
Confidence 44565 89999999999 8999999999999999875443 345555544 466654
No 99
>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=94.57 E-value=0.0098 Score=62.83 Aligned_cols=144 Identities=24% Similarity=0.297 Sum_probs=52.2
Q ss_pred CccEEEEEEEeCCCc--EEEEcccccCCCCeEEEEEecCCeEEeE---EEEEEcCCCceEEEEECCCCcccccccCCCCC
Q 001280 66 GASYATGFVVDKRRG--IILTNRHVVKPGPVVAEAMFVNREEIPV---YPIYRDPVHDFGFFRYDPSAIQFLNYDEIPLA 140 (1108)
Q Consensus 66 ~~~~GSGfvV~~~~G--~ILTn~HVV~~~~~~~~v~~~d~~~~~a---~vv~~d~~~DlAlLk~d~~~~~~~~~~~l~l~ 140 (1108)
..++|+. |...+| .++|++||... +..+ ..+.+|+.++. +.++.+...|++||+..+.-...+....+.+.
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 432255 99999999995 4433 34456666654 36677899999999998431111111221111
Q ss_pred -CcccCCCCEEEEEecCCCCCCeEEEE-EEEEecCCCCCCCCCCcccccceEEEEeeecCCCCCCCceecccCcEEEEee
Q 001280 141 -PEAACVGLEIRVVGNDSGEKVSILAG-TLARLDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNA 218 (1108)
Q Consensus 141 -~~~~~~G~~V~~iG~p~g~~~si~~G-~is~~~~~~~~~~~~~~~~~~~~~i~~~a~~~~G~SGgPv~n~~G~vVGi~~ 218 (1108)
...+..| .+..+ ....+ ..+.-.. ++. -.+ .++..-+...+|.||.|.++.+ ++||++.
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 1111000 00011 11111 1111111 111 111 1578888999999999999999 9999998
Q ss_pred cc---cCCCCcccccCh
Q 001280 219 GS---KSSSASAFFLPL 232 (1108)
Q Consensus 219 ~~---~~~~~~~falPi 232 (1108)
+. ....+.++..|+
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 333445554444
No 100
>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=94.36 E-value=0.04 Score=68.75 Aligned_cols=55 Identities=24% Similarity=0.342 Sum_probs=41.9
Q ss_pred EEEEeeecCCCCCCCceecccCcEEEEeecccCC-----------CCcccccChHHHHHHHHHHHh
Q 001280 190 YMQAASGTKGGSSGSPVIDWQGRAVALNAGSKSS-----------SASAFFLPLERVVRALRFLQE 244 (1108)
Q Consensus 190 ~i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~~-----------~~~~falPi~~i~~~l~~l~~ 244 (1108)
.+.++..+.+|||||||+|.+|++|||+.-+.-. ...+..+-+..|+.+|+.+-.
T Consensus 623 ~FlstnDitGGNSGSPvlN~~GeLVGl~FDgn~Esl~~D~~fdp~~~R~I~VDiRyvL~~ldkv~g 688 (698)
T PF10459_consen 623 NFLSTNDITGGNSGSPVLNAKGELVGLAFDGNWESLSGDIAFDPELNRTIHVDIRYVLWALDKVYG 688 (698)
T ss_pred EEEeccCcCCCCCCCccCCCCceEEEEeecCchhhcccccccccccceeEEEEHHHHHHHHHHHhC
Confidence 3688889999999999999999999999654311 233455777788888877643
No 101
>KOG3542 consensus cAMP-regulated guanine nucleotide exchange factor [Signal transduction mechanisms]
Probab=94.13 E-value=0.037 Score=65.38 Aligned_cols=55 Identities=25% Similarity=0.421 Sum_probs=42.3
Q ss_pred CCeEEEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCceEEEE
Q 001280 1006 GHGVYVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEFVRVR 1061 (1108)
Q Consensus 1006 ~~gV~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~v~l~ 1061 (1108)
+.|+||.+|.|||-|++.||+.||.|++|||+...++.. .++..-...++.+.|.
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 348999999999999999999999999999999998743 3333332334544444
No 102
>KOG3532 consensus Predicted protein kinase [General function prediction only]
Probab=93.85 E-value=0.13 Score=61.22 Aligned_cols=57 Identities=26% Similarity=0.352 Sum_probs=45.6
Q ss_pred CCceEEEEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEE
Q 001280 296 ETGLLVVDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIER 353 (1108)
Q Consensus 296 ~~G~lVv~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~V~R 353 (1108)
...++-|..|++++||.+ .|++||++++|||.+|++..+...++..-.|+ +.+.++|
T Consensus 396 ~~~~v~v~tv~~ns~a~k~~~~~gdvlvai~~~pi~s~~q~~~~~~s~~~~-~~~l~~~ 453 (1051)
T KOG3532|consen 396 TNRAVKVCTVEDNSLADKAAFKPGDVLVAINNVPIRSERQATRFLQSTTGD-LTVLVER 453 (1051)
T ss_pred CceEEEEEEecCCChhhHhcCCCcceEEEecCccchhHHHHHHHHHhcccc-eEEEEee
Confidence 344555689999999999 99999999999999999999998888765454 3333333
No 103
>KOG3552 consensus FERM domain protein FRM-8 [General function prediction only]
Probab=93.54 E-value=0.072 Score=65.50 Aligned_cols=53 Identities=28% Similarity=0.547 Sum_probs=41.2
Q ss_pred EEEEEecCCCccccCCCCCCEEEEECCEEeCCh--hHHHHHHhcCCCCeEEEEEEE
Q 001280 300 LVVDSVVPGGPAHLRLEPGDVLVRVNGEVITQF--LKLETLLDDGVDKNIELLIER 353 (1108)
Q Consensus 300 lVv~~V~~~spA~~gL~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g~~v~l~V~R 353 (1108)
+||..|.+|||+..+|++||.|++|||++|.+. +.+..++.. .-+.|.|+|.+
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 445799999999999999999999999999874 444444432 34567788766
No 104
>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=93.37 E-value=1 Score=46.82 Aligned_cols=139 Identities=14% Similarity=0.149 Sum_probs=78.0
Q ss_pred CccEEEEEEEeCCCcEEEEcccccCCCCeEEEEEecCCeEEeEE--EEEEcCC---CceEEEEECCCCcccccccC-CCC
Q 001280 66 GASYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVY--PIYRDPV---HDFGFFRYDPSAIQFLNYDE-IPL 139 (1108)
Q Consensus 66 ~~~~GSGfvV~~~~G~ILTn~HVV~~~~~~~~v~~~d~~~~~a~--vv~~d~~---~DlAlLk~d~~~~~~~~~~~-l~l 139 (1108)
+...++|+.|- +.++|.++|.-. ...+.+ ++..++.. +...+.. .|+++++++... ++-++.. ++
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-DGVEYKVDDSVVLVDRDGVDTDLTLVKLPRNP-KFRDIRKFFP- 93 (172)
T ss_dssp EEEEEEEEEEE--BTEEEEEGGGGG----CSEEEE-TTEEEEEEEEEEEEETTSSEEEEEEEEEESSS--B--GGGGSB-
T ss_pred ceEEEecceEe--eeEEEEECcCCC----cEEEEE-CCEEEEeeeeEEEecCCCcceeEEEEEccCCc-ccCchhhhhc-
Confidence 56678888887 459999999322 222332 45555433 2234544 599999996422 1112221 11
Q ss_pred CCcccCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCcccccceEEEEeeecCCCCCCCceec---ccCcEEEE
Q 001280 140 APEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVID---WQGRAVAL 216 (1108)
Q Consensus 140 ~~~~~~~G~~V~~iG~p~g~~~si~~G~is~~~~~~~~~~~~~~~~~~~~~i~~~a~~~~G~SGgPv~n---~~G~vVGi 216 (1108)
.......+...++-++......+..+.+...+.- ... ... ....+...++..+|+-||||+. ..++++||
T Consensus 94 -~~~~~~~~~~l~v~~~~~~~~~~~v~~v~~~~~i-~~~-g~~----~~~~~~Y~~~t~~G~CG~~l~~~~~~~~~i~Gi 166 (172)
T PF00548_consen 94 -ESIPEYPECVLLVNSTKFPRMIVEVGFVTNFGFI-NLS-GTT----TPRSLKYKAPTKPGMCGSPLVSRIGGQGKIIGI 166 (172)
T ss_dssp -SSGGTEEEEEEEEESSSSTCEEEEEEEEEEEEEE-EET-TEE----EEEEEEEESEEETTGTTEEEEESCGGTTEEEEE
T ss_pred -cccccCCCcEEEEECCCCccEEEEEEEEeecCcc-ccC-CCE----eeEEEEEccCCCCCccCCeEEEeeccCccEEEE
Confidence 1222445555555444333334444444444331 000 011 1246888999999999999984 36799999
Q ss_pred eecc
Q 001280 217 NAGS 220 (1108)
Q Consensus 217 ~~~~ 220 (1108)
+.++
T Consensus 167 HvaG 170 (172)
T PF00548_consen 167 HVAG 170 (172)
T ss_dssp EEEE
T ss_pred Eecc
Confidence 9875
No 105
>KOG3532 consensus Predicted protein kinase [General function prediction only]
Probab=93.32 E-value=0.17 Score=60.48 Aligned_cols=46 Identities=22% Similarity=0.324 Sum_probs=41.9
Q ss_pred ceEEEEeecCCCHHhHh-ccCCCEEEEECCEEcCChhHHHHHHHhcc
Q 001280 899 QVLRVKGCLAGSKAENM-LEQGDMMLAINKQPVTCFHDIENACQALD 944 (1108)
Q Consensus 899 ~~~~V~~V~~~s~A~~a-L~~GDiIlsVnG~~V~~~~dl~~~l~~~~ 944 (1108)
+.+.|..|.++++|.++ |++||++++|||.+|++.+++...++...
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 99999999999999999999998886444
No 106
>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=93.28 E-value=0.055 Score=53.08 Aligned_cols=31 Identities=29% Similarity=0.359 Sum_probs=21.9
Q ss_pred EEEeeecCCCCCCCceecccCcEEEEeeccc
Q 001280 191 MQAASGTKGGSSGSPVIDWQGRAVALNAGSK 221 (1108)
Q Consensus 191 i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~ 221 (1108)
...+....+|+||+|+||.+|++|||...+.
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 3444557889999999999999999986654
No 107
>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=92.46 E-value=0.51 Score=57.20 Aligned_cols=121 Identities=17% Similarity=0.295 Sum_probs=73.1
Q ss_pred cCCCceEEEEECCCC---------cc------cccccCCCCC--CcccCCCCEEEEEecCCCCCCeEEEEEEEEecCCCC
Q 001280 114 DPVHDFGFFRYDPSA---------IQ------FLNYDEIPLA--PEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAP 176 (1108)
Q Consensus 114 d~~~DlAlLk~d~~~---------~~------~~~~~~l~l~--~~~~~~G~~V~~iG~p~g~~~si~~G~is~~~~~~~ 176 (1108)
....|+||+++++.- +. .+.+..+-.. -..+..|.+|+=+|.-.|. +.|.+.+..-.
