Query 036272
Match_columns 383
No_of_seqs 151 out of 1710
Neff 10.0
Searched_HMMs 46136
Date Fri Mar 29 11:04:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036272.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036272hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03732 Retrotrans_gag: Retro 99.6 8.2E-15 1.8E-19 109.6 7.6 90 77-166 2-96 (96)
2 PF08284 RVP_2: Retroviral asp 99.4 3.3E-12 7.2E-17 100.6 9.0 77 302-378 17-93 (135)
3 PF13975 gag-asp_proteas: gag- 99.3 1.3E-11 2.8E-16 86.2 7.9 65 303-367 5-70 (72)
4 cd05484 retropepsin_like_LTR_2 99.3 2E-11 4.3E-16 89.9 9.0 70 308-378 2-71 (91)
5 cd05479 RP_DDI RP_DDI; retrope 99.2 7E-11 1.5E-15 92.2 9.0 74 305-378 15-88 (124)
6 PF03564 DUF1759: Protein of u 99.0 3.9E-09 8.5E-14 85.1 10.5 124 47-174 1-139 (145)
7 PF13650 Asp_protease_2: Aspar 99.0 4.7E-09 1E-13 77.1 8.7 72 309-382 1-73 (90)
8 PF09668 Asp_protease: Asparty 98.8 1.1E-08 2.4E-13 78.2 7.3 75 304-378 22-96 (124)
9 cd05481 retropepsin_like_LTR_1 98.8 1.3E-08 2.8E-13 74.7 7.1 68 310-378 2-73 (93)
10 TIGR02281 clan_AA_DTGA clan AA 98.8 6.4E-08 1.4E-12 74.9 9.3 77 304-382 9-86 (121)
11 cd05483 retropepsin_like_bacte 98.8 5.4E-08 1.2E-12 72.4 8.7 74 306-381 2-75 (96)
12 PF00098 zf-CCHC: Zinc knuckle 98.7 8.8E-09 1.9E-13 50.2 1.2 17 252-268 2-18 (18)
13 PF12384 Peptidase_A2B: Ty3 tr 98.7 1.7E-07 3.7E-12 73.4 8.9 75 304-378 32-106 (177)
14 cd05480 NRIP_C NRIP_C; putativ 98.6 8.9E-08 1.9E-12 68.7 5.7 70 309-378 1-72 (103)
15 PF00077 RVP: Retroviral aspar 98.6 5.5E-08 1.2E-12 73.0 4.7 71 305-379 4-74 (100)
16 cd06095 RP_RTVL_H_like Retrope 98.5 5.3E-07 1.1E-11 65.4 7.3 65 310-379 2-67 (86)
17 COG3577 Predicted aspartyl pro 98.4 1.9E-06 4.2E-11 70.4 8.0 76 305-382 104-180 (215)
18 PF14893 PNMA: PNMA 98.3 1.1E-05 2.3E-10 72.8 12.5 135 39-173 161-315 (331)
19 cd00303 retropepsin_like Retro 98.1 2.3E-05 4.9E-10 56.4 8.8 69 310-378 2-71 (92)
20 TIGR03698 clan_AA_DTGF clan AA 98.0 2.6E-05 5.6E-10 58.9 7.9 59 315-377 14-73 (107)
21 KOG0012 DNA damage inducible p 98.0 7.7E-06 1.7E-10 72.4 5.6 73 305-378 234-307 (380)
22 PF05585 DUF1758: Putative pep 97.9 2.2E-05 4.8E-10 64.5 5.8 45 316-361 11-55 (164)
23 cd06094 RP_Saci_like RP_Saci_l 97.7 5.2E-05 1.1E-09 53.8 4.5 59 315-378 7-66 (89)
24 PF14223 UBN2: gag-polypeptide 97.7 0.0003 6.5E-09 54.4 8.7 93 104-196 5-115 (119)
25 cd05482 HIV_retropepsin_like R 97.5 0.00042 9.2E-09 49.7 6.4 63 310-376 2-64 (87)
26 PF12382 Peptidase_A2E: Retrot 97.5 0.00022 4.8E-09 50.8 4.8 61 317-378 47-107 (137)
27 PF13696 zf-CCHC_2: Zinc knuck 97.4 5E-05 1.1E-09 42.4 0.8 18 251-268 9-26 (32)
28 PF02160 Peptidase_A3: Caulifl 97.2 0.00067 1.4E-08 56.3 5.6 62 316-378 19-80 (201)
29 PF14227 UBN2_2: gag-polypepti 96.8 0.015 3.2E-07 44.8 9.8 93 103-195 5-112 (119)
30 smart00343 ZnF_C2HC zinc finge 96.8 0.00055 1.2E-08 37.0 0.8 17 252-268 1-17 (26)
31 PF14787 zf-CCHC_5: GAG-polypr 96.4 0.001 2.2E-08 38.0 0.4 22 250-271 2-23 (36)
32 PF13917 zf-CCHC_3: Zinc knuck 96.4 0.0015 3.2E-08 39.4 0.9 19 250-268 4-22 (42)
33 COG5082 AIR1 Arginine methyltr 95.8 0.0032 6.9E-08 51.4 0.7 22 246-267 56-77 (190)
34 PF02023 SCAN: SCAN domain; I 95.8 0.035 7.5E-07 40.7 6.0 71 122-192 6-86 (95)
35 PF14244 UBN2_3: gag-polypepti 95.7 0.081 1.8E-06 42.7 8.5 107 40-147 6-134 (152)
36 COG5082 AIR1 Arginine methyltr 95.4 0.0055 1.2E-07 50.1 0.6 19 251-269 98-117 (190)
37 PF14392 zf-CCHC_4: Zinc knuck 95.3 0.0059 1.3E-07 38.7 0.5 19 250-268 31-49 (49)
38 PF15288 zf-CCHC_6: Zinc knuck 94.6 0.016 3.5E-07 34.3 1.0 20 251-270 2-23 (40)
39 PTZ00368 universal minicircle 94.1 0.021 4.5E-07 45.9 1.0 17 252-268 105-121 (148)
40 COG5550 Predicted aspartyl pro 94.1 0.16 3.4E-06 38.5 5.6 56 317-376 26-82 (125)
41 PF02093 Gag_p30: Gag P30 core 93.8 0.26 5.7E-06 41.2 6.8 70 122-191 126-206 (211)
42 COG5222 Uncharacterized conser 93.2 0.13 2.9E-06 44.7 4.4 18 251-268 177-194 (427)
43 PTZ00368 universal minicircle 91.8 0.07 1.5E-06 42.9 0.9 17 252-268 2-18 (148)
44 KOG4400 E3 ubiquitin ligase in 89.6 0.19 4.2E-06 44.6 1.8 18 251-268 144-161 (261)
45 cd07936 SCAN SCAN oligomerizat 89.6 1.5 3.3E-05 31.3 6.0 68 123-190 6-83 (85)
46 KOG0109 RNA-binding protein LA 89.5 0.14 3E-06 44.6 0.7 21 251-271 161-181 (346)
47 smart00431 SCAN leucine rich r 83.8 4.6 0.0001 30.5 6.0 69 123-191 6-84 (113)
48 cd05470 pepsin_retropepsin_lik 74.8 2.6 5.6E-05 31.5 2.4 26 311-336 3-30 (109)
49 KOG0119 Splicing factor 1/bran 73.9 1.4 3E-05 41.6 0.8 19 251-269 286-304 (554)
50 cd05474 SAP_like SAPs, pepsin- 72.6 15 0.00032 33.0 7.2 24 309-332 5-30 (295)
51 KOG2673 Uncharacterized conser 71.4 1.7 3.7E-05 40.6 0.8 21 251-271 129-149 (485)
52 KOG0341 DEAD-box protein abstr 69.1 2 4.3E-05 39.6 0.6 22 250-271 570-591 (610)
53 PF12353 eIF3g: Eukaryotic tra 68.3 2.3 4.9E-05 33.1 0.8 22 249-271 105-126 (128)
54 KOG2044 5'-3' exonuclease HKE1 67.6 2.1 4.7E-05 42.9 0.6 20 250-269 260-279 (931)
55 KOG4400 E3 ubiquitin ligase in 66.3 2.7 5.9E-05 37.3 1.0 23 249-271 163-185 (261)
56 PF00607 Gag_p24: gag gene pro 65.7 7.1 0.00015 33.2 3.3 63 125-187 125-193 (206)
57 KOG0107 Alternative splicing f 63.4 3.2 7E-05 33.7 0.8 18 251-268 101-118 (195)
58 PF03539 Spuma_A9PTase: Spumav 58.6 18 0.0004 28.5 4.1 57 314-377 2-58 (163)
59 cd06098 phytepsin Phytepsin, a 58.4 25 0.00054 32.1 5.8 23 318-340 211-233 (317)
60 PF13961 DUF4219: Domain of un 58.3 16 0.00034 19.7 2.7 21 47-68 1-21 (27)
61 COG5179 TAF1 Transcription ini 57.9 4.2 9.1E-05 39.7 0.6 19 251-269 938-958 (968)
62 KOG3116 Predicted C3H1-type Zn 55.6 3.5 7.6E-05 32.2 -0.2 21 251-271 28-48 (177)
63 KOG2560 RNA splicing factor - 54.6 3.3 7.2E-05 38.8 -0.6 19 249-267 111-129 (529)
64 PF14223 UBN2: gag-polypeptide 52.5 69 0.0015 24.1 6.6 63 48-110 38-107 (119)
65 PF00026 Asp: Eukaryotic aspar 52.3 16 0.00035 33.1 3.5 25 309-333 4-30 (317)
66 cd06097 Aspergillopepsin_like 52.1 14 0.00031 32.9 3.1 26 309-334 3-30 (278)
67 cd06096 Plasmepsin_5 Plasmepsi 51.4 21 0.00045 32.8 4.1 41 317-360 231-271 (326)
68 cd05476 pepsin_A_like_plant Ch 50.7 26 0.00056 31.0 4.5 25 309-333 4-30 (265)
69 PF05515 Viral_NABP: Viral nuc 49.8 31 0.00068 26.4 4.0 24 245-268 57-80 (124)
70 cd05476 pepsin_A_like_plant Ch 48.1 24 0.00053 31.1 3.9 19 318-336 177-195 (265)
71 cd05478 pepsin_A Pepsin A, asp 45.8 25 0.00055 32.0 3.7 30 311-340 194-229 (317)
72 cd05472 cnd41_like Chloroplast 45.7 20 0.00044 32.3 3.1 21 319-339 173-193 (299)
73 KOG3794 CBF1-interacting corep 44.9 8.6 0.00019 35.3 0.5 23 249-271 123-147 (453)
74 cd05488 Proteinase_A_fungi Fun 44.5 53 0.0012 30.0 5.7 28 307-334 11-40 (320)
75 cd05472 cnd41_like Chloroplast 42.7 39 0.00083 30.5 4.4 40 309-358 4-45 (299)
76 cd05485 Cathepsin_D_like Cathe 41.1 30 0.00066 31.7 3.5 22 318-339 211-232 (329)
77 cd05477 gastricsin Gastricsins 41.0 31 0.00067 31.4 3.6 22 318-339 202-223 (318)
78 cd05486 Cathespin_E Cathepsin 40.7 31 0.00066 31.5 3.5 22 318-339 199-220 (316)
79 COG1644 RPB10 DNA-directed RNA 38.3 13 0.00029 24.4 0.5 9 251-259 5-13 (63)
80 cd05473 beta_secretase_like Be 38.3 33 0.00072 32.0 3.4 21 319-339 213-233 (364)
81 cd06098 phytepsin Phytepsin, a 37.3 35 0.00075 31.2 3.2 29 306-334 10-40 (317)
82 cd05487 renin_like Renin stimu 36.8 35 0.00075 31.3 3.2 27 307-333 9-37 (326)
83 cd05477 gastricsin Gastricsins 36.6 35 0.00077 31.1 3.2 27 308-334 5-33 (318)
84 PF14227 UBN2_2: gag-polypepti 36.2 1.8E+02 0.0038 21.9 6.6 39 47-85 35-78 (119)
85 PF02761 Cbl_N2: CBL proto-onc 35.1 31 0.00068 24.5 1.9 51 82-132 5-57 (85)
86 cd05490 Cathepsin_D2 Cathepsin 34.6 40 0.00086 30.8 3.2 27 307-333 7-35 (325)
87 cd05475 nucellin_like Nucellin 34.5 38 0.00083 30.1 3.0 24 309-332 5-30 (273)
88 cd06097 Aspergillopepsin_like 34.3 31 0.00068 30.7 2.4 23 317-339 198-220 (278)
89 PF14543 TAXi_N: Xylanase inhi 34.2 44 0.00095 27.1 3.1 25 309-333 3-29 (164)
90 PLN00032 DNA-directed RNA poly 34.0 18 0.00039 24.6 0.6 9 251-259 5-13 (71)
91 cd06096 Plasmepsin_5 Plasmepsi 33.3 46 0.001 30.5 3.4 27 308-334 5-33 (326)
92 cd05478 pepsin_A Pepsin A, asp 32.3 45 0.00097 30.4 3.1 29 306-334 10-40 (317)
93 cd05471 pepsin_like Pepsin-lik 32.1 46 0.00099 29.4 3.1 28 309-336 3-32 (283)
94 smart00647 IBR In Between Ring 31.6 24 0.00051 23.1 0.9 16 251-266 49-64 (64)
95 PF14541 TAXi_C: Xylanase inhi 31.5 35 0.00075 27.6 2.0 22 318-339 30-51 (161)
96 KOG3497 DNA-directed RNA polym 31.3 17 0.00037 23.6 0.1 9 251-259 5-13 (69)
97 PF01194 RNA_pol_N: RNA polyme 31.0 22 0.00047 23.4 0.6 9 251-259 5-13 (60)
98 KOG2629 Peroxisomal membrane a 30.6 1.9E+02 0.0042 25.8 6.4 117 18-147 49-169 (300)
99 PTZ00147 plasmepsin-1; Provisi 30.3 54 0.0012 31.7 3.4 28 307-334 140-169 (453)
100 cd05473 beta_secretase_like Be 30.3 50 0.0011 30.8 3.1 27 308-334 5-33 (364)
101 cd05485 Cathepsin_D_like Cathe 30.3 50 0.0011 30.3 3.1 29 306-334 11-41 (329)
102 PRK04016 DNA-directed RNA poly 29.3 24 0.00051 23.4 0.5 9 251-259 5-13 (62)
103 cd05490 Cathepsin_D2 Cathepsin 29.3 41 0.0009 30.7 2.4 22 318-339 207-228 (325)
104 cd05486 Cathespin_E Cathepsin 28.8 54 0.0012 29.8 3.0 26 309-334 3-30 (316)
105 PF03461 TRCF: TRCF domain; I 28.4 37 0.00081 25.0 1.6 32 88-119 21-52 (101)
106 COG0282 ackA Acetate kinase [E 28.3 42 0.00091 31.3 2.1 46 325-370 179-224 (396)
107 PTZ00013 plasmepsin 4 (PM4); P 27.9 65 0.0014 31.2 3.5 28 308-335 140-169 (450)
108 PF01485 IBR: IBR domain; Int 27.9 22 0.00048 23.2 0.3 16 251-266 49-64 (64)
109 PF14420 Clr5: Clr5 domain 27.3 1.2E+02 0.0026 19.4 3.6 45 100-144 3-50 (54)
110 cd05471 pepsin_like Pepsin-lik 26.9 49 0.0011 29.2 2.4 25 316-340 201-225 (283)
111 cd05487 renin_like Renin stimu 26.9 79 0.0017 28.9 3.8 22 318-339 208-229 (326)
112 KOG0314 Predicted E3 ubiquitin 26.8 31 0.00067 32.9 1.1 20 250-269 158-177 (448)
113 KOG4437 ATP-dependent DNA liga 26.1 2.6E+02 0.0056 25.6 6.5 163 47-212 189-371 (482)
114 PLN03146 aspartyl protease fam 25.9 65 0.0014 31.0 3.1 20 319-338 309-328 (431)
115 PF05741 zf-nanos: Nanos RNA b 25.8 29 0.00063 22.4 0.5 18 251-268 34-54 (55)
116 cd05488 Proteinase_A_fungi Fun 24.8 52 0.0011 30.0 2.2 23 318-340 206-228 (320)
117 PF00649 Copper-fist: Copper f 24.3 42 0.00092 20.0 0.9 17 251-268 9-25 (40)
118 PLN03146 aspartyl protease fam 23.9 72 0.0016 30.7 3.0 28 306-333 84-113 (431)
119 TIGR03778 VPDSG_CTERM VPDSG-CT 23.8 23 0.00051 18.9 -0.2 20 322-341 2-21 (26)
120 cd05489 xylanase_inhibitor_I_l 23.7 75 0.0016 29.7 3.0 22 319-340 231-252 (362)
121 PTZ00165 aspartyl protease; Pr 23.0 82 0.0018 30.8 3.2 31 306-336 120-152 (482)
122 smart00545 JmjN Small domain f 22.5 1E+02 0.0023 18.6 2.4 26 44-69 2-31 (42)
123 KOG0119 Splicing factor 1/bran 22.1 39 0.00084 32.4 0.8 19 251-269 262-280 (554)
124 PTZ00013 plasmepsin 4 (PM4); P 21.7 64 0.0014 31.2 2.2 22 318-339 332-353 (450)
125 PF03732 Retrotrans_gag: Retro 21.1 1.9E+02 0.0041 20.2 4.2 32 51-82 61-94 (96)
126 PRK05978 hypothetical protein; 20.8 50 0.0011 26.4 1.0 13 249-262 32-44 (148)
127 KOG2985 Uncharacterized conser 20.5 33 0.00072 29.6 -0.0 22 250-271 81-102 (306)
No 1
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=99.57 E-value=8.2e-15 Score=109.59 Aligned_cols=90 Identities=23% Similarity=0.469 Sum_probs=81.4
Q ss_pred HhhhhcccchhhHHHHhhhcCCC--CCHHHHHHHHHhhhcCcccc-cHHHHhhcccc-cccHhhHHHHHHHHHHHhCC-C
Q 036272 77 LAAYHLENDAQLWFQQRKNQGHL--VTWDGLKAGLLAKFAATEYE-DSFGDLCKLKQ-TGTVSDYQPQFERLLARAGS-L 151 (383)
Q Consensus 77 ~~~~~L~g~A~~w~~~~~~~~~~--~~w~~~~~~l~~~F~~~~~~-~~~~~l~~~~q-~~sv~~Y~~~f~~l~~~~~~-~ 151 (383)
++..+|+|.|..||..+...... .+|++|++.|.++|.++... .+..+|.+++| +++|.+|+.+|+.|+..++. +
T Consensus 2 ~~~~~L~g~A~~w~~~~~~~~~~~~~~W~~~~~~~~~~f~~~~~~~~~~~~l~~l~Q~~esv~~y~~rf~~l~~~~~~~~ 81 (96)
T PF03732_consen 2 LFPSFLKGPARQWYRNLRPNEIRDFITWEEFKDAFRKRFFPPDRKEQARQELNSLRQGNESVREYVNRFRELARRAPPPM 81 (96)
T ss_pred CchHhccCHHHHHHHHhHhcCCCCCCCHHHHHHHHHHHHhhhhccccchhhhhhhhccCCcHHHHHHHHHHHHHHCCCCc
Confidence 67899999999999998764443 49999999999999998876 57788999999 99999999999999999984 9
Q ss_pred CHHHHHHHHHhhcch
Q 036272 152 TDKQEAACFISGLKD 166 (383)
Q Consensus 152 ~e~~~~~~f~~gL~~ 166 (383)
+++.++.+|++||+|
T Consensus 82 ~e~~~v~~f~~GL~~ 96 (96)
T PF03732_consen 82 DEEMLVERFIRGLRP 96 (96)
T ss_pred CHHHHHHHHHHCCCC
Confidence 999999999999975
No 2
>PF08284 RVP_2: Retroviral aspartyl protease; InterPro: IPR013242 This region defines single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases.
Probab=99.36 E-value=3.3e-12 Score=100.56 Aligned_cols=77 Identities=31% Similarity=0.454 Sum_probs=69.3
Q ss_pred CCCcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272 302 QTPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE 378 (383)
Q Consensus 302 ~~~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~ 378 (383)
..+..+...+.|++.++.+|||||||+|||+.++|.+++++..+.....++.++|+.+.+.+.|..+++.++|+.|.
T Consensus 17 ~~~~vi~g~~~I~~~~~~vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~~V~~~g~~~~~~~~~~~~~~~i~g~~~~ 93 (135)
T PF08284_consen 17 ESPDVITGTFLINSIPASVLIDSGATHSFISSSFAKKLGLPLEPLPRPIVVSAPGGSINCEGVCPDVPLSIQGHEFV 93 (135)
T ss_pred CCCCeEEEEEEeccEEEEEEEecCCCcEEccHHHHHhcCCEEEEccCeeEEecccccccccceeeeEEEEECCeEEE
Confidence 35678999999999999999999999999999999999999998876666667788888999999999999999875
No 3
>PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease
Probab=99.30 E-value=1.3e-11 Score=86.20 Aligned_cols=65 Identities=28% Similarity=0.431 Sum_probs=59.0
Q ss_pred CCcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCC-ceEEEEeCCCeEecCceeec
Q 036272 303 TPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSC-LFSVVVANGERLSSPGRCKG 367 (383)
Q Consensus 303 ~~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~-~~~v~~~~g~~~~~~~~~~~ 367 (383)
.+..+++.+.|+|..+.+||||||++|||++++|++|+++..... ...+.++||+.....|....
T Consensus 5 ~~g~~~v~~~I~g~~~~alvDtGat~~fis~~~a~rLgl~~~~~~~~~~v~~a~g~~~~~~g~~~~ 70 (72)
T PF13975_consen 5 DPGLMYVPVSIGGVQVKALVDTGATHNFISESLAKRLGLPLEKPPSPIRVKLANGSVIEIRGVAEN 70 (72)
T ss_pred cCCEEEEEEEECCEEEEEEEeCCCcceecCHHHHHHhCCCcccCCCCEEEEECCCCccccceEEEe
Confidence 346789999999999999999999999999999999999998877 89999999999999887643
No 4
>cd05484 retropepsin_like_LTR_2 Retropepsins_like_LTR, pepsin-like aspartate proteases. Retropepsin of retrotransposons with long terminal repeats are pepsin-like aspartate proteases. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classif
Probab=99.29 E-value=2e-11 Score=89.94 Aligned_cols=70 Identities=19% Similarity=0.194 Sum_probs=63.5
Q ss_pred EEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272 308 RVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE 378 (383)
Q Consensus 308 ~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~ 378 (383)
.+.+.|||+++.+||||||++|||+++.+.+++.+........+..++|..+...|.+ .+.+.++|.++.
T Consensus 2 ~~~~~Ing~~i~~lvDTGA~~svis~~~~~~lg~~~~~~~~~~v~~a~G~~~~~~G~~-~~~v~~~~~~~~ 71 (91)
T cd05484 2 TVTLLVNGKPLKFQLDTGSAITVISEKTWRKLGSPPLKPTKKRLRTATGTKLSVLGQI-LVTVKYGGKTKV 71 (91)
T ss_pred EEEEEECCEEEEEEEcCCcceEEeCHHHHHHhCCCccccccEEEEecCCCEeeEeEEE-EEEEEECCEEEE
Confidence 5778999999999999999999999999999998876556789999999999999998 699999999754
No 5
>cd05479 RP_DDI RP_DDI; retropepsin-like domain of DNA damage inducible protein. The family represents the retropepsin-like domain of DNA damage inducible protein. DNA damage inducible protein has a retropepsin-like domain and an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain. This CD represents the retropepsin-like domain of DDI.
Probab=99.21 E-value=7e-11 Score=92.17 Aligned_cols=74 Identities=12% Similarity=0.191 Sum_probs=62.7
Q ss_pred cceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272 305 HTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE 378 (383)
Q Consensus 305 ~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~ 378 (383)
..+++.+.|||.++.+||||||++|||+.++|+++|++........+..+.+......|.+..+++.|+|+.|.
T Consensus 15 ~~~~v~~~Ing~~~~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~ 88 (124)
T cd05479 15 PMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRIHLAQVKIGNLFLP 88 (124)
T ss_pred eEEEEEEEECCEEEEEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCCCcEEEeEEEEEEEEECCEEee
Confidence 56889999999999999999999999999999999998765444555555545577788888899999999875
No 6
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=98.99 E-value=3.9e-09 Score=85.07 Aligned_cols=124 Identities=12% Similarity=0.141 Sum_probs=99.8
Q ss_pred ccCCCChHHHHHHHH---HHHHH-hCCchhhHHHHhhhhcccchhhHHHHhhhcCCCCCHHHHHHHHHhhhcCcccc--c
Q 036272 47 YDGSEDPTLWICRAE---QFFEF-QGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYE--D 120 (383)
Q Consensus 47 F~G~~d~~~w~~~~e---~~~~~-~~~~d~~k~~~~~~~L~g~A~~w~~~~~~~~~~~~w~~~~~~l~~~F~~~~~~--~ 120 (383)
|+| |+.+|..+.+ ..... ..++|..|..+|..+|+|+|+.-+.++.. ...+|...++.|.++|+.+... .
T Consensus 1 F~G--~~~~~~~F~~~F~~~v~~n~~~~d~~K~~~L~~~L~G~A~~~i~~~~~--~~~~Y~~a~~~L~~~yg~~~~i~~~ 76 (145)
T PF03564_consen 1 FDG--DPSEWPEFIDQFDSLVHENPDLSDIEKLNYLRSCLKGEAKELIRGLPL--SEENYEEAWELLEERYGNPRRIIQA 76 (145)
T ss_pred CCC--CHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHhcchHHHHHHcccc--cchhhHHHHHHHHHHhCCchHHHHH
Confidence 899 7866555444 44444 57899999999999999999999998864 4579999999999999999853 4
Q ss_pred HHHHhhcccc-----cccHhhHHHHHHHHHHHhC----CCCHHHHHHHHHhhcchhHHhHccc
Q 036272 121 SFGDLCKLKQ-----TGTVSDYQPQFERLLARAG----SLTDKQEAACFISGLKDGLRADVRA 174 (383)
Q Consensus 121 ~~~~l~~~~q-----~~sv~~Y~~~f~~l~~~~~----~~~e~~~~~~f~~gL~~~l~~~l~~ 174 (383)
...+|.++.. .+.+..++..++.+...+. ..++..++..++..||+.++..|..
T Consensus 77 ~~~~l~~l~~~~~~d~~~L~~~~~~v~~~i~~L~~lg~~~~~~~l~~~i~~KLp~~~~~~w~~ 139 (145)
T PF03564_consen 77 LLEELRNLPPISNDDPEALRSLVDKVNNCIRALKALGVNVDDPLLISIILSKLPPEIREKWEE 139 (145)
T ss_pred HHHHHhccccccchhHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHCCHHHHHHHHH
Confidence 6677877774 5677888888888877762 3467789999999999999998864
No 7
>PF13650 Asp_protease_2: Aspartyl protease
Probab=98.95 E-value=4.7e-09 Score=77.13 Aligned_cols=72 Identities=25% Similarity=0.373 Sum_probs=58.2
Q ss_pred EEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCC-ceEEEEeCCCeEecCceeeceEEEecCeeeeeeec
Q 036272 309 VHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSC-LFSVVVANGERLSSPGRCKGVRLTLQDVPIENIEA 382 (383)
Q Consensus 309 ~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~-~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~~~~~ 382 (383)
|.+.+||+++.+||||||+.++|+++++++++++..+.. ...+..++|......+. .-.++|++.++.++.+
T Consensus 1 V~v~vng~~~~~liDTGa~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~--~~~i~ig~~~~~~~~~ 73 (90)
T PF13650_consen 1 VPVKVNGKPVRFLIDTGASISVISRSLAKKLGLKPRPKSVPISVSGAGGSVTVYRGR--VDSITIGGITLKNVPF 73 (90)
T ss_pred CEEEECCEEEEEEEcCCCCcEEECHHHHHHcCCCCcCCceeEEEEeCCCCEEEEEEE--EEEEEECCEEEEeEEE
Confidence 357899999999999999999999999999999887764 56777888884443333 3489999999987654
No 8
>PF09668 Asp_protease: Aspartyl protease; InterPro: IPR019103 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This family of eukaryotic aspartyl proteases have a fold similar to retroviral proteases which implies they function proteolytically during regulated protein turnover []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 3S8I_A 2I1A_B.
Probab=98.84 E-value=1.1e-08 Score=78.23 Aligned_cols=75 Identities=15% Similarity=0.225 Sum_probs=50.8
Q ss_pred CcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272 304 PHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE 378 (383)
Q Consensus 304 ~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~ 378 (383)
...+++.+.+||++++|+|||||.+|+||.++|+++||...-.....-....-....+.|..-.+++.|++..++
T Consensus 22 v~mLyI~~~ing~~vkA~VDtGAQ~tims~~~a~r~gL~~lid~r~~g~a~GvG~~~i~G~Ih~~~l~ig~~~~~ 96 (124)
T PF09668_consen 22 VSMLYINCKINGVPVKAFVDTGAQSTIMSKSCAERCGLMRLIDKRFAGVAKGVGTQKILGRIHSVQLKIGGLFFP 96 (124)
T ss_dssp ----EEEEEETTEEEEEEEETT-SS-EEEHHHHHHTTGGGGEEGGG-EE-------EEEEEEEEEEEEETTEEEE
T ss_pred cceEEEEEEECCEEEEEEEeCCCCccccCHHHHHHcCChhhccccccccccCCCcCceeEEEEEEEEEECCEEEE
Confidence 357999999999999999999999999999999999995432222222222225667888888899999997664
No 9
>cd05481 retropepsin_like_LTR_1 Retropepsins_like_LTR; pepsin-like aspartate protease from retrotransposons with long terminal repeats. Retropepsin of retrotransposons with long terminal repeats are pepsin-like aspartate proteases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identifi
Probab=98.83 E-value=1.3e-08 Score=74.69 Aligned_cols=68 Identities=16% Similarity=0.214 Sum_probs=59.1
Q ss_pred EEEEcC-eEEEEEeeCCCcchhccHHHHHHhC---CccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272 310 HSQISK-IPLTILIDSGSTHNYLHHRFAKITR---IKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE 378 (383)
Q Consensus 310 ~~~i~~-~~v~~LiDsGAt~s~Is~~~~~~l~---l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~ 378 (383)
.+.++| .+++++|||||++|+|+.+++++|+ .+....+...+..++|+.+...|. ..+.+.+++..+.
T Consensus 2 ~~~i~g~~~v~~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~~~G~-~~~~v~~~~~~~~ 73 (93)
T cd05481 2 DMKINGKQSVKFQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIPVEGG-VKLKCRYRNPKYN 73 (93)
T ss_pred ceEeCCceeEEEEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEeeeeEE-EEEEEEECCcEEE
Confidence 356788 9999999999999999999999998 555566678999999999999999 4699999988754
No 10
>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family. This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Sequences in the seed alignment and those scoring above the trusted cutoff are Proteobacterial; homologs scroing between trusted and noise are found in Pyrobaculum aerophilum str. IM2 (archaeal), Pirellula sp. (Planctomycetes), and Nostoc sp. PCC 7120 (Cyanobacteria).
Probab=98.76 E-value=6.4e-08 Score=74.90 Aligned_cols=77 Identities=18% Similarity=0.261 Sum_probs=61.5
Q ss_pred CcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCC-ceEEEEeCCCeEecCceeeceEEEecCeeeeeeec
Q 036272 304 PHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSC-LFSVVVANGERLSSPGRCKGVRLTLQDVPIENIEA 382 (383)
Q Consensus 304 ~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~-~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~~~~~ 382 (383)
...+.+.+.|||.++.+||||||++++|+.++|++|++...... ...+..++|.... .....-.|.|+++.++++.+
T Consensus 9 ~g~~~v~~~InG~~~~flVDTGAs~t~is~~~A~~Lgl~~~~~~~~~~~~ta~G~~~~--~~~~l~~l~iG~~~~~nv~~ 86 (121)
T TIGR02281 9 DGHFYATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIKA--ARVTLDRVAIGGIVVNDVDA 86 (121)
T ss_pred CCeEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCcccCCceEEEEeCCCcEEE--EEEEeCEEEECCEEEeCcEE
Confidence 35688999999999999999999999999999999999765433 4667778886442 33344678999999888765
No 11
>cd05483 retropepsin_like_bacteria Bacterial aspartate proteases, retropepsin-like protease family. This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.
Probab=98.76 E-value=5.4e-08 Score=72.35 Aligned_cols=74 Identities=19% Similarity=0.266 Sum_probs=59.9
Q ss_pred ceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeeeeee
Q 036272 306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIENIE 381 (383)
Q Consensus 306 ~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~~~~ 381 (383)
.+.+.+.+|+.++.+||||||++++|++.+++++++...+.....+..++|........ .-.|.|++..|.++.
T Consensus 2 ~~~v~v~i~~~~~~~llDTGa~~s~i~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~--~~~i~ig~~~~~~~~ 75 (96)
T cd05483 2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAARVR--LDSLQIGGITLRNVP 75 (96)
T ss_pred cEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCccCCCcEEEEecCCCccceEEE--cceEEECCcEEeccE
Confidence 36788999999999999999999999999999998744444566777788876665544 567899999887764
No 12
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.66 E-value=8.8e-09 Score=50.18 Aligned_cols=17 Identities=29% Similarity=0.866 Sum_probs=16.0
Q ss_pred cccccCCCcccccccce
Q 036272 252 LCYSCDENYTVGHKCKK 268 (383)
Q Consensus 252 ~Cf~C~~~GH~a~~Cp~ 268 (383)
.||+|++.||++++||+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 69999999999999985
No 13
>PF12384 Peptidase_A2B: Ty3 transposon peptidase; InterPro: IPR024650 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. Ty3 is a gypsy-type, retrovirus-like, element found in the budding yeast. The Ty3 aspartyl protease is required for processing of the viral polyprotein into its mature species [].
Probab=98.66 E-value=1.7e-07 Score=73.43 Aligned_cols=75 Identities=13% Similarity=0.205 Sum_probs=64.6
Q ss_pred CcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272 304 PHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE 378 (383)
Q Consensus 304 ~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~ 378 (383)
..+..+++.++|.++.+|+||||-.|||+.+.+++|+|+....++..++..-+.........+.+++.+++..+.
T Consensus 32 g~T~~v~l~~~~t~i~vLfDSGSPTSfIr~di~~kL~L~~~~app~~fRG~vs~~~~~tsEAv~ld~~i~n~~i~ 106 (177)
T PF12384_consen 32 GKTAIVQLNCKGTPIKVLFDSGSPTSFIRSDIVEKLELPTHDAPPFRFRGFVSGESATTSEAVTLDFYIDNKLID 106 (177)
T ss_pred CcEEEEEEeecCcEEEEEEeCCCccceeehhhHHhhCCccccCCCEEEeeeccCCceEEEEeEEEEEEECCeEEE
Confidence 356778888999999999999999999999999999999999999999977655555556667799999998875
No 14
>cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein. Proteins in this family have been described as probable nuclear receptor interacting proteins. The C-terminal domain of this family is homologous to the retroviral aspartyl protease domain. The domain is structurally related to one lobe of the pepsin molecule. The conserved active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.
Probab=98.62 E-value=8.9e-08 Score=68.66 Aligned_cols=70 Identities=17% Similarity=0.156 Sum_probs=53.6
Q ss_pred EEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccc-cC-CceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272 309 VHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPE-RS-CLFSVVVANGERLSSPGRCKGVRLTLQDVPIE 378 (383)
Q Consensus 309 ~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~-~~-~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~ 378 (383)
+.+++||.+++|+|||||.+|+||+..|+++||... .. ..--+..+-|...+.+|..-.+++.|++..++
T Consensus 1 vnCk~nG~~vkAfVDsGaQ~timS~~caercgL~r~v~~~r~~g~A~gvgt~~kiiGrih~~~ikig~~~~~ 72 (103)
T cd05480 1 VSCQCAGKELRALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSLPTSVKVIGQIERLVLQLGQLTVE 72 (103)
T ss_pred CceeECCEEEEEEEecCCchhhcCHHHHHHcChHhhhhhccccccccCCCcceeEeeEEEEEEEEeCCEEee
Confidence 357899999999999999999999999999998633 22 11122223455578889988999999987654
No 15
>PF00077 RVP: Retroviral aspartyl protease The Prosite entry also includes Pfam:PF00026; InterPro: IPR018061 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to the MEROPS peptidase family A2 (retropepsin family, clan AA), subfamily A2A. The family includes the single domain aspartic proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). Retroviral aspartyl protease is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins.; PDB: 3D3T_B 3SQF_A 1NSO_A 2HB3_A 2HS2_A 2HS1_B 3K4V_A 3GGV_C 1HTG_B 2FDE_A ....
Probab=98.60 E-value=5.5e-08 Score=72.97 Aligned_cols=71 Identities=15% Similarity=0.159 Sum_probs=55.8
Q ss_pred cceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeeee
Q 036272 305 HTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIEN 379 (383)
Q Consensus 305 ~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~~ 379 (383)
....+.+.++|.++.|||||||++|+|+++.+..+... +.....+..++|.. ...|.. .+.+.+++..+.+
T Consensus 4 ~rp~i~v~i~g~~i~~LlDTGA~vsiI~~~~~~~~~~~--~~~~~~v~~~~g~~-~~~~~~-~~~v~~~~~~~~~ 74 (100)
T PF00077_consen 4 NRPYITVKINGKKIKALLDTGADVSIISEKDWKKLGPP--PKTSITVRGAGGSS-SILGST-TVEVKIGGKEFNH 74 (100)
T ss_dssp SSSEEEEEETTEEEEEEEETTBSSEEESSGGSSSTSSE--EEEEEEEEETTEEE-EEEEEE-EEEEEETTEEEEE
T ss_pred CCceEEEeECCEEEEEEEecCCCcceeccccccccccc--ccCCceeccCCCcc-eeeeEE-EEEEEEECccceE
Confidence 34678889999999999999999999999988877654 33345565566666 666654 6999999998876
No 16
>cd06095 RP_RTVL_H_like Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements. This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where
Probab=98.50 E-value=5.3e-07 Score=65.39 Aligned_cols=65 Identities=14% Similarity=0.228 Sum_probs=48.2
Q ss_pred EEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeece-EEEecCeeeee
Q 036272 310 HSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGV-RLTLQDVPIEN 379 (383)
Q Consensus 310 ~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~-~v~i~~~~~~~ 379 (383)
.+.|||.++.+||||||+.++|+...++++. .......+..++|........ .+ .|.++++++.+
T Consensus 2 ~v~InG~~~~fLvDTGA~~tii~~~~a~~~~---~~~~~~~v~gagG~~~~~v~~--~~~~v~vg~~~~~~ 67 (86)
T cd06095 2 TITVEGVPIVFLVDTGATHSVLKSDLGPKQE---LSTTSVLIRGVSGQSQQPVTT--YRTLVDLGGHTVSH 67 (86)
T ss_pred EEEECCEEEEEEEECCCCeEEECHHHhhhcc---CCCCcEEEEeCCCcccccEEE--eeeEEEECCEEEEE
Confidence 4679999999999999999999999999972 233567777788876212222 23 47888887764
No 17
>COG3577 Predicted aspartyl protease [General function prediction only]
Probab=98.36 E-value=1.9e-06 Score=70.40 Aligned_cols=76 Identities=20% Similarity=0.287 Sum_probs=63.5
Q ss_pred cceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCC-ceEEEEeCCCeEecCceeeceEEEecCeeeeeeec
Q 036272 305 HTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSC-LFSVVVANGERLSSPGRCKGVRLTLQDVPIENIEA 382 (383)
Q Consensus 305 ~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~-~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~~~~~ 382 (383)
..+.+.+.|||+.+.+|||||||...++++.|+++|+..-+.. +..+.++||......= +.=.|.|+++.+.+++|
T Consensus 104 GHF~a~~~VNGk~v~fLVDTGATsVal~~~dA~RlGid~~~l~y~~~v~TANG~~~AA~V--~Ld~v~IG~I~~~nV~A 180 (215)
T COG3577 104 GHFEANGRVNGKKVDFLVDTGATSVALNEEDARRLGIDLNSLDYTITVSTANGRARAAPV--TLDRVQIGGIRVKNVDA 180 (215)
T ss_pred CcEEEEEEECCEEEEEEEecCcceeecCHHHHHHhCCCccccCCceEEEccCCccccceE--EeeeEEEccEEEcCchh
Confidence 4688899999999999999999999999999999999887765 6888889998654432 23567888888888876
No 18
>PF14893 PNMA: PNMA
Probab=98.31 E-value=1.1e-05 Score=72.75 Aligned_cols=135 Identities=21% Similarity=0.270 Sum_probs=104.8
Q ss_pred CCCCCCCCccCCCCh-------HHHHHHHHHHHHHhC-CchhhHHHHhhhhcccchhhHHHHhhhcCCCCCHHHHHHHHH
Q 036272 39 LAKLDFPCYDGSEDP-------TLWICRAEQFFEFQG-TSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLL 110 (383)
Q Consensus 39 ~~~~~~p~F~G~~d~-------~~w~~~~e~~~~~~~-~~d~~k~~~~~~~L~g~A~~w~~~~~~~~~~~~w~~~~~~l~ 110 (383)
+.-.+++.|+|...+ +.|+.++...+..-. ++|.++...+...|.|+|..+.+.+....+..+-.++++.|.
T Consensus 161 ~~y~~L~iFSG~~~~~~gee~fe~Wl~~a~~~v~~W~~~~e~ekrrrlle~L~GpA~~~~r~l~~~nP~~t~~~~l~aL~ 240 (331)
T PF14893_consen 161 IAYRDLRIFSGREEPAPGEESFESWLEHANEMVKKWNDVSEEEKRRRLLESLRGPALDSRRKLQKKNPKQTAQDCLKALG 240 (331)
T ss_pred hhhhhhhhhcCCCCCCCCcccHHHHHHHHHHHHHhccCCchhhchhhhHHhcccHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence 334567799997433 479999987776544 789999999999999999999999877677789999999999
Q ss_pred hhhcCcccc-cHHHHhhcccc--cccHhhHHHHHHHHHHHh---CCC----CHHHHHHHHHhh-c-chhHHhHcc
Q 036272 111 AKFAATEYE-DSFGDLCKLKQ--TGTVSDYQPQFERLLARA---GSL----TDKQEAACFISG-L-KDGLRADVR 173 (383)
Q Consensus 111 ~~F~~~~~~-~~~~~l~~~~q--~~sv~~Y~~~f~~l~~~~---~~~----~e~~~~~~f~~g-L-~~~l~~~l~ 173 (383)
..|+++... +...++.+..| +|++.+|+.+++.+...+ +.+ .+...+..++.+ . ...++.+++
T Consensus 241 ~~Fg~~es~~~~~~kf~~~~Q~~~E~ls~yv~RlE~lLqkav~k~a~~p~~adq~rl~q~l~~a~~~e~lq~klr 315 (331)
T PF14893_consen 241 QVFGSSESRETLEAKFLNTFQEPGEKLSAYVKRLESLLQKAVEKGAIKPSEADQVRLRQVLSGAVLSESLQDKLR 315 (331)
T ss_pred HhcCCcccHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHhcCCCccccCHHHHHHHHccCCCCHHHHHHHH
Confidence 999999986 57778878777 999999999999998885 222 345555565544 3 444555443
No 19
>cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples
Probab=98.12 E-value=2.3e-05 Score=56.36 Aligned_cols=69 Identities=22% Similarity=0.330 Sum_probs=54.5
Q ss_pred EEEEcCeEEEEEeeCCCcchhccHHHHHHhCC-ccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272 310 HSQISKIPLTILIDSGSTHNYLHHRFAKITRI-KPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE 378 (383)
Q Consensus 310 ~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l-~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~ 378 (383)
.+.+++..+.+|+|+||++++++..++.++++ .........+...+|......+.+..+.+.+.+.++.
T Consensus 2 ~~~~~~~~~~~liDtgs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~ 71 (92)
T cd00303 2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFT 71 (92)
T ss_pred EEEECCEEEEEEEcCCCcccccCHHHHHHcCCCcccCCCceEEEecCCCEeccCcEEEEEEEEeCCEEEE
Confidence 35578899999999999999999999999987 4444456677778888777777766788888876654
No 20
>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family. Members of this protein family are clan AA aspartic proteases, related to family TIGR02281. These proteins resemble retropepsins, pepsin-like proteases of retroviruses such as HIV. Members of this family are found in archaea and bacteria.
Probab=98.04 E-value=2.6e-05 Score=58.89 Aligned_cols=59 Identities=12% Similarity=0.153 Sum_probs=47.2
Q ss_pred CeEEEEEeeCCCcchh-ccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeee
Q 036272 315 KIPLTILIDSGSTHNY-LHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPI 377 (383)
Q Consensus 315 ~~~v~~LiDsGAt~s~-Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~ 377 (383)
..++.+||||||+..+ |+.+.|++||++... ...+.++||......- ....|.++|+..
T Consensus 14 ~~~v~~LVDTGat~~~~l~~~~a~~lgl~~~~--~~~~~tA~G~~~~~~v--~~~~v~igg~~~ 73 (107)
T TIGR03698 14 FMEVRALVDTGFSGFLLVPPDIVNKLGLPELD--QRRVYLADGREVLTDV--AKASIIINGLEI 73 (107)
T ss_pred ceEEEEEEECCCCeEEecCHHHHHHcCCCccc--CcEEEecCCcEEEEEE--EEEEEEECCEEE
Confidence 3489999999999997 999999999997754 5689999997555543 357788888765
No 21
>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]
Probab=98.04 E-value=7.7e-06 Score=72.39 Aligned_cols=73 Identities=15% Similarity=0.257 Sum_probs=57.7
Q ss_pred cceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCC-ceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272 305 HTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSC-LFSVVVANGERLSSPGRCKGVRLTLQDVPIE 378 (383)
Q Consensus 305 ~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~-~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~ 378 (383)
..++|++.|||++|+|+|||||..|+||..+|+++||...=.+ -.-+.-+-| ..+++|..-.++|.|.+..++
T Consensus 234 ~ML~iN~~ing~~VKAfVDsGaq~timS~~Caer~gL~rlid~r~~g~a~gvg-~~ki~g~Ih~~~lki~~~~l~ 307 (380)
T KOG0012|consen 234 TMLYINCEINGVPVKAFVDSGAQTTIMSAACAERCGLNRLIDKRFQGEARGVG-TEKILGRIHQAQLKIEDLYLP 307 (380)
T ss_pred eEEEEEEEECCEEEEEEEcccchhhhhhHHHHHHhChHHHhhhhhhccccCCC-cccccceeEEEEEEeccEeec
Confidence 4689999999999999999999999999999999998554322 222222333 778889888999999877653
No 22
>PF05585 DUF1758: Putative peptidase (DUF1758); InterPro: IPR008737 This is a family of nematode proteins of unknown function []. However, it seems likely that these proteins act as aspartic peptidases.
Probab=97.90 E-value=2.2e-05 Score=64.52 Aligned_cols=45 Identities=16% Similarity=0.278 Sum_probs=33.9
Q ss_pred eEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEec
Q 036272 316 IPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSS 361 (383)
Q Consensus 316 ~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~ 361 (383)
.++++|+||||+.|||+++++++|+|+..+.....+ ...|.....
T Consensus 11 ~~~~~LlDsGSq~SfIt~~la~~L~L~~~~~~~~~~-~~~g~~~~~ 55 (164)
T PF05585_consen 11 VEARALLDSGSQRSFITESLANKLNLPGTGEKILVI-GTFGSSSPK 55 (164)
T ss_pred EEEEEEEecCCchhHHhHHHHHHhCCCCCCceEEEE-eccCccCcc
Confidence 478999999999999999999999998877653333 333443333
No 23
>cd06094 RP_Saci_like RP_Saci_like, retropepsin family. Retropepsin on retrotransposons with long terminal repeats (LTR) including Saci-1, -2 and -3 of Schistosoma mansoni. Retropepsins are related to fungal and mammalian pepsins. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified
Probab=97.73 E-value=5.2e-05 Score=53.84 Aligned_cols=59 Identities=22% Similarity=0.313 Sum_probs=46.0
Q ss_pred CeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCe-eee
Q 036272 315 KIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDV-PIE 378 (383)
Q Consensus 315 ~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~-~~~ 378 (383)
...+.+||||||.+|+|.....+.. ....+..+..+||..+.+-|.. .+.|.++.+ +|+
T Consensus 7 ~s~~~fLVDTGA~vSviP~~~~~~~----~~~~~~~l~AANgt~I~tyG~~-~l~ldlGlrr~~~ 66 (89)
T cd06094 7 TSGLRFLVDTGAAVSVLPASSTKKS----LKPSPLTLQAANGTPIATYGTR-SLTLDLGLRRPFA 66 (89)
T ss_pred CCCcEEEEeCCCceEeecccccccc----ccCCceEEEeCCCCeEeeeeeE-EEEEEcCCCcEEe
Confidence 3457899999999999999877653 2334578999999999999964 588888764 554
No 24
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=97.69 E-value=0.0003 Score=54.39 Aligned_cols=93 Identities=13% Similarity=0.178 Sum_probs=72.9
Q ss_pred HHHHHHHhhhcCccc---c---cHHHHhhcccc--cccHhhHHHHHHHHHHHhC----CCCHHHHHHHHHhhcchhHHhH
Q 036272 104 GLKAGLLAKFAATEY---E---DSFGDLCKLKQ--TGTVSDYQPQFERLLARAG----SLTDKQEAACFISGLKDGLRAD 171 (383)
Q Consensus 104 ~~~~~l~~~F~~~~~---~---~~~~~l~~~~q--~~sv~~Y~~~f~~l~~~~~----~~~e~~~~~~f~~gL~~~l~~~ 171 (383)
++++.|...|..... . .+..+|.+++. ++++.+|+.+|..++..+. .+++..++..+++|||+.....
T Consensus 5 e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~g~~i~d~~~v~~iL~~Lp~~y~~~ 84 (119)
T PF14223_consen 5 EAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAIGKPISDEDLVSKILRSLPPSYDTF 84 (119)
T ss_pred HHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhcCCcccchhHHHHHHhcCCchhHHH
Confidence 566677778887765 3 35678888884 9999999999999998882 5789999999999999876655
Q ss_pred cc---cc-CCC--CHHHHHHHHHHHHHHHhh
Q 036272 172 VR---AQ-NPQ--NLSAAIGLARNYELKAQE 196 (383)
Q Consensus 172 l~---~~-~~~--~l~~~~~~a~~~e~~~~~ 196 (383)
+. .. +.. ++++++......|.....
T Consensus 85 ~~~i~~~~~~~~~t~~el~~~L~~~E~~~~~ 115 (119)
T PF14223_consen 85 VTAIRNSKDLPKMTLEELISRLLAEEMRLKS 115 (119)
T ss_pred HHHHHhcCCCCcCCHHHHHHHHHHHHHHHHH
Confidence 54 22 334 899999999998876543
No 25
>cd05482 HIV_retropepsin_like Retropepsins, pepsin-like aspartate proteases. This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This gro
Probab=97.49 E-value=0.00042 Score=49.71 Aligned_cols=63 Identities=11% Similarity=-0.011 Sum_probs=41.8
Q ss_pred EEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCee
Q 036272 310 HSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVP 376 (383)
Q Consensus 310 ~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~ 376 (383)
.+.++|+.+.+|+||||++++|++..+... .........+.+-|..+...... .+.+++++..
T Consensus 2 ~~~i~g~~~~~llDTGAd~Tvi~~~~~p~~---w~~~~~~~~i~GIGG~~~~~~~~-~v~i~i~~~~ 64 (87)
T cd05482 2 TLYINGKLFEGLLDTGADVSIIAENDWPKN---WPIQPAPSNLTGIGGAITPSQSS-VLLLEIDGEG 64 (87)
T ss_pred EEEECCEEEEEEEccCCCCeEEcccccCCC---CccCCCCeEEEeccceEEEEEEe-eEEEEEcCCe
Confidence 467889999999999999999998543221 10111235555666655555443 5888888753
No 26
>PF12382 Peptidase_A2E: Retrotransposon peptidase; InterPro: IPR024648 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. This entry represents a small family of fungal retroviral aspartyl peptidases.
Probab=97.48 E-value=0.00022 Score=50.75 Aligned_cols=61 Identities=11% Similarity=0.172 Sum_probs=41.2
Q ss_pred EEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272 317 PLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE 378 (383)
Q Consensus 317 ~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~ 378 (383)
.+-+||||||.+++|.+..++.++|+..|.....+. +.--....-.+...+.+.++|+.+.
T Consensus 47 sipclidtgaq~niiteetvrahklptrpw~~sviy-ggvyp~kinrkt~kl~i~lngisik 107 (137)
T PF12382_consen 47 SIPCLIDTGAQVNIITEETVRAHKLPTRPWSQSVIY-GGVYPNKINRKTIKLNINLNGISIK 107 (137)
T ss_pred cceeEEccCceeeeeehhhhhhccCCCCcchhheEe-ccccccccccceEEEEEEecceEEE
Confidence 446899999999999999999999999887543222 2111222333344566677776553
No 27
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=97.42 E-value=5e-05 Score=42.43 Aligned_cols=18 Identities=17% Similarity=0.438 Sum_probs=16.9
Q ss_pred ccccccCCCcccccccce
Q 036272 251 ELCYSCDENYTVGHKCKK 268 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~Cp~ 268 (383)
..|+.|+++||+.++||.
T Consensus 9 Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CEeecCCCCCccHhHCCC
Confidence 679999999999999996
No 28
>PF02160 Peptidase_A3: Cauliflower mosaic virus peptidase (A3); InterPro: IPR000588 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of sequences contain an aspartic peptidase signature that belongs to MEROPS peptidase family A3, subfamily A3A (cauliflower mosaic virus-type endopeptidase, clan AA). Cauliflower mosaic virus belongs to the Retro-transcribing viruses, which have a double-stranded DNA genome. The genome includes an open reading frame (ORF V) that shows similarities to the pol gene of retroviruses. This ORF codes for a polyprotein that includes a reverse transcriptase, which, on the basis of a DTG triplet near the N terminus, was suggested to include an aspartic protease. The presence of an aspartic protease has been confirmed by mutational studies, implicating Asp-45 in catalysis. The protease releases itself from the polyprotein and is involved in reactions required to process the ORF IV polyprotein, which includes the viral coat protein []. The viral aspartic peptidase signature has also been found associated with a polyprotein encoded by integrated pararetrovirus-like sequences in the genome of Nicotiana tabacum (Common tobacco) []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis
Probab=97.23 E-value=0.00067 Score=56.31 Aligned_cols=62 Identities=15% Similarity=0.147 Sum_probs=48.3
Q ss_pred eEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272 316 IPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE 378 (383)
Q Consensus 316 ~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~ 378 (383)
..+.++|||||+++++++..+-.-...- ...+..|..+|++......++..+.+.|.|..|.
T Consensus 19 ~~~~~~vDTGAt~C~~~~~iiP~e~we~-~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~ 80 (201)
T PF02160_consen 19 FNYHCYVDTGATICCASKKIIPEEYWEK-SKKPIKVKGANGSIIQINKKAKNGKIQIADKIFR 80 (201)
T ss_pred EEEEEEEeCCCceEEecCCcCCHHHHHh-CCCcEEEEEecCCceEEEEEecCceEEEccEEEe
Confidence 4678999999999998887652211111 1125789999999999999999999999998885
No 29
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=96.84 E-value=0.015 Score=44.85 Aligned_cols=93 Identities=18% Similarity=0.226 Sum_probs=72.2
Q ss_pred HHHHHHHHhhhcCcccc---cHHHHhhcccc--cccHhhHHHHHHHHHHHhC----CCCHHHHHHHHHhhcchhHHhHcc
Q 036272 103 DGLKAGLLAKFAATEYE---DSFGDLCKLKQ--TGTVSDYQPQFERLLARAG----SLTDKQEAACFISGLKDGLRADVR 173 (383)
Q Consensus 103 ~~~~~~l~~~F~~~~~~---~~~~~l~~~~q--~~sv~~Y~~~f~~l~~~~~----~~~e~~~~~~f~~gL~~~l~~~l~ 173 (383)
.++++.|...|...... ...++|..++. +.++.+|+.+|+.+...+. .++++.++..++.+||+.....+.
T Consensus 5 ~~~W~~L~~~y~~~~~~~~~~l~~kl~~~k~~~~~~v~~hi~~~~~l~~~L~~~g~~i~d~~~~~~lL~sLP~sy~~~~~ 84 (119)
T PF14227_consen 5 KEMWDKLKKKYEKKSFANKIYLLRKLYSLKMDEGGSVRDHINEFRSLVNQLKSLGVPIDDEDKVIILLSSLPPSYDSFVT 84 (119)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHhHhccchhHHHHHHHHHHHHHhhccccccchHHHHHHHHHHcCCHhHHHHHH
Confidence 35667788888887763 35678888876 7899999999999999983 468999999999999998776663
Q ss_pred c--c----CCCCHHHHHHHHHHHHHHHh
Q 036272 174 A--Q----NPQNLSAAIGLARNYELKAQ 195 (383)
Q Consensus 174 ~--~----~~~~l~~~~~~a~~~e~~~~ 195 (383)
. . ...++++++......|....
T Consensus 85 ~l~~~~~~~~~tl~~v~~~L~~ee~~~~ 112 (119)
T PF14227_consen 85 ALLYSKPEDELTLEEVKSKLLQEEERRK 112 (119)
T ss_pred HHHccCCCCCcCHHHHHHHHHHHHHHHH
Confidence 2 2 34688888888877665443
No 30
>smart00343 ZnF_C2HC zinc finger.
Probab=96.76 E-value=0.00055 Score=36.98 Aligned_cols=17 Identities=29% Similarity=0.907 Sum_probs=15.6
Q ss_pred cccccCCCcccccccce
Q 036272 252 LCYSCDENYTVGHKCKK 268 (383)
Q Consensus 252 ~Cf~C~~~GH~a~~Cp~ 268 (383)
.||+|++.||++++||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 49999999999999984
No 31
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=96.42 E-value=0.001 Score=37.99 Aligned_cols=22 Identities=18% Similarity=0.510 Sum_probs=13.1
Q ss_pred CccccccCCCcccccccceeEE
Q 036272 250 QELCYSCDENYTVGHKCKKLFF 271 (383)
Q Consensus 250 ~~~Cf~C~~~GH~a~~Cp~~~~ 271 (383)
.++|++|++..|.+++|....-
T Consensus 2 ~~~CprC~kg~Hwa~~C~sk~d 23 (36)
T PF14787_consen 2 PGLCPRCGKGFHWASECRSKTD 23 (36)
T ss_dssp --C-TTTSSSCS-TTT---TCC
T ss_pred CccCcccCCCcchhhhhhhhhc
Confidence 3689999999999999986543
No 32
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=96.35 E-value=0.0015 Score=39.43 Aligned_cols=19 Identities=16% Similarity=0.424 Sum_probs=17.2
Q ss_pred CccccccCCCcccccccce
Q 036272 250 QELCYSCDENYTVGHKCKK 268 (383)
Q Consensus 250 ~~~Cf~C~~~GH~a~~Cp~ 268 (383)
...|.+|++.||+..+|++
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 3679999999999999994
No 33
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=95.82 E-value=0.0032 Score=51.44 Aligned_cols=22 Identities=27% Similarity=0.779 Sum_probs=18.2
Q ss_pred hhhcCccccccCCCcccccccc
Q 036272 246 RRREQELCYSCDENYTVGHKCK 267 (383)
Q Consensus 246 ~~~~~~~Cf~C~~~GH~a~~Cp 267 (383)
.+.+...||+||+.||+++|||
T Consensus 56 ~~~~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 56 IREENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccccccchhcccCcccccCC
Confidence 3345567999999999999999
No 34
>PF02023 SCAN: SCAN domain; InterPro: IPR003309 A number of C2H2-zinc finger proteins contain a highly conserved N-terminal motif termed the SCAN domain. The SCAN domain may play an important role in the assembly and function of this newly defined subclass of transcriptional regulators [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3LHR_B 4E6S_A 2FI2_A 1Y7Q_A.
Probab=95.77 E-value=0.035 Score=40.71 Aligned_cols=71 Identities=17% Similarity=0.244 Sum_probs=53.2
Q ss_pred HHHhhcccc--cccHhhHHHHHHHHHHHh--CCC-C-----HHHHHHHHHhhcchhHHhHccccCCCCHHHHHHHHHHHH
Q 036272 122 FGDLCKLKQ--TGTVSDYQPQFERLLARA--GSL-T-----DKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYE 191 (383)
Q Consensus 122 ~~~l~~~~q--~~sv~~Y~~~f~~l~~~~--~~~-~-----e~~~~~~f~~gL~~~l~~~l~~~~~~~l~~~~~~a~~~e 191 (383)
..+|+..+. +++..+++.++..|+..= +.. + |-.++..|+..||++++..+..+.|.+..++..+|..+.
T Consensus 6 r~~FR~~~~~~~~~p~e~~~rL~~l~~~WL~pe~~tkeqi~ellvlEQFL~~lP~e~~~wV~e~~p~s~~ea~~Lae~~~ 85 (95)
T PF02023_consen 6 RQRFRSFQYQEGEGPREFLSRLRELCDRWLQPEVHTKEQILELLVLEQFLNILPPEVQTWVRERKPESAEEAVALAEDYQ 85 (95)
T ss_dssp HHHHHT--CCTTTSHHHHHHHHHHHHHHHH-TTTS-HHHHHHHHHHHHHHHHS-HHHHHHHHTCS-SSHHHHHHHHHHHH
T ss_pred HHHHhCCCCCCCCCHHHHHHHHHHHHHHhCccccCcHHHHHHHHHHHHHHHHCCHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence 345555554 788899999999887654 222 2 346788999999999999999999999999999998876
Q ss_pred H
Q 036272 192 L 192 (383)
Q Consensus 192 ~ 192 (383)
.
T Consensus 86 ~ 86 (95)
T PF02023_consen 86 R 86 (95)
T ss_dssp C
T ss_pred H
Confidence 3
No 35
>PF14244 UBN2_3: gag-polypeptide of LTR copia-type
Probab=95.67 E-value=0.081 Score=42.74 Aligned_cols=107 Identities=16% Similarity=0.170 Sum_probs=69.0
Q ss_pred CCCCCCCccCCCChHHHHHHHHHHHHHhCC----------chhhHHHHhh-hhcccchhhHHHHhhhc------CCCCCH
Q 036272 40 AKLDFPCYDGSEDPTLWICRAEQFFEFQGT----------SLENQVKLAA-YHLENDAQLWFQQRKNQ------GHLVTW 102 (383)
Q Consensus 40 ~~~~~p~F~G~~d~~~w~~~~e~~~~~~~~----------~d~~k~~~~~-~~L~g~A~~w~~~~~~~------~~~~~w 102 (383)
..+.+++++|+ |+..|...++.++...+. |+.....|.. ..-...+..|+...... ....+=
T Consensus 6 ~~i~~~kL~g~-NY~~W~~~~~~~L~~~~l~~~i~g~~~~P~~~~~~~~~W~~~d~~v~swl~~sis~~i~~~i~~~~ta 84 (152)
T PF14244_consen 6 QPITSIKLNGS-NYLSWSQQMEMALRGKGLWGFIDGTIPKPPETDPAYEKWERKDQLVLSWLLNSISPDILSTIIFCETA 84 (152)
T ss_pred CcccccCCCCc-cHHHHHHHHHHHHHhCCCcccccCccccccccchhhhhHHHhhhHHHHHHHHhhcHHHHhhhHhhhhH
Confidence 34556788995 999999999999987542 1111111111 12233355566442110 012344
Q ss_pred HHHHHHHHhhhcCcc-cc---cHHHHhhcccc-cccHhhHHHHHHHHHHH
Q 036272 103 DGLKAGLLAKFAATE-YE---DSFGDLCKLKQ-TGTVSDYQPQFERLLAR 147 (383)
Q Consensus 103 ~~~~~~l~~~F~~~~-~~---~~~~~l~~~~q-~~sv~~Y~~~f~~l~~~ 147 (383)
.++.+.|..+|.... .. +...+|..++| +.++.+|+.+|..|...
T Consensus 85 k~~W~~L~~~f~~~~~~~r~~~L~~~l~~~kq~~~sv~ey~~~lk~l~~~ 134 (152)
T PF14244_consen 85 KEIWDALKERFSQKSNASRVFQLRNELHSLKQGDKSVTEYFNKLKSLWQE 134 (152)
T ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHhHH
Confidence 467788888898777 32 46688999999 99999999999999843
No 36
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=95.37 E-value=0.0055 Score=50.05 Aligned_cols=19 Identities=26% Similarity=0.753 Sum_probs=16.8
Q ss_pred ccccccCCCccccccc-cee
Q 036272 251 ELCYSCDENYTVGHKC-KKL 269 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~C-p~~ 269 (383)
.+||+||+.||++++| |++
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~~ 117 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPSK 117 (190)
T ss_pred cccccccccCccccccCccc
Confidence 5799999999999999 554
No 37
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=95.31 E-value=0.0059 Score=38.68 Aligned_cols=19 Identities=21% Similarity=0.676 Sum_probs=17.0
Q ss_pred CccccccCCCcccccccce
Q 036272 250 QELCYSCDENYTVGHKCKK 268 (383)
Q Consensus 250 ~~~Cf~C~~~GH~a~~Cp~ 268 (383)
...||+||..||...+||+
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 3579999999999999984
No 38
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=94.59 E-value=0.016 Score=34.26 Aligned_cols=20 Identities=15% Similarity=0.386 Sum_probs=16.3
Q ss_pred ccccccCCCcccc--cccceeE
Q 036272 251 ELCYSCDENYTVG--HKCKKLF 270 (383)
Q Consensus 251 ~~Cf~C~~~GH~a--~~Cp~~~ 270 (383)
.+|.+||..||++ +.||...
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 4699999999998 5698643
No 39
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=94.13 E-value=0.021 Score=45.94 Aligned_cols=17 Identities=24% Similarity=0.837 Sum_probs=10.9
Q ss_pred cccccCCCcccccccce
Q 036272 252 LCYSCDENYTVGHKCKK 268 (383)
Q Consensus 252 ~Cf~C~~~GH~a~~Cp~ 268 (383)
.||+|++.||++++||.
T Consensus 105 ~C~~Cg~~gH~~~~C~~ 121 (148)
T PTZ00368 105 ACYNCGGEGHISRDCPN 121 (148)
T ss_pred hhcccCcCCcchhcCCC
Confidence 56666666666666655
No 40
>COG5550 Predicted aspartyl protease [Posttranslational modification, protein turnover, chaperones]
Probab=94.11 E-value=0.16 Score=38.53 Aligned_cols=56 Identities=20% Similarity=0.178 Sum_probs=42.4
Q ss_pred EEEEEeeCCCc-chhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCee
Q 036272 317 PLTILIDSGST-HNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVP 376 (383)
Q Consensus 317 ~v~~LiDsGAt-~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~ 376 (383)
....|||||.+ -..|+.+.+++++++... ...+..++|+...+.= ....+.|+|+.
T Consensus 26 ~~~~LiDTGFtg~lvlp~~vaek~~~~~~~--~~~~~~a~~~~v~t~V--~~~~iki~g~e 82 (125)
T COG5550 26 VYDELIDTGFTGYLVLPPQVAEKLGLPLFS--TIRIVLADGGVVKTSV--ALATIKIDGVE 82 (125)
T ss_pred EeeeEEecCCceeEEeCHHHHHhcCCCccC--ChhhhhhcCCEEEEEE--EEEEEEECCEE
Confidence 33459999999 899999999999986654 4677888888776633 24677788754
No 41
>PF02093 Gag_p30: Gag P30 core shell protein; InterPro: IPR003036 P30 is essential for viral assembly []. Cleavage of P70 in vitro can be accompanied by a shift from a concentrically coiled internal strand ("immature") to a collapsed ("mature") form of the virus core [].; GO: 0019068 virion assembly; PDB: 3BP9_U 1U7K_D 2Y4Z_A 1BM4_A.
Probab=93.81 E-value=0.26 Score=41.15 Aligned_cols=70 Identities=13% Similarity=0.186 Sum_probs=20.4
Q ss_pred HHHhhcccc--cccHhhHHHHHHHHHHHhCCCCHH------HHHHHHHhhcchhHHhHccccC---CCCHHHHHHHHHHH
Q 036272 122 FGDLCKLKQ--TGTVSDYQPQFERLLARAGSLTDK------QEAACFISGLKDGLRADVRAQN---PQNLSAAIGLARNY 190 (383)
Q Consensus 122 ~~~l~~~~q--~~sv~~Y~~~f~~l~~~~~~~~e~------~~~~~f~~gL~~~l~~~l~~~~---~~~l~~~~~~a~~~ 190 (383)
+.++..+.| +|+...|+.++++..+.--.++++ .+...|+.---++|++++.... -.++.++++.|..+
T Consensus 126 lsKv~~v~Qg~~EsPs~FLeRL~ea~r~yTp~dP~~~~~~~~v~~~Fi~QsapDIrkKLq~~eg~~~~~l~~Ll~~A~kV 205 (211)
T PF02093_consen 126 LSKVREVTQGPNESPSAFLERLREAYRKYTPFDPESPEGQASVAMSFITQSAPDIRKKLQKLEGLQGKTLSELLKEAEKV 205 (211)
T ss_dssp --S--TTTTTGGGHHHHHHHHHHHHHHHTS--------------------------------------------------
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHHHhcCCCCCCCCccchhHHHHHHHhccHHHHHHHHhhcCcccCCHHHHHHHHHHH
Confidence 344556677 899999999999998877434322 5777899999999999998654 57889999988765
Q ss_pred H
Q 036272 191 E 191 (383)
Q Consensus 191 e 191 (383)
-
T Consensus 206 f 206 (211)
T PF02093_consen 206 F 206 (211)
T ss_dssp -
T ss_pred H
Confidence 4
No 42
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.24 E-value=0.13 Score=44.72 Aligned_cols=18 Identities=22% Similarity=0.628 Sum_probs=16.6
Q ss_pred ccccccCCCcccccccce
Q 036272 251 ELCYSCDENYTVGHKCKK 268 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~Cp~ 268 (383)
..||+||++||+...||.
T Consensus 177 Y~CyRCGqkgHwIqnCpT 194 (427)
T COG5222 177 YVCYRCGQKGHWIQNCPT 194 (427)
T ss_pred eeEEecCCCCchhhcCCC
Confidence 579999999999999985
No 43
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=91.80 E-value=0.07 Score=42.87 Aligned_cols=17 Identities=24% Similarity=0.737 Sum_probs=14.5
Q ss_pred cccccCCCcccccccce
Q 036272 252 LCYSCDENYTVGHKCKK 268 (383)
Q Consensus 252 ~Cf~C~~~GH~a~~Cp~ 268 (383)
+||+|++.||++++||.
T Consensus 2 ~C~~C~~~GH~~~~c~~ 18 (148)
T PTZ00368 2 VCYRCGGVGHQSRECPN 18 (148)
T ss_pred cCCCCCCCCcCcccCcC
Confidence 58888888888888886
No 44
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=89.65 E-value=0.19 Score=44.60 Aligned_cols=18 Identities=33% Similarity=0.879 Sum_probs=16.2
Q ss_pred ccccccCCCcccccccce
Q 036272 251 ELCYSCDENYTVGHKCKK 268 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~Cp~ 268 (383)
..||+||+.||+.++||.
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~ 161 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPE 161 (261)
T ss_pred CccCCCCcCCcchhhCCC
Confidence 569999999999999994
No 45
>cd07936 SCAN SCAN oligomerization domain. The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.
Probab=89.56 E-value=1.5 Score=31.32 Aligned_cols=68 Identities=16% Similarity=0.125 Sum_probs=51.7
Q ss_pred HHhhcccc--cccHhhHHHHHHHHHHHh--CC-CC-----HHHHHHHHHhhcchhHHhHccccCCCCHHHHHHHHHHH
Q 036272 123 GDLCKLKQ--TGTVSDYQPQFERLLARA--GS-LT-----DKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNY 190 (383)
Q Consensus 123 ~~l~~~~q--~~sv~~Y~~~f~~l~~~~--~~-~~-----e~~~~~~f~~gL~~~l~~~l~~~~~~~l~~~~~~a~~~ 190 (383)
.+++.+.. ..+..+++.++++|+..= +. -+ +-..+..|+.-|+++++..+..+.|.+-.++..++..+
T Consensus 6 ~~FR~f~~~~~~~p~eal~~L~eLc~~WLrpe~~tkeqilelLVlEQfl~~lp~e~q~~v~~~~p~s~eea~~l~e~~ 83 (85)
T cd07936 6 QRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLAEDL 83 (85)
T ss_pred HHHhccccCCCCChHHHHHHHHHHHHHHcchhhcCHHHHHHHHHHHHHhhhCCHHHHHHHHhcCCCCHHHHHHHHHHh
Confidence 34455443 778889999998887764 11 12 23577889999999999999999999999999988654
No 46
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=89.46 E-value=0.14 Score=44.63 Aligned_cols=21 Identities=19% Similarity=0.377 Sum_probs=18.3
Q ss_pred ccccccCCCcccccccceeEE
Q 036272 251 ELCYSCDENYTVGHKCKKLFF 271 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~Cp~~~~ 271 (383)
..||.||+.||.+++||..+.
T Consensus 161 ~~cyrcGkeghwskEcP~~~~ 181 (346)
T KOG0109|consen 161 SGCYRCGKEGHWSKECPVDRT 181 (346)
T ss_pred HHheeccccccccccCCccCC
Confidence 459999999999999997654
No 47
>smart00431 SCAN leucine rich region.
Probab=83.80 E-value=4.6 Score=30.49 Aligned_cols=69 Identities=20% Similarity=0.228 Sum_probs=52.5
Q ss_pred HHhhcccc--cccHhhHHHHHHHHHHHh--CCC-C-----HHHHHHHHHhhcchhHHhHccccCCCCHHHHHHHHHHHH
Q 036272 123 GDLCKLKQ--TGTVSDYQPQFERLLARA--GSL-T-----DKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYE 191 (383)
Q Consensus 123 ~~l~~~~q--~~sv~~Y~~~f~~l~~~~--~~~-~-----e~~~~~~f~~gL~~~l~~~l~~~~~~~l~~~~~~a~~~e 191 (383)
.+++++.. ..+..+++.++++|+..= +.. + +-..+.+|+.-|+.+++..+..+.|.+-++++.++....
T Consensus 6 ~~FR~f~y~e~~gp~eaL~~L~eLc~~WLrPe~~tKeqilElLVlEQFL~ilP~e~q~wv~~~~p~sgeeav~l~E~l~ 84 (113)
T smart00431 6 QRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLLEDLE 84 (113)
T ss_pred HHhhccccCCCCChHHHHHHHHHHHHhhcChhhhhHHHHHHHHHHHHHhccCcHHHHHHHHhcCCCCHHHHHHHHHHhc
Confidence 34555544 678889999998887764 111 2 224678899999999999999999999999999987664
No 48
>cd05470 pepsin_retropepsin_like Cellular and retroviral pepsin-like aspartate proteases. This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site
Probab=74.83 E-value=2.6 Score=31.45 Aligned_cols=26 Identities=19% Similarity=0.330 Sum_probs=20.3
Q ss_pred EEEcC--eEEEEEeeCCCcchhccHHHH
Q 036272 311 SQISK--IPLTILIDSGSTHNYLHHRFA 336 (383)
Q Consensus 311 ~~i~~--~~v~~LiDsGAt~s~Is~~~~ 336 (383)
+.|+. .++.++|||||+..+|...-.
T Consensus 3 i~vGtP~q~~~~~~DTGSs~~Wv~~~~c 30 (109)
T cd05470 3 IGIGTPPQTFNVLLDTGSSNLWVPSVDC 30 (109)
T ss_pred EEeCCCCceEEEEEeCCCCCEEEeCCCC
Confidence 45554 789999999999998876643
No 49
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=73.93 E-value=1.4 Score=41.61 Aligned_cols=19 Identities=21% Similarity=0.455 Sum_probs=17.2
Q ss_pred ccccccCCCccccccccee
Q 036272 251 ELCYSCDENYTVGHKCKKL 269 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~Cp~~ 269 (383)
+.|++|+..||+++||+..
T Consensus 286 n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 286 NVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccCCcccccccCCCc
Confidence 4899999999999999865
No 50
>cd05474 SAP_like SAPs, pepsin-like proteinases secreted from pathogens to degrade host proteins. SAPs (Secreted aspartic proteinases) are secreted from a group of pathogenic fungi, predominantly Candida species. They are secreted from the pathogen to degrade host proteins. SAP is one of the most significant extracellular hydrolytic enzymes produced by C. albicans. SAP proteins, encoded by a family of 10 SAP genes. All 10 SAP genes of C. albicans encode preproenzymes, approximately 60 amino acid longer than the mature enzyme, which are processed when transported via the secretory pathway. The mature enzymes contain sequence motifs typical for all aspartyl proteinases, including the two conserved aspartate residues other active site and conserved cysteine residues implicated in the maintenance of the three-dimensional structure. Most Sap proteins contain putative N-glycosylation sites, but it remains to be determined which Sap proteins are glycosylated. This family of aspartate proteases
Probab=72.61 E-value=15 Score=33.01 Aligned_cols=24 Identities=21% Similarity=0.454 Sum_probs=20.2
Q ss_pred EEEEEcC--eEEEEEeeCCCcchhcc
Q 036272 309 VHSQISK--IPLTILIDSGSTHNYLH 332 (383)
Q Consensus 309 ~~~~i~~--~~v~~LiDsGAt~s~Is 332 (383)
+.+.|+. +++.++|||||+...|.
T Consensus 5 ~~i~iGtp~q~~~v~~DTgS~~~wv~ 30 (295)
T cd05474 5 AELSVGTPPQKVTVLLDTGSSDLWVP 30 (295)
T ss_pred EEEEECCCCcEEEEEEeCCCCcceee
Confidence 4556665 78999999999999998
No 51
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=71.39 E-value=1.7 Score=40.64 Aligned_cols=21 Identities=19% Similarity=0.561 Sum_probs=17.8
Q ss_pred ccccccCCCcccccccceeEE
Q 036272 251 ELCYSCDENYTVGHKCKKLFF 271 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~Cp~~~~ 271 (383)
-.||||+..-|-.++||.++.
T Consensus 129 ~~CFNC~g~~hsLrdC~rp~d 149 (485)
T KOG2673|consen 129 DPCFNCGGTPHSLRDCPRPFD 149 (485)
T ss_pred ccccccCCCCCccccCCCccc
Confidence 349999999999999998653
No 52
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=69.09 E-value=2 Score=39.59 Aligned_cols=22 Identities=23% Similarity=0.229 Sum_probs=18.7
Q ss_pred CccccccCCCcccccccceeEE
Q 036272 250 QELCYSCDENYTVGHKCKKLFF 271 (383)
Q Consensus 250 ~~~Cf~C~~~GH~a~~Cp~~~~ 271 (383)
..-|-+||..||...+||+...
T Consensus 570 ~kGCayCgGLGHRItdCPKle~ 591 (610)
T KOG0341|consen 570 EKGCAYCGGLGHRITDCPKLEA 591 (610)
T ss_pred ccccccccCCCcccccCchhhh
Confidence 3469999999999999998543
No 53
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=68.28 E-value=2.3 Score=33.10 Aligned_cols=22 Identities=18% Similarity=0.217 Sum_probs=17.5
Q ss_pred cCccccccCCCcccccccceeEE
Q 036272 249 EQELCYSCDENYTVGHKCKKLFF 271 (383)
Q Consensus 249 ~~~~Cf~C~~~GH~a~~Cp~~~~ 271 (383)
....|.+|+ ..|+...||.+-.
T Consensus 105 ~~v~CR~Ck-GdH~T~~CPyKd~ 126 (128)
T PF12353_consen 105 SKVKCRICK-GDHWTSKCPYKDT 126 (128)
T ss_pred ceEEeCCCC-CCcccccCCcccc
Confidence 345799997 7899999997543
No 54
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=67.59 E-value=2.1 Score=42.89 Aligned_cols=20 Identities=15% Similarity=0.521 Sum_probs=17.3
Q ss_pred CccccccCCCccccccccee
Q 036272 250 QELCYSCDENYTVGHKCKKL 269 (383)
Q Consensus 250 ~~~Cf~C~~~GH~a~~Cp~~ 269 (383)
+..||-||+.||.+.+|.-.
T Consensus 260 ~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 260 PRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred cccchhhcccCCcHhhcCCc
Confidence 35699999999999999754
No 55
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=66.33 E-value=2.7 Score=37.27 Aligned_cols=23 Identities=13% Similarity=0.320 Sum_probs=20.0
Q ss_pred cCccccccCCCcccccccceeEE
Q 036272 249 EQELCYSCDENYTVGHKCKKLFF 271 (383)
Q Consensus 249 ~~~~Cf~C~~~GH~a~~Cp~~~~ 271 (383)
..+.||.|++.||.+++||....
T Consensus 163 ~~~~c~~c~~~~h~~~~C~~~~~ 185 (261)
T KOG4400|consen 163 KGGTCFRCGKVGHGSRDCPSKQK 185 (261)
T ss_pred CCCccccCCCcceecccCCcccc
Confidence 46889999999999999997544
No 56
>PF00607 Gag_p24: gag gene protein p24 (core nucleocapsid protein); InterPro: IPR000721 The Gag protein from retroviruses, also known as p24, forms the inner protein layer of the nucleocapsid. This protein performs highly complex orchestrated tasks during the assembly, budding, maturation and infection stages of the viral replication cycle. During viral assembly, the proteins form membrane associations and self-associations that ultimately result in budding of an immature virion from the infected cell. Gag precursors also function during viral assembly to selectively bind and package two plus strands of genomic RNA. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.; GO: 0016032 viral reproduction; PDB: 1BMX_A 1SJH_C 1SJE_C 1U57_A 1FGL_B 1G03_A 2XT1_A 2JO0_A 2L6E_A 2HJL_C ....
Probab=65.72 E-value=7.1 Score=33.23 Aligned_cols=63 Identities=14% Similarity=0.170 Sum_probs=44.3
Q ss_pred hhcccc--cccHhhHHHHHHHHHHHhCCC---CHHHHHHHHHhhcchhHHhHccccCC-CCHHHHHHHH
Q 036272 125 LCKLKQ--TGTVSDYQPQFERLLARAGSL---TDKQEAACFISGLKDGLRADVRAQNP-QNLSAAIGLA 187 (383)
Q Consensus 125 l~~~~q--~~sv~~Y~~~f~~l~~~~~~~---~e~~~~~~f~~gL~~~l~~~l~~~~~-~~l~~~~~~a 187 (383)
+.+++| +|++.+|+.||..-+.....- .+..+....+.+-+++-+..+....+ .+|+|.+..+
T Consensus 125 ~~~I~QGp~Epf~dFv~rl~~a~~~~~~~~~~~~~~~~~L~~eNAN~~C~~~~~~l~~~~~lee~~~~C 193 (206)
T PF00607_consen 125 FTKIKQGPKEPFADFVDRLQKAIRREQGENEVKNILIRQLAYENANPDCRRIIRPLGKDAPLEEMIRAC 193 (206)
T ss_dssp GGGH-S-TTSHHHHHHHHHHHHHHCSSSTHHHHHHHHHHHHHHTS-HHHHHHHHHH-TTSTHHHHHHHT
T ss_pred HHHhhhccccchHHHHHHHHHHHhhcccccchhhHHHHHhhhccchHHHHHHHHccCCCCCHHHHHHHh
Confidence 356788 999999999999888876421 23345566678888888888875554 6898888765
No 57
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=63.45 E-value=3.2 Score=33.67 Aligned_cols=18 Identities=39% Similarity=1.069 Sum_probs=16.1
Q ss_pred ccccccCCCcccccccce
Q 036272 251 ELCYSCDENYTVGHKCKK 268 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~Cp~ 268 (383)
..|++||+.||+.+.|..
T Consensus 101 ~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 101 GFCYRCGERGHIGRNCKD 118 (195)
T ss_pred cccccCCCcccccccccc
Confidence 449999999999999976
No 58
>PF03539 Spuma_A9PTase: Spumavirus aspartic protease (A9); InterPro: IPR001641 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to MEROPS peptidase family A9 (spumapepsin family, clan AA). Foamy viruses are single-stranded enveloped retroviruses that have been noted to infect monkeys, cats and humans. In the human virus, the aspartic protease is encoded by the retroviral gag gene [], and in monkeys by the pol gene []. At present, the virus has not been proven to cause any particular disease. However, studies have shown Human foamy virus causes neurological disorders in infected mice []. It is not clear whether the Foamy virus/spumavirus proteases share a common evolutionary origin with other aspartic proteases. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 2JYS_A.
Probab=58.58 E-value=18 Score=28.48 Aligned_cols=57 Identities=12% Similarity=0.078 Sum_probs=35.0
Q ss_pred cCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeee
Q 036272 314 SKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPI 377 (383)
Q Consensus 314 ~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~ 377 (383)
.|..+.+--||||+++.|.+.+... -.|.....+....|+..-.+- .+.+.|+|+-+
T Consensus 2 kg~~l~~~wDsga~ITCiP~~fl~~----E~Pi~~~~i~Tihg~~~~~vY---Yl~fKi~grkv 58 (163)
T PF03539_consen 2 KGTKLKGHWDSGAQITCIPESFLEE----EQPIGKTLIKTIHGEKEQDVY---YLTFKINGRKV 58 (163)
T ss_dssp TTEEEEEEE-TT-SSEEEEGGGTTT-------SEEEEEE-SS-EEEEEEE---EEEEEESS-EE
T ss_pred CCceeeEEecCCCeEEEccHHHhCc----cccccceEEEEecCceeccEE---EEEEEEcCeEE
Confidence 4788999999999999999987543 234445666777776544333 47777777654
No 59
>cd06098 phytepsin Phytepsin, a plant homolog of mammalian lysosomal pepsins. Phytepsin, a plant homolog of mammalian lysosomal pepsins, resides in grains, roots, stems, leaves and flowers. Phytepsin may participate in metabolic turnover and in protein processing events. In addition, it highly expressed in several plant tissues undergoing apoptosis. Phytepsin contains an internal region consisting of about 100 residues not present in animal or microbial pepsins. This region is thus called a plant specific insert. The insert is highly similar to saponins, which are lysosomal sphingolipid-activating proteins in mammalian cells. The saponin-like domain may have a role in the vacuolar targeting of phytepsin. Phytepsin, as its animal counterparts, possesses a topology typical of all aspartic proteases. They are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved fro
Probab=58.35 E-value=25 Score=32.08 Aligned_cols=23 Identities=13% Similarity=0.042 Sum_probs=20.5
Q ss_pred EEEEeeCCCcchhccHHHHHHhC
Q 036272 318 LTILIDSGSTHNYLHHRFAKITR 340 (383)
Q Consensus 318 v~~LiDsGAt~s~Is~~~~~~l~ 340 (383)
..++||||++..++..++++.+.
T Consensus 211 ~~aivDTGTs~~~lP~~~~~~i~ 233 (317)
T cd06098 211 CAAIADSGTSLLAGPTTIVTQIN 233 (317)
T ss_pred cEEEEecCCcceeCCHHHHHhhh
Confidence 46899999999999999998775
No 60
>PF13961 DUF4219: Domain of unknown function (DUF4219)
Probab=58.34 E-value=16 Score=19.65 Aligned_cols=21 Identities=29% Similarity=0.591 Sum_probs=18.1
Q ss_pred ccCCCChHHHHHHHHHHHHHhC
Q 036272 47 YDGSEDPTLWICRAEQFFEFQG 68 (383)
Q Consensus 47 F~G~~d~~~w~~~~e~~~~~~~ 68 (383)
|+| +|+..|..+++.++....
T Consensus 1 l~g-~NY~~W~~~M~~~L~~~~ 21 (27)
T PF13961_consen 1 LDG-TNYSTWKIRMKAYLESQD 21 (27)
T ss_pred CCc-cCHHHHHHHHHHHHHHcc
Confidence 788 599999999999998765
No 61
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=57.92 E-value=4.2 Score=39.68 Aligned_cols=19 Identities=21% Similarity=0.551 Sum_probs=15.8
Q ss_pred ccccccCCCcccccc--ccee
Q 036272 251 ELCYSCDENYTVGHK--CKKL 269 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~--Cp~~ 269 (383)
.+|-+||+.||+..+ ||..
T Consensus 938 r~C~nCGQvGHmkTNK~CP~f 958 (968)
T COG5179 938 RTCGNCGQVGHMKTNKACPKF 958 (968)
T ss_pred eecccccccccccccccCccc
Confidence 479999999999765 9864
No 62
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=55.59 E-value=3.5 Score=32.21 Aligned_cols=21 Identities=19% Similarity=0.232 Sum_probs=18.0
Q ss_pred ccccccCCCcccccccceeEE
Q 036272 251 ELCYSCDENYTVGHKCKKLFF 271 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~Cp~~~~ 271 (383)
..|..|.+.||+.-.|...+.
T Consensus 28 ~rCQKClq~GHWtYECk~kRk 48 (177)
T KOG3116|consen 28 ARCQKCLQAGHWTYECKNKRK 48 (177)
T ss_pred hhHHHHHhhccceeeecCcee
Confidence 369999999999999987554
No 63
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=54.57 E-value=3.3 Score=38.76 Aligned_cols=19 Identities=16% Similarity=0.405 Sum_probs=17.2
Q ss_pred cCccccccCCCcccccccc
Q 036272 249 EQELCYSCDENYTVGHKCK 267 (383)
Q Consensus 249 ~~~~Cf~C~~~GH~a~~Cp 267 (383)
+.+-|-|||..||..++|-
T Consensus 111 RKGACeNCGAmtHk~KDCm 129 (529)
T KOG2560|consen 111 RKGACENCGAMTHKVKDCM 129 (529)
T ss_pred hhhhhhhhhhhhcchHHHh
Confidence 5578999999999999994
No 64
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=52.50 E-value=69 Score=24.14 Aligned_cols=63 Identities=21% Similarity=0.201 Sum_probs=40.4
Q ss_pred cCCCChHHHHHHHHHHHHH-----hCCchhhHHHHhhhhcccchhhHHHHhhhcCCCC--CHHHHHHHHH
Q 036272 48 DGSEDPTLWICRAEQFFEF-----QGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLV--TWDGLKAGLL 110 (383)
Q Consensus 48 ~G~~d~~~w~~~~e~~~~~-----~~~~d~~k~~~~~~~L~g~A~~w~~~~~~~~~~~--~w~~~~~~l~ 110 (383)
.+.+.+.+|+..+..+..- ..++|.+.+..++..|...=......+....... +++++...|.
T Consensus 38 ~~~~sv~~y~~~~~~i~~~L~~~g~~i~d~~~v~~iL~~Lp~~y~~~~~~i~~~~~~~~~t~~el~~~L~ 107 (119)
T PF14223_consen 38 KDGESVDEYISRLKEIVDELRAIGKPISDEDLVSKILRSLPPSYDTFVTAIRNSKDLPKMTLEELISRLL 107 (119)
T ss_pred cccccHHHHHHHHHHhhhhhhhcCCcccchhHHHHHHhcCCchhHHHHHHHHhcCCCCcCCHHHHHHHHH
Confidence 3445778888888877643 2467888888888888644444444444333333 6777777765
No 65
>PF00026 Asp: Eukaryotic aspartyl protease The Prosite entry also includes Pfam:PF00077.; InterPro: IPR001461 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to MEROPS peptidase family A1 (pepsin family, clan AA). The type example is pepsin A from Homo sapiens (Human) . More than 70 aspartic peptidases, from all from eukaryotic organisms, have been identified. These include pepsins, cathepsins, and renins. The enzymes are synthesised with signal peptides, and the proenzymes are secreted or passed into the lysosomal/endosomal system, where acidification leads to autocatalytic activation. Most members of the pepsin family specifically cleave bonds in peptides that are at least six residues in length, with hydrophobic residues in both the P1 and P1' positions []. Crystallography has shown the active site to form a groove across the junction of the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors within the active site []. Specificity is determined by several hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. Cysteine residues are well conserved within the pepsin family, pepsin itself containing three disulphide loops. The first loop is found in all but the fungal enzymes, and is usually around five residues in length, but is longer in barrierpepsin and candidapepsin; the second loop is also small and found only in the animal enzymes; and the third loop is the largest, found in all members of the family, except for the cysteine-free polyporopepsin. The loops are spread unequally throughout the two lobes, suggesting that they formed after the initial gene duplication and fusion event []. This family does not include the retroviral nor retrotransposon aspartic proteases which are much smaller and appear to be homologous to the single domain aspartic proteases.; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 1CZI_E 3CMS_A 1CMS_A 4CMS_A 1YG9_A 2NR6_A 3LIZ_A 1FLH_A 3UTL_A 1QRP_E ....
Probab=52.33 E-value=16 Score=33.09 Aligned_cols=25 Identities=24% Similarity=0.537 Sum_probs=20.9
Q ss_pred EEEEEc--CeEEEEEeeCCCcchhccH
Q 036272 309 VHSQIS--KIPLTILIDSGSTHNYLHH 333 (383)
Q Consensus 309 ~~~~i~--~~~v~~LiDsGAt~s~Is~ 333 (383)
+.+.|+ .+++.++|||||+..+|..
T Consensus 4 ~~v~iGtp~q~~~~~iDTGS~~~wv~~ 30 (317)
T PF00026_consen 4 INVTIGTPPQTFRVLIDTGSSDTWVPS 30 (317)
T ss_dssp EEEEETTTTEEEEEEEETTBSSEEEEB
T ss_pred EEEEECCCCeEEEEEEecccceeeece
Confidence 456676 7899999999999998874
No 66
>cd06097 Aspergillopepsin_like Aspergillopepsin_like, aspartic proteases of fungal origin. The members of this family are aspartic proteases of fungal origin, including aspergillopepsin, rhizopuspepsin, endothiapepsin, and rodosporapepsin. The various fungal species in this family may be the most economically important genus of fungi. They may serve as virulence factors or as industrial aids. For example, Aspergillopepsin from A. fumigatus is involved in invasive aspergillosis owing to its elastolytic activity and Aspergillopepsins from the mold A. saitoi are used in fermentation industry. Aspartic proteinases are a group of proteolytic enzymes in which the scissile peptide bond is attacked by a nucleophilic water molecule activated by two aspartic residues in a DT(S)G motif at the active site. They have a similar fold composed of two beta-barrel domains. Between the N-terminal and C-terminal domains, each of which contributes one catalytic aspartic residue, there is an extended active-
Probab=52.10 E-value=14 Score=32.94 Aligned_cols=26 Identities=19% Similarity=0.354 Sum_probs=20.9
Q ss_pred EEEEEcC--eEEEEEeeCCCcchhccHH
Q 036272 309 VHSQISK--IPLTILIDSGSTHNYLHHR 334 (383)
Q Consensus 309 ~~~~i~~--~~v~~LiDsGAt~s~Is~~ 334 (383)
+.+.|++ +++.++|||||+..+|...
T Consensus 3 ~~i~vGtP~Q~~~v~~DTGS~~~wv~~~ 30 (278)
T cd06097 3 TPVKIGTPPQTLNLDLDTGSSDLWVFSS 30 (278)
T ss_pred eeEEECCCCcEEEEEEeCCCCceeEeeC
Confidence 4556665 7899999999999998654
No 67
>cd06096 Plasmepsin_5 Plasmepsins are a class of aspartic proteinases produced by the plasmodium parasite. The family contains a group of aspartic proteinases homologous to plasmepsin 5. Plasmepsins are a class of at least 10 enzymes produced by the plasmodium parasite. Through their haemoglobin-degrading activity, they are an important cause of symptoms in malaria sufferers. This family of enzymes is a potential target for anti-malarial drugs. Plasmepsins are aspartic acid proteases, which means their active site contains two aspartic acid residues. These two aspartic acid residue act respectively as proton donor and proton acceptor, catalyzing the hydrolysis of peptide bond in proteins. Aspartic proteinases are composed of two structurally similar beta barrel lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The catalytic Asp residues are contained in an Asp-Thr-Gly-Ser/thr motif in both N- and C-terminal l
Probab=51.37 E-value=21 Score=32.76 Aligned_cols=41 Identities=20% Similarity=0.221 Sum_probs=29.6
Q ss_pred EEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEe
Q 036272 317 PLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLS 360 (383)
Q Consensus 317 ~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~ 360 (383)
...++||||.+.+++.+..++++.-.. +.+.+.+.+|..+.
T Consensus 231 ~~~aivDSGTs~~~lp~~~~~~l~~~~---P~i~~~f~~g~~~~ 271 (326)
T cd06096 231 GLGMLVDSGSTLSHFPEDLYNKINNFF---PTITIIFENNLKID 271 (326)
T ss_pred CCCEEEeCCCCcccCCHHHHHHHHhhc---CcEEEEEcCCcEEE
Confidence 345899999999999999999875333 34555665555444
No 68
>cd05476 pepsin_A_like_plant Chroloplast Nucleoids DNA-binding Protease and Nucellin, pepsin-like aspartic proteases from plants. This family contains pepsin like aspartic proteases from plants including Chloroplast Nucleoids DNA-binding Protease and Nucellin. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco and Nucellins are important regulators of nucellar cell's progressive degradation after ovule fertilization. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which
Probab=50.67 E-value=26 Score=30.98 Aligned_cols=25 Identities=24% Similarity=0.523 Sum_probs=19.6
Q ss_pred EEEEEc--CeEEEEEeeCCCcchhccH
Q 036272 309 VHSQIS--KIPLTILIDSGSTHNYLHH 333 (383)
Q Consensus 309 ~~~~i~--~~~v~~LiDsGAt~s~Is~ 333 (383)
+.+.|+ .+.+.++|||||+...|..
T Consensus 4 ~~i~iGtP~q~~~v~~DTGSs~~wv~~ 30 (265)
T cd05476 4 VTLSIGTPPQPFSLIVDTGSDLTWTQC 30 (265)
T ss_pred EEEecCCCCcceEEEecCCCCCEEEcC
Confidence 455565 4688999999999988863
No 69
>PF05515 Viral_NABP: Viral nucleic acid binding ; InterPro: IPR008891 This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP).
Probab=49.76 E-value=31 Score=26.40 Aligned_cols=24 Identities=17% Similarity=0.656 Sum_probs=18.6
Q ss_pred HhhhcCccccccCCCcccccccce
Q 036272 245 QRRREQELCYSCDENYTVGHKCKK 268 (383)
Q Consensus 245 ~~~~~~~~Cf~C~~~GH~a~~Cp~ 268 (383)
.+.++-+.||.||+.-|--..|+.
T Consensus 57 RRAkR~~~C~~CG~~l~~~~~C~~ 80 (124)
T PF05515_consen 57 RRAKRYNRCFKCGRYLHNNGNCRR 80 (124)
T ss_pred HHHHHhCccccccceeecCCcCCC
Confidence 344456889999998888888983
No 70
>cd05476 pepsin_A_like_plant Chroloplast Nucleoids DNA-binding Protease and Nucellin, pepsin-like aspartic proteases from plants. This family contains pepsin like aspartic proteases from plants including Chloroplast Nucleoids DNA-binding Protease and Nucellin. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco and Nucellins are important regulators of nucellar cell's progressive degradation after ovule fertilization. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which
Probab=48.11 E-value=24 Score=31.14 Aligned_cols=19 Identities=37% Similarity=0.396 Sum_probs=16.7
Q ss_pred EEEEeeCCCcchhccHHHH
Q 036272 318 LTILIDSGSTHNYLHHRFA 336 (383)
Q Consensus 318 v~~LiDsGAt~s~Is~~~~ 336 (383)
..++||||++..++.+.++
T Consensus 177 ~~ai~DTGTs~~~lp~~~~ 195 (265)
T cd05476 177 GGTIIDSGTTLTYLPDPAY 195 (265)
T ss_pred CcEEEeCCCcceEcCcccc
Confidence 3589999999999998876
No 71
>cd05478 pepsin_A Pepsin A, aspartic protease produced in gastric mucosa of mammals. Pepsin, a well-known aspartic protease, is produced by the human gastric mucosa in seven different zymogen isoforms, subdivided into two types: pepsinogen A and pepsinogen C. The prosequence of the zymogens are self cleaved under acidic pH. The mature enzymes are called pepsin A and pepsin C, correspondingly. The well researched porcine pepsin is also in this pepsin A family. Pepsins play an integral role in the digestion process of vertebrates. Pepsins are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. More recently evolved enzymes have similar three-dimensional structures, however their amino acid sequences are more divergent except for the conserved catalytic site motif. Pepsins specifically cleave bonds in peptides which
Probab=45.84 E-value=25 Score=32.03 Aligned_cols=30 Identities=10% Similarity=0.028 Sum_probs=23.4
Q ss_pred EEEcCeEE------EEEeeCCCcchhccHHHHHHhC
Q 036272 311 SQISKIPL------TILIDSGSTHNYLHHRFAKITR 340 (383)
Q Consensus 311 ~~i~~~~v------~~LiDsGAt~s~Is~~~~~~l~ 340 (383)
+.|++..+ .++||||++..++.+..++.+.
T Consensus 194 v~v~g~~~~~~~~~~~iiDTGts~~~lp~~~~~~l~ 229 (317)
T cd05478 194 VTINGQVVACSGGCQAIVDTGTSLLVGPSSDIANIQ 229 (317)
T ss_pred EEECCEEEccCCCCEEEECCCchhhhCCHHHHHHHH
Confidence 34555543 6899999999999999887753
No 72
>cd05472 cnd41_like Chloroplast Nucleoids DNA-binding Protease, catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco. Antisense tobacco with reduced amount of CND41 maintained green leaves and constant protein levels, especially Rubisco. CND41 has DNA-binding as well as aspartic protease activities. The pepsin-like aspartic protease domain is located at the C-terminus of the protein. The enzyme is characterized by having two aspartic protease catalytic site motifs, the Asp-Thr-Gly-Ser in the N-terminal and Asp-Ser-Gly-Ser in the C-terminal region. Aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. This fami
Probab=45.66 E-value=20 Score=32.31 Aligned_cols=21 Identities=24% Similarity=0.238 Sum_probs=18.7
Q ss_pred EEEeeCCCcchhccHHHHHHh
Q 036272 319 TILIDSGSTHNYLHHRFAKIT 339 (383)
Q Consensus 319 ~~LiDsGAt~s~Is~~~~~~l 339 (383)
.++||||++.+++.+.+++.+
T Consensus 173 ~~ivDSGTt~~~lp~~~~~~l 193 (299)
T cd05472 173 GVIIDSGTVITRLPPSAYAAL 193 (299)
T ss_pred CeEEeCCCcceecCHHHHHHH
Confidence 589999999999999888765
No 73
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=44.91 E-value=8.6 Score=35.35 Aligned_cols=23 Identities=13% Similarity=0.299 Sum_probs=17.8
Q ss_pred cCccccccCCCccccc--ccceeEE
Q 036272 249 EQELCYSCDENYTVGH--KCKKLFF 271 (383)
Q Consensus 249 ~~~~Cf~C~~~GH~a~--~Cp~~~~ 271 (383)
+...|+.|++-||+.. +||-.-.
T Consensus 123 RNVrC~kChkwGH~n~DreCplf~~ 147 (453)
T KOG3794|consen 123 RNVRCLKCHKWGHINTDRECPLFGK 147 (453)
T ss_pred eeeeEEeecccccccCCccCcchhh
Confidence 4467999999999954 6986443
No 74
>cd05488 Proteinase_A_fungi Fungal Proteinase A , aspartic proteinase superfamily. Fungal Proteinase A, a proteolytic enzyme distributed among a variety of organisms, is a member of the aspartic proteinase superfamily. In Saccharomyces cerevisiae, targeted to the vacuole as a zymogen, activation of proteinases A at acidic pH can occur by two different pathways: a one-step process to release mature proteinase A, involving the intervention of proteinase B, or a step-wise pathway via the auto-activation product known as pseudo-proteinase A. Once active, S. cerevisiae proteinase A is essential to the activities of other yeast vacuolar hydrolases, including proteinase B and carboxypeptidase Y. The mature enzyme is bilobal, with each lobe providing one of the two catalytically essential aspartic acid residues in the active site. The crystal structure of free proteinase A shows that flap loop is atypically pointing directly into the S(1) pocket of the enzyme. Proteinase A preferentially hydro
Probab=44.54 E-value=53 Score=29.95 Aligned_cols=28 Identities=11% Similarity=0.280 Sum_probs=22.4
Q ss_pred eEEEEEEc--CeEEEEEeeCCCcchhccHH
Q 036272 307 MRVHSQIS--KIPLTILIDSGSTHNYLHHR 334 (383)
Q Consensus 307 ~~~~~~i~--~~~v~~LiDsGAt~s~Is~~ 334 (383)
..+.+.|+ .+++.++|||||+..+|...
T Consensus 11 Y~~~i~iGtp~q~~~v~~DTGSs~~wv~~~ 40 (320)
T cd05488 11 YFTDITLGTPPQKFKVILDTGSSNLWVPSV 40 (320)
T ss_pred EEEEEEECCCCcEEEEEEecCCcceEEEcC
Confidence 45666776 47899999999999998654
No 75
>cd05472 cnd41_like Chloroplast Nucleoids DNA-binding Protease, catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco. Antisense tobacco with reduced amount of CND41 maintained green leaves and constant protein levels, especially Rubisco. CND41 has DNA-binding as well as aspartic protease activities. The pepsin-like aspartic protease domain is located at the C-terminus of the protein. The enzyme is characterized by having two aspartic protease catalytic site motifs, the Asp-Thr-Gly-Ser in the N-terminal and Asp-Ser-Gly-Ser in the C-terminal region. Aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. This fami
Probab=42.74 E-value=39 Score=30.47 Aligned_cols=40 Identities=23% Similarity=0.506 Sum_probs=26.5
Q ss_pred EEEEEc--CeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCe
Q 036272 309 VHSQIS--KIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGER 358 (383)
Q Consensus 309 ~~~~i~--~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~ 358 (383)
+.+.|+ .+++.++|||||+...|... +.....+..++|..
T Consensus 4 ~~i~iGtP~q~~~v~~DTGSs~~Wv~c~----------~c~~~~i~Yg~Gs~ 45 (299)
T cd05472 4 VTVGLGTPARDQTVIVDTGSDLTWVQCQ----------PCCLYQVSYGDGSY 45 (299)
T ss_pred EEEecCCCCcceEEEecCCCCcccccCC----------CCCeeeeEeCCCce
Confidence 445565 46899999999999888421 11345566666654
No 76
>cd05485 Cathepsin_D_like Cathepsin_D_like, pepsin family of proteinases. Cathepsin D is the major aspartic proteinase of the lysosomal compartment where it functions in protein catabolism. It is a member of the pepsin family of proteinases. This enzyme is distinguished from other members of the pepsin family by two features that are characteristic of lysosomal hydrolases. First, mature Cathepsin D is found predominantly in a two-chain form due to a posttranslational cleavage event. Second, it contains phosphorylated, N-linked oligosaccharides that target the enzyme to lysosomes via mannose-6-phosphate receptors. Cathepsin D preferentially attacks peptide bonds flanked by bulky hydrophobic amino acids and its pH optimum is between pH 2.8 and 4.0. Two active site aspartic acid residues are essential for the catalytic activity of aspartic proteinases. Like other aspartic proteinases, Cathepsin D is a bilobed molecule; the two evolutionary related lobes are mostly made up of beta-sheets an
Probab=41.10 E-value=30 Score=31.74 Aligned_cols=22 Identities=9% Similarity=-0.090 Sum_probs=19.4
Q ss_pred EEEEeeCCCcchhccHHHHHHh
Q 036272 318 LTILIDSGSTHNYLHHRFAKIT 339 (383)
Q Consensus 318 v~~LiDsGAt~s~Is~~~~~~l 339 (383)
..++||||++..++.+..++.+
T Consensus 211 ~~~iiDSGtt~~~lP~~~~~~l 232 (329)
T cd05485 211 CQAIADTGTSLIAGPVDEIEKL 232 (329)
T ss_pred cEEEEccCCcceeCCHHHHHHH
Confidence 3699999999999999988765
No 77
>cd05477 gastricsin Gastricsins, asparate proteases produced in gastric mucosa. Gastricsin is also called pepsinogen C. Gastricsins are produced in gastric mucosa of mammals. It is synthesized by the chief cells in the stomach as an inactive zymogen. It is self-converted to a mature enzyme under acidic conditions. Human gastricsin is distributed throughout all parts of the stomach. Gastricsin is synthesized as an inactive progastricsin that has an approximately 40 residue prosequence. It is self-converting to a mature enzyme being triggered by a drop in pH from neutrality to acidic conditions. Like other aspartic proteases, gastricsin are characterized by two catalytic aspartic residues at the active site, and display optimal activity at acidic pH. Mature enzyme has a pseudo-2-fold symmetry that passes through the active site between the catalytic aspartate residues. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic aspartate residue, with an exten
Probab=40.99 E-value=31 Score=31.43 Aligned_cols=22 Identities=9% Similarity=0.163 Sum_probs=19.3
Q ss_pred EEEEeeCCCcchhccHHHHHHh
Q 036272 318 LTILIDSGSTHNYLHHRFAKIT 339 (383)
Q Consensus 318 v~~LiDsGAt~s~Is~~~~~~l 339 (383)
..++||||.+..++.+.+++.+
T Consensus 202 ~~~iiDSGtt~~~lP~~~~~~l 223 (318)
T cd05477 202 CQAIVDTGTSLLTAPQQVMSTL 223 (318)
T ss_pred ceeeECCCCccEECCHHHHHHH
Confidence 3689999999999999988765
No 78
>cd05486 Cathespin_E Cathepsin E, non-lysosomal aspartic protease. Cathepsin E is an intracellular, non-lysosomal aspartic protease expressed in a variety of cells and tissues. The protease has proposed physiological roles in antigen presentation by the MHC class II system, in the biogenesis of the vasoconstrictor peptide endothelin, and in neurodegeneration associated with brain ischemia and aging. Cathepsin E is the only A1 aspartic protease that exists as a homodimer with a disulfide bridge linking the two monomers. Like many other aspartic proteases, it is synthesized as a zymogen which is catalytically inactive towards its natural substrates at neutral pH and which auto-activates in an acidic environment. The overall structure follows the general fold of aspartic proteases of the A1 family, it is composed of two structurally similar beta barrel lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The catalyt
Probab=40.74 E-value=31 Score=31.46 Aligned_cols=22 Identities=14% Similarity=0.015 Sum_probs=19.0
Q ss_pred EEEEeeCCCcchhccHHHHHHh
Q 036272 318 LTILIDSGSTHNYLHHRFAKIT 339 (383)
Q Consensus 318 v~~LiDsGAt~s~Is~~~~~~l 339 (383)
..++||||++..++....++.+
T Consensus 199 ~~aiiDTGTs~~~lP~~~~~~l 220 (316)
T cd05486 199 CQAIVDTGTSLITGPSGDIKQL 220 (316)
T ss_pred CEEEECCCcchhhcCHHHHHHH
Confidence 3699999999999999887765
No 79
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=38.31 E-value=13 Score=24.37 Aligned_cols=9 Identities=33% Similarity=0.936 Sum_probs=7.5
Q ss_pred ccccccCCC
Q 036272 251 ELCYSCDEN 259 (383)
Q Consensus 251 ~~Cf~C~~~ 259 (383)
.+||.||+.
T Consensus 5 iRCFsCGkv 13 (63)
T COG1644 5 VRCFSCGKV 13 (63)
T ss_pred eEeecCCCC
Confidence 579999984
No 80
>cd05473 beta_secretase_like Beta-secretase, aspartic-acid protease important in the pathogenesis of Alzheimer's disease. Beta-secretase also called BACE (beta-site of APP cleaving enzyme) or memapsin-2. Beta-secretase is an aspartic-acid protease important in the pathogenesis of Alzheimer's disease, and in the formation of myelin sheaths in peripheral nerve cells. It cleaves amyloid precursor protein (APP) to reveal the N-terminus of the beta-amyloid peptides. The beta-amyloid peptides are the major components of the amyloid plaques formed in the brain of patients with Alzheimer's disease (AD). Since BACE mediates one of the cleavages responsible for generation of AD, it is regarded as a potential target for pharmacological intervention in AD. Beta-secretase is a member of pepsin family of aspartic proteases. Same as other aspartic proteases, beta-secretase is a bilobal enzyme, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two
Probab=38.27 E-value=33 Score=31.99 Aligned_cols=21 Identities=24% Similarity=0.336 Sum_probs=18.6
Q ss_pred EEEeeCCCcchhccHHHHHHh
Q 036272 319 TILIDSGSTHNYLHHRFAKIT 339 (383)
Q Consensus 319 ~~LiDsGAt~s~Is~~~~~~l 339 (383)
.++||||++.+++....++.+
T Consensus 213 ~~ivDSGTs~~~lp~~~~~~l 233 (364)
T cd05473 213 KAIVDSGTTNLRLPVKVFNAA 233 (364)
T ss_pred cEEEeCCCcceeCCHHHHHHH
Confidence 589999999999999988764
No 81
>cd06098 phytepsin Phytepsin, a plant homolog of mammalian lysosomal pepsins. Phytepsin, a plant homolog of mammalian lysosomal pepsins, resides in grains, roots, stems, leaves and flowers. Phytepsin may participate in metabolic turnover and in protein processing events. In addition, it highly expressed in several plant tissues undergoing apoptosis. Phytepsin contains an internal region consisting of about 100 residues not present in animal or microbial pepsins. This region is thus called a plant specific insert. The insert is highly similar to saponins, which are lysosomal sphingolipid-activating proteins in mammalian cells. The saponin-like domain may have a role in the vacuolar targeting of phytepsin. Phytepsin, as its animal counterparts, possesses a topology typical of all aspartic proteases. They are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved fro
Probab=37.27 E-value=35 Score=31.16 Aligned_cols=29 Identities=17% Similarity=0.263 Sum_probs=22.6
Q ss_pred ceEEEEEEc--CeEEEEEeeCCCcchhccHH
Q 036272 306 TMRVHSQIS--KIPLTILIDSGSTHNYLHHR 334 (383)
Q Consensus 306 ~~~~~~~i~--~~~v~~LiDsGAt~s~Is~~ 334 (383)
...+.+.|+ .+++.++|||||+..+|...
T Consensus 10 ~Y~~~i~iGtP~Q~~~v~~DTGSs~lWv~~~ 40 (317)
T cd06098 10 QYFGEIGIGTPPQKFTVIFDTGSSNLWVPSS 40 (317)
T ss_pred EEEEEEEECCCCeEEEEEECCCccceEEecC
Confidence 345566776 57899999999999988754
No 82
>cd05487 renin_like Renin stimulates production of angiotensin and thus affects blood pressure. Renin, also known as angiotensinogenase, is a circulating enzyme that participates in the renin-angiotensin system that mediates extracellular volume, arterial vasoconstriction, and consequently mean arterial blood pressure. The enzyme is secreted by the kidneys from specialized juxtaglomerular cells in response to decreases in glomerular filtration rate (a consequence of low blood volume), diminished filtered sodium chloride and sympathetic nervous system innervation. The enzyme circulates in the blood stream and hydrolyzes angiotensinogen secreted from the liver into the peptide angiotensin I. Angiotensin I is further cleaved in the lungs by endothelial bound angiotensin converting enzyme (ACE) into angiotensin II, the final active peptide. Renin is a member of the aspartic protease family. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Aspartate r
Probab=36.81 E-value=35 Score=31.27 Aligned_cols=27 Identities=15% Similarity=0.268 Sum_probs=21.9
Q ss_pred eEEEEEEc--CeEEEEEeeCCCcchhccH
Q 036272 307 MRVHSQIS--KIPLTILIDSGSTHNYLHH 333 (383)
Q Consensus 307 ~~~~~~i~--~~~v~~LiDsGAt~s~Is~ 333 (383)
..+.+.|+ .+++.++|||||+...|..
T Consensus 9 y~~~i~iGtP~q~~~v~~DTGSs~~Wv~~ 37 (326)
T cd05487 9 YYGEIGIGTPPQTFKVVFDTGSSNLWVPS 37 (326)
T ss_pred EEEEEEECCCCcEEEEEEeCCccceEEcc
Confidence 44566676 6788999999999999964
No 83
>cd05477 gastricsin Gastricsins, asparate proteases produced in gastric mucosa. Gastricsin is also called pepsinogen C. Gastricsins are produced in gastric mucosa of mammals. It is synthesized by the chief cells in the stomach as an inactive zymogen. It is self-converted to a mature enzyme under acidic conditions. Human gastricsin is distributed throughout all parts of the stomach. Gastricsin is synthesized as an inactive progastricsin that has an approximately 40 residue prosequence. It is self-converting to a mature enzyme being triggered by a drop in pH from neutrality to acidic conditions. Like other aspartic proteases, gastricsin are characterized by two catalytic aspartic residues at the active site, and display optimal activity at acidic pH. Mature enzyme has a pseudo-2-fold symmetry that passes through the active site between the catalytic aspartate residues. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic aspartate residue, with an exten
Probab=36.62 E-value=35 Score=31.05 Aligned_cols=27 Identities=19% Similarity=0.267 Sum_probs=21.2
Q ss_pred EEEEEEcC--eEEEEEeeCCCcchhccHH
Q 036272 308 RVHSQISK--IPLTILIDSGSTHNYLHHR 334 (383)
Q Consensus 308 ~~~~~i~~--~~v~~LiDsGAt~s~Is~~ 334 (383)
.+.+.|+. +++.++|||||+...|...
T Consensus 5 ~~~i~iGtP~q~~~v~~DTGS~~~wv~~~ 33 (318)
T cd05477 5 YGEISIGTPPQNFLVLFDTGSSNLWVPSV 33 (318)
T ss_pred EEEEEECCCCcEEEEEEeCCCccEEEccC
Confidence 44566663 7899999999999999753
No 84
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=36.22 E-value=1.8e+02 Score=21.86 Aligned_cols=39 Identities=13% Similarity=0.012 Sum_probs=27.3
Q ss_pred ccCCCChHHHHHHHHHHHHH-----hCCchhhHHHHhhhhcccc
Q 036272 47 YDGSEDPTLWICRAEQFFEF-----QGTSLENQVKLAAYHLEND 85 (383)
Q Consensus 47 F~G~~d~~~w~~~~e~~~~~-----~~~~d~~k~~~~~~~L~g~ 85 (383)
|+...++.+|+..|+..+.. ..++|...+.+++..|-..
T Consensus 35 ~~~~~~v~~hi~~~~~l~~~L~~~g~~i~d~~~~~~lL~sLP~s 78 (119)
T PF14227_consen 35 MDEGGSVRDHINEFRSLVNQLKSLGVPIDDEDKVIILLSSLPPS 78 (119)
T ss_pred hccchhHHHHHHHHHHHHHhhccccccchHHHHHHHHHHcCCHh
Confidence 34335788999999988764 2467888888887777433
No 85
>PF02761 Cbl_N2: CBL proto-oncogene N-terminus, EF hand-like domain; InterPro: IPR014741 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the EF hand-like domain.; GO: 0005509 calcium ion binding; PDB: 3OP0_A 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B ....
Probab=35.05 E-value=31 Score=24.52 Aligned_cols=51 Identities=10% Similarity=0.180 Sum_probs=32.2
Q ss_pred cccchhhHHHHhhhcCCCCCHHHHHHHHHhhhcCcccc--cHHHHhhcccccc
Q 036272 82 LENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYE--DSFGDLCKLKQTG 132 (383)
Q Consensus 82 L~g~A~~w~~~~~~~~~~~~w~~~~~~l~~~F~~~~~~--~~~~~l~~~~q~~ 132 (383)
.+.+|..+|...-.......|.+|...|.+.+.-.... .+++...-+.++.
T Consensus 5 TK~eA~~FW~~~Fg~r~IVPW~~F~~~L~~~h~~~~~~~~~aLk~TiDlT~n~ 57 (85)
T PF02761_consen 5 TKAEAAEFWKTSFGKRTIVPWSEFRQALQKVHPISSGLEAMALKSTIDLTCND 57 (85)
T ss_dssp SSHHHHHHHHHHHTT-SEEEHHHHHHHHHHHS--SSHHHHHHHHHHH-TTSSS
T ss_pred ccHHHHHHHHHHCCCCeEeeHHHHHHHHHHhcCCCchHHHHHHHHHHhcccCC
Confidence 45678888877544456799999999999988866532 3444444555533
No 86
>cd05490 Cathepsin_D2 Cathepsin_D2, pepsin family of proteinases. Cathepsin D is the major aspartic proteinase of the lysosomal compartment where it functions in protein catabolism. It is a member of the pepsin family of proteinases. This enzyme is distinguished from other members of the pepsin family by two features that are characteristic of lysosomal hydrolases. First, mature Cathepsin D is found predominantly in a two-chain form due to a posttranslational cleavage event. Second, it contains phosphorylated, N-linked oligosaccharides that target the enzyme to lysosomes via mannose-6-phosphate receptors. Cathepsin D preferentially attacks peptide bonds flanked by bulky hydrophobic amino acids and its pH optimum is between pH 2.8 and 4.0. Two active site aspartic acid residues are essential for the catalytic activity of aspartic proteinases. Like other aspartic proteinases, Cathepsin D is a bilobed molecule; the two evolutionary related lobes are mostly made up of beta-sheets and flank
Probab=34.60 E-value=40 Score=30.85 Aligned_cols=27 Identities=19% Similarity=0.298 Sum_probs=20.9
Q ss_pred eEEEEEEc--CeEEEEEeeCCCcchhccH
Q 036272 307 MRVHSQIS--KIPLTILIDSGSTHNYLHH 333 (383)
Q Consensus 307 ~~~~~~i~--~~~v~~LiDsGAt~s~Is~ 333 (383)
..+.+.|+ .+++.++|||||+...|..
T Consensus 7 Y~~~i~iGtP~q~~~v~~DTGSs~~Wv~~ 35 (325)
T cd05490 7 YYGEIGIGTPPQTFTVVFDTGSSNLWVPS 35 (325)
T ss_pred EEEEEEECCCCcEEEEEEeCCCccEEEEc
Confidence 34556666 4789999999999998854
No 87
>cd05475 nucellin_like Nucellins, plant aspartic proteases specifically expressed in nucellar cells during degradation. Nucellins are important regulators of nucellar cell's progressive degradation after ovule fertilization. This degradation is a characteristic of programmed cell death. Nucellins are plant aspartic proteases specifically expressed in nucellar cells during degradation. The enzyme is characterized by having two aspartic protease catalytic site motifs, the Asp-Thr-Gly-Ser in the N-terminal and Asp-Ser-Gly-Ser in the C-terminal region, and two other regions nearly identical to two regions of plant aspartic proteases. Aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. Although the three-dimensional structures of the two lobes are very similar, the amino acid sequences are more d
Probab=34.51 E-value=38 Score=30.07 Aligned_cols=24 Identities=33% Similarity=0.484 Sum_probs=19.2
Q ss_pred EEEEEc--CeEEEEEeeCCCcchhcc
Q 036272 309 VHSQIS--KIPLTILIDSGSTHNYLH 332 (383)
Q Consensus 309 ~~~~i~--~~~v~~LiDsGAt~s~Is 332 (383)
+.+.|+ .+.+.+++||||+...|.
T Consensus 5 ~~i~iGtP~q~~~v~~DTGS~~~Wv~ 30 (273)
T cd05475 5 VTINIGNPPKPYFLDIDTGSDLTWLQ 30 (273)
T ss_pred EEEEcCCCCeeEEEEEccCCCceEEe
Confidence 445555 578899999999999985
No 88
>cd06097 Aspergillopepsin_like Aspergillopepsin_like, aspartic proteases of fungal origin. The members of this family are aspartic proteases of fungal origin, including aspergillopepsin, rhizopuspepsin, endothiapepsin, and rodosporapepsin. The various fungal species in this family may be the most economically important genus of fungi. They may serve as virulence factors or as industrial aids. For example, Aspergillopepsin from A. fumigatus is involved in invasive aspergillosis owing to its elastolytic activity and Aspergillopepsins from the mold A. saitoi are used in fermentation industry. Aspartic proteinases are a group of proteolytic enzymes in which the scissile peptide bond is attacked by a nucleophilic water molecule activated by two aspartic residues in a DT(S)G motif at the active site. They have a similar fold composed of two beta-barrel domains. Between the N-terminal and C-terminal domains, each of which contributes one catalytic aspartic residue, there is an extended active-
Probab=34.29 E-value=31 Score=30.70 Aligned_cols=23 Identities=17% Similarity=0.255 Sum_probs=19.7
Q ss_pred EEEEEeeCCCcchhccHHHHHHh
Q 036272 317 PLTILIDSGSTHNYLHHRFAKIT 339 (383)
Q Consensus 317 ~v~~LiDsGAt~s~Is~~~~~~l 339 (383)
...++||||++..++.+.+++.+
T Consensus 198 ~~~~iiDSGTs~~~lP~~~~~~l 220 (278)
T cd06097 198 GFSAIADTGTTLILLPDAIVEAY 220 (278)
T ss_pred CceEEeecCCchhcCCHHHHHHH
Confidence 45799999999999998887765
No 89
>PF14543 TAXi_N: Xylanase inhibitor N-terminal; PDB: 3HD8_A 3VLB_A 3VLA_A 3AUP_D 1T6G_A 1T6E_X 2B42_A.
Probab=34.20 E-value=44 Score=27.14 Aligned_cols=25 Identities=24% Similarity=0.577 Sum_probs=17.6
Q ss_pred EEEEEcC--eEEEEEeeCCCcchhccH
Q 036272 309 VHSQISK--IPLTILIDSGSTHNYLHH 333 (383)
Q Consensus 309 ~~~~i~~--~~v~~LiDsGAt~s~Is~ 333 (383)
+.+.|+. +++.++|||||+.+.+.-
T Consensus 3 ~~~~iGtP~~~~~lvvDtgs~l~W~~C 29 (164)
T PF14543_consen 3 VSVSIGTPPQPFSLVVDTGSDLTWVQC 29 (164)
T ss_dssp EEEECTCTTEEEEEEEETT-SSEEEET
T ss_pred EEEEeCCCCceEEEEEECCCCceEEcC
Confidence 3445543 588999999999988744
No 90
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=33.99 E-value=18 Score=24.63 Aligned_cols=9 Identities=22% Similarity=0.910 Sum_probs=7.6
Q ss_pred ccccccCCC
Q 036272 251 ELCYSCDEN 259 (383)
Q Consensus 251 ~~Cf~C~~~ 259 (383)
.+||.||+.
T Consensus 5 VRCFTCGkv 13 (71)
T PLN00032 5 VRCFTCGKV 13 (71)
T ss_pred eeecCCCCC
Confidence 579999985
No 91
>cd06096 Plasmepsin_5 Plasmepsins are a class of aspartic proteinases produced by the plasmodium parasite. The family contains a group of aspartic proteinases homologous to plasmepsin 5. Plasmepsins are a class of at least 10 enzymes produced by the plasmodium parasite. Through their haemoglobin-degrading activity, they are an important cause of symptoms in malaria sufferers. This family of enzymes is a potential target for anti-malarial drugs. Plasmepsins are aspartic acid proteases, which means their active site contains two aspartic acid residues. These two aspartic acid residue act respectively as proton donor and proton acceptor, catalyzing the hydrolysis of peptide bond in proteins. Aspartic proteinases are composed of two structurally similar beta barrel lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The catalytic Asp residues are contained in an Asp-Thr-Gly-Ser/thr motif in both N- and C-terminal l
Probab=33.33 E-value=46 Score=30.48 Aligned_cols=27 Identities=15% Similarity=0.203 Sum_probs=20.8
Q ss_pred EEEEEEc--CeEEEEEeeCCCcchhccHH
Q 036272 308 RVHSQIS--KIPLTILIDSGSTHNYLHHR 334 (383)
Q Consensus 308 ~~~~~i~--~~~v~~LiDsGAt~s~Is~~ 334 (383)
.+.+.|+ .+++.++|||||+...|...
T Consensus 5 ~~~i~vGtP~Q~~~v~~DTGS~~~wv~~~ 33 (326)
T cd06096 5 FIDIFIGNPPQKQSLILDTGSSSLSFPCS 33 (326)
T ss_pred EEEEEecCCCeEEEEEEeCCCCceEEecC
Confidence 3455665 47889999999999988654
No 92
>cd05478 pepsin_A Pepsin A, aspartic protease produced in gastric mucosa of mammals. Pepsin, a well-known aspartic protease, is produced by the human gastric mucosa in seven different zymogen isoforms, subdivided into two types: pepsinogen A and pepsinogen C. The prosequence of the zymogens are self cleaved under acidic pH. The mature enzymes are called pepsin A and pepsin C, correspondingly. The well researched porcine pepsin is also in this pepsin A family. Pepsins play an integral role in the digestion process of vertebrates. Pepsins are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. More recently evolved enzymes have similar three-dimensional structures, however their amino acid sequences are more divergent except for the conserved catalytic site motif. Pepsins specifically cleave bonds in peptides which
Probab=32.31 E-value=45 Score=30.37 Aligned_cols=29 Identities=17% Similarity=0.261 Sum_probs=22.3
Q ss_pred ceEEEEEEc--CeEEEEEeeCCCcchhccHH
Q 036272 306 TMRVHSQIS--KIPLTILIDSGSTHNYLHHR 334 (383)
Q Consensus 306 ~~~~~~~i~--~~~v~~LiDsGAt~s~Is~~ 334 (383)
...+.+.|+ .+++.++|||||+..+|...
T Consensus 10 ~Y~~~i~vGtp~q~~~v~~DTGS~~~wv~~~ 40 (317)
T cd05478 10 EYYGTISIGTPPQDFTVIFDTGSSNLWVPSV 40 (317)
T ss_pred EEEEEEEeCCCCcEEEEEEeCCCccEEEecC
Confidence 344566676 47899999999999999743
No 93
>cd05471 pepsin_like Pepsin-like aspartic proteases, bilobal enzymes that cleave bonds in peptides at acidic pH. Pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, renin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (renin, cathepsin D and E, pepsin) or commercially (chymosin) important. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Aspartate residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. Most members of the pepsin family specifically cleave bonds in peptides that are at least six residues in length, with hydrophobic residu
Probab=32.12 E-value=46 Score=29.40 Aligned_cols=28 Identities=14% Similarity=0.253 Sum_probs=21.0
Q ss_pred EEEEEcC--eEEEEEeeCCCcchhccHHHH
Q 036272 309 VHSQISK--IPLTILIDSGSTHNYLHHRFA 336 (383)
Q Consensus 309 ~~~~i~~--~~v~~LiDsGAt~s~Is~~~~ 336 (383)
+.+.|+. +++.++|||||+...|.....
T Consensus 3 ~~i~iGtp~q~~~l~~DTGS~~~wv~~~~c 32 (283)
T cd05471 3 GEITIGTPPQKFSVIFDTGSSLLWVPSSNC 32 (283)
T ss_pred EEEEECCCCcEEEEEEeCCCCCEEEecCCC
Confidence 3455554 488999999999998877643
No 94
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=31.62 E-value=24 Score=23.12 Aligned_cols=16 Identities=19% Similarity=0.804 Sum_probs=13.1
Q ss_pred ccccccCCCccccccc
Q 036272 251 ELCYSCDENYTVGHKC 266 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~C 266 (383)
..||+|+..+|.-..|
T Consensus 49 ~fC~~C~~~~H~~~~C 64 (64)
T smart00647 49 SFCFRCKVPWHSPVSC 64 (64)
T ss_pred eECCCCCCcCCCCCCC
Confidence 4699999999976655
No 95
>PF14541 TAXi_C: Xylanase inhibitor C-terminal; PDB: 3AUP_D 3HD8_A 1T6G_A 1T6E_X 2B42_A 3VLB_A 3VLA_A.
Probab=31.50 E-value=35 Score=27.55 Aligned_cols=22 Identities=32% Similarity=0.327 Sum_probs=17.5
Q ss_pred EEEEeeCCCcchhccHHHHHHh
Q 036272 318 LTILIDSGSTHNYLHHRFAKIT 339 (383)
Q Consensus 318 v~~LiDsGAt~s~Is~~~~~~l 339 (383)
-.++||||.+.+++.+.+...|
T Consensus 30 g~~iiDSGT~~T~L~~~~y~~l 51 (161)
T PF14541_consen 30 GGTIIDSGTTYTYLPPPVYDAL 51 (161)
T ss_dssp CSEEE-SSSSSEEEEHHHHHHH
T ss_pred CCEEEECCCCccCCcHHHHHHH
Confidence 3578999999999999877664
No 96
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=31.26 E-value=17 Score=23.62 Aligned_cols=9 Identities=22% Similarity=0.881 Sum_probs=7.4
Q ss_pred ccccccCCC
Q 036272 251 ELCYSCDEN 259 (383)
Q Consensus 251 ~~Cf~C~~~ 259 (383)
.+||.||+.
T Consensus 5 iRCFtCGKv 13 (69)
T KOG3497|consen 5 IRCFTCGKV 13 (69)
T ss_pred eEeeecccc
Confidence 469999984
No 97
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=30.95 E-value=22 Score=23.44 Aligned_cols=9 Identities=22% Similarity=0.910 Sum_probs=6.6
Q ss_pred ccccccCCC
Q 036272 251 ELCYSCDEN 259 (383)
Q Consensus 251 ~~Cf~C~~~ 259 (383)
.+||.||+.
T Consensus 5 VRCFTCGkv 13 (60)
T PF01194_consen 5 VRCFTCGKV 13 (60)
T ss_dssp SS-STTTSB
T ss_pred eecCCCCCC
Confidence 579999984
No 98
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=30.58 E-value=1.9e+02 Score=25.82 Aligned_cols=117 Identities=12% Similarity=0.003 Sum_probs=59.5
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCChHHHHHHHHHHHHHhCCchhhHHHHhhhhcccchhhHHHHhhhcC
Q 036272 18 RNWGPQGQGGAGYAGGLVAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQG 97 (383)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~F~G~~d~~~w~~~~e~~~~~~~~~d~~k~~~~~~~L~g~A~~w~~~~~~~~ 97 (383)
-.+++.++.+..++-.+..+.+..+.|+.+-+. +..+| |-...-..+ +.|..+-+ .+.|+..+-...
T Consensus 49 ~~~d~s~~~p~~~~~~~~~p~~~~~~P~~~~~~-rwrdy---~vmAvi~aG------i~y~~y~~---~K~YV~P~~l~~ 115 (300)
T KOG2629|consen 49 PAQDVSKQIPTANQVVSGGPPLLIIQPQQNVLR-RWRDY---FVMAVILAG------IAYAAYRF---VKSYVLPRFLGE 115 (300)
T ss_pred ccccccccCCCcccccCCCchhhhcCCCccchh-hHHHH---HHHHHHHhh------HHHHHHHH---HHHHHHHHhhCc
Confidence 344566677766666666666666777766553 33333 222222112 12221111 233333322223
Q ss_pred CCCCHHHHHHHHHhhhcCcccc--cHHHHhhcccc--cccHhhHHHHHHHHHHH
Q 036272 98 HLVTWDGLKAGLLAKFAATEYE--DSFGDLCKLKQ--TGTVSDYQPQFERLLAR 147 (383)
Q Consensus 98 ~~~~w~~~~~~l~~~F~~~~~~--~~~~~l~~~~q--~~sv~~Y~~~f~~l~~~ 147 (383)
...-+++-+..|.+.|..-... +...++...+| ...-.+|...+..|...
T Consensus 116 ~~~k~e~~k~~Ld~~~~~~~~~~~~l~~~va~v~q~~~~qq~Els~~L~~l~~~ 169 (300)
T KOG2629|consen 116 SKDKLEADKRQLDDQFDKAAKSLNALMDEVAQVSQLLATQQSELSRALASLKNT 169 (300)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3235788888888888876653 23344555554 33344666666655554
No 99
>PTZ00147 plasmepsin-1; Provisional
Probab=30.33 E-value=54 Score=31.75 Aligned_cols=28 Identities=11% Similarity=0.233 Sum_probs=22.2
Q ss_pred eEEEEEEc--CeEEEEEeeCCCcchhccHH
Q 036272 307 MRVHSQIS--KIPLTILIDSGSTHNYLHHR 334 (383)
Q Consensus 307 ~~~~~~i~--~~~v~~LiDsGAt~s~Is~~ 334 (383)
....+.|+ .+++.++|||||+...|...
T Consensus 140 Y~~~I~IGTP~Q~f~Vi~DTGSsdlWVps~ 169 (453)
T PTZ00147 140 SYGEAKLGDNGQKFNFIFDTGSANLWVPSI 169 (453)
T ss_pred EEEEEEECCCCeEEEEEEeCCCCcEEEeec
Confidence 44566676 67899999999999998654
No 100
>cd05473 beta_secretase_like Beta-secretase, aspartic-acid protease important in the pathogenesis of Alzheimer's disease. Beta-secretase also called BACE (beta-site of APP cleaving enzyme) or memapsin-2. Beta-secretase is an aspartic-acid protease important in the pathogenesis of Alzheimer's disease, and in the formation of myelin sheaths in peripheral nerve cells. It cleaves amyloid precursor protein (APP) to reveal the N-terminus of the beta-amyloid peptides. The beta-amyloid peptides are the major components of the amyloid plaques formed in the brain of patients with Alzheimer's disease (AD). Since BACE mediates one of the cleavages responsible for generation of AD, it is regarded as a potential target for pharmacological intervention in AD. Beta-secretase is a member of pepsin family of aspartic proteases. Same as other aspartic proteases, beta-secretase is a bilobal enzyme, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two
Probab=30.29 E-value=50 Score=30.80 Aligned_cols=27 Identities=26% Similarity=0.342 Sum_probs=21.0
Q ss_pred EEEEEEc--CeEEEEEeeCCCcchhccHH
Q 036272 308 RVHSQIS--KIPLTILIDSGSTHNYLHHR 334 (383)
Q Consensus 308 ~~~~~i~--~~~v~~LiDsGAt~s~Is~~ 334 (383)
.+.+.|+ .+++.++|||||+...|...
T Consensus 5 ~~~i~iGtP~Q~~~v~~DTGSs~lWv~~~ 33 (364)
T cd05473 5 YIEMLIGTPPQKLNILVDTGSSNFAVAAA 33 (364)
T ss_pred EEEEEecCCCceEEEEEecCCcceEEEcC
Confidence 4556665 47899999999999988654
No 101
>cd05485 Cathepsin_D_like Cathepsin_D_like, pepsin family of proteinases. Cathepsin D is the major aspartic proteinase of the lysosomal compartment where it functions in protein catabolism. It is a member of the pepsin family of proteinases. This enzyme is distinguished from other members of the pepsin family by two features that are characteristic of lysosomal hydrolases. First, mature Cathepsin D is found predominantly in a two-chain form due to a posttranslational cleavage event. Second, it contains phosphorylated, N-linked oligosaccharides that target the enzyme to lysosomes via mannose-6-phosphate receptors. Cathepsin D preferentially attacks peptide bonds flanked by bulky hydrophobic amino acids and its pH optimum is between pH 2.8 and 4.0. Two active site aspartic acid residues are essential for the catalytic activity of aspartic proteinases. Like other aspartic proteinases, Cathepsin D is a bilobed molecule; the two evolutionary related lobes are mostly made up of beta-sheets an
Probab=30.27 E-value=50 Score=30.30 Aligned_cols=29 Identities=14% Similarity=0.268 Sum_probs=22.7
Q ss_pred ceEEEEEEc--CeEEEEEeeCCCcchhccHH
Q 036272 306 TMRVHSQIS--KIPLTILIDSGSTHNYLHHR 334 (383)
Q Consensus 306 ~~~~~~~i~--~~~v~~LiDsGAt~s~Is~~ 334 (383)
...+.+.|+ .+++.++|||||+..+|...
T Consensus 11 ~Y~~~i~vGtP~q~~~v~~DTGSs~~Wv~~~ 41 (329)
T cd05485 11 QYYGVITIGTPPQSFKVVFDTGSSNLWVPSK 41 (329)
T ss_pred eEEEEEEECCCCcEEEEEEcCCCccEEEecC
Confidence 345567776 47899999999999988754
No 102
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=29.35 E-value=24 Score=23.41 Aligned_cols=9 Identities=22% Similarity=0.910 Sum_probs=7.5
Q ss_pred ccccccCCC
Q 036272 251 ELCYSCDEN 259 (383)
Q Consensus 251 ~~Cf~C~~~ 259 (383)
..||.||+.
T Consensus 5 vRCFTCGkv 13 (62)
T PRK04016 5 VRCFTCGKV 13 (62)
T ss_pred eEecCCCCC
Confidence 579999984
No 103
>cd05490 Cathepsin_D2 Cathepsin_D2, pepsin family of proteinases. Cathepsin D is the major aspartic proteinase of the lysosomal compartment where it functions in protein catabolism. It is a member of the pepsin family of proteinases. This enzyme is distinguished from other members of the pepsin family by two features that are characteristic of lysosomal hydrolases. First, mature Cathepsin D is found predominantly in a two-chain form due to a posttranslational cleavage event. Second, it contains phosphorylated, N-linked oligosaccharides that target the enzyme to lysosomes via mannose-6-phosphate receptors. Cathepsin D preferentially attacks peptide bonds flanked by bulky hydrophobic amino acids and its pH optimum is between pH 2.8 and 4.0. Two active site aspartic acid residues are essential for the catalytic activity of aspartic proteinases. Like other aspartic proteinases, Cathepsin D is a bilobed molecule; the two evolutionary related lobes are mostly made up of beta-sheets and flank
Probab=29.34 E-value=41 Score=30.71 Aligned_cols=22 Identities=9% Similarity=0.039 Sum_probs=19.6
Q ss_pred EEEEeeCCCcchhccHHHHHHh
Q 036272 318 LTILIDSGSTHNYLHHRFAKIT 339 (383)
Q Consensus 318 v~~LiDsGAt~s~Is~~~~~~l 339 (383)
..++||||++..++....++.+
T Consensus 207 ~~aiiDSGTt~~~~p~~~~~~l 228 (325)
T cd05490 207 CEAIVDTGTSLITGPVEEVRAL 228 (325)
T ss_pred CEEEECCCCccccCCHHHHHHH
Confidence 4799999999999999888766
No 104
>cd05486 Cathespin_E Cathepsin E, non-lysosomal aspartic protease. Cathepsin E is an intracellular, non-lysosomal aspartic protease expressed in a variety of cells and tissues. The protease has proposed physiological roles in antigen presentation by the MHC class II system, in the biogenesis of the vasoconstrictor peptide endothelin, and in neurodegeneration associated with brain ischemia and aging. Cathepsin E is the only A1 aspartic protease that exists as a homodimer with a disulfide bridge linking the two monomers. Like many other aspartic proteases, it is synthesized as a zymogen which is catalytically inactive towards its natural substrates at neutral pH and which auto-activates in an acidic environment. The overall structure follows the general fold of aspartic proteases of the A1 family, it is composed of two structurally similar beta barrel lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The catalyt
Probab=28.75 E-value=54 Score=29.83 Aligned_cols=26 Identities=19% Similarity=0.330 Sum_probs=19.8
Q ss_pred EEEEEc--CeEEEEEeeCCCcchhccHH
Q 036272 309 VHSQIS--KIPLTILIDSGSTHNYLHHR 334 (383)
Q Consensus 309 ~~~~i~--~~~v~~LiDsGAt~s~Is~~ 334 (383)
..+.|+ .+++.++|||||+...|...
T Consensus 3 ~~i~iGtP~Q~~~v~~DTGSs~~Wv~s~ 30 (316)
T cd05486 3 GQISIGTPPQNFTVIFDTGSSNLWVPSI 30 (316)
T ss_pred EEEEECCCCcEEEEEEcCCCccEEEecC
Confidence 344555 57889999999999988643
No 105
>PF03461 TRCF: TRCF domain; InterPro: IPR005118 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript.; GO: 0003684 damaged DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0006281 DNA repair; PDB: 2QSR_A 2EYQ_A.
Probab=28.42 E-value=37 Score=25.05 Aligned_cols=32 Identities=13% Similarity=0.221 Sum_probs=19.5
Q ss_pred hHHHHhhhcCCCCCHHHHHHHHHhhhcCcccc
Q 036272 88 LWFQQRKNQGHLVTWDGLKAGLLAKFAATEYE 119 (383)
Q Consensus 88 ~w~~~~~~~~~~~~w~~~~~~l~~~F~~~~~~ 119 (383)
.+|+.+.........+++.+.|..+||+...+
T Consensus 21 ~~Yrrl~~~~~~~el~~l~~El~DRFG~~P~e 52 (101)
T PF03461_consen 21 ELYRRLASAESEEELEDLREELIDRFGPLPEE 52 (101)
T ss_dssp HHHHHHHC--SHHHHHHHHHHHHHHH-S--HH
T ss_pred HHHHHHhhCCCHHHHHHHHHHHHHHcCCCcHH
Confidence 35666654455567778899999999987754
No 106
>COG0282 ackA Acetate kinase [Energy production and conversion]
Probab=28.31 E-value=42 Score=31.30 Aligned_cols=46 Identities=26% Similarity=0.364 Sum_probs=37.3
Q ss_pred CCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEE
Q 036272 325 GSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRL 370 (383)
Q Consensus 325 GAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v 370 (383)
|=+|.||+..+++.|+.+..+...+..=++||.++.....=..|+-
T Consensus 179 GtSh~YVs~~aa~~L~k~~~~l~~I~~HLGNGASicAiknGkSvDT 224 (396)
T COG0282 179 GTSHKYVSQRAAEILGKPLEDLNLITCHLGNGASICAIKNGKSVDT 224 (396)
T ss_pred ccchHHHHHHHHHHhCCCccccCEEEEEecCchhhhhhhCCeeecc
Confidence 7789999999999999988888888888899988777654444443
No 107
>PTZ00013 plasmepsin 4 (PM4); Provisional
Probab=27.89 E-value=65 Score=31.18 Aligned_cols=28 Identities=11% Similarity=0.297 Sum_probs=21.8
Q ss_pred EEEEEEc--CeEEEEEeeCCCcchhccHHH
Q 036272 308 RVHSQIS--KIPLTILIDSGSTHNYLHHRF 335 (383)
Q Consensus 308 ~~~~~i~--~~~v~~LiDsGAt~s~Is~~~ 335 (383)
...+.|+ +.++.++|||||+...|...-
T Consensus 140 y~~i~IGTP~Q~f~vi~DTGSsdlWV~s~~ 169 (450)
T PTZ00013 140 YGEGEVGDNHQKFMLIFDTGSANLWVPSKK 169 (450)
T ss_pred EEEEEECCCCeEEEEEEeCCCCceEEeccc
Confidence 3455665 688999999999999997543
No 108
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=27.88 E-value=22 Score=23.22 Aligned_cols=16 Identities=38% Similarity=1.138 Sum_probs=12.6
Q ss_pred ccccccCCCccccccc
Q 036272 251 ELCYSCDENYTVGHKC 266 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~C 266 (383)
..||.|++..|....|
T Consensus 49 ~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 49 EFCFKCGEPWHEGVTC 64 (64)
T ss_dssp EECSSSTSESCTTS-H
T ss_pred cCccccCcccCCCCCC
Confidence 5699999999987665
No 109
>PF14420 Clr5: Clr5 domain
Probab=27.33 E-value=1.2e+02 Score=19.36 Aligned_cols=45 Identities=11% Similarity=0.244 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHhhhcCcccc--cHHHHhhcccc-cccHhhHHHHHHHH
Q 036272 100 VTWDGLKAGLLAKFAATEYE--DSFGDLCKLKQ-TGTVSDYQPQFERL 144 (383)
Q Consensus 100 ~~w~~~~~~l~~~F~~~~~~--~~~~~l~~~~q-~~sv~~Y~~~f~~l 144 (383)
..|+..+..+..-|...... +....+..... ..+...|-.+|...
T Consensus 3 ~~We~~K~~I~~LY~~e~~tl~~v~~~M~~~~~F~at~rqy~~r~~~W 50 (54)
T PF14420_consen 3 EDWEPHKEEIERLYIDENKTLEEVMEIMKEEHGFKATKRQYKRRFKKW 50 (54)
T ss_pred chHHHHHHHHHHHHHhCCCcHHHHHHHHHHHhCCCcCHHHHHHHHHHc
Confidence 57999999999888755543 33444433333 77888888888753
No 110
>cd05471 pepsin_like Pepsin-like aspartic proteases, bilobal enzymes that cleave bonds in peptides at acidic pH. Pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, renin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (renin, cathepsin D and E, pepsin) or commercially (chymosin) important. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Aspartate residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. Most members of the pepsin family specifically cleave bonds in peptides that are at least six residues in length, with hydrophobic residu
Probab=26.92 E-value=49 Score=29.20 Aligned_cols=25 Identities=20% Similarity=0.141 Sum_probs=21.6
Q ss_pred eEEEEEeeCCCcchhccHHHHHHhC
Q 036272 316 IPLTILIDSGSTHNYLHHRFAKITR 340 (383)
Q Consensus 316 ~~v~~LiDsGAt~s~Is~~~~~~l~ 340 (383)
....++||||++..++.+.+++.|-
T Consensus 201 ~~~~~iiDsGt~~~~lp~~~~~~l~ 225 (283)
T cd05471 201 GGGGAIVDSGTSLIYLPSSVYDAIL 225 (283)
T ss_pred CCcEEEEecCCCCEeCCHHHHHHHH
Confidence 3568999999999999999888764
No 111
>cd05487 renin_like Renin stimulates production of angiotensin and thus affects blood pressure. Renin, also known as angiotensinogenase, is a circulating enzyme that participates in the renin-angiotensin system that mediates extracellular volume, arterial vasoconstriction, and consequently mean arterial blood pressure. The enzyme is secreted by the kidneys from specialized juxtaglomerular cells in response to decreases in glomerular filtration rate (a consequence of low blood volume), diminished filtered sodium chloride and sympathetic nervous system innervation. The enzyme circulates in the blood stream and hydrolyzes angiotensinogen secreted from the liver into the peptide angiotensin I. Angiotensin I is further cleaved in the lungs by endothelial bound angiotensin converting enzyme (ACE) into angiotensin II, the final active peptide. Renin is a member of the aspartic protease family. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Aspartate r
Probab=26.88 E-value=79 Score=28.92 Aligned_cols=22 Identities=14% Similarity=0.045 Sum_probs=18.8
Q ss_pred EEEEeeCCCcchhccHHHHHHh
Q 036272 318 LTILIDSGSTHNYLHHRFAKIT 339 (383)
Q Consensus 318 v~~LiDsGAt~s~Is~~~~~~l 339 (383)
..++||||++..++....++.+
T Consensus 208 ~~aiiDSGts~~~lP~~~~~~l 229 (326)
T cd05487 208 CTAVVDTGASFISGPTSSISKL 229 (326)
T ss_pred CEEEECCCccchhCcHHHHHHH
Confidence 3589999999999999877765
No 112
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.81 E-value=31 Score=32.89 Aligned_cols=20 Identities=15% Similarity=0.296 Sum_probs=17.7
Q ss_pred CccccccCCCccccccccee
Q 036272 250 QELCYSCDENYTVGHKCKKL 269 (383)
Q Consensus 250 ~~~Cf~C~~~GH~a~~Cp~~ 269 (383)
.+.|++|+++||....||..
T Consensus 158 sy~c~rc~~~g~wikacptv 177 (448)
T KOG0314|consen 158 SYKCVKCPTPGPWIKACPTV 177 (448)
T ss_pred CcceecCCCCCccceecccc
Confidence 36899999999999999863
No 113
>KOG4437 consensus ATP-dependent DNA ligase III [Replication, recombination and repair]
Probab=26.08 E-value=2.6e+02 Score=25.60 Aligned_cols=163 Identities=14% Similarity=0.123 Sum_probs=0.0
Q ss_pred ccCCCChHHHHHHH--HHHHHHhCCchhhHHHHhhhhcccchhhHHHHhhhcCCCCCHHHHHHHHHhhhcCcccc---cH
Q 036272 47 YDGSEDPTLWICRA--EQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYE---DS 121 (383)
Q Consensus 47 F~G~~d~~~w~~~~--e~~~~~~~~~d~~k~~~~~~~L~g~A~~w~~~~~~~~~~~~w~~~~~~l~~~F~~~~~~---~~ 121 (383)
||| |..-|+..+ |.--+.|+++|...+.++..-|.=-...-++.+.......+..-|-+.= +.|.+.... +.
T Consensus 189 FDG--DL~LWL~FLIRESD~R~YNl~DkKLI~lfsKiLn~~~~~~~~~Y~~~S~~~~i~i~~~~~-K~~~~~K~~~siQ~ 265 (482)
T KOG4437|consen 189 FDG--DLYLWLKFLIRESDKRVYNLNDKKLIKLFSKILNCNPDDMARDYEQGSVSETIRVFFEQS-KSFPPAKSLLTIQE 265 (482)
T ss_pred CCc--chhhhhhhhhcccccccccccHHHHHHHHHHHHccChHHHHHHHHhccchhhhhhhHhhc-cCCCCcccceeHHH
Q ss_pred HHH-hhcccccccHhhHHHHHHHHHHHh-------------CCCCHHHHHHHHHhhcchhHHhHccccCCCCH-HHHHHH
Q 036272 122 FGD-LCKLKQTGTVSDYQPQFERLLARA-------------GSLTDKQEAACFISGLKDGLRADVRAQNPQNL-SAAIGL 186 (383)
Q Consensus 122 ~~~-l~~~~q~~sv~~Y~~~f~~l~~~~-------------~~~~e~~~~~~f~~gL~~~l~~~l~~~~~~~l-~~~~~~ 186 (383)
..+ |.++..-+.-.+-.+.+..++.++ .+++...-..+++.||.|..-......+..++ +..+.-
T Consensus 266 ~D~~L~rLSKi~~~D~~~~~L~~~A~R~~~~~L~~iIRLIr~~L~~~s~A~~iL~~~~P~A~E~F~S~~L~~ViEr~~~N 345 (482)
T KOG4437|consen 266 VDEFLLRLSKLTKEDEQQQALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALDPNAYEAFKSRNLQDVVERVLHN 345 (482)
T ss_pred HHHHHHHHhcccchHHHHHHHHHHHHhcccchHHHHHHHHHHHhccCCChhHHHhccCCCcHHHHHhcCHHHHHHHHHHh
Q ss_pred HHHHHHHHhhhhccCCCCCCCcccCC
Q 036272 187 ARNYELKAQEIRRSVNPTFSSSVRNS 212 (383)
Q Consensus 187 a~~~e~~~~~~~~~~~~~~~~~~~~~ 212 (383)
+...+......+...-+.+-....+.
T Consensus 346 ~~~~~~~~~~~~~~s~~s~~~s~~Q~ 371 (482)
T KOG4437|consen 346 AQEVEKEPGQRRALSVQASLMTPVQP 371 (482)
T ss_pred HHHHhhCccccccccchhhhcCCcCh
No 114
>PLN03146 aspartyl protease family protein; Provisional
Probab=25.88 E-value=65 Score=30.95 Aligned_cols=20 Identities=40% Similarity=0.534 Sum_probs=17.1
Q ss_pred EEEeeCCCcchhccHHHHHH
Q 036272 319 TILIDSGSTHNYLHHRFAKI 338 (383)
Q Consensus 319 ~~LiDsGAt~s~Is~~~~~~ 338 (383)
.++||||++.+++.+...+.
T Consensus 309 ~~iiDSGTt~t~Lp~~~y~~ 328 (431)
T PLN03146 309 NIIIDSGTTLTLLPSDFYSE 328 (431)
T ss_pred cEEEeCCccceecCHHHHHH
Confidence 47999999999999996554
No 115
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=25.82 E-value=29 Score=22.41 Aligned_cols=18 Identities=22% Similarity=0.401 Sum_probs=7.0
Q ss_pred ccccccCCCc---ccccccce
Q 036272 251 ELCYSCDENY---TVGHKCKK 268 (383)
Q Consensus 251 ~~Cf~C~~~G---H~a~~Cp~ 268 (383)
..|-.||..| |..+-||.
T Consensus 34 y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp ---TTT---GGG---GGG-TT
T ss_pred CcCCCCcCcCccccccccCcC
Confidence 5799999866 66667875
No 116
>cd05488 Proteinase_A_fungi Fungal Proteinase A , aspartic proteinase superfamily. Fungal Proteinase A, a proteolytic enzyme distributed among a variety of organisms, is a member of the aspartic proteinase superfamily. In Saccharomyces cerevisiae, targeted to the vacuole as a zymogen, activation of proteinases A at acidic pH can occur by two different pathways: a one-step process to release mature proteinase A, involving the intervention of proteinase B, or a step-wise pathway via the auto-activation product known as pseudo-proteinase A. Once active, S. cerevisiae proteinase A is essential to the activities of other yeast vacuolar hydrolases, including proteinase B and carboxypeptidase Y. The mature enzyme is bilobal, with each lobe providing one of the two catalytically essential aspartic acid residues in the active site. The crystal structure of free proteinase A shows that flap loop is atypically pointing directly into the S(1) pocket of the enzyme. Proteinase A preferentially hydro
Probab=24.78 E-value=52 Score=30.02 Aligned_cols=23 Identities=22% Similarity=0.263 Sum_probs=19.8
Q ss_pred EEEEeeCCCcchhccHHHHHHhC
Q 036272 318 LTILIDSGSTHNYLHHRFAKITR 340 (383)
Q Consensus 318 v~~LiDsGAt~s~Is~~~~~~l~ 340 (383)
..++||||++..++...+++.+.
T Consensus 206 ~~~ivDSGtt~~~lp~~~~~~l~ 228 (320)
T cd05488 206 TGAAIDTGTSLIALPSDLAEMLN 228 (320)
T ss_pred CeEEEcCCcccccCCHHHHHHHH
Confidence 36899999999999999888653
No 117
>PF00649 Copper-fist: Copper fist DNA binding domain; InterPro: IPR001083 Some fungal transcription factors contain an N-terminal domain, the copper fist, which seems to be involved in copper-dependent DNA-binding [, ]. These proteins activate the transcription of the metallothionein gene in response to copper. Metallothionein maintains copper levels in yeast [, ]. The copper fist domain, which is similar in structure to metallothionein itself, undergoes a large conformational change on copper-binding that allows DNA-binding. The domain contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet []. Conserved residues form a basic patch that may be important for DNA binding. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0005507 copper ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1CO4_A.
Probab=24.28 E-value=42 Score=19.96 Aligned_cols=17 Identities=24% Similarity=0.434 Sum_probs=11.4
Q ss_pred ccccccCCCcccccccce
Q 036272 251 ELCYSCDENYTVGHKCKK 268 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~Cp~ 268 (383)
.-|-.|-+ ||.+..|.+
T Consensus 9 yAC~~Cir-GHRss~C~H 25 (40)
T PF00649_consen 9 YACESCIR-GHRSSTCNH 25 (40)
T ss_dssp EEETTTTT-TSGGGG---
T ss_pred EEhhhhhC-ccccCcccC
Confidence 34778877 999999975
No 118
>PLN03146 aspartyl protease family protein; Provisional
Probab=23.90 E-value=72 Score=30.66 Aligned_cols=28 Identities=18% Similarity=0.345 Sum_probs=21.7
Q ss_pred ceEEEEEEc--CeEEEEEeeCCCcchhccH
Q 036272 306 TMRVHSQIS--KIPLTILIDSGSTHNYLHH 333 (383)
Q Consensus 306 ~~~~~~~i~--~~~v~~LiDsGAt~s~Is~ 333 (383)
...+.+.|+ .+++.+++||||+...|.-
T Consensus 84 ~Y~v~i~iGTPpq~~~vi~DTGS~l~Wv~C 113 (431)
T PLN03146 84 EYLMNISIGTPPVPILAIADTGSDLIWTQC 113 (431)
T ss_pred cEEEEEEcCCCCceEEEEECCCCCcceEcC
Confidence 455666776 4678999999999999853
No 119
>TIGR03778 VPDSG_CTERM VPDSG-CTERM exosortase interaction domain. Through in silico analysis, we previously described the PEP-CTERM/exosortase system (PubMed:16930487). This model describes a PEP-CTERM-like variant C-terminal protein sorting signal, as found at the C-terminus of twenty otherwise unrelated proteins in Verrucomicrobiae bacterium DG1235. The variant motif, VPDSG, seems an intermediate between the VPEP motif (TIGR02595) of typical exosortase systems and the classical LPXTG of sortase in Gram-positive bacteria.
Probab=23.82 E-value=23 Score=18.86 Aligned_cols=20 Identities=30% Similarity=0.270 Sum_probs=14.4
Q ss_pred eeCCCcchhccHHHHHHhCC
Q 036272 322 IDSGSTHNYLHHRFAKITRI 341 (383)
Q Consensus 322 iDsGAt~s~Is~~~~~~l~l 341 (383)
-|+|||..+..-.+.--+.+
T Consensus 2 PDsGST~~Ll~~~l~~l~~~ 21 (26)
T TIGR03778 2 PDSGSTLALLGLGLLGLLGL 21 (26)
T ss_pred CCchhHHHHHHHHHHHHHHH
Confidence 38999998887776655544
No 120
>cd05489 xylanase_inhibitor_I_like TAXI-I inhibits degradation of xylan in the cell wall. Xylanase inhibitor-I (TAXI-I) is a member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases. Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms. Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and colonization by antagonists. Xylanases of fungal and bacterial pathogens are the key enzymes in the degradation of xylan in the cell wall. Plants secrete proteins that inhibit these degradation glycosidases, including xylanase. Surprisingly, TAXI-I displays structural homology with the pepsin-like family of aspartic proteases but is proteolytically nonfunctional, because one or more residues of the essential catalytic triad are absent. The structure of the TAXI-inhibitor, Aspergillus niger xylanase I complex, illustrates the ability
Probab=23.65 E-value=75 Score=29.70 Aligned_cols=22 Identities=5% Similarity=0.004 Sum_probs=18.3
Q ss_pred EEEeeCCCcchhccHHHHHHhC
Q 036272 319 TILIDSGSTHNYLHHRFAKITR 340 (383)
Q Consensus 319 ~~LiDsGAt~s~Is~~~~~~l~ 340 (383)
-++||||.+.+++.+.+.+.+.
T Consensus 231 g~iiDSGTs~t~lp~~~y~~l~ 252 (362)
T cd05489 231 GVKLSTVVPYTVLRSDIYRAFT 252 (362)
T ss_pred cEEEecCCceEEECHHHHHHHH
Confidence 4899999999998888776643
No 121
>PTZ00165 aspartyl protease; Provisional
Probab=22.96 E-value=82 Score=30.80 Aligned_cols=31 Identities=13% Similarity=0.260 Sum_probs=23.9
Q ss_pred ceEEEEEEcC--eEEEEEeeCCCcchhccHHHH
Q 036272 306 TMRVHSQISK--IPLTILIDSGSTHNYLHHRFA 336 (383)
Q Consensus 306 ~~~~~~~i~~--~~v~~LiDsGAt~s~Is~~~~ 336 (383)
.....+.|+. +++.+++||||+...|....+
T Consensus 120 ~Y~~~I~IGTPpQ~f~Vv~DTGSS~lWVps~~C 152 (482)
T PTZ00165 120 QYFGEIQVGTPPKSFVVVFDTGSSNLWIPSKEC 152 (482)
T ss_pred eEEEEEEeCCCCceEEEEEeCCCCCEEEEchhc
Confidence 3456667764 789999999999999976543
No 122
>smart00545 JmjN Small domain found in the jumonji family of transcription factors. To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).
Probab=22.52 E-value=1e+02 Score=18.61 Aligned_cols=26 Identities=23% Similarity=0.409 Sum_probs=17.4
Q ss_pred CCCccCC----CChHHHHHHHHHHHHHhCC
Q 036272 44 FPCYDGS----EDPTLWICRAEQFFEFQGT 69 (383)
Q Consensus 44 ~p~F~G~----~d~~~w~~~~e~~~~~~~~ 69 (383)
.|+|..+ .|+..|+..++.....+++
T Consensus 2 iPvf~Pt~eEF~Dp~~yi~~i~~~~~~yGi 31 (42)
T smart00545 2 IPVFYPTMEEFKDPLAYISKIRPQAEKYGI 31 (42)
T ss_pred CCeEcCCHHHHHCHHHHHHHHHHHHhhCCE
Confidence 4667665 5677788888776655543
No 123
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=22.09 E-value=39 Score=32.38 Aligned_cols=19 Identities=16% Similarity=0.370 Sum_probs=17.4
Q ss_pred ccccccCCCccccccccee
Q 036272 251 ELCYSCDENYTVGHKCKKL 269 (383)
Q Consensus 251 ~~Cf~C~~~GH~a~~Cp~~ 269 (383)
..|-+||..||...+||..
T Consensus 262 ~~c~~cg~~~H~q~~cp~r 280 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGR 280 (554)
T ss_pred ccccccCCCccccccCCcc
Confidence 4799999999999999976
No 124
>PTZ00013 plasmepsin 4 (PM4); Provisional
Probab=21.68 E-value=64 Score=31.20 Aligned_cols=22 Identities=23% Similarity=0.320 Sum_probs=19.0
Q ss_pred EEEEeeCCCcchhccHHHHHHh
Q 036272 318 LTILIDSGSTHNYLHHRFAKIT 339 (383)
Q Consensus 318 v~~LiDsGAt~s~Is~~~~~~l 339 (383)
..++||||++..++.++.++.+
T Consensus 332 ~~aIlDSGTSli~lP~~~~~~i 353 (450)
T PTZ00013 332 ANVIVDSGTTTITAPSEFLNKF 353 (450)
T ss_pred cceEECCCCccccCCHHHHHHH
Confidence 4699999999999999887754
No 125
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=21.08 E-value=1.9e+02 Score=20.24 Aligned_cols=32 Identities=16% Similarity=0.016 Sum_probs=17.1
Q ss_pred CChHHHHHHHHHHHHHhC--CchhhHHHHhhhhc
Q 036272 51 EDPTLWICRAEQFFEFQG--TSLENQVKLAAYHL 82 (383)
Q Consensus 51 ~d~~~w~~~~e~~~~~~~--~~d~~k~~~~~~~L 82 (383)
+.+.+|+..|+..+.... +++..++..+..-|
T Consensus 61 esv~~y~~rf~~l~~~~~~~~~e~~~v~~f~~GL 94 (96)
T PF03732_consen 61 ESVREYVNRFRELARRAPPPMDEEMLVERFIRGL 94 (96)
T ss_pred CcHHHHHHHHHHHHHHCCCCcCHHHHHHHHHHCC
Confidence 455566666665555444 55555555554433
No 126
>PRK05978 hypothetical protein; Provisional
Probab=20.77 E-value=50 Score=26.39 Aligned_cols=13 Identities=23% Similarity=0.442 Sum_probs=10.1
Q ss_pred cCccccccCCCccc
Q 036272 249 EQELCYSCDENYTV 262 (383)
Q Consensus 249 ~~~~Cf~C~~~GH~ 262 (383)
-.++|.+||+ ||+
T Consensus 32 l~grCP~CG~-G~L 44 (148)
T PRK05978 32 FRGRCPACGE-GKL 44 (148)
T ss_pred HcCcCCCCCC-Ccc
Confidence 4578999999 555
No 127
>KOG2985 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.51 E-value=33 Score=29.62 Aligned_cols=22 Identities=14% Similarity=0.460 Sum_probs=18.4
Q ss_pred CccccccCCCcccccccceeEE
Q 036272 250 QELCYSCDENYTVGHKCKKLFF 271 (383)
Q Consensus 250 ~~~Cf~C~~~GH~a~~Cp~~~~ 271 (383)
.+-|-+||.+||+.-+|.+.-.
T Consensus 81 sg~ckRcg~~ghl~fqcRn~~~ 102 (306)
T KOG2985|consen 81 SGSCKRCGRVGHLTFQCRNFLS 102 (306)
T ss_pred ccchhhccccchhhHHHhhhhh
Confidence 3679999999999999986443
Done!