Query 040033
Match_columns 158
No_of_seqs 144 out of 791
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 04:25:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040033.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040033hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08284 RVP_2: Retroviral asp 99.9 1.4E-25 3.1E-30 163.3 11.7 84 74-158 17-124 (135)
2 cd05479 RP_DDI RP_DDI; retrope 99.9 4.3E-21 9.4E-26 137.7 11.9 82 76-158 14-119 (124)
3 cd05484 retropepsin_like_LTR_2 99.6 1.3E-15 2.8E-20 103.4 9.1 67 80-147 2-91 (91)
4 PF09668 Asp_protease: Asparty 99.6 2.2E-15 4.7E-20 108.0 10.3 79 76-155 22-124 (124)
5 TIGR02281 clan_AA_DTGA clan AA 99.5 1.4E-13 2.9E-18 98.5 10.6 82 75-156 8-114 (121)
6 PF13650 Asp_protease_2: Aspar 99.5 2.9E-13 6.3E-18 90.3 9.0 65 81-145 1-90 (90)
7 PF00077 RVP: Retroviral aspar 99.5 6.3E-13 1.4E-17 91.2 9.2 72 79-151 6-97 (100)
8 cd05480 NRIP_C NRIP_C; putativ 99.4 5.3E-13 1.1E-17 91.4 8.3 75 82-157 2-102 (103)
9 cd05483 retropepsin_like_bacte 99.4 2.1E-12 4.4E-17 87.0 9.4 70 78-147 2-96 (96)
10 PF12384 Peptidase_A2B: Ty3 tr 99.3 3.4E-11 7.3E-16 89.4 9.8 79 73-151 29-131 (177)
11 TIGR03698 clan_AA_DTGF clan AA 99.3 3.5E-11 7.5E-16 84.3 9.4 70 87-158 14-104 (107)
12 cd06095 RP_RTVL_H_like Retrope 99.2 6.1E-11 1.3E-15 79.7 8.5 65 82-147 2-86 (86)
13 cd00303 retropepsin_like Retro 99.2 1.6E-10 3.6E-15 73.9 8.1 66 82-147 2-92 (92)
14 KOG0012 DNA damage inducible p 99.1 1.4E-10 3.1E-15 95.1 6.7 80 77-157 234-337 (380)
15 PF13975 gag-asp_proteas: gag- 99.0 8.5E-10 1.8E-14 71.9 5.6 41 75-115 5-45 (72)
16 COG3577 Predicted aspartyl pro 98.9 7.7E-09 1.7E-13 79.4 7.6 82 74-155 101-207 (215)
17 PF02160 Peptidase_A3: Caulifl 98.6 1E-07 2.3E-12 73.3 6.3 69 88-157 19-110 (201)
18 cd05481 retropepsin_like_LTR_1 98.4 1.7E-06 3.6E-11 59.1 7.6 61 83-144 3-90 (93)
19 cd06094 RP_Saci_like RP_Saci_l 98.2 2.8E-06 6.1E-11 57.4 5.3 61 88-150 8-88 (89)
20 PF00098 zf-CCHC: Zinc knuckle 98.2 6.1E-07 1.3E-11 43.1 0.9 17 31-47 2-18 (18)
21 PF05585 DUF1758: Putative pep 98.2 4E-06 8.6E-11 62.5 5.5 28 88-115 11-38 (164)
22 COG5550 Predicted aspartyl pro 98.1 2.7E-05 5.9E-10 55.5 8.3 70 86-157 23-113 (125)
23 cd05482 HIV_retropepsin_like R 97.9 6.5E-05 1.4E-09 50.7 6.5 66 82-147 2-87 (87)
24 PF13696 zf-CCHC_2: Zinc knuck 96.7 0.00073 1.6E-08 37.0 0.8 19 30-48 9-27 (32)
25 smart00343 ZnF_C2HC zinc finge 95.9 0.0036 7.8E-08 32.4 0.9 18 31-48 1-18 (26)
26 PF13917 zf-CCHC_3: Zinc knuck 95.7 0.0045 9.7E-08 36.1 0.8 18 30-47 5-22 (42)
27 PF12382 Peptidase_A2E: Retrot 95.2 0.051 1.1E-06 37.6 4.9 65 79-143 35-124 (137)
28 PF14787 zf-CCHC_5: GAG-polypr 95.1 0.0074 1.6E-07 33.7 0.4 19 30-48 3-21 (36)
29 COG5082 AIR1 Arginine methyltr 94.7 0.012 2.7E-07 45.0 0.9 21 26-46 56-77 (190)
30 PF05618 Zn_protease: Putative 94.2 0.14 3E-06 37.4 5.4 33 117-149 89-124 (138)
31 COG5082 AIR1 Arginine methyltr 93.9 0.024 5.2E-07 43.4 0.9 19 30-48 98-117 (190)
32 PF14392 zf-CCHC_4: Zinc knuck 93.2 0.028 6E-07 33.6 0.2 22 26-47 27-49 (49)
33 COG4067 Uncharacterized protei 93.1 0.26 5.6E-06 36.6 5.2 38 117-155 113-152 (162)
34 PTZ00368 universal minicircle 91.2 0.089 1.9E-06 38.4 0.9 17 31-47 2-18 (148)
35 KOG4400 E3 ubiquitin ligase in 90.9 0.092 2E-06 42.0 0.7 18 30-47 144-161 (261)
36 COG5222 Uncharacterized conser 90.1 0.21 4.4E-06 41.1 2.1 19 30-48 177-195 (427)
37 cd05476 pepsin_A_like_plant Ch 89.3 1.4 3E-05 34.9 6.3 62 90-157 177-254 (265)
38 cd05477 gastricsin Gastricsins 89.2 1.8 3.8E-05 35.1 7.0 67 90-157 202-309 (318)
39 PTZ00368 universal minicircle 88.9 0.17 3.7E-06 36.9 0.8 18 30-47 104-121 (148)
40 PTZ00013 plasmepsin 4 (PM4); P 87.3 2 4.3E-05 37.3 6.4 26 81-106 141-168 (450)
41 cd05470 pepsin_retropepsin_lik 86.8 0.79 1.7E-05 30.9 3.1 25 82-106 2-28 (109)
42 cd05478 pepsin_A Pepsin A, asp 86.1 2.8 6E-05 34.0 6.4 74 83-157 194-309 (317)
43 PTZ00147 plasmepsin-1; Provisi 85.7 3.1 6.7E-05 36.1 6.8 26 80-105 141-168 (453)
44 PF15288 zf-CCHC_6: Zinc knuck 85.3 0.45 9.7E-06 27.3 1.0 18 31-48 3-22 (40)
45 cd06096 Plasmepsin_5 Plasmepsi 84.6 2.2 4.7E-05 34.9 5.2 68 89-157 231-314 (326)
46 cd05474 SAP_like SAPs, pepsin- 84.3 4.1 9E-05 32.3 6.5 64 81-145 5-80 (295)
47 KOG0109 RNA-binding protein LA 81.4 0.76 1.6E-05 37.7 1.2 17 32-48 163-179 (346)
48 cd06097 Aspergillopepsin_like 79.3 1.6 3.4E-05 34.7 2.4 68 89-157 198-270 (278)
49 cd05471 pepsin_like Pepsin-lik 79.2 2.7 5.9E-05 32.8 3.7 61 88-157 201-275 (283)
50 PF00026 Asp: Eukaryotic aspar 78.0 3.7 8E-05 32.7 4.2 26 80-105 3-30 (317)
51 PF05515 Viral_NABP: Viral nuc 75.8 1.2 2.6E-05 31.8 0.7 18 30-47 63-80 (124)
52 cd06097 Aspergillopepsin_like 74.0 4.3 9.4E-05 32.2 3.6 25 81-105 3-29 (278)
53 PF13821 DUF4187: Domain of un 73.0 1.9 4.1E-05 26.4 1.0 22 26-47 22-49 (55)
54 KOG0341 DEAD-box protein abstr 69.8 2.1 4.4E-05 36.9 0.9 19 30-48 571-589 (610)
55 KOG4400 E3 ubiquitin ligase in 69.7 1.8 3.9E-05 34.5 0.5 19 30-48 93-111 (261)
56 smart00647 IBR In Between Ring 69.6 2.2 4.9E-05 25.9 0.8 16 30-45 49-64 (64)
57 PF12353 eIF3g: Eukaryotic tra 68.5 2.6 5.6E-05 30.3 1.0 18 30-48 107-124 (128)
58 PF03539 Spuma_A9PTase: Spumav 68.5 16 0.00035 27.1 5.2 63 85-150 1-84 (163)
59 cd05472 cnd41_like Chloroplast 67.3 6.7 0.00015 31.4 3.4 21 91-111 173-193 (299)
60 cd06098 phytepsin Phytepsin, a 65.9 11 0.00023 30.7 4.3 26 80-105 12-39 (317)
61 PF01485 IBR: IBR domain; Int 65.8 1.7 3.7E-05 26.4 -0.3 16 30-45 49-64 (64)
62 KOG0119 Splicing factor 1/bran 64.0 3.4 7.5E-05 36.2 1.1 19 30-48 286-304 (554)
63 cd05487 renin_like Renin stimu 62.6 12 0.00026 30.4 4.1 25 81-105 11-37 (326)
64 cd05490 Cathepsin_D2 Cathepsin 62.4 12 0.00027 30.2 4.1 25 80-104 8-34 (325)
65 cd05476 pepsin_A_like_plant Ch 62.1 9.9 0.00021 29.9 3.4 65 81-145 4-88 (265)
66 cd05477 gastricsin Gastricsins 61.2 14 0.0003 29.9 4.1 25 81-105 6-32 (318)
67 cd06098 phytepsin Phytepsin, a 60.5 12 0.00026 30.3 3.7 74 83-157 197-309 (317)
68 cd05475 nucellin_like Nucellin 59.7 14 0.0003 29.3 3.9 24 81-104 5-30 (273)
69 cd05485 Cathepsin_D_like Cathe 59.6 12 0.00026 30.6 3.5 67 90-157 211-321 (329)
70 COG2383 Uncharacterized conser 59.4 2.7 5.9E-05 29.0 -0.2 18 140-157 51-68 (109)
71 KOG0107 Alternative splicing f 59.1 4.7 0.0001 30.8 1.0 18 30-47 101-118 (195)
72 cd05473 beta_secretase_like Be 58.3 11 0.00025 31.1 3.3 20 91-110 213-232 (364)
73 cd05486 Cathespin_E Cathepsin 57.8 9.8 0.00021 30.8 2.7 29 83-111 186-220 (316)
74 cd05486 Cathespin_E Cathepsin 57.5 15 0.00033 29.6 3.8 24 82-105 4-29 (316)
75 cd05478 pepsin_A Pepsin A, asp 57.2 17 0.00037 29.4 4.1 26 80-105 12-39 (317)
76 cd05473 beta_secretase_like Be 56.4 16 0.00035 30.2 3.8 25 81-105 6-32 (364)
77 cd06096 Plasmepsin_5 Plasmepsi 56.3 18 0.0004 29.4 4.1 25 81-105 6-32 (326)
78 cd05472 cnd41_like Chloroplast 56.3 11 0.00024 30.1 2.8 65 81-145 4-89 (299)
79 cd05488 Proteinase_A_fungi Fun 55.7 18 0.0004 29.3 4.0 27 79-105 11-39 (320)
80 cd05485 Cathepsin_D_like Cathe 55.6 19 0.00041 29.4 4.1 27 80-106 13-41 (329)
81 PF14543 TAXi_N: Xylanase inhi 51.7 24 0.00052 25.9 3.8 23 81-103 3-27 (164)
82 cd05471 pepsin_like Pepsin-lik 51.2 22 0.00048 27.5 3.7 26 82-107 4-31 (283)
83 KOG2673 Uncharacterized conser 49.9 11 0.00023 32.9 1.7 19 30-48 129-147 (485)
84 cd05489 xylanase_inhibitor_I_l 46.7 29 0.00062 29.0 3.9 20 91-110 231-250 (362)
85 PLN03146 aspartyl protease fam 46.5 23 0.00051 30.3 3.4 19 91-109 309-327 (431)
86 PTZ00165 aspartyl protease; Pr 44.1 34 0.00073 30.0 4.0 28 79-106 121-150 (482)
87 KOG2560 RNA splicing factor - 43.6 5.8 0.00013 34.5 -0.7 19 28-46 111-129 (529)
88 PF14541 TAXi_C: Xylanase inhi 42.1 22 0.00047 25.9 2.2 23 89-111 29-51 (161)
89 cd05487 renin_like Renin stimu 41.9 31 0.00067 28.0 3.3 22 90-111 208-229 (326)
90 cd05490 Cathepsin_D2 Cathepsin 41.6 19 0.00041 29.2 2.0 22 90-111 207-228 (325)
91 PLN03146 aspartyl protease fam 40.9 35 0.00076 29.3 3.6 26 79-104 85-112 (431)
92 KOG2044 5'-3' exonuclease HKE1 38.1 11 0.00025 35.0 0.2 19 30-48 261-279 (931)
93 KOG0119 Splicing factor 1/bran 37.1 19 0.00041 31.8 1.3 34 15-48 240-280 (554)
94 cd05488 Proteinase_A_fungi Fun 36.6 28 0.00062 28.1 2.3 67 90-157 206-312 (320)
95 KOG4584 Uncharacterized conser 35.7 24 0.00051 29.3 1.6 22 122-143 196-217 (348)
96 PTZ00147 plasmepsin-1; Provisi 35.6 53 0.0011 28.5 3.9 22 89-110 332-353 (453)
97 PTZ00165 aspartyl protease; Pr 34.8 53 0.0012 28.8 3.8 23 89-111 327-349 (482)
98 cd05474 SAP_like SAPs, pepsin- 34.6 30 0.00065 27.3 2.1 69 88-157 177-286 (295)
99 TIGR02854 spore_II_GA sigma-E 33.9 59 0.0013 26.4 3.7 35 77-111 157-202 (288)
100 PF03419 Peptidase_U4: Sporula 33.4 65 0.0014 26.0 3.9 34 78-111 157-201 (293)
101 PTZ00013 plasmepsin 4 (PM4); P 31.7 31 0.00068 29.9 1.8 23 89-111 331-353 (450)
102 COG1644 RPB10 DNA-directed RNA 30.3 24 0.00051 22.2 0.6 13 30-42 5-18 (63)
103 KOG3497 DNA-directed RNA polym 28.4 26 0.00056 22.0 0.6 8 31-38 6-13 (69)
104 PF00026 Asp: Eukaryotic aspar 28.1 54 0.0012 25.9 2.6 68 89-157 199-308 (317)
105 PF13395 HNH_4: HNH endonuclea 26.3 24 0.00051 21.1 0.1 9 32-40 1-9 (54)
106 smart00400 ZnF_CHCC zinc finge 25.6 34 0.00074 20.3 0.8 11 30-40 24-34 (55)
107 PF11880 DUF3400: Domain of un 25.6 60 0.0013 19.0 1.7 23 125-149 9-31 (45)
108 PF13771 zf-HC5HC2H: PHD-like 25.0 49 0.0011 21.4 1.5 19 30-48 37-55 (90)
109 PHA00689 hypothetical protein 24.9 18 0.00038 21.8 -0.6 18 24-41 12-29 (62)
110 PF13717 zinc_ribbon_4: zinc-r 24.6 24 0.00052 19.4 -0.1 23 18-40 13-36 (36)
111 PLN00032 DNA-directed RNA poly 23.8 31 0.00068 22.3 0.3 9 30-38 5-13 (71)
112 PRK04016 DNA-directed RNA poly 23.1 31 0.00067 21.7 0.2 9 30-38 5-13 (62)
113 PF04746 DUF575: Protein of un 22.8 45 0.00098 22.7 1.0 12 138-149 28-39 (101)
114 KOG1339 Aspartyl protease [Pos 20.8 97 0.0021 26.1 2.9 22 87-108 57-78 (398)
No 1
>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=99.93 E-value=1.4e-25 Score=163.35 Aligned_cols=84 Identities=40% Similarity=0.676 Sum_probs=79.0
Q ss_pred ccCceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------------------EEEEECCEEEEEEE
Q 040033 74 RASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------------------VNLILQGVYVIVDF 129 (158)
Q Consensus 74 ~~~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------------------A~i~i~g~~~~~~~ 129 (158)
..++.|...+.|+++++.+|||||||||||++++|++++++. .++.++|++|..+|
T Consensus 17 ~~~~vi~g~~~I~~~~~~vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~~V~~~g~~~~~~~~~~~~~~~i~g~~~~~dl 96 (135)
T PF08284_consen 17 ESPDVITGTFLINSIPASVLIDSGATHSFISSSFAKKLGLPLEPLPRPIVVSAPGGSINCEGVCPDVPLSIQGHEFVVDL 96 (135)
T ss_pred CCCCeEEEEEEeccEEEEEEEecCCCcEEccHHHHHhcCCEEEEccCeeEEecccccccccceeeeEEEEECCeEEEeee
Confidence 457889999999999999999999999999999999999887 18899999999999
Q ss_pred EEecCCCCcEEechhHhhhcCCceeeecC
Q 040033 130 NLRELEGYDVVLGTQWLRTLEPILWDFAS 158 (158)
Q Consensus 130 ~v~~~~~~dvILG~dwL~~~~~i~idw~~ 158 (158)
.|+++.++|||||||||.+|+| .|||.+
T Consensus 97 ~vl~l~~~DvILGm~WL~~~~~-~IDw~~ 124 (135)
T PF08284_consen 97 LVLDLGGYDVILGMDWLKKHNP-VIDWAT 124 (135)
T ss_pred EEecccceeeEeccchHHhCCC-EEEccC
Confidence 9999999999999999999999 899974
No 2
>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=99.86 E-value=4.3e-21 Score=137.71 Aligned_cols=82 Identities=21% Similarity=0.321 Sum_probs=75.6
Q ss_pred CceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------------------EEEEECCEEEEEEEEE
Q 040033 76 SETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------------------VNLILQGVYVIVDFNL 131 (158)
Q Consensus 76 ~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------------------A~i~i~g~~~~~~~~v 131 (158)
...+.+.+.|||+++.+||||||++|||+.++|+++|++. .++.+++.++.++|.|
T Consensus 14 ~~~~~v~~~Ing~~~~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~~~~~V 93 (124)
T cd05479 14 VPMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRIHLAQVKIGNLFLPCSFTV 93 (124)
T ss_pred eeEEEEEEEECCEEEEEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCCCcEEEeEEEEEEEEECCEEeeeEEEE
Confidence 4578899999999999999999999999999999999853 1888999999999999
Q ss_pred ecCCCCcEEechhHhhhcCCceeeecC
Q 040033 132 RELEGYDVVLGTQWLRTLEPILWDFAS 158 (158)
Q Consensus 132 ~~~~~~dvILG~dwL~~~~~i~idw~~ 158 (158)
+++..+|+|||||||++++. .|||++
T Consensus 94 l~~~~~d~ILG~d~L~~~~~-~ID~~~ 119 (124)
T cd05479 94 LEDDDVDFLIGLDMLKRHQC-VIDLKE 119 (124)
T ss_pred ECCCCcCEEecHHHHHhCCe-EEECCC
Confidence 99999999999999999995 899974
No 3
>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=99.64 E-value=1.3e-15 Score=103.40 Aligned_cols=67 Identities=19% Similarity=0.226 Sum_probs=61.1
Q ss_pred EEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE-----------------------EEEEECCEEEEEEEEEecCCC
Q 040033 80 RINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI-----------------------VNLILQGVYVIVDFNLRELEG 136 (158)
Q Consensus 80 ~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~-----------------------A~i~i~g~~~~~~~~v~~~~~ 136 (158)
.+.+.|||+++.+||||||++|||+++.+.+++.+. ..+++++.++.++|+|++..
T Consensus 2 ~~~~~Ing~~i~~lvDTGA~~svis~~~~~~lg~~~~~~~~~~v~~a~G~~~~~~G~~~~~v~~~~~~~~~~~~v~~~~- 80 (91)
T cd05484 2 TVTLLVNGKPLKFQLDTGSAITVISEKTWRKLGSPPLKPTKKRLRTATGTKLSVLGQILVTVKYGGKTKVLTLYVVKNE- 80 (91)
T ss_pred EEEEEECCEEEEEEEcCCcceEEeCHHHHHHhCCCccccccEEEEecCCCEeeEeEEEEEEEEECCEEEEEEEEEEECC-
Confidence 467899999999999999999999999999999753 17788999999999999998
Q ss_pred CcEEechhHhh
Q 040033 137 YDVVLGTQWLR 147 (158)
Q Consensus 137 ~dvILG~dwL~ 147 (158)
++.|||+|||.
T Consensus 81 ~~~lLG~~wl~ 91 (91)
T cd05484 81 GLNLLGRDWLD 91 (91)
T ss_pred CCCccChhhcC
Confidence 99999999984
No 4
>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=99.64 E-value=2.2e-15 Score=107.97 Aligned_cols=79 Identities=24% Similarity=0.381 Sum_probs=67.3
Q ss_pred CceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------------------EEEEECCEEEEEEEEE
Q 040033 76 SETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------------------VNLILQGVYVIVDFNL 131 (158)
Q Consensus 76 ~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------------------A~i~i~g~~~~~~~~v 131 (158)
...+.+.+.|||++++|+|||||.+|.||.++|+++|+.. +++++++..+.+.|.|
T Consensus 22 v~mLyI~~~ing~~vkA~VDtGAQ~tims~~~a~r~gL~~lid~r~~g~a~GvG~~~i~G~Ih~~~l~ig~~~~~~s~~V 101 (124)
T PF09668_consen 22 VSMLYINCKINGVPVKAFVDTGAQSTIMSKSCAERCGLMRLIDKRFAGVAKGVGTQKILGRIHSVQLKIGGLFFPCSFTV 101 (124)
T ss_dssp ----EEEEEETTEEEEEEEETT-SS-EEEHHHHHHTTGGGGEEGGG-EE-------EEEEEEEEEEEEETTEEEEEEEEE
T ss_pred cceEEEEEEECCEEEEEEEeCCCCccccCHHHHHHcCChhhccccccccccCCCcCceeEEEEEEEEEECCEEEEEEEEE
Confidence 4567889999999999999999999999999999999864 2889999999999999
Q ss_pred ecCCCCcEEechhHhhhcCCceee
Q 040033 132 RELEGYDVVLGTQWLRTLEPILWD 155 (158)
Q Consensus 132 ~~~~~~dvILG~dwL~~~~~i~id 155 (158)
++-...|+|||.|||++|+. .||
T Consensus 102 le~~~~d~llGld~L~~~~c-~ID 124 (124)
T PF09668_consen 102 LEDQDVDLLLGLDMLKRHKC-CID 124 (124)
T ss_dssp ETTSSSSEEEEHHHHHHTT--EEE
T ss_pred eCCCCcceeeeHHHHHHhCc-ccC
Confidence 99889999999999999997 676
No 5
>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=99.52 E-value=1.4e-13 Score=98.49 Aligned_cols=82 Identities=21% Similarity=0.239 Sum_probs=72.1
Q ss_pred cCceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE-----------E------------EEEECCEEEE-EEEE
Q 040033 75 ASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI-----------V------------NLILQGVYVI-VDFN 130 (158)
Q Consensus 75 ~~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~-----------A------------~i~i~g~~~~-~~~~ 130 (158)
...++.+++.|||+++.+||||||++++|++++|+++|+.. | .+.+++..+. +.+.
T Consensus 8 ~~g~~~v~~~InG~~~~flVDTGAs~t~is~~~A~~Lgl~~~~~~~~~~~~ta~G~~~~~~~~l~~l~iG~~~~~nv~~~ 87 (121)
T TIGR02281 8 GDGHFYATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIKAARVTLDRVAIGGIVVNDVDAM 87 (121)
T ss_pred CCCeEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCcccCCceEEEEeCCCcEEEEEEEeCEEEECCEEEeCcEEE
Confidence 35678899999999999999999999999999999999875 1 7888998888 8899
Q ss_pred EecCC-CCcEEechhHhhhcCCceeee
Q 040033 131 LRELE-GYDVVLGTQWLRTLEPILWDF 156 (158)
Q Consensus 131 v~~~~-~~dvILG~dwL~~~~~i~idw 156 (158)
|++.. ..+.+||||||.++..+.+|-
T Consensus 88 v~~~~~~~~~LLGm~fL~~~~~~~~~~ 114 (121)
T TIGR02281 88 VAEGGALSESLLGMSFLNRLSRFTVRG 114 (121)
T ss_pred EeCCCcCCceEcCHHHHhccccEEEEC
Confidence 99886 358999999999998877774
No 6
>PF13650 Asp_protease_2: Aspartyl protease
Probab=99.48 E-value=2.9e-13 Score=90.28 Aligned_cols=65 Identities=22% Similarity=0.330 Sum_probs=58.3
Q ss_pred EEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE-----------------------EEEEECCEEE-EEEEEEec-CC
Q 040033 81 INGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI-----------------------VNLILQGVYV-IVDFNLRE-LE 135 (158)
Q Consensus 81 ~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~-----------------------A~i~i~g~~~-~~~~~v~~-~~ 135 (158)
++++|||+++.+||||||+.++|++++++++++.. ..+++++..+ .+++.+++ ..
T Consensus 1 V~v~vng~~~~~liDTGa~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~~~~i~ig~~~~~~~~~~v~~~~~ 80 (90)
T PF13650_consen 1 VPVKVNGKPVRFLIDTGASISVISRSLAKKLGLKPRPKSVPISVSGAGGSVTVYRGRVDSITIGGITLKNVPFLVVDLGD 80 (90)
T ss_pred CEEEECCEEEEEEEcCCCCcEEECHHHHHHcCCCCcCCceeEEEEeCCCCEEEEEEEEEEEEECCEEEEeEEEEEECCCC
Confidence 46889999999999999999999999999998775 1888999888 58899999 56
Q ss_pred CCcEEechhH
Q 040033 136 GYDVVLGTQW 145 (158)
Q Consensus 136 ~~dvILG~dw 145 (158)
.+|+|||+||
T Consensus 81 ~~~~iLG~df 90 (90)
T PF13650_consen 81 PIDGILGMDF 90 (90)
T ss_pred CCEEEeCCcC
Confidence 8999999998
No 7
>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=99.45 E-value=6.3e-13 Score=91.18 Aligned_cols=72 Identities=22% Similarity=0.226 Sum_probs=63.8
Q ss_pred EEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE--------------------EEEEECCEEEEEEEEEecCCCCc
Q 040033 79 LRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI--------------------VNLILQGVYVIVDFNLRELEGYD 138 (158)
Q Consensus 79 i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~--------------------A~i~i~g~~~~~~~~v~~~~~~d 138 (158)
-.+.+.++|+++.+||||||+.|+|+++.++...... +.+.+++..+...|+|++....|
T Consensus 6 p~i~v~i~g~~i~~LlDTGA~vsiI~~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~v~~~~~~~~~~~~v~~~~~~~ 85 (100)
T PF00077_consen 6 PYITVKINGKKIKALLDTGADVSIISEKDWKKLGPPPKTSITVRGAGGSSSILGSTTVEVKIGGKEFNHTFLVVPDLPMN 85 (100)
T ss_dssp SEEEEEETTEEEEEEEETTBSSEEESSGGSSSTSSEEEEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEESSTCSSE
T ss_pred ceEEEeECCEEEEEEEecCCCcceecccccccccccccCCceeccCCCcceeeeEEEEEEEEECccceEEEEecCCCCCC
Confidence 3578999999999999999999999999998775532 18889999999999999987788
Q ss_pred EEechhHhhhcCC
Q 040033 139 VVLGTQWLRTLEP 151 (158)
Q Consensus 139 vILG~dwL~~~~~ 151 (158)
|||+|||++++.
T Consensus 86 -ILG~D~L~~~~~ 97 (100)
T PF00077_consen 86 -ILGRDFLKKLNA 97 (100)
T ss_dssp -EEEHHHHTTTTC
T ss_pred -EeChhHHHHcCC
Confidence 999999999986
No 8
>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=99.45 E-value=5.3e-13 Score=91.41 Aligned_cols=75 Identities=20% Similarity=0.184 Sum_probs=68.9
Q ss_pred EEEECCEeeEEEecCCCceeEECHHHHHHcCCeE--------------------------EEEEECCEEEEEEEEEecCC
Q 040033 82 NGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI--------------------------VNLILQGVYVIVDFNLRELE 135 (158)
Q Consensus 82 ~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~--------------------------A~i~i~g~~~~~~~~v~~~~ 135 (158)
..++||++++|+|||||-+|+||..+|+++|+.. |++++++..+...|.|++-.
T Consensus 2 nCk~nG~~vkAfVDsGaQ~timS~~caercgL~r~v~~~r~~g~A~gvgt~~kiiGrih~~~ikig~~~~~CSftVld~~ 81 (103)
T cd05480 2 SCQCAGKELRALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSLPTSVKVIGQIERLVLQLGQLTVECSAQVVDDN 81 (103)
T ss_pred ceeECCEEEEEEEecCCchhhcCHHHHHHcChHhhhhhccccccccCCCcceeEeeEEEEEEEEeCCEEeeEEEEEEcCC
Confidence 4679999999999999999999999999999863 28889999999999999988
Q ss_pred CCcEEechhHhhhcCCceeeec
Q 040033 136 GYDVVLGTQWLRTLEPILWDFA 157 (158)
Q Consensus 136 ~~dvILG~dwL~~~~~i~idw~ 157 (158)
+.|++||.|-|++|.. .||.+
T Consensus 82 ~~d~llGLdmLkrhqc-~IdL~ 102 (103)
T cd05480 82 EKNFSLGLQTLKSLKC-VINLE 102 (103)
T ss_pred CcceEeeHHHHhhcce-eeecc
Confidence 9999999999999998 79864
No 9
>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=99.41 E-value=2.1e-12 Score=87.03 Aligned_cols=70 Identities=21% Similarity=0.318 Sum_probs=62.0
Q ss_pred eEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE----------E------------EEEECCEEEE-EEEEEecC
Q 040033 78 TLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI----------V------------NLILQGVYVI-VDFNLREL 134 (158)
Q Consensus 78 ~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~----------A------------~i~i~g~~~~-~~~~v~~~ 134 (158)
.+.+++.||++++.+||||||++++|+..+++++++.. | .+++++..+. ..+.+++.
T Consensus 2 ~~~v~v~i~~~~~~~llDTGa~~s~i~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~ig~~~~~~~~~~v~d~ 81 (96)
T cd05483 2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAARVRLDSLQIGGITLRNVPAVVLPG 81 (96)
T ss_pred cEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCccCCCcEEEEecCCCccceEEEcceEEECCcEEeccEEEEeCC
Confidence 46789999999999999999999999999999988522 1 8889999887 68999999
Q ss_pred CC--CcEEechhHhh
Q 040033 135 EG--YDVVLGTQWLR 147 (158)
Q Consensus 135 ~~--~dvILG~dwL~ 147 (158)
.. .|.|||+|||+
T Consensus 82 ~~~~~~gIlG~d~l~ 96 (96)
T cd05483 82 DALGVDGLLGMDFLR 96 (96)
T ss_pred cccCCceEeChHHhC
Confidence 87 99999999984
No 10
>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=99.28 E-value=3.4e-11 Score=89.37 Aligned_cols=79 Identities=16% Similarity=0.216 Sum_probs=72.2
Q ss_pred cccCceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE---------------------E---EEEECCEEEEEE
Q 040033 73 VRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI---------------------V---NLILQGVYVIVD 128 (158)
Q Consensus 73 ~~~~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~---------------------A---~i~i~g~~~~~~ 128 (158)
-.-..+...+..++|.++.+|+||||-.|||+..++.+|+++. | ++.+++..+.+.
T Consensus 29 Pevg~T~~v~l~~~~t~i~vLfDSGSPTSfIr~di~~kL~L~~~~app~~fRG~vs~~~~~tsEAv~ld~~i~n~~i~i~ 108 (177)
T PF12384_consen 29 PEVGKTAIVQLNCKGTPIKVLFDSGSPTSFIRSDIVEKLELPTHDAPPFRFRGFVSGESATTSEAVTLDFYIDNKLIDIA 108 (177)
T ss_pred cccCcEEEEEEeecCcEEEEEEeCCCccceeehhhHHhhCCccccCCCEEEeeeccCCceEEEEeEEEEEEECCeEEEEE
Confidence 3345778889999999999999999999999999999999987 1 788999999999
Q ss_pred EEEecCCCCcEEechhHhhhcCC
Q 040033 129 FNLRELEGYDVVLGTQWLRTLEP 151 (158)
Q Consensus 129 ~~v~~~~~~dvILG~dwL~~~~~ 151 (158)
++|++..++|+|+|.+.|+++..
T Consensus 109 aYV~d~m~~dlIIGnPiL~ryp~ 131 (177)
T PF12384_consen 109 AYVTDNMDHDLIIGNPILDRYPT 131 (177)
T ss_pred EEEeccCCcceEeccHHHhhhHH
Confidence 99999999999999999999875
No 11
>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=99.28 E-value=3.5e-11 Score=84.30 Aligned_cols=70 Identities=19% Similarity=0.229 Sum_probs=59.3
Q ss_pred CEeeEEEecCCCceeE-ECHHHHHHcCCeE--------------------EEEEECCEEEEEEEEEecCCCCcEEechhH
Q 040033 87 NISPIVLVDSGSTHNF-ISDTFAKKVKNFI--------------------VNLILQGVYVIVDFNLRELEGYDVVLGTQW 145 (158)
Q Consensus 87 ~~~v~aLiDSGat~sf-I~~~~a~~~~~~~--------------------A~i~i~g~~~~~~~~v~~~~~~dvILG~dw 145 (158)
..++.+||||||+..+ |++++|+++|+.. +.+.++|.+....+.+.+..+ +++|||.|
T Consensus 14 ~~~v~~LVDTGat~~~~l~~~~a~~lgl~~~~~~~~~tA~G~~~~~~v~~~~v~igg~~~~~~v~~~~~~~-~~LLG~~~ 92 (107)
T TIGR03698 14 FMEVRALVDTGFSGFLLVPPDIVNKLGLPELDQRRVYLADGREVLTDVAKASIIINGLEIDAFVESLGYVD-EPLLGTEL 92 (107)
T ss_pred ceEEEEEEECCCCeEEecCHHHHHHcCCCcccCcEEEecCCcEEEEEEEEEEEEECCEEEEEEEEecCCCC-ccEecHHH
Confidence 3589999999999998 9999999999886 178889988866666666656 89999999
Q ss_pred hhhcCCceeeecC
Q 040033 146 LRTLEPILWDFAS 158 (158)
Q Consensus 146 L~~~~~i~idw~~ 158 (158)
|.+++. .+||++
T Consensus 93 L~~l~l-~id~~~ 104 (107)
T TIGR03698 93 LEGLGI-VIDYRN 104 (107)
T ss_pred HhhCCE-EEehhh
Confidence 999984 899974
No 12
>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=99.24 E-value=6.1e-11 Score=79.73 Aligned_cols=65 Identities=25% Similarity=0.272 Sum_probs=54.6
Q ss_pred EEEECCEeeEEEecCCCceeEECHHHHHHcCCeE-------E-------------EEEECCEEEEEEEEEecCCCCcEEe
Q 040033 82 NGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI-------V-------------NLILQGVYVIVDFNLRELEGYDVVL 141 (158)
Q Consensus 82 ~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~-------A-------------~i~i~g~~~~~~~~v~~~~~~dvIL 141 (158)
.+.|||+++.+|+||||+++.|++..++++.... | .+.+++++....+.+++-. .+.||
T Consensus 2 ~v~InG~~~~fLvDTGA~~tii~~~~a~~~~~~~~~~~v~gagG~~~~~v~~~~~~v~vg~~~~~~~~~v~~~~-~~~lL 80 (86)
T cd06095 2 TITVEGVPIVFLVDTGATHSVLKSDLGPKQELSTTSVLIRGVSGQSQQPVTTYRTLVDLGGHTVSHSFLVVPNC-PDPLL 80 (86)
T ss_pred EEEECCEEEEEEEECCCCeEEECHHHhhhccCCCCcEEEEeCCCcccccEEEeeeEEEECCEEEEEEEEEEcCC-CCcEe
Confidence 5789999999999999999999999999852211 0 3788999999999888753 69999
Q ss_pred chhHhh
Q 040033 142 GTQWLR 147 (158)
Q Consensus 142 G~dwL~ 147 (158)
|||||.
T Consensus 81 G~dfL~ 86 (86)
T cd06095 81 GRDLLS 86 (86)
T ss_pred chhhcC
Confidence 999984
No 13
>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=99.18 E-value=1.6e-10 Score=73.92 Aligned_cols=66 Identities=41% Similarity=0.663 Sum_probs=57.3
Q ss_pred EEEECCEeeEEEecCCCceeEECHHHHHHcCC-eE------------------------EEEEECCEEEEEEEEEecCCC
Q 040033 82 NGRIGNISPIVLVDSGSTHNFISDTFAKKVKN-FI------------------------VNLILQGVYVIVDFNLRELEG 136 (158)
Q Consensus 82 ~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~-~~------------------------A~i~i~g~~~~~~~~v~~~~~ 136 (158)
.+.+++.++.+|+|+||++++++..++.+++. .. ..+.+++..+...|++++...
T Consensus 2 ~~~~~~~~~~~liDtgs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~ 81 (92)
T cd00303 2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS 81 (92)
T ss_pred EEEECCEEEEEEEcCCCcccccCHHHHHHcCCCcccCCCceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcCCC
Confidence 46688999999999999999999999999876 22 055677888999999999999
Q ss_pred CcEEechhHhh
Q 040033 137 YDVVLGTQWLR 147 (158)
Q Consensus 137 ~dvILG~dwL~ 147 (158)
+|+|||+|||.
T Consensus 82 ~~~ilG~~~l~ 92 (92)
T cd00303 82 YDVILGRPWLE 92 (92)
T ss_pred cCEEecccccC
Confidence 99999999984
No 14
>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]
Probab=99.11 E-value=1.4e-10 Score=95.07 Aligned_cols=80 Identities=24% Similarity=0.353 Sum_probs=74.1
Q ss_pred ceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------------------EEEEECCEEEEEEEEEe
Q 040033 77 ETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------------------VNLILQGVYVIVDFNLR 132 (158)
Q Consensus 77 ~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------------------A~i~i~g~~~~~~~~v~ 132 (158)
..+.+.+.|||++|+|+|||||-.|.||.++|+++|+.. +.++++...+...|.|+
T Consensus 234 ~ML~iN~~ing~~VKAfVDsGaq~timS~~Caer~gL~rlid~r~~g~a~gvg~~ki~g~Ih~~~lki~~~~l~c~ftV~ 313 (380)
T KOG0012|consen 234 TMLYINCEINGVPVKAFVDSGAQTTIMSAACAERCGLNRLIDKRFQGEARGVGTEKILGRIHQAQLKIEDLYLPCSFTVL 313 (380)
T ss_pred eEEEEEEEECCEEEEEEEcccchhhhhhHHHHHHhChHHHhhhhhhccccCCCcccccceeEEEEEEeccEeeccceEEe
Confidence 446778999999999999999999999999999999876 28899999999999999
Q ss_pred cCCCCcEEechhHhhhcCCceeeec
Q 040033 133 ELEGYDVVLGTQWLRTLEPILWDFA 157 (158)
Q Consensus 133 ~~~~~dvILG~dwL~~~~~i~idw~ 157 (158)
+-.+.|+.||.|-|++|+. .||.+
T Consensus 314 d~~~~d~llGLd~Lrr~~c-cIdL~ 337 (380)
T KOG0012|consen 314 DRRDMDLLLGLDMLRRHQC-CIDLK 337 (380)
T ss_pred cCCCcchhhhHHHHHhccc-eeecc
Confidence 9999999999999999998 79975
No 15
>PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease
Probab=99.00 E-value=8.5e-10 Score=71.85 Aligned_cols=41 Identities=34% Similarity=0.539 Sum_probs=38.3
Q ss_pred cCceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE
Q 040033 75 ASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI 115 (158)
Q Consensus 75 ~~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~ 115 (158)
....+++.+.|+++.+.+||||||++|||++++|+++|++.
T Consensus 5 ~~g~~~v~~~I~g~~~~alvDtGat~~fis~~~a~rLgl~~ 45 (72)
T PF13975_consen 5 DPGLMYVPVSIGGVQVKALVDTGATHNFISESLAKRLGLPL 45 (72)
T ss_pred cCCEEEEEEEECCEEEEEEEeCCCcceecCHHHHHHhCCCc
Confidence 45788999999999999999999999999999999999877
No 16
>COG3577 Predicted aspartyl protease [General function prediction only]
Probab=98.88 E-value=7.7e-09 Score=79.44 Aligned_cols=82 Identities=23% Similarity=0.285 Sum_probs=70.0
Q ss_pred ccCceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------------E-----EEEECCEEEE-EEE
Q 040033 74 RASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------------V-----NLILQGVYVI-VDF 129 (158)
Q Consensus 74 ~~~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------------A-----~i~i~g~~~~-~~~ 129 (158)
+...++...+.|||+.+.+|||||||.-.+++.-|+++|+.. | .++|++..+. ++.
T Consensus 101 ~~~GHF~a~~~VNGk~v~fLVDTGATsVal~~~dA~RlGid~~~l~y~~~v~TANG~~~AA~V~Ld~v~IG~I~~~nV~A 180 (215)
T COG3577 101 SRDGHFEANGRVNGKKVDFLVDTGATSVALNEEDARRLGIDLNSLDYTITVSTANGRARAAPVTLDRVQIGGIRVKNVDA 180 (215)
T ss_pred cCCCcEEEEEEECCEEEEEEEecCcceeecCHHHHHHhCCCccccCCceEEEccCCccccceEEeeeEEEccEEEcCchh
Confidence 345678889999999999999999999999999999999876 1 7888988887 788
Q ss_pred EEecCC-CCcEEechhHhhhcCCceee
Q 040033 130 NLRELE-GYDVVLGTQWLRTLEPILWD 155 (158)
Q Consensus 130 ~v~~~~-~~dvILG~dwL~~~~~i~id 155 (158)
+|++-+ --..+|||.||.+++-.+.+
T Consensus 181 ~V~~~g~L~~sLLGMSfL~rL~~fq~~ 207 (215)
T COG3577 181 MVAEDGALDESLLGMSFLNRLSGFQVD 207 (215)
T ss_pred heecCCccchhhhhHHHHhhccceEec
Confidence 999766 67789999999998765443
No 17
>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=98.60 E-value=1e-07 Score=73.34 Aligned_cols=69 Identities=23% Similarity=0.334 Sum_probs=53.3
Q ss_pred EeeEEEecCCCceeEECHHHH-----HHcCCeE----E--------------EEEECCEEEEEEEEEecCCCCcEEechh
Q 040033 88 ISPIVLVDSGSTHNFISDTFA-----KKVKNFI----V--------------NLILQGVYVIVDFNLRELEGYDVVLGTQ 144 (158)
Q Consensus 88 ~~v~aLiDSGat~sfI~~~~a-----~~~~~~~----A--------------~i~i~g~~~~~~~~v~~~~~~dvILG~d 144 (158)
..+.++|||||+.++++..+. +++.-+. | .+.+.|+.|...+.-.--.+.|+|||++
T Consensus 19 ~~~~~~vDTGAt~C~~~~~iiP~e~we~~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~IP~iYq~~~g~d~IlG~N 98 (201)
T PF02160_consen 19 FNYHCYVDTGATICCASKKIIPEEYWEKSKKPIKVKGANGSIIQINKKAKNGKIQIADKIFRIPTIYQQESGIDIILGNN 98 (201)
T ss_pred EEEEEEEeCCCceEEecCCcCCHHHHHhCCCcEEEEEecCCceEEEEEecCceEEEccEEEeccEEEEecCCCCEEecch
Confidence 567899999999999887654 4444322 2 7889999999865444336899999999
Q ss_pred HhhhcCCceeeec
Q 040033 145 WLRTLEPILWDFA 157 (158)
Q Consensus 145 wL~~~~~i~idw~ 157 (158)
|++.+.| -+.|.
T Consensus 99 F~r~y~P-fiq~~ 110 (201)
T PF02160_consen 99 FLRLYEP-FIQTE 110 (201)
T ss_pred HHHhcCC-cEEEc
Confidence 9999999 47774
No 18
>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=98.41 E-value=1.7e-06 Score=59.06 Aligned_cols=61 Identities=18% Similarity=0.172 Sum_probs=50.6
Q ss_pred EEECC-EeeEEEecCCCceeEECHHHHHHcC---CeE----------E-------------EEEECCEEEEEEEEEecCC
Q 040033 83 GRIGN-ISPIVLVDSGSTHNFISDTFAKKVK---NFI----------V-------------NLILQGVYVIVDFNLRELE 135 (158)
Q Consensus 83 ~~i~~-~~v~aLiDSGat~sfI~~~~a~~~~---~~~----------A-------------~i~i~g~~~~~~~~v~~~~ 135 (158)
..|++ +++++++||||+.|+|+.+..++++ .+. | .+.+++..+.++|+|++..
T Consensus 3 ~~i~g~~~v~~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~~~G~~~~~v~~~~~~~~~~f~Vvd~~ 82 (93)
T cd05481 3 MKINGKQSVKFQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIPVEGGVKLKCRYRNPKYNLTFQVVKEE 82 (93)
T ss_pred eEeCCceeEEEEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEeeeeEEEEEEEEECCcEEEEEEEEECCC
Confidence 56888 9999999999999999999999987 222 1 7778999999999999975
Q ss_pred CCcEEechh
Q 040033 136 GYDVVLGTQ 144 (158)
Q Consensus 136 ~~dvILG~d 144 (158)
..-|||.+
T Consensus 83 -~~~lLG~~ 90 (93)
T cd05481 83 -GPPLLGAK 90 (93)
T ss_pred -CCceEccc
Confidence 55667764
No 19
>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=98.23 E-value=2.8e-06 Score=57.36 Aligned_cols=61 Identities=21% Similarity=0.278 Sum_probs=46.8
Q ss_pred EeeEEEecCCCceeEECHHHHHHc-C-CeE---E--------------EEEECC-EEEEEEEEEecCCCCcEEechhHhh
Q 040033 88 ISPIVLVDSGSTHNFISDTFAKKV-K-NFI---V--------------NLILQG-VYVIVDFNLRELEGYDVVLGTQWLR 147 (158)
Q Consensus 88 ~~v~aLiDSGat~sfI~~~~a~~~-~-~~~---A--------------~i~i~g-~~~~~~~~v~~~~~~dvILG~dwL~ 147 (158)
-.+..||||||.+|.|.....++. . .+. | .+.++. +.|.-.|.|.+.. .-|||.|||+
T Consensus 8 s~~~fLVDTGA~vSviP~~~~~~~~~~~~~~l~AANgt~I~tyG~~~l~ldlGlrr~~~w~FvvAdv~--~pIlGaDfL~ 85 (89)
T cd06094 8 SGLRFLVDTGAAVSVLPASSTKKSLKPSPLTLQAANGTPIATYGTRSLTLDLGLRRPFAWNFVVADVP--HPILGADFLQ 85 (89)
T ss_pred CCcEEEEeCCCceEeeccccccccccCCceEEEeCCCCeEeeeeeEEEEEEcCCCcEEeEEEEEcCCC--cceecHHHHH
Confidence 357899999999999999988863 1 111 1 455564 4888899998875 4799999999
Q ss_pred hcC
Q 040033 148 TLE 150 (158)
Q Consensus 148 ~~~ 150 (158)
.|+
T Consensus 86 ~~~ 88 (89)
T cd06094 86 HYG 88 (89)
T ss_pred HcC
Confidence 886
No 20
>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=98.18 E-value=6.1e-07 Score=43.09 Aligned_cols=17 Identities=6% Similarity=0.001 Sum_probs=15.9
Q ss_pred ceeecCCCCCCCccCCc
Q 040033 31 VCATIATKSFPRDIGER 47 (158)
Q Consensus 31 ~Cf~Cg~~gH~~~~C~~ 47 (158)
.||+|++.||++++||+
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 59999999999999985
No 21
>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=98.16 E-value=4e-06 Score=62.51 Aligned_cols=28 Identities=32% Similarity=0.485 Sum_probs=26.1
Q ss_pred EeeEEEecCCCceeEECHHHHHHcCCeE
Q 040033 88 ISPIVLVDSGSTHNFISDTFAKKVKNFI 115 (158)
Q Consensus 88 ~~v~aLiDSGat~sfI~~~~a~~~~~~~ 115 (158)
.++.+|+||||..|||++++|++++++.
T Consensus 11 ~~~~~LlDsGSq~