T Consensus 540 ~~LsD~AIIkV~~~~~~~N~LGddi~f~~~dP~l~f~NlyV~~~~~~~~~G~~VfK~GrTTgy----T~G~lNg~klv-- 613 (695)
T PF08192_consen 540 KRLSDWAIIKVNKERKCQNYLGDDIQFNEPDPTLMFQNLYVREVVSNLVPGMEVFKVGRTTGY----TTGILNGIKLV-- 613 (695)
T ss_pred ccccceEEEEeCCCceecCCCCccccccCCCccccccccchhhhhhccCCCCeEEEecccCCc----cceEecceEEE--
Confidence 344699999997532 11 1111111110 2346789999999987775 45555544211
Q ss_pred CCCCCCcccccceEEEEe----eecCCCCCCCceecccCc------EEEEeecccCC-CCcccccChHHHHHHHHHH
Q 001280 177 HYKKDGYNDFNTFYMQAA----SGTKGGSSGSPVIDWQGR------AVALNAGSKSS-SASAFFLPLERVVRALRFL 242 (1108)
Q Consensus 177 ~~~~~~~~~~~~~~i~~~----a~~~~G~SGgPv~n~~G~------vVGi~~~~~~~-~~~~falPi~~i~~~l~~l 242 (1108)
.+..... . -.+++... +=..+|.||+-|++.-+. |+||..+.... ..++++.|+..|+.=|+.+
T Consensus 614 yw~dG~i-~-s~efvV~s~~~~~Fa~~GDSGS~VLtk~~d~~~gLgvvGMlhsydge~kqfglftPi~~il~rl~~v 688 (695)
T PF08192_consen 614 YWADGKI-Q-SSEFVVSSDNNPAFASGGDSGSWVLTKLEDNNKGLGVVGMLHSYDGEQKQFGLFTPINEILDRLEEV 688 (695)
T ss_pred EecCCCe-E-EEEEEEecCCCccccCCCCcccEEEecccccccCceeeEEeeecCCccceeeccCcHHHHHHHHHHh
Confidence 1111111 1 12334444 335789999999986555 99998774433 5788999999988777665
No 108
>KOG3571 consensus Dishevelled 3 and related proteins [General function prediction only]
Probab=91.76 E-value=0.45 Score=55.39 Aligned_cols=63 Identities=21% Similarity=0.327 Sum_probs=48.3
Q ss_pred eeeccccccCCchhhhhcCCCCCCCCeEEEEEecCCChhhhcC-CCCCCEEEEECCeecCCH--HHHHHHHHcC
Q 001280 982 INWCGCIVQDPHPAVRALGFLPEEGHGVYVARWCHGSPVHRYG-LYALQWIVEINGKRTPDL--EAFVNVTKEI 1052 (1108)
Q Consensus 982 ~~~~G~~~~~p~~~vr~~~~lp~~~~gV~V~~v~~gSpA~~~G-L~~gD~I~~VNg~~v~~l--~~f~~~v~~~ 1052 (1108)
+.|+|+.+.--. ...+..|+||.++.+|++-+.-| +.+||.|+.||.....++ ++.+.+|+++
T Consensus 260 vnfLGiSivgqs--------n~rgDggIYVgsImkgGAVA~DGRIe~GDMiLQVNevsFENmSNd~AVrvLREa 325 (626)
T KOG3571|consen 260 VNFLGISIVGQS--------NARGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNEVSFENMSNDQAVRVLREA 325 (626)
T ss_pred cccceeEeeccc--------CcCCCCceEEeeeccCceeeccCccCccceEEEeeecchhhcCchHHHHHHHHH
Confidence 457887764422 11123589999999999877665 899999999999999988 7888888774
No 109
>KOG3550 consensus Receptor targeting protein Lin-7 [Extracellular structures]
Probab=91.73 E-value=0.38 Score=47.08 Aligned_cols=52 Identities=23% Similarity=0.286 Sum_probs=42.0
Q ss_pred eEEEEEecCCChhhhc-CCCCCCEEEEECCeecCCH--HHHHHHHHcCCCCceEEEE
Q 001280 1008 GVYVARWCHGSPVHRY-GLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVR 1061 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~-GL~~gD~I~~VNg~~v~~l--~~f~~~v~~~~~~~~v~l~ 1061 (1108)
-+||+++.||+-|++- ||+.||.+++|||..+..- +-.+++++.. -..|+|.
T Consensus 116 piyisriipggvadrhgglkrgdqllsvngvsvege~hekavellkaa--~gsvklv 170 (207)
T KOG3550|consen 116 PIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKAA--VGSVKLV 170 (207)
T ss_pred ceEEEeecCCccccccCcccccceeEeecceeecchhhHHHHHHHHHh--cCcEEEE
Confidence 4799999999999986 7999999999999998765 5567777763 3346655
No 110
>KOG1892 consensus Actin filament-binding protein Afadin [Cytoskeleton]
Probab=89.71 E-value=0.4 Score=59.32 Aligned_cols=61 Identities=31% Similarity=0.478 Sum_probs=49.8
Q ss_pred CCCceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChhHHHHH-HhcCCCCeEEEEEEECCE
Q 001280 295 GETGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFLKLETL-LDDGVDKNIELLIERGGI 356 (1108)
Q Consensus 295 ~~~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~~l~~~-l~~~~g~~v~l~V~R~g~ 356 (1108)
..-|+|| ..|.+|++|+. -|+.||.|++|||..+-...+-+.+ |....|..|.+.|...|.
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 89999999998 5999999999999998887666543 566778889998876543
No 111
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=89.70 E-value=8.8 Score=43.10 Aligned_cols=106 Identities=11% Similarity=0.110 Sum_probs=58.0
Q ss_pred CCCceEEEEECCC---CcccccccCCCCCCcccCCCCEEEEEecCCCCCCeEEEEEEEEecCCCCCCCCCCcccccceEE
Q 001280 115 PVHDFGFFRYDPS---AIQFLNYDEIPLAPEAACVGLEIRVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYM 191 (1108)
Q Consensus 115 ~~~DlAlLk~d~~---~~~~~~~~~l~l~~~~~~~G~~V~~iG~p~g~~~si~~G~is~~~~~~~~~~~~~~~~~~~~~i 191 (1108)
...++.||+++.+ ...+.=+ +=.+.....|+.+.+.|+...... ....+.-..... ....+
T Consensus 159 ~~~~~mIlEl~~~~~~~~~~~Cl---~~~~~~~~~~~~~~~yg~~~~~~~--~~~~~~i~~~~~-----------~~~~~ 222 (282)
T PF03761_consen 159 RPYSPMILELEEDFSKNVSPPCL---ADSSTNWEKGDEVDVYGFNSTGKL--KHRKLKITNCTK-----------CAYSI 222 (282)
T ss_pred cccceEEEEEcccccccCCCEEe---CCCccccccCceEEEeecCCCCeE--EEEEEEEEEeec-----------cceeE
Confidence 3468899999765 2222222 223455778999999998322221 111111111100 11124
Q ss_pred EEeeecCCCCCCCcee---cccCcEEEEeecccCCC--CcccccChHHHH
Q 001280 192 QAASGTKGGSSGSPVI---DWQGRAVALNAGSKSSS--ASAFFLPLERVV 236 (1108)
Q Consensus 192 ~~~a~~~~G~SGgPv~---n~~G~vVGi~~~~~~~~--~~~falPi~~i~ 236 (1108)
........|.+|||++ |.+-.|||+.+.+.... ...+++.+...+
T Consensus 223 ~~~~~~~~~d~Gg~lv~~~~gr~tlIGv~~~~~~~~~~~~~~f~~v~~~~ 272 (282)
T PF03761_consen 223 CTKQYSCKGDRGGPLVKNINGRWTLIGVGASGNYECNKNNSYFFNVSWYQ 272 (282)
T ss_pred ecccccCCCCccCeEEEEECCCEEEEEEEccCCCcccccccEEEEHHHhh
Confidence 5555667899999997 33445999987655322 245556555444
No 112
>KOG3542 consensus cAMP-regulated guanine nucleotide exchange factor [Signal transduction mechanisms]
Probab=89.24 E-value=0.32 Score=57.87 Aligned_cols=53 Identities=19% Similarity=0.252 Sum_probs=41.7
Q ss_pred CeEEEE--CCCChhHHcCCCCCCEEEEeCCeecCCHHHHHHHHHhcCCCCeEEEEE
Q 001280 398 GLVYVA--EPGYMLFRAGVPRHAIIKKFAGEEISRLEDLISVLSKLSRGARVPIEY 451 (1108)
Q Consensus 398 ~gv~v~--~~~~~a~~aGl~~Gd~I~~Vng~~v~~l~~~~~~i~~~~~~~~v~l~~ 451 (1108)
-|+||. .||+.|.++||+.||.|++||||...++ .+.+++.-+.++..+.|.+
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 379999 4999999999999999999999999998 5566666555544444433
No 113
>KOG3627 consensus Trypsin [Amino acid transport and metabolism]
Probab=89.21 E-value=8.8 Score=42.17 Aligned_cols=147 Identities=17% Similarity=0.133 Sum_probs=73.0
Q ss_pred EEEEEEEeCCCcEEEEcccccCCCC-eEEEEEec---------CC---eEEeE-EEEEEcC-------C-CceEEEEECC
Q 001280 69 YATGFVVDKRRGIILTNRHVVKPGP-VVAEAMFV---------NR---EEIPV-YPIYRDP-------V-HDFGFFRYDP 126 (1108)
Q Consensus 69 ~GSGfvV~~~~G~ILTn~HVV~~~~-~~~~v~~~---------d~---~~~~a-~vv~~d~-------~-~DlAlLk~d~ 126 (1108)
.+.|.+|++ .+|||++|++.... ....|.+. ++ ..... +++ .|+ . +|||+|+++.
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 39999999999531 03334332 11 11111 222 332 2 7999999985
Q ss_pred C-CcccccccCCCCCCc----ccCCCCEEEEEecCCCC----C-C-eEEEEEEEEecC--CCCCCCCC-CcccccceEEE
Q 001280 127 S-AIQFLNYDEIPLAPE----AACVGLEIRVVGNDSGE----K-V-SILAGTLARLDR--DAPHYKKD-GYNDFNTFYMQ 192 (1108)
Q Consensus 127 ~-~~~~~~~~~l~l~~~----~~~~G~~V~~iG~p~g~----~-~-si~~G~is~~~~--~~~~~~~~-~~~~~~~~~i~ 192 (1108)
. .+. ..+.++.|... ....+....+.|+.... . . ......+..+.. -...++.. ...+ ..+-
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 3 221 13344444311 13444888888865321 1 1 122122222221 00111110 0001 1122
Q ss_pred Ee-----eecCCCCCCCceeccc---CcEEEEeecccC
Q 001280 193 AA-----SGTKGGSSGSPVIDWQ---GRAVALNAGSKS 222 (1108)
Q Consensus 193 ~~-----a~~~~G~SGgPv~n~~---G~vVGi~~~~~~ 222 (1108)
+. ..+-.|.|||||+-.+ ..++||.+.+..
T Consensus 192 a~~~~~~~~~C~GDSGGPLv~~~~~~~~~~GivS~G~~ 229 (256)
T KOG3627|consen 192 AGGPEGGKDACQGDSGGPLVCEDNGRWVLVGIVSWGSG 229 (256)
T ss_pred eCccCCCCccccCCCCCeEEEeeCCcEEEEEEEEecCC
Confidence 21 2245589999998654 699999988754
No 114
>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=88.36 E-value=1.9 Score=44.84 Aligned_cols=83 Identities=19% Similarity=0.272 Sum_probs=55.6
Q ss_pred hhHHHHHHHhccCCCCCCCeEEEEEEe---CCEEE--EEEEeecccCCCCCcceeeeccccccCCchhhhhcCCCCCCCC
Q 001280 933 FHDIENACQALDKDGEDNGKLDITIFR---QGREI--ELQVGTDVRDGNGTTRVINWCGCIVQDPHPAVRALGFLPEEGH 1007 (1108)
Q Consensus 933 ~~dl~~~l~~~~~g~~~~~~v~l~V~R---~g~~~--~v~v~~~~~~~~~t~~~~~~~G~~~~~p~~~vr~~~~lp~~~~ 1007 (1108)
..++...+...+.| +.+.++|.+ .|+.. ++.+++.+.. ....| ..-+|+.+.. +..
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 44566666555665 889999987 45544 4555554332 22223 3345766543 123
Q ss_pred eEEEEEecCCChhhhcCCCCCCEEEEE
Q 001280 1008 GVYVARWCHGSPVHRYGLYALQWIVEI 1034 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~GL~~gD~I~~V 1034 (1108)
.+.|..+..||||+++|+.-+..|++|
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 689999999999999999999989887
No 115
>KOG3552 consensus FERM domain protein FRM-8 [General function prediction only]
Probab=88.21 E-value=0.57 Score=58.11 Aligned_cols=56 Identities=20% Similarity=0.318 Sum_probs=43.0
Q ss_pred ceEEEEeecCCCHHhHhccCCCEEEEECCEEcCC--hhHHHHHHHhccCCCCCCCeEEEEEEeC
Q 001280 899 QVLRVKGCLAGSKAENMLEQGDMMLAINKQPVTC--FHDIENACQALDKDGEDNGKLDITIFRQ 960 (1108)
Q Consensus 899 ~~~~V~~V~~~s~A~~aL~~GDiIlsVnG~~V~~--~~dl~~~l~~~~~g~~~~~~v~l~V~R~ 960 (1108)
.-++|..|.+|+|+...|++||.|+.|||++|.. |+.+..++. .. .+.|.++|.+-
T Consensus 75 rPviVr~VT~GGps~GKL~PGDQIl~vN~Epv~daprervIdlvR---ac---e~sv~ltV~qP 132 (1298)
T KOG3552|consen 75 RPVIVRFVTEGGPSIGKLQPGDQILAVNGEPVKDAPRERVIDLVR---AC---ESSVNLTVCQP 132 (1298)
T ss_pred CceEEEEecCCCCccccccCCCeEEEecCcccccccHHHHHHHHH---HH---hhhcceEEecc
Confidence 3477999999999998899999999999999987 444444442 22 25688888874
No 116
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=87.15 E-value=1.6 Score=51.15 Aligned_cols=54 Identities=31% Similarity=0.532 Sum_probs=47.6
Q ss_pred EecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCe---EEEEEEE-CCEE
Q 001280 304 SVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKN---IELLIER-GGIS 357 (1108)
Q Consensus 304 ~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~---v~l~V~R-~g~~ 357 (1108)
.+..+++|.. +|++||.++++|++++.+|.++...+....+.. +.+.+.| ++..
T Consensus 135 ~v~~~s~a~~a~l~~Gd~iv~~~~~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~ 193 (375)
T COG0750 135 EVAPKSAAALAGLRPGDRIVAVDGEKVASWDDVRRLLVAAAGDVFNLLTILVIRLDGEA 193 (375)
T ss_pred ecCCCCHHHHcCCCCCCEEEeECCEEccCHHHHHHHHHhccCCcccceEEEEEecccee
Confidence 6888999999 999999999999999999999998887766666 8899999 6655
No 117
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=86.51 E-value=0.92 Score=51.50 Aligned_cols=46 Identities=22% Similarity=0.278 Sum_probs=42.6
Q ss_pred CCeEEEEEecCCChhhhc-CCCCCCEEEEECCeecCCHHHHHHHHHc
Q 001280 1006 GHGVYVARWCHGSPVHRY-GLYALQWIVEINGKRTPDLEAFVNVTKE 1051 (1108)
Q Consensus 1006 ~~gV~V~~v~~gSpA~~~-GL~~gD~I~~VNg~~v~~l~~f~~~v~~ 1051 (1108)
+.||.|++|...||+..+ ||.+||.|+++||-|+.+-+|+.+.++.
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 458999999999999866 9999999999999999999999999887
No 118
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=85.98 E-value=1.3 Score=47.85 Aligned_cols=54 Identities=20% Similarity=0.408 Sum_probs=46.9
Q ss_pred eEEEEEecCCChhhhcCC-CCCCEEEEECCeec--CCHHHHHHHHHcCCCCceEEEE
Q 001280 1008 GVYVARWCHGSPVHRYGL-YALQWIVEINGKRT--PDLEAFVNVTKEIEHGEFVRVR 1061 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~GL-~~gD~I~~VNg~~v--~~l~~f~~~v~~~~~~~~v~l~ 1061 (1108)
|++|++..+|+-|+--|| ..+|.|++|||..| +++|+..+++-++..|--|+++
T Consensus 195 GIFISRlVpGGLAeSTGLLaVnDEVlEVNGIEVaGKTLDQVTDMMvANshNLIiTVk 251 (358)
T KOG3606|consen 195 GIFISRLVPGGLAESTGLLAVNDEVLEVNGIEVAGKTLDQVTDMMVANSHNLIITVK 251 (358)
T ss_pred ceEEEeecCCccccccceeeecceeEEEcCEEeccccHHHHHHHHhhcccceEEEec
Confidence 899999999999999986 78999999999887 5889999999887666666654
No 119
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=85.64 E-value=2.8 Score=49.25 Aligned_cols=58 Identities=17% Similarity=0.252 Sum_probs=49.0
Q ss_pred EEEEecCCChhhhcCCCCCCEEEEECCeecCCHHHHHHHHHcCCCCce---EEEEEEEe-CCeE
Q 001280 1010 YVARWCHGSPVHRYGLYALQWIVEINGKRTPDLEAFVNVTKEIEHGEF---VRVRTVHL-NGKP 1069 (1108)
Q Consensus 1010 ~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l~~f~~~v~~~~~~~~---v~l~~v~r-dg~~ 1069 (1108)
++..+..+|+|.++|+++||.|+++|++++.++++..+.+.... +.. +.+. +.| ++..
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 34478899999999999999999999999999999999988865 444 6777 556 7776
No 120
>KOG0606 consensus Microtubule-associated serine/threonine kinase and related proteins [Signal transduction mechanisms; General function prediction only]
Probab=85.27 E-value=1.2 Score=57.00 Aligned_cols=51 Identities=29% Similarity=0.378 Sum_probs=43.8
Q ss_pred EEEEecCCChhhhcCCCCCCEEEEECCeecCCH--HHHHHHHHcCCCCceEEEEE
Q 001280 1010 YVARWCHGSPVHRYGLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRT 1062 (1108)
Q Consensus 1010 ~V~~v~~gSpA~~~GL~~gD~I~~VNg~~v~~l--~~f~~~v~~~~~~~~v~l~~ 1062 (1108)
.|..|..||||..+||.++|.|++|||+++..+ .++.+.+-+ .|..+.+++
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 688999999999999999999999999999988 577777775 367777763
No 121
>KOG1892 consensus Actin filament-binding protein Afadin [Cytoskeleton]
Probab=85.16 E-value=1 Score=56.00 Aligned_cols=67 Identities=21% Similarity=0.314 Sum_probs=50.3
Q ss_pred hcCCCccceEEEEeecCCCHHhHh--ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCE
Q 001280 892 KKDPVRRQVLRVKGCLAGSKAENM--LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGR 962 (1108)
Q Consensus 892 ~~~~~~~~~~~V~~V~~~s~A~~a--L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~ 962 (1108)
+...++.-|+||+.|.+|++|+.- |+.||.+|+|||+..-..++-+.+-.....| ..|.+.|-..|.
T Consensus 953 kGaGq~klGIYvKsVV~GgaAd~DGRL~aGDQLLsVdG~SLiGisQErAA~lmtrtg----~vV~leVaKqgA 1021 (1629)
T KOG1892|consen 953 KGAGQRKLGIYVKSVVEGGAADHDGRLEAGDQLLSVDGHSLIGISQERAARLMTRTG----NVVHLEVAKQGA 1021 (1629)
T ss_pred ccCCccccceEEEEeccCCccccccccccCceeeeecCcccccccHHHHHHHHhccC----CeEEEehhhhhh
Confidence 345667789999999999999855 9999999999999887765544333234444 778888875554
No 122
>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=84.66 E-value=13 Score=38.57 Aligned_cols=151 Identities=14% Similarity=0.127 Sum_probs=77.7
Q ss_pred ccccccEEEEEEEcCcccccCCcccceeeEEEEEEEeeCCceEEEEeCceecCCCceEEEEeecCCeEE--eEEEEEeeC
Q 001280 622 SVIEPTLVMFEVHVPPSCMIDGVHSQHFFGTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEI--PGEVVFLHP 699 (1108)
Q Consensus 622 ~~~~~S~V~V~~~~~~~~~~dg~~~~~~~GsG~iId~~~~~G~IlTnr~~V~~~~~~i~V~~~~~~~~~--~a~vv~~dp 699 (1108)
..+.+-++.|++ . ...+.++++-|. ..+.|.++| .... ..+.+. +..+ ...+.-.+.
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--EEPE--DTIYID--GVEYKVDDSVVLVDR 67 (172)
T ss_dssp HHHHHHEEEEEE--T---------TEEEEEEEEEEE----BTEEEEEGG--GGGC--SEEEET--TEEEEEEEEEEEEET
T ss_pred HHHhccEEEEEe--C---------CceEEEecceEe----eeEEEEECc--CCCc--EEEEEC--CEEEEeeeeEEEecC
Confidence 345566666655 2 567889988888 568888878 2222 233333 4433 224444555
Q ss_pred C---CcEEEEEECCC-CCCcccccceeccccCCCccCCCCCEEEEEeeCCCCCceeeeeeEeccccccccCCCCCCcccc
Q 001280 700 V---HNFALIAYDPS-SLGVAGASVVRAAELLPEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRA 775 (1108)
Q Consensus 700 ~---~dlAilk~d~~-~l~~~~~~~v~~~~l~~~~~l~~G~~V~~vG~p~~~~~~~~~~~Vt~~~~~~~i~~~~~~~y~~ 775 (1108)
. .|+++++++.. .+. .-.+-+. +.. -...+.+.++=.+........-+.|+. .+.+.....+.+
T Consensus 68 ~~~~~Dl~~v~l~~~~kfr----DIrk~~~--~~~-~~~~~~~l~v~~~~~~~~~~~v~~v~~---~~~i~~~g~~~~-- 135 (172)
T PF00548_consen 68 DGVDTDLTLVKLPRNPKFR----DIRKFFP--ESI-PEYPECVLLVNSTKFPRMIVEVGFVTN---FGFINLSGTTTP-- 135 (172)
T ss_dssp TSSEEEEEEEEEESSS-B------GGGGSB--SSG-GTEEEEEEEEESSSSTCEEEEEEEEEE---EEEEEETTEEEE--
T ss_pred CCcceeEEEEEccCCcccC----chhhhhc--ccc-ccCCCcEEEEECCCCccEEEEEEEEee---cCccccCCCEee--
Confidence 4 59999999542 221 1111122 221 144555656644433333333344442 333322111111
Q ss_pred ccceEEEEecc-cCCCCCceEEcC---CeeEEEEEee
Q 001280 776 MNMEVIELDTD-FGSTFSGVLTDE---HGRVQAIWGS 808 (1108)
Q Consensus 776 ~~~~~I~~d~~-ig~~sGGpL~d~---~G~VvGi~~~ 808 (1108)
..+.=+++ ..+.|||+|+.. .++++||..+
T Consensus 136 ---~~~~Y~~~t~~G~CG~~l~~~~~~~~~i~GiHva 169 (172)
T PF00548_consen 136 ---RSLKYKAPTKPGMCGSPLVSRIGGQGKIIGIHVA 169 (172)
T ss_dssp ---EEEEEESEEETTGTTEEEEESCGGTTEEEEEEEE
T ss_pred ---EEEEEccCCCCCccCCeEEEeeccCccEEEEEec
Confidence 22333332 234599999864 4799999876
No 123
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=83.71 E-value=2.7 Score=45.43 Aligned_cols=60 Identities=20% Similarity=0.385 Sum_probs=45.1
Q ss_pred CCCceEEEEEecCCCcccc-C-CCCCCEEEEECCEEeC--ChhHHHHHHhcCCCCeEEEEEEECCE
Q 001280 295 GETGLLVVDSVVPGGPAHL-R-LEPGDVLVRVNGEVIT--QFLKLETLLDDGVDKNIELLIERGGI 356 (1108)
Q Consensus 295 ~~~G~lVv~~V~~~spA~~-g-L~~GD~Il~VnG~~v~--~~~~l~~~l~~~~g~~v~l~V~R~g~ 356 (1108)
.-.|++| ++..|++-|+. | |...|.+++|||..|. +..++..++..+. ..+-++|.-..+
T Consensus 192 kvpGIFI-SRlVpGGLAeSTGLLaVnDEVlEVNGIEVaGKTLDQVTDMMvANs-hNLIiTVkPANQ 255 (358)
T KOG3606|consen 192 KVPGIFI-SRLVPGGLAESTGLLAVNDEVLEVNGIEVAGKTLDQVTDMMVANS-HNLIITVKPANQ 255 (358)
T ss_pred ccCceEE-EeecCCccccccceeeecceeEEEcCEEeccccHHHHHHHHhhcc-cceEEEeccccc
Confidence 5678888 89999999999 6 7789999999999994 5677776664321 356667654433
No 124
>KOG0609 consensus Calcium/calmodulin-dependent serine protein kinase/membrane-associated guanylate kinase [Signal transduction mechanisms]
Probab=83.19 E-value=2 Score=51.14 Aligned_cols=74 Identities=24% Similarity=0.362 Sum_probs=57.8
Q ss_pred eEEEEEecCCChhhhcCC-CCCCEEEEECCeecCCH--HHHHHHHHcCCCCceEEEEEEEeC---CeEEEEEEEeCCccC
Q 001280 1008 GVYVARWCHGSPVHRYGL-YALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVHLN---GKPRVLTLKQDLHYW 1081 (1108)
Q Consensus 1008 gV~V~~v~~gSpA~~~GL-~~gD~I~~VNg~~v~~l--~~f~~~v~~~~~~~~v~l~~v~rd---g~~~~~~lk~d~~y~ 1081 (1108)
.++|.++..|+.|++-|+ +.||.|.+|||..+.+. +++.+++++.. |. ++++++--- .....+-++.-.+|+
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-GS-ITFKIIPSYRPPPQQQVVFVRALFDYD 224 (542)
T ss_pred ccEEeeeccCCcchhccceeeccchheecCeecccCCHHHHHHHHHhCC-Cc-EEEEEcccccCCCceeeeeehhhcCcC
Confidence 469999999999999985 89999999999998875 89999999865 44 777743321 233346788888898
Q ss_pred cc
Q 001280 1082 PT 1083 (1108)
Q Consensus 1082 pt 1083 (1108)
|-
T Consensus 225 P~ 226 (542)
T KOG0609|consen 225 PK 226 (542)
T ss_pred cc
Confidence 86
No 125
>KOG3651 consensus Protein kinase C, alpha binding protein [Signal transduction mechanisms]
Probab=82.39 E-value=2.4 Score=46.34 Aligned_cols=54 Identities=26% Similarity=0.406 Sum_probs=40.5
Q ss_pred CceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChhHHH--HHHhcCCCCeEEEEEE
Q 001280 297 TGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFLKLE--TLLDDGVDKNIELLIE 352 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~~l~--~~l~~~~g~~v~l~V~ 352 (1108)
-.++|| .|..++||++ .++.||.|++|||..|..-..+. .++.... +.|++++-
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 346776 9999999999 59999999999999998766554 4444332 35666654
No 126
>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=82.33 E-value=1.2 Score=43.24 Aligned_cols=32 Identities=34% Similarity=0.509 Sum_probs=25.9
Q ss_pred EEEeeecCCCCCCCceecccCcEEEEeecccC
Q 001280 191 MQAASGTKGGSSGSPVIDWQGRAVALNAGSKS 222 (1108)
Q Consensus 191 i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~~ 222 (1108)
..-...-.+|.||-|++|..|+||||+.++.+
T Consensus 97 tip~g~g~~GDSGRpi~DNsGrVVaIVLGG~n 128 (158)
T PF00944_consen 97 TIPTGVGKPGDSGRPIFDNSGRVVAIVLGGAN 128 (158)
T ss_dssp EEETTS-STTSTTEEEESTTSBEEEEEEEEEE
T ss_pred EeccCCCCCCCCCCccCcCCCCEEEEEecCCC
Confidence 33445568899999999999999999988754
No 127
>KOG3551 consensus Syntrophins (type beta) [Extracellular structures]
Probab=80.82 E-value=1.4 Score=49.90 Aligned_cols=55 Identities=24% Similarity=0.296 Sum_probs=42.4
Q ss_pred CCceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChhHHHHHH-hcCCCCeEEEEE
Q 001280 296 ETGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFLKLETLL-DDGVDKNIELLI 351 (1108)
Q Consensus 296 ~~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~~l~~~l-~~~~g~~v~l~V 351 (1108)
.-.+|| +.+.++=.|++ -|..||.|++|||+.+.+..+-+..- .++.|+.|.++|
T Consensus 109 kMPIlI-SKIFkGlAADQt~aL~~gDaIlSVNG~dL~~AtHdeAVqaLKraGkeV~lev 166 (506)
T KOG3551|consen 109 KMPILI-SKIFKGLAADQTGALFLGDAILSVNGEDLRDATHDEAVQALKRAGKEVLLEV 166 (506)
T ss_pred CCceeh-hHhccccccccccceeeccEEEEecchhhhhcchHHHHHHHHhhCceeeeee
Confidence 344555 89999999998 69999999999999998877665544 456788766554
No 128
>KOG3571 consensus Dishevelled 3 and related proteins [General function prediction only]
Probab=77.28 E-value=3.3 Score=48.55 Aligned_cols=70 Identities=20% Similarity=0.337 Sum_probs=53.8
Q ss_pred CeEEEEC--CCChhHHcC-CCCCCEEEEeCCeecCCHH--HHHHHHHhcCCCCeEEEEEeeecccccceEEEEEEecCCC
Q 001280 398 GLVYVAE--PGYMLFRAG-VPRHAIIKKFAGEEISRLE--DLISVLSKLSRGARVPIEYSSYTDRHRRKSVLVTIDRHEW 472 (1108)
Q Consensus 398 ~gv~v~~--~~~~a~~aG-l~~Gd~I~~Vng~~v~~l~--~~~~~i~~~~~~~~v~l~~~~~~~~~~~~~~~l~idR~~~ 472 (1108)
+|+||.+ ++++-+..| +.+||.|++||.....|+. +.+++|+..- |++.++.+++-. .|
T Consensus 277 ggIYVgsImkgGAVA~DGRIe~GDMiLQVNevsFENmSNd~AVrvLREaV---------------~~~gPi~ltvAk-~~ 340 (626)
T KOG3571|consen 277 GGIYVGSIMKGGAVALDGRIEPGDMILQVNEVSFENMSNDQAVRVLREAV---------------SRPGPIKLTVAK-CW 340 (626)
T ss_pred CceEEeeeccCceeeccCccCccceEEEeeecchhhcCchHHHHHHHHHh---------------ccCCCeEEEEee-cc
Confidence 6899994 888888887 9999999999999998875 8888888863 234667788877 77
Q ss_pred CCCCeeEEecC
Q 001280 473 YAPPQIYTRND 483 (1108)
Q Consensus 473 ~~~~~~~~r~d 483 (1108)
-...+-+.+.+
T Consensus 341 DP~~q~~fTip 351 (626)
T KOG3571|consen 341 DPNPQSYFTIP 351 (626)
T ss_pred CCCCcccccCC
Confidence 65555544443
No 129
>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=75.36 E-value=26 Score=43.25 Aligned_cols=125 Identities=17% Similarity=0.191 Sum_probs=68.9
Q ss_pred eCCCcEEEEEECCCC-----CCcccc--cceeccccCCC------ccCCCCCEEEEEeeCCCCCceeeeeeEeccccccc
Q 001280 698 HPVHNFALIAYDPSS-----LGVAGA--SVVRAAELLPE------PALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALN 764 (1108)
Q Consensus 698 dp~~dlAilk~d~~~-----l~~~~~--~~v~~~~l~~~------~~l~~G~~V~~vG~p~~~~~~~~~~~Vt~~~~~~~ 764 (1108)
....|+|||+++... +..... .+=.++.|.+. ..+..|..|+=+|..-++. +|.|.++.. ..
T Consensus 540 ~~LsD~AIIkV~~~~~~~N~LGddi~f~~~dP~l~f~NlyV~~~~~~~~~G~~VfK~GrTTgyT----~G~lNg~kl-vy 614 (695)
T PF08192_consen 540 KRLSDWAIIKVNKERKCQNYLGDDIQFNEPDPTLMFQNLYVREVVSNLVPGMEVFKVGRTTGYT----TGILNGIKL-VY 614 (695)
T ss_pred ccccceEEEEeCCCceecCCCCccccccCCCccccccccchhhhhhccCCCCeEEEecccCCcc----ceEecceEE-EE
Confidence 456799999998653 221000 01112233221 2467899999999887774 555554321 11
Q ss_pred cCCCCCCccccccceEEEEe---ccc--CCCCCceEEcCCee------EEEEEeeccccccccCCCCCcceeEecccHHH
Q 001280 765 ISSADCPRYRAMNMEVIELD---TDF--GSTFSGVLTDEHGR------VQAIWGSFSTQVKFGCSSSEDHQFVRGIPIYT 833 (1108)
Q Consensus 765 i~~~~~~~y~~~~~~~I~~d---~~i--g~~sGGpL~d~~G~------VvGi~~~~~~~~~~~~~~~~~~~~~~aipi~~ 833 (1108)
...... .-.+++-.. ..+ ++.||..+++.-+. |+||..+|-++ -.+|.+-.|+..
T Consensus 615 w~dG~i-----~s~efvV~s~~~~~Fa~~GDSGS~VLtk~~d~~~gLgvvGMlhsydge---------~kqfglftPi~~ 680 (695)
T PF08192_consen 615 WADGKI-----QSSEFVVSSDNNPAFASGGDSGSWVLTKLEDNNKGLGVVGMLHSYDGE---------QKQFGLFTPINE 680 (695)
T ss_pred ecCCCe-----EEEEEEEecCCCccccCCCCcccEEEecccccccCceeeEEeeecCCc---------cceeeccCcHHH
Confidence 111111 112333322 123 33578888786555 99999998654 356655678777
Q ss_pred HHHHHHHH
Q 001280 834 ISRVLDKI 841 (1108)
Q Consensus 834 i~~vl~~l 841 (1108)
|+.=|++.
T Consensus 681 il~rl~~v 688 (695)
T PF08192_consen 681 ILDRLEEV 688 (695)
T ss_pred HHHHHHHh
Confidence 76655554
No 130
>KOG3551 consensus Syntrophins (type beta) [Extracellular structures]
Probab=75.16 E-value=2.8 Score=47.56 Aligned_cols=51 Identities=22% Similarity=0.363 Sum_probs=44.6
Q ss_pred EEEEEecCCChhhhcC-CCCCCEEEEECCeecCCH--HHHHHHHHcCCCCceEEEE
Q 001280 1009 VYVARWCHGSPVHRYG-LYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVR 1061 (1108)
Q Consensus 1009 V~V~~v~~gSpA~~~G-L~~gD~I~~VNg~~v~~l--~~f~~~v~~~~~~~~v~l~ 1061 (1108)
++|+.+.+|-.|+|.+ |..||.|++|||....+. |+.++++|. .|+.|.+.
T Consensus 112 IlISKIFkGlAADQt~aL~~gDaIlSVNG~dL~~AtHdeAVqaLKr--aGkeV~le 165 (506)
T KOG3551|consen 112 ILISKIFKGLAADQTGALFLGDAILSVNGEDLRDATHDEAVQALKR--AGKEVLLE 165 (506)
T ss_pred eehhHhccccccccccceeeccEEEEecchhhhhcchHHHHHHHHh--hCceeeee
Confidence 5899999999999985 899999999999998877 888889886 58888776
No 131
>KOG3549 consensus Syntrophins (type gamma) [Extracellular structures]
Probab=73.94 E-value=4.2 Score=45.43 Aligned_cols=53 Identities=21% Similarity=0.354 Sum_probs=40.6
Q ss_pred EEEEEecCCCcccc-C-CCCCCEEEEECCEEeCChhHHHHH-HhcCCCCeEEEEEE
Q 001280 300 LVVDSVVPGGPAHL-R-LEPGDVLVRVNGEVITQFLKLETL-LDDGVDKNIELLIE 352 (1108)
Q Consensus 300 lVv~~V~~~spA~~-g-L~~GD~Il~VnG~~v~~~~~l~~~-l~~~~g~~v~l~V~ 352 (1108)
+||+.+..+-.|+. | |-.||-|+.|||..|+.-.+-+.. +..+.|+.|+++|.
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 45588888888888 4 889999999999999886554432 24567888888774
No 132
>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=72.14 E-value=10 Score=35.82 Aligned_cols=52 Identities=10% Similarity=0.117 Sum_probs=32.7
Q ss_pred EEEEeCCCcEEEEcccccCCCCeEEEEEecCCeEEeEEEEEEcCCCceEEEEECCCCccccccc
Q 001280 72 GFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYPIYRDPVHDFGFFRYDPSAIQFLNYD 135 (1108)
Q Consensus 72 GfvV~~~~G~ILTn~HVV~~~~~~~~v~~~d~~~~~a~vv~~d~~~DlAlLk~d~~~~~~~~~~ 135 (1108)
++-|. +|..+|+.||.+.... + ++.++ +++ ...-|+++++.....++.++++
T Consensus 3 avHIG--nG~~vt~tHva~~~~~-v-----~g~~f--~~~--~~~ge~~~v~~~~~~~p~~~ig 54 (105)
T PF03510_consen 3 AVHIG--NGRYVTVTHVAKSSDS-V-----DGQPF--KIV--KTDGELCWVQSPLVHLPAAQIG 54 (105)
T ss_pred eEEeC--CCEEEEEEEEeccCce-E-----cCcCc--EEE--EeccCEEEEECCCCCCCeeEec
Confidence 45565 7999999999994321 1 22222 223 3445999999987665655554
No 133
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=71.59 E-value=5.5 Score=45.53 Aligned_cols=46 Identities=22% Similarity=0.258 Sum_probs=39.3
Q ss_pred CCCceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChhHHHHHHhc
Q 001280 295 GETGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFLKLETLLDD 341 (1108)
Q Consensus 295 ~~~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~~l~~~l~~ 341 (1108)
...|+.| .+|...||+.. ||.+||+|.++||-+|.+.++..+-++.
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 3467777 69999999988 9999999999999999998887776644
No 134
>KOG3651 consensus Protein kinase C, alpha binding protein [Signal transduction mechanisms]
Probab=71.45 E-value=9.1 Score=42.07 Aligned_cols=57 Identities=16% Similarity=0.134 Sum_probs=41.9
Q ss_pred CccceEEEEeecCCCHHhHh--ccCCCEEEEECCEEcCChh--HHHHHHHhccCCCCCCCeEEEEEE
Q 001280 896 VRRQVLRVKGCLAGSKAENM--LEQGDMMLAINKQPVTCFH--DIENACQALDKDGEDNGKLDITIF 958 (1108)
Q Consensus 896 ~~~~~~~V~~V~~~s~A~~a--L~~GDiIlsVnG~~V~~~~--dl~~~l~~~~~g~~~~~~v~l~V~ 958 (1108)
.....++|..|-.++||++- ++.||.|++|||..|..-. ++..+++... +.+.+.+.
T Consensus 27 pyCPClYiVQvFD~tPAa~dG~i~~GDEi~avNg~svKGktKveVAkmIQ~~~------~eV~IhyN 87 (429)
T KOG3651|consen 27 PYCPCLYIVQVFDKTPAAKDGRIRCGDEIVAVNGISVKGKTKVEVAKMIQVSL------NEVKIHYN 87 (429)
T ss_pred CcCCeEEEEEeccCCchhccCccccCCeeEEecceeecCccHHHHHHHHHHhc------cceEEEeh
Confidence 34567889999999999976 9999999999999998654 4445553222 34666654
No 135
>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=69.55 E-value=2.9 Score=49.21 Aligned_cols=30 Identities=33% Similarity=0.489 Sum_probs=24.8
Q ss_pred EEEEeeecCCCCCCCceecccCcEEEEeec
Q 001280 190 YMQAASGTKGGSSGSPVIDWQGRAVALNAG 219 (1108)
Q Consensus 190 ~i~~~a~~~~G~SGgPv~n~~G~vVGi~~~ 219 (1108)
++.-...+.+|+||+.|+|.+|++|||..|
T Consensus 345 y~~~~~~l~gGaSGS~V~n~~~~lvGIy~g 374 (374)
T PF01732_consen 345 YLIDNYSLGGGASGSMVINQNNELVGIYFG 374 (374)
T ss_pred hcccccCCCCCCCcCeEECCCCCEEEEeCC
Confidence 344455788999999999999999999753
No 136
>KOG0609 consensus Calcium/calmodulin-dependent serine protein kinase/membrane-associated guanylate kinase [Signal transduction mechanisms]
Probab=69.43 E-value=8.6 Score=45.94 Aligned_cols=52 Identities=31% Similarity=0.441 Sum_probs=41.1
Q ss_pred EEEEEecCCCcccc-C-CCCCCEEEEECCEEeCCh--hHHHHHHhcCCCCeEEEEEE
Q 001280 300 LVVDSVVPGGPAHL-R-LEPGDVLVRVNGEVITQF--LKLETLLDDGVDKNIELLIE 352 (1108)
Q Consensus 300 lVv~~V~~~spA~~-g-L~~GD~Il~VnG~~v~~~--~~l~~~l~~~~g~~v~l~V~ 352 (1108)
.+|.++..|+-+++ | |..||.|++|||..+.+- .++..+|....| .|++.|.
T Consensus 148 ~~vARI~~GG~~~r~glL~~GD~i~EvNGi~v~~~~~~e~q~~l~~~~G-~itfkii 203 (542)
T KOG0609|consen 148 VVVARIMHGGMADRQGLLHVGDEILEVNGISVANKSPEELQELLRNSRG-SITFKII 203 (542)
T ss_pred cEEeeeccCCcchhccceeeccchheecCeecccCCHHHHHHHHHhCCC-cEEEEEc
Confidence 44479999999999 4 999999999999999764 678888866544 5666654
No 137
>KOG0606 consensus Microtubule-associated serine/threonine kinase and related proteins [Signal transduction mechanisms; General function prediction only]
Probab=63.37 E-value=10 Score=49.04 Aligned_cols=48 Identities=35% Similarity=0.520 Sum_probs=37.0
Q ss_pred EEEecCCCcccc-CCCCCCEEEEECCEEeCChhHHH--HHHhcCCCCeEEEE
Q 001280 302 VDSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLE--TLLDDGVDKNIELL 350 (1108)
Q Consensus 302 v~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~--~~l~~~~g~~v~l~ 350 (1108)
|..|.+++||.. ||++||.|+.+||+++....+-+ ++|.. .|..+.+.
T Consensus 662 v~sv~egsPA~~agls~~DlIthvnge~v~gl~H~ev~~Lll~-~gn~v~~~ 712 (1205)
T KOG0606|consen 662 VGSVEEGSPAFEAGLSAGDLITHVNGEPVHGLVHTEVMELLLK-SGNKVTLR 712 (1205)
T ss_pred eeeecCCCCccccCCCccceeEeccCcccchhhHHHHHHHHHh-cCCeeEEE
Confidence 378899999998 99999999999999998875533 44443 35555554
No 138
>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=60.06 E-value=44 Score=34.98 Aligned_cols=80 Identities=21% Similarity=0.151 Sum_probs=51.0
Q ss_pred hhHHHHHHh-cCCCCeEEEEEEE---CCEEEEEEE---cccccccCCCcccccCCeEEccCCHHHhhccCcCCCeEEEEC
Q 001280 332 FLKLETLLD-DGVDKNIELLIER---GGISMTVNL---VQDLHSITPDYFLEVSGAVIHPLSYQQARNFRFPCGLVYVAE 404 (1108)
Q Consensus 332 ~~~l~~~l~-~~~g~~v~l~V~R---~g~~~~~~v---~~~~~~~~~~~~~~~~G~~~~~l~~q~~~~~~~~~~gv~v~~ 404 (1108)
..++.+.+. ...|+.+.++|.+ .|+..+.++ +.+-. +...-+.-.|+.+.+. .+.+.|.+
T Consensus 62 ~~~~~~~~~~~~~g~~lrl~V~G~~~~G~~~~k~v~lpl~~~~--~g~eRL~~~GL~l~~e-----------~~~~~Vd~ 128 (183)
T PF11874_consen 62 PSELVQVAEQLPPGSSLRLRVEGPDFEGDPVTKTVLLPLGDGA--DGEERLEAAGLTLMEE-----------GGKVIVDE 128 (183)
T ss_pred HHHHHHHHhcCCCCCEEEEEEEccCCCCCceEEEEEEEcCCCC--CHHHHHHhCCCEEEee-----------CCEEEEEe
Confidence 345666664 4778999999998 466555544 33221 2222233446665532 14566774
Q ss_pred --CCChhHHcCCCCCCEEEEeC
Q 001280 405 --PGYMLFRAGVPRHAIIKKFA 424 (1108)
Q Consensus 405 --~~~~a~~aGl~~Gd~I~~Vn 424 (1108)
.||+|+++|+.-+|.|.+|-
T Consensus 129 v~fgS~A~~~g~d~d~~I~~v~ 150 (183)
T PF11874_consen 129 VEFGSPAEKAGIDFDWEITEVE 150 (183)
T ss_pred cCCCCHHHHcCCCCCcEEEEEE
Confidence 69999999999999888763
No 139
>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=58.98 E-value=24 Score=38.43 Aligned_cols=56 Identities=23% Similarity=0.353 Sum_probs=47.4
Q ss_pred EEEEEecCCChhhhc-CCCCCCEEEEECCeecCCH--HHHHHHHHcCCCCceEEEEEEE
Q 001280 1009 VYVARWCHGSPVHRY-GLYALQWIVEINGKRTPDL--EAFVNVTKEIEHGEFVRVRTVH 1064 (1108)
Q Consensus 1009 V~V~~v~~gSpA~~~-GL~~gD~I~~VNg~~v~~l--~~f~~~v~~~~~~~~v~l~~v~ 1064 (1108)
.+|..+.+||--.+. .+..||.|.+|||+.+-.+ .+..+.+++++.++.++|+++.
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 377888888877765 4689999999999999888 5778999999999999999754
No 140
>KOG3549 consensus Syntrophins (type gamma) [Extracellular structures]
Probab=56.66 E-value=14 Score=41.48 Aligned_cols=54 Identities=19% Similarity=0.156 Sum_probs=39.1
Q ss_pred EEEEeecCCCHHhHh--ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEE
Q 001280 901 LRVKGCLAGSKAENM--LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIF 958 (1108)
Q Consensus 901 ~~V~~V~~~s~A~~a--L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~ 958 (1108)
++|+++..+-.|+.. |=.||-|+.|||..|+.-.+-+..-.+...| +.++++|.
T Consensus 82 vviSkI~kdQaAd~tG~LFvGDAilqvNGi~v~~c~HeevV~iLRNAG----deVtlTV~ 137 (505)
T KOG3549|consen 82 VVISKIYKDQAADITGQLFVGDAILQVNGIYVTACPHEEVVNILRNAG----DEVTLTVK 137 (505)
T ss_pred EEeehhhhhhhhhhcCceEeeeeeEEeccEEeecCChHHHHHHHHhcC----CEEEEEeH
Confidence 568888888877765 8899999999999999865433222223344 77787775
No 141
>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=55.21 E-value=7.9 Score=37.84 Aligned_cols=113 Identities=19% Similarity=0.230 Sum_probs=56.8
Q ss_pred EEEEEeCCCcEEEEcccccCCCCeEEEEEecCCeEEeEEEEEEcCCCceEEEEECCCCcccccccCCCCCCcccCCCCEE
Q 001280 71 TGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYPIYRDPVHDFGFFRYDPSAIQFLNYDEIPLAPEAACVGLEI 150 (1108)
Q Consensus 71 SGfvV~~~~G~ILTn~HVV~~~~~~~~v~~~d~~~~~a~vv~~d~~~DlAlLk~d~~~~~~~~~~~l~l~~~~~~~G~~V 150 (1108)
-|+.| +|.+-|.+|-.... .+--..| +....+.+...|+..-...+..- .+.+.... -..+
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---SLTPCTCG------SSDL 75 (148)
T ss_dssp EEEEE---TTEEEEEHHHHTTS----EEEBTTS---EB-ESEEETTTTEEEEE-STTB-----BBB-SSS------SSEE
T ss_pred ehhEE---ccEEEEEEecCCcc----cccCCCC---cceEeEEcCCCCCcccccccccc---cCCccccC------CccE
Confidence 46666 47999999976631 1211222 34556788889998877754321 12222111 2356
Q ss_pred EEEecCCCCCCeEEEEEEEEecCCCCCCCCCCcccccceEEEEeeecCCCCCCCceecccCcEEEEeec
Q 001280 151 RVVGNDSGEKVSILAGTLARLDRDAPHYKKDGYNDFNTFYMQAASGTKGGSSGSPVIDWQGRAVALNAG 219 (1108)
Q Consensus 151 ~~iG~p~g~~~si~~G~is~~~~~~~~~~~~~~~~~~~~~i~~~a~~~~G~SGgPv~n~~G~vVGi~~~ 219 (1108)
++|-+... +..+ .+.+. .+.. -..-.-.+...|+||||++=.+|.+|||..+
T Consensus 76 ylVtr~~~----v~p~--rr~gd--------~~~~---L~sp~pis~lkGSSGgPiLC~~GH~vG~f~a 127 (148)
T PF02907_consen 76 YLVTRDAD----VIPV--RRRGD--------SRAS---LLSPRPISDLKGSSGGPILCPSGHAVGMFRA 127 (148)
T ss_dssp EEE-TTS-----EEEE--EEEST--------TEEE---EEEEEEHHHHTT-TT-EEEETTSEEEEEEEE
T ss_pred EEEeccCc----Eeee--EEcCC--------CceE---ecCCceeEEEecCCCCcccCCCCCEEEEEEE
Confidence 66654432 1121 11110 0000 0011222345799999999999999999744
No 142
>COG5233 GRH1 Peripheral Golgi membrane protein [Intracellular trafficking and secretion]
Probab=50.37 E-value=35 Score=38.11 Aligned_cols=68 Identities=13% Similarity=-0.005 Sum_probs=43.6
Q ss_pred cCCChhhhcCCCCC-CEEE-EECCeecCCHHHHHHHHHcCCCCceEEEEE-EEeCCeEEEEEEEeCCccCc
Q 001280 1015 CHGSPVHRYGLYAL-QWIV-EINGKRTPDLEAFVNVTKEIEHGEFVRVRT-VHLNGKPRVLTLKQDLHYWP 1082 (1108)
Q Consensus 1015 ~~gSpA~~~GL~~g-D~I~-~VNg~~v~~l~~f~~~v~~~~~~~~v~l~~-v~rdg~~~~~~lk~d~~y~p 1082 (1108)
.+++|++.++|.|. |+|. .=+|++..--+-.++=+..++-+-...|.+ ...+...+.+|+..+.|+-|
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 68899999999774 3444 567888755544444444446566666642 23366778888877766544
No 143
>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=50.33 E-value=12 Score=36.89 Aligned_cols=28 Identities=25% Similarity=0.519 Sum_probs=18.1
Q ss_pred EEEEecccCCCCCceEEcCCeeEEEEEee
Q 001280 780 VIELDTDFGSTFSGVLTDEHGRVQAIWGS 808 (1108)
Q Consensus 780 ~I~~d~~ig~~sGGpL~d~~G~VvGi~~~ 808 (1108)
++.+|-.-|+ ||-|++|.+|+|+||-..
T Consensus 89 ~~~~d~~~Gs-SGSpi~n~~g~ivGlYg~ 116 (132)
T PF00949_consen 89 AIDLDFPKGS-SGSPIFNQNGEIVGLYGN 116 (132)
T ss_dssp EE---S-TTG-TT-EEEETTSCEEEEEEE
T ss_pred eeecccCCCC-CCCceEcCCCcEEEEEcc
Confidence 3445544455 899999999999999654
No 144
>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=46.64 E-value=27 Score=37.14 Aligned_cols=56 Identities=20% Similarity=0.322 Sum_probs=44.4
Q ss_pred ceEEEEeeecCCCCCCCceecc----cCcEEEEeecccCCCCcccccCh--HHHHHHHHHHH
Q 001280 188 TFYMQAASGTKGGSSGSPVIDW----QGRAVALNAGSKSSSASAFFLPL--ERVVRALRFLQ 243 (1108)
Q Consensus 188 ~~~i~~~a~~~~G~SGgPv~n~----~G~vVGi~~~~~~~~~~~falPi--~~i~~~l~~l~ 243 (1108)
...++..++...|+-|||++=. --+++||+.++..+.+.+||-++ +.+++++..|.
T Consensus 168 r~gleY~~~t~~GdCGs~i~~~~t~~~RKIvGiHVAG~~~~~~gYAe~itQEDL~~A~~~l~ 229 (231)
T PF12381_consen 168 RQGLEYQMPTMNGDCGSPIVRNNTQMVRKIVGIHVAGSANHAMGYAESITQEDLMRAINKLE 229 (231)
T ss_pred eeeeeEECCCcCCCccceeeEcchhhhhhhheeeecccccccceehhhhhHHHHHHHHHhhc
Confidence 3456888899999999999732 36899999999887888998555 67888877764
No 145
>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=45.10 E-value=73 Score=37.20 Aligned_cols=136 Identities=24% Similarity=0.354 Sum_probs=68.4
Q ss_pred cEEEEEEEeCCCcEEEEcccccCCCCeEEEEEecCCeEEeEEEEEEcCCCceEEEEECCCCcccccccCCCCCCcccCCC
Q 001280 68 SYATGFVVDKRRGIILTNRHVVKPGPVVAEAMFVNREEIPVYPIYRDPVHDFGFFRYDPSAIQFLNYDEIPLAPEAACVG 147 (1108)
Q Consensus 68 ~~GSGfvV~~~~G~ILTn~HVV~~~~~~~~v~~~d~~~~~a~vv~~d~~~DlAlLk~d~~~~~~~~~~~l~l~~~~~~~G 147 (1108)
+.|-||-|+++ +++|+-||++.+...++= ++..-+..+..-+|+-++|... +.+ ++.-+-| .+....|
T Consensus 379 GsGWGfWVS~~--lfITttHViP~g~~E~FG-------v~i~~i~vh~sGeF~~~rFpk~-iRP-DvtgmiL-EeGapEG 446 (535)
T PF05416_consen 379 GSGWGFWVSPT--LFITTTHVIPPGAKEAFG-------VPISQIQVHKSGEFCRFRFPKP-IRP-DVTGMIL-EEGAPEG 446 (535)
T ss_dssp TTEEEEESSSS--EEEEEGGGS-STTSEETT-------EECGGEEEEEETTEEEEEESS--SST-TS---EE--SS--TT
T ss_pred CCceeeeecce--EEEEeeeecCCcchhhhC-------CChhHeEEeeccceEEEecCCC-CCC-Cccceee-ccCCCCc
Confidence 56889999976 999999999976543321 1222345566678888888532 211 2222111 2234455
Q ss_pred CEEEE-EecCCCCC--CeEEEEEEEEecCCCCCCCCCCcccccceEEEE-------eeecCCCCCCCceecccCc---EE
Q 001280 148 LEIRV-VGNDSGEK--VSILAGTLARLDRDAPHYKKDGYNDFNTFYMQA-------ASGTKGGSSGSPVIDWQGR---AV 214 (1108)
Q Consensus 148 ~~V~~-iG~p~g~~--~si~~G~is~~~~~~~~~~~~~~~~~~~~~i~~-------~a~~~~G~SGgPv~n~~G~---vV 214 (1108)
.-..+ |=.|.|+- +.+..|..+...-.-...+ . ...++.+ |-.+.||.-|.|-+=..|+ |+
T Consensus 447 tV~siLiKR~sGEllpLAvRMgt~AsmkIqgr~v~-----G-Q~GMLLTGaNAK~mDLGT~PGDCGcPYvyKrgNd~VV~ 520 (535)
T PF05416_consen 447 TVCSILIKRPSGELLPLAVRMGTHASMKIQGRTVH-----G-QMGMLLTGANAKGMDLGTIPGDCGCPYVYKRGNDWVVI 520 (535)
T ss_dssp -EEEEEEE-TTSBEEEEEEEEEEEEEEEETTEEEE-----E-EEEEETTSTT-SSTTTS--TTGTT-EEEEEETTEEEEE
T ss_pred eEEEEEEEcCCccchhhhhhhccceeEEEcceeec-----c-eeeeeeecCCccccccCCCCCCCCCceeeecCCcEEEE
Confidence 55443 34666644 4455565544321100000 0 0111111 2346789999999876664 88
Q ss_pred EEeeccc
Q 001280 215 ALNAGSK 221 (1108)
Q Consensus 215 Gi~~~~~ 221 (1108)
|++++..
T Consensus 521 GVH~AAt 527 (535)
T PF05416_consen 521 GVHAAAT 527 (535)
T ss_dssp EEEEEE-
T ss_pred EEEehhc
Confidence 9987643
No 146
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=44.50 E-value=37 Score=30.26 Aligned_cols=48 Identities=27% Similarity=0.492 Sum_probs=33.0
Q ss_pred EEeEEEEEeeCCCcEEEEEECCCCCCcccccceeccccCCCccCCCCCEEEE-EeeC
Q 001280 689 EIPGEVVFLHPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYL-VGLS 744 (1108)
Q Consensus 689 ~~~a~vv~~dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~-vG~p 744 (1108)
-+|++|+..+...++|++.+-.--- .|. +.|-++ .++.||.|++ +||.
T Consensus 4 aiPgqI~~I~~~~~~A~Vd~gGvkr------eV~-l~Lv~~-~v~~GdyVLVHvGfA 52 (82)
T COG0298 4 AIPGQIVEIDDNNHLAIVDVGGVKR------EVN-LDLVGE-EVKVGDYVLVHVGFA 52 (82)
T ss_pred ccccEEEEEeCCCceEEEEeccEeE------EEE-eeeecC-ccccCCEEEEEeeEE
Confidence 4789999999988899999854211 111 233333 3799999998 6764
No 147
>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=34.52 E-value=44 Score=32.61 Aligned_cols=33 Identities=9% Similarity=0.125 Sum_probs=25.5
Q ss_pred ceEEEEeeecCCCCCCCceecccCcEEEEeeccc
Q 001280 188 TFYMQAASGTKGGSSGSPVIDWQGRAVALNAGSK 221 (1108)
Q Consensus 188 ~~~i~~~a~~~~G~SGgPv~n~~G~vVGi~~~~~ 221 (1108)
..++....+..||.-||+|+=..| |+||.+++.
T Consensus 78 ~~~l~g~Gp~~PGdCGg~L~C~HG-ViGi~Tagg 110 (127)
T PF00947_consen 78 YNLLIGEGPAEPGDCGGILRCKHG-VIGIVTAGG 110 (127)
T ss_dssp ECEEEEE-SSSTT-TCSEEEETTC-EEEEEEEEE
T ss_pred cCceeecccCCCCCCCceeEeCCC-eEEEEEeCC
Confidence 446778889999999999995555 999998864
No 148
>KOG4407 consensus Predicted Rho GTPase-activating protein [General function prediction only]
Probab=33.89 E-value=28 Score=45.67 Aligned_cols=87 Identities=7% Similarity=0.063 Sum_probs=61.3
Q ss_pred EEecCCCcccc-CCCCCCEEEEECCEEeCChhHHHHHHhcCCCCeEEEEEEECCEEEEEEEcccccccCCCcccccCCeE
Q 001280 303 DSVVPGGPAHL-RLEPGDVLVRVNGEVITQFLKLETLLDDGVDKNIELLIERGGISMTVNLVQDLHSITPDYFLEVSGAV 381 (1108)
Q Consensus 303 ~~V~~~spA~~-gL~~GD~Il~VnG~~v~~~~~l~~~l~~~~g~~v~l~V~R~g~~~~~~v~~~~~~~~~~~~~~~~G~~ 381 (1108)
..+..++++.. |+-.||.|+.|||..+.+-..+--.+..+. +
T Consensus 101 ~Q~~s~~~~~nsG~~s~~~v~~itG~e~~~~TS~~~~~vk~~-e------------------------------------ 143 (1973)
T KOG4407|consen 101 PQEASSAAGSNSGSSSSVGVAGITGLEPTSPTSLPPYQVKAM-E------------------------------------ 143 (1973)
T ss_pred chhcccCcccccCcccccceeeecccccCCCccccHHHHhhh-h------------------------------------
Confidence 34556788888 999999999999998876544332222110 0
Q ss_pred EccCCHHHhhccCcCCCeEEEE--CCCChhHHcCCCCCCEEEEeCCeecCCHH--HHHHHHHhcCC
Q 001280 382 IHPLSYQQARNFRFPCGLVYVA--EPGYMLFRAGVPRHAIIKKFAGEEISRLE--DLISVLSKLSR 443 (1108)
Q Consensus 382 ~~~l~~q~~~~~~~~~~gv~v~--~~~~~a~~aGl~~Gd~I~~Vng~~v~~l~--~~~~~i~~~~~ 443 (1108)
-+|+. ++.+++..+.|+-||.|+.||++|+..+. +.+..++..+.
T Consensus 144 -----------------T~~~~eV~~n~~~~~a~LQ~~~~V~~v~~q~~A~i~~s~~~S~~~qt~~ 192 (1973)
T KOG4407|consen 144 -----------------TIFIKEVQANGPAHYANLQTGDRVLMVNNQPIAGIAYSTIVSMIKQTPA 192 (1973)
T ss_pred -----------------hhhhhhhccCChhHHHhhhccceeEEeecCcccchhhhhhhhhhccCCC
Confidence 01111 36788888899999999999999998875 66666666543
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=31.53 E-value=1.1e+02 Score=26.21 Aligned_cols=32 Identities=16% Similarity=0.162 Sum_probs=26.3
Q ss_pred eEEEEeecCCeEEeEEEEEeeCCCcEEEEEECC
Q 001280 678 DVMLSFAAFPIEIPGEVVFLHPVHNFALIAYDP 710 (1108)
Q Consensus 678 ~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~d~ 710 (1108)
.+.++... |.+++|+|+.+|....+.|||-..
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 35566664 889999999999999999998544
No 150
>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=30.69 E-value=41 Score=36.74 Aligned_cols=55 Identities=18% Similarity=0.260 Sum_probs=41.8
Q ss_pred eEEEEeecCCCHHhHh--ccCCCEEEEECCEEcCChhHHH--HHHHhccCCCCCCCeEEEEEE
Q 001280 900 VLRVKGCLAGSKAENM--LEQGDMMLAINKQPVTCFHDIE--NACQALDKDGEDNGKLDITIF 958 (1108)
Q Consensus 900 ~~~V~~V~~~s~A~~a--L~~GDiIlsVnG~~V~~~~dl~--~~l~~~~~g~~~~~~v~l~V~ 958 (1108)
-..|+++.++|..... ++.||.|-+|||+.|-.+++.+ .+|..+..| ++.++.+.
T Consensus 150 yAFIKrIkegsvidri~~i~VGd~IEaiNge~ivG~RHYeVArmLKel~rg----e~ftlrLi 208 (334)
T KOG3938|consen 150 YAFIKRIKEGSVIDRIEAICVGDHIEAINGESIVGKRHYEVARMLKELPRG----ETFTLRLI 208 (334)
T ss_pred eeeeEeecCCchhhhhhheeHHhHHHhhcCccccchhHHHHHHHHHhcccC----CeeEEEee
Confidence 3458899999998876 9999999999999999998865 455444444 55555444
No 151
>KOG1738 consensus Membrane-associated guanylate kinase-interacting protein/connector enhancer of KSR-like [Nucleotide transport and metabolism]
Probab=27.95 E-value=34 Score=41.81 Aligned_cols=37 Identities=19% Similarity=0.427 Sum_probs=32.8
Q ss_pred CceEEEEEecCCCcccc--CCCCCCEEEEECCEEeCChh
Q 001280 297 TGLLVVDSVVPGGPAHL--RLEPGDVLVRVNGEVITQFL 333 (1108)
Q Consensus 297 ~G~lVv~~V~~~spA~~--gL~~GD~Il~VnG~~v~~~~ 333 (1108)
.|.-++..+.+++||+. .|.+||.++.||+..+..|+
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 56666788999999998 89999999999999998884
No 152
>KOG4371 consensus Membrane-associated protein tyrosine phosphatase PTP-BAS and related proteins, contain FERM domain [Signal transduction mechanisms]
Probab=27.01 E-value=1.5e+02 Score=38.70 Aligned_cols=115 Identities=14% Similarity=0.115 Sum_probs=59.6
Q ss_pred CCCCCCEEEEECCEEeCChhHHHHHH-hcCCCCeEEEEEEECCEE-EEEEEcccccccCCCcccccCCeEEccCCHHHh-
Q 001280 314 RLEPGDVLVRVNGEVITQFLKLETLL-DDGVDKNIELLIERGGIS-MTVNLVQDLHSITPDYFLEVSGAVIHPLSYQQA- 390 (1108)
Q Consensus 314 gL~~GD~Il~VnG~~v~~~~~l~~~l-~~~~g~~v~l~V~R~g~~-~~~~v~~~~~~~~~~~~~~~~G~~~~~l~~q~~- 390 (1108)
-|+.||+|+.+||..+..-.+....- ....|+.|.|-|+|..-. ........+.. +..+.-.-+...+..-+..
T Consensus 1186 d~~~g~~l~~~n~i~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~d~~~~s~~~~---~~~l~~~~~~~~p~~~~~~~ 1262 (1332)
T KOG4371|consen 1186 DIRVGDVLLYVNGIAVEGKVHQEVVAMLRGGGDRVVLGVQRPPPAYSDQHHASSTSA---SAPLISVMLLKKPMATLGLS 1262 (1332)
T ss_pred CcchhhhhhhccceeeechhhHHHHHHHhccCceEEEEeecCCcccccchhhhhhcc---cchhhhheeeeccccccccc
Confidence 79999999999998777655544333 345678899999995332 11111111100 0000000011111111000
Q ss_pred hccCcCCCeEEEEC--CCChhH-HcCCCCCCEEEEeCCeecCCH
Q 001280 391 RNFRFPCGLVYVAE--PGYMLF-RAGVPRHAIIKKFAGEEISRL 431 (1108)
Q Consensus 391 ~~~~~~~~gv~v~~--~~~~a~-~aGl~~Gd~I~~Vng~~v~~l 431 (1108)
-.-..+.+|+++.. ..+.|. ...++.||.+.+.+|+++--.
T Consensus 1263 ~~~~~~s~~~~~~~~~~~~~a~~~~~~r~g~~~~~~~~~~~~~~ 1306 (1332)
T KOG4371|consen 1263 LAKRTMSDGIFIRNIAQDSAASSEGTLRVGDRLVSLDGEPVDGF 1306 (1332)
T ss_pred ccccCcCCceeeecccccccccccccccccceeeccCCccCCCC
Confidence 00011235677663 222222 223899999999999998544
No 153
>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=26.73 E-value=87 Score=30.83 Aligned_cols=23 Identities=26% Similarity=0.174 Sum_probs=19.7
Q ss_pred CCCceEEcCCeeEEEEEeecccc
Q 001280 790 TFSGVLTDEHGRVQAIWGSFSTQ 812 (1108)
Q Consensus 790 ~sGGpL~d~~G~VvGi~~~~~~~ 812 (1108)
.||=|++|..|+||||.+.-.++
T Consensus 107 DSGRpi~DNsGrVVaIVLGG~ne 129 (158)
T PF00944_consen 107 DSGRPIFDNSGRVVAIVLGGANE 129 (158)
T ss_dssp STTEEEESTTSBEEEEEEEEEEE
T ss_pred CCCCccCcCCCCEEEEEecCCCC
Confidence 68999999999999998875444
No 154
>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=26.24 E-value=1.3e+02 Score=26.16 Aligned_cols=44 Identities=27% Similarity=0.437 Sum_probs=29.3
Q ss_pred EEeEEEEEeeCCCcEEEEEECCCCCCcccccceeccccCCCccCCCCCEEEEE
Q 001280 689 EIPGEVVFLHPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLV 741 (1108)
Q Consensus 689 ~~~a~vv~~dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~v 741 (1108)
-+|++|+..+..-+.|++.+....-. |. +.|-+ ++++||+|++-
T Consensus 4 ~iP~~Vv~v~~~~~~A~v~~~G~~~~------V~-~~lv~--~v~~Gd~VLVH 47 (68)
T PF01455_consen 4 AIPGRVVEVDEDGGMAVVDFGGVRRE------VS-LALVP--DVKVGDYVLVH 47 (68)
T ss_dssp CEEEEEEEEETTTTEEEEEETTEEEE------EE-GTTCT--SB-TT-EEEEE
T ss_pred cccEEEEEEeCCCCEEEEEcCCcEEE------EE-EEEeC--CCCCCCEEEEe
Confidence 47999999998899999998753111 11 22322 37999999985
No 155
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=26.12 E-value=1e+02 Score=26.62 Aligned_cols=31 Identities=19% Similarity=0.251 Sum_probs=27.0
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 708 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~ 708 (1108)
..|.|.+.+ ++++.|++.++|+..|+.+-..
T Consensus 11 ~~V~V~Lk~-g~~~~G~L~~~D~~mNlvL~~~ 41 (67)
T cd01726 11 RPVVVKLNS-GVDYRGILACLDGYMNIALEQT 41 (67)
T ss_pred CeEEEEECC-CCEEEEEEEEEccceeeEEeeE
Confidence 358899998 9999999999999999987554
No 156
>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=25.32 E-value=1.3e+02 Score=25.21 Aligned_cols=31 Identities=16% Similarity=0.144 Sum_probs=27.0
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 708 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~ 708 (1108)
..+.|.+.+ ++.+.|++.+.|...|+.+-..
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 157
>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=25.06 E-value=1.2e+02 Score=27.11 Aligned_cols=30 Identities=17% Similarity=0.203 Sum_probs=26.4
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEEE
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIA 707 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk 707 (1108)
..+.|.+.+ ++.+.|++.++|...|+.+=.
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 468899998 999999999999999998643
No 158
>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=23.37 E-value=1.2e+02 Score=27.16 Aligned_cols=31 Identities=10% Similarity=0.145 Sum_probs=26.4
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 708 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~ 708 (1108)
..+.|++.+ ++.+.|.+.++|...|+.|=..
T Consensus 11 ~~V~V~l~d-gR~~~G~L~~~D~~~NlVL~~~ 41 (79)
T cd01717 11 YRLRVTLQD-GRQFVGQFLAFDKHMNLVLSDC 41 (79)
T ss_pred CEEEEEECC-CcEEEEEEEEEcCccCEEcCCE
Confidence 357899998 9999999999999999976443
No 159
>PF09342 DUF1986: Domain of unknown function (DUF1986); InterPro: IPR015420 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found in serine endopeptidases belonging to MEROPS peptidase family S1A (clan PA). It is found in unusual mosaic proteins, which are encoded by the Drosophila nudel gene (see P98159 from SWISSPROT). Nudel is involved in defining embryonic dorsoventral polarity. Three proteases; ndl, gd and snk process easter to create active easter. Active easter defines cell identities along the dorsal-ventral continuum by activating the spz ligand for the Tl receptor in the ventral region of the embryo. Nudel, pipe and windbeutel together trigger the protease cascade within the extraembryonic perivitelline compartment which induces dorsoventral polarity of the Drosophila embryo [].
Probab=23.30 E-value=6.7e+02 Score=27.65 Aligned_cols=90 Identities=14% Similarity=0.195 Sum_probs=53.1
Q ss_pred CccEEEEEEEeCCCcEEEEcccccCCCC---eEEEEEecCCeEE-----------eEEEEEEcCCCceEEEEECCCC-cc
Q 001280 66 GASYATGFVVDKRRGIILTNRHVVKPGP---VVAEAMFVNREEI-----------PVYPIYRDPVHDFGFFRYDPSA-IQ 130 (1108)
Q Consensus 66 ~~~~GSGfvV~~~~G~ILTn~HVV~~~~---~~~~v~~~d~~~~-----------~a~vv~~d~~~DlAlLk~d~~~-~~ 130 (1108)
+...+||++|+++ |||++..++.+-. .-+.+.+..++.+ ...-+..=+..+++||.++.+. +.
T Consensus 26 G~~~CsgvLlD~~--WlLvsssCl~~I~L~~~YvsallG~~Kt~~~v~Gp~EQI~rVD~~~~V~~S~v~LLHL~~~~~fT 103 (267)
T PF09342_consen 26 GRYWCSGVLLDPH--WLLVSSSCLRGISLSHHYVSALLGGGKTYLSVDGPHEQISRVDCFKDVPESNVLLLHLEQPANFT 103 (267)
T ss_pred CeEEEEEEEeccc--eEEEeccccCCcccccceEEEEecCcceecccCCChheEEEeeeeeeccccceeeeeecCcccce
Confidence 5678999999976 9999999998521 1344455544432 2222222377899999997542 21
Q ss_pred -cccccCCCCCCcccCCCCEEEEEecCC
Q 001280 131 -FLNYDEIPLAPEAACVGLEIRVVGNDS 157 (1108)
Q Consensus 131 -~~~~~~l~l~~~~~~~G~~V~~iG~p~ 157 (1108)
++.-.-+|=........+..++||...
T Consensus 104 r~VlP~flp~~~~~~~~~~~CVAVg~d~ 131 (267)
T PF09342_consen 104 RYVLPTFLPETSNENESDDECVAVGHDD 131 (267)
T ss_pred eeecccccccccCCCCCCCceEEEEccc
Confidence 111011111123444556888999776
No 160
>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=22.93 E-value=1.2e+02 Score=26.17 Aligned_cols=31 Identities=19% Similarity=0.261 Sum_probs=27.0
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 708 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~ 708 (1108)
..|.|.+.+ |+.+.|+++++|...|+.+=..
T Consensus 12 ~~V~V~Lk~-g~~~~G~L~~~D~~mNi~L~~~ 42 (68)
T cd01722 12 KPVIVKLKW-GMEYKGTLVSVDSYMNLQLANT 42 (68)
T ss_pred CEEEEEECC-CcEEEEEEEEECCCEEEEEeeE
Confidence 358899998 9999999999999999987554
No 161
>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=22.73 E-value=1.5e+02 Score=26.42 Aligned_cols=31 Identities=10% Similarity=0.038 Sum_probs=26.5
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 708 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~ 708 (1108)
..+.|++.| |+.+.|++.++|...|+.+=..
T Consensus 11 ~~v~V~l~d-gR~~~G~l~~~D~~~NivL~~~ 41 (75)
T cd06168 11 RTMRIHMTD-GRTLVGVFLCTDRDCNIILGSA 41 (75)
T ss_pred CeEEEEEcC-CeEEEEEEEEEcCCCcEEecCc
Confidence 358899998 9999999999999999976443
No 162
>KOG4371 consensus Membrane-associated protein tyrosine phosphatase PTP-BAS and related proteins, contain FERM domain [Signal transduction mechanisms]
Probab=22.42 E-value=1.2e+02 Score=39.56 Aligned_cols=117 Identities=14% Similarity=0.170 Sum_probs=63.8
Q ss_pred ccCCCEEEEECCEEcCChhHHHHHHHhccCCCCCCCeEEEEEEeCCEEEEEEEeecccCCCCCcceeeeccccccCCchh
Q 001280 916 LEQGDMMLAINKQPVTCFHDIENACQALDKDGEDNGKLDITIFRQGREIELQVGTDVRDGNGTTRVINWCGCIVQDPHPA 995 (1108)
Q Consensus 916 L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~g~~~~~~v~l~V~R~g~~~~v~v~~~~~~~~~t~~~~~~~G~~~~~p~~~ 995 (1108)
|+.||+++.+||..+.---.....- .+..+ ++.+.+-|.|..- .....+....... +. ....-.++..|...
T Consensus 1187 ~~~g~~l~~~n~i~~~~~~~~~~~~-~~~~~---~~~~~~~~~r~~~-~~~d~~~~s~~~~--~~-~l~~~~~~~~p~~~ 1258 (1332)
T KOG4371|consen 1187 IRVGDVLLYVNGIAVEGKVHQEVVA-MLRGG---GDRVVLGVQRPPP-AYSDQHHASSTSA--SA-PLISVMLLKKPMAT 1258 (1332)
T ss_pred cchhhhhhhccceeeechhhHHHHH-HHhcc---CceEEEEeecCCc-ccccchhhhhhcc--cc-hhhhheeeeccccc
Confidence 9999999999998877543333222 23333 4789999998532 1122222111100 00 00001122222211
Q ss_pred hhh-c-CCCCCCCCeEEEEEecCCChhhhcC-CCCCCEEEEECCeecCCH
Q 001280 996 VRA-L-GFLPEEGHGVYVARWCHGSPVHRYG-LYALQWIVEINGKRTPDL 1042 (1108)
Q Consensus 996 vr~-~-~~lp~~~~gV~V~~v~~gSpA~~~G-L~~gD~I~~VNg~~v~~l 1042 (1108)
... + ..-++ .|+++..+..++.|.-.| ++.||.+.+.+|+++..+
T Consensus 1259 ~~~~~~~~~~s--~~~~~~~~~~~~~a~~~~~~r~g~~~~~~~~~~~~~~ 1306 (1332)
T KOG4371|consen 1259 LGLSLAKRTMS--DGIFIRNIAQDSAASSEGTLRVGDRLVSLDGEPVDGF 1306 (1332)
T ss_pred ccccccccCcC--CceeeecccccccccccccccccceeeccCCccCCCC
Confidence 110 0 11122 367777777777666554 899999999999998765
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=22.35 E-value=1.1e+02 Score=27.49 Aligned_cols=29 Identities=17% Similarity=0.165 Sum_probs=25.9
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEE
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALI 706 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAil 706 (1108)
..|.|.+.+ ++.+.|++.++|.+.|+.+=
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 468899998 99999999999999999863
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=22.02 E-value=1.5e+02 Score=26.06 Aligned_cols=57 Identities=14% Similarity=0.151 Sum_probs=37.8
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEEEECCCCCCcccccceeccccCCCccCCCCCEEEEEe
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLVG 742 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~vG 742 (1108)
..|.|.+.+ ++.+.|++.++|...|+.+=...... . ....-+++.- +-+|+.|..|+
T Consensus 11 k~V~V~L~~-g~~~~G~L~~~D~~mNlvL~~~~E~~-~-----~~~~~~lg~v--~IRG~~I~~i~ 67 (72)
T cd01719 11 KKLSLKLNG-NRKVSGILRGFDPFMNLVLDDAVEVN-S-----GGEKNNIGMV--VIRGNSIVMLE 67 (72)
T ss_pred CeEEEEECC-CeEEEEEEEEEcccccEEeccEEEEc-c-----CCceeEeceE--EECCCEEEEEE
Confidence 357888998 99999999999999999874431100 0 0011244332 56788888776
No 165
>KOG1738 consensus Membrane-associated guanylate kinase-interacting protein/connector enhancer of KSR-like [Nucleotide transport and metabolism]
Probab=21.76 E-value=1e+02 Score=37.91 Aligned_cols=46 Identities=22% Similarity=0.271 Sum_probs=37.1
Q ss_pred ceEEEEeecCCCHHhHh--ccCCCEEEEECCEEcCChhHHHHHHHhccC
Q 001280 899 QVLRVKGCLAGSKAENM--LEQGDMMLAINKQPVTCFHDIENACQALDK 945 (1108)
Q Consensus 899 ~~~~V~~V~~~s~A~~a--L~~GDiIlsVnG~~V~~~~dl~~~l~~~~~ 945 (1108)
+..+|..+.++|||... |..||.|+.||++.|-.| ++..++..+..
T Consensus 225 g~h~~s~~~e~Spad~~~kI~dgdEv~qiN~qtvVgw-qlk~vV~sL~~ 272 (638)
T KOG1738|consen 225 GPHVTSKIFEQSPADYRQKILDGDEVLQINEQTVVGW-QLKVVVSSLRE 272 (638)
T ss_pred CceeccccccCChHHHhhcccCccceeeecccccccc-hhHhHHhhccc
Confidence 33457788899999976 999999999999999988 57777755543
No 166
>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=21.53 E-value=1.5e+02 Score=26.74 Aligned_cols=31 Identities=16% Similarity=0.183 Sum_probs=26.6
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 708 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~ 708 (1108)
..+.|.+.+ ++.+.|++.++|...|+.+=..
T Consensus 13 k~V~V~l~~-gr~~~G~L~~~D~~mNlvL~~~ 43 (81)
T cd01729 13 KKIRVKFQG-GREVTGILKGYDQLLNLVLDDT 43 (81)
T ss_pred CeEEEEECC-CcEEEEEEEEEcCcccEEecCE
Confidence 458899998 9999999999999999977443
No 167
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=21.21 E-value=1.5e+02 Score=26.00 Aligned_cols=31 Identities=23% Similarity=0.158 Sum_probs=27.3
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 708 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~ 708 (1108)
..|.|.+.+ |+.+.|++.++|+..|+.+=..
T Consensus 15 k~V~V~lk~-g~~~~G~L~~~D~~mNlvL~d~ 45 (72)
T PRK00737 15 SPVLVRLKG-GREFRGELQGYDIHMNLVLDNA 45 (72)
T ss_pred CEEEEEECC-CCEEEEEEEEEcccceeEEeeE
Confidence 358899998 9999999999999999987765
No 168
>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=21.15 E-value=1.5e+02 Score=25.54 Aligned_cols=31 Identities=16% Similarity=0.191 Sum_probs=27.6
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEEEE
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAY 708 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~ 708 (1108)
..|.|.+.+ ++.+.|++.++|...|+.+-..
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 458899998 9999999999999999988765
No 169
>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=20.97 E-value=1.7e+02 Score=26.00 Aligned_cols=60 Identities=15% Similarity=0.078 Sum_probs=38.3
Q ss_pred ceEEEEeecCCeEEeEEEEEeeCCCcEEEEEECCCCCCcccccceeccccCCCccCCCCCEEEEEe
Q 001280 677 SDVMLSFAAFPIEIPGEVVFLHPVHNFALIAYDPSSLGVAGASVVRAAELLPEPALRRGDSVYLVG 742 (1108)
Q Consensus 677 ~~i~V~~~~~~~~~~a~vv~~dp~~dlAilk~d~~~l~~~~~~~v~~~~l~~~~~l~~G~~V~~vG 742 (1108)
..|.|.+.+ ++.+.|.+.++|+..|+.+=......... .......++. -+-+|+.|..+|
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 457899998 99999999999999999774432110000 0000122332 267788888887
No 170
>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=20.89 E-value=6.7e+02 Score=26.87 Aligned_cols=133 Identities=13% Similarity=0.036 Sum_probs=47.6
Q ss_pred EEEEEEEeeCCceEEEEeCceecCCCceEEEEeecCCeEEe---EEEEEeeCCCcEEEEEECCCCCCcccccceeccccC
Q 001280 651 GTGVIIYHSQSMGLVVVDKNTVAISASDVMLSFAAFPIEIP---GEVVFLHPVHNFALIAYDPSSLGVAGASVVRAAELL 727 (1108)
Q Consensus 651 GsG~iId~~~~~G~IlTnr~~V~~~~~~i~V~~~~~~~~~~---a~vv~~dp~~dlAilk~d~~~l~~~~~~~v~~~~l~ 727 (1108)
|.+..|..-...-..+|+ +||......+... .+ |+.++ -+.++.+...|++||+..+.-. ++-.++.+.|.
T Consensus 30 Gya~cv~l~~g~~~L~ta-~Hv~~~~~~~~~~-k~-g~kipl~~f~~~~~~~~~D~~il~~P~n~~---s~Lg~k~~~~~ 103 (203)
T PF02122_consen 30 GYATCVRLFDGEDALLTA-RHVWSRPSKVTSL-KT-GEKIPLAEFTDLLESRIADFVILRGPPNWE---SKLGVKAAQLS 103 (203)
T ss_dssp ----EEEE----EEEEE--HHHHTSSS---EE-ET-TEEEE--S-EEEEE-TTT-EEEEE--HHHH---HHHT-----B-
T ss_pred ccceEEECcCCccceecc-cccCCCccceeEc-CC-CCcccchhChhhhCCCccCEEEEecCcCHH---HHhCccccccc
Confidence 334444322235577899 5566555544433 33 54433 3566788999999999985422 12344556665
Q ss_pred CCccCCCCCEEEEEeeCCCCCceeeeeeEeccccccccCCCCCCccccccceEEEEe-cccCCCCCceEEcCCeeEEEEE
Q 001280 728 PEPALRRGDSVYLVGLSRSLQATSRKSIVTNPCAALNISSADCPRYRAMNMEVIELD-TDFGSTFSGVLTDEHGRVQAIW 806 (1108)
Q Consensus 728 ~~~~l~~G~~V~~vG~p~~~~~~~~~~~Vt~~~~~~~i~~~~~~~y~~~~~~~I~~d-~~ig~~sGGpL~d~~G~VvGi~ 806 (1108)
...++..| --.-+.........+ +..|. +.+ .. ++.+- .+.++.||-|+++.. +|+|+.
T Consensus 104 ~~~~~~~g-------~~~~y~~~~~~~~~~----sa~i~----g~~---~~-~~~vls~T~~G~SGtp~y~g~-~vvGvH 163 (203)
T PF02122_consen 104 QNSQLAKG-------PVSFYGFSSGEWPCS----SAKIP----GTE---GK-FASVLSNTSPGWSGTPYYSGK-NVVGVH 163 (203)
T ss_dssp ---SEEEE-------ESSTTSEEEEEEEEE----E-S--------S---TT-EEEE-----TT-TT-EEE-SS--EEEEE
T ss_pred chhhhCCC-------CeeeeeecCCCceec----cCccc----ccc---Cc-CCceEcCCCCCCCCCCeEECC-CceEee
Confidence 44322221 111111111112222 11111 111 11 22222 223345899999999 999998
Q ss_pred eec
Q 001280 807 GSF 809 (1108)
Q Consensus 807 ~~~ 809 (1108)
...
T Consensus 164 ~G~ 166 (203)
T PF02122_consen 164 TGS 166 (203)
T ss_dssp EEE
T ss_pred cCc
Confidence 765
No 171
>PF15436 PGBA_N: Plasminogen-binding protein pgbA N-terminal
Probab=20.76 E-value=6.1e+02 Score=27.49 Aligned_cols=66 Identities=11% Similarity=0.072 Sum_probs=40.4
Q ss_pred cccccCCCCeEEEEEe-cCCeEEeEEEEEEcCCCceEEEEECCCCcccccccCCCCCCcccCCCCEEEE
Q 001280 85 NRHVVKPGPVVAEAMF-VNREEIPVYPIYRDPVHDFGFFRYDPSAIQFLNYDEIPLAPEAACVGLEIRV 152 (1108)
Q Consensus 85 n~HVV~~~~~~~~v~~-~d~~~~~a~vv~~d~~~DlAlLk~d~~~~~~~~~~~l~l~~~~~~~G~~V~~ 152 (1108)
+.+..-+....+...| .+...+-|+.+-.....+.|.+|+.+-+ .+.-..||...-.++.||+|+.
T Consensus 22 ~~~l~vG~SGiV~h~~~~~~~~IiA~a~V~~~~~g~A~~kf~~fd--~L~Q~aLP~p~~~pk~GD~vil 88 (218)
T PF15436_consen 22 APDLKVGESGIVVHKFDKDHSSIIARAVVISKKNGVAKAKFSVFD--SLKQDALPTPKMVPKKGDEVIL 88 (218)
T ss_pred CCccccCCceEEEEEecCCcceeeeEEEEEEecCCeeEEEEeehh--hhhhhcCCCCccccCCCCEEEE
Confidence 4444443333444455 5666677776666667889999986521 1223445555667899999886
No 172
>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=20.01 E-value=2.4e+02 Score=31.23 Aligned_cols=19 Identities=11% Similarity=0.183 Sum_probs=15.3
Q ss_pred CCCceEEcCCeeEEEEEee
Q 001280 790 TFSGVLTDEHGRVQAIWGS 808 (1108)
Q Consensus 790 ~sGGpL~d~~G~VvGi~~~ 808 (1108)
.||.|++..+|.+||+.+.
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 4899999999999999875
Done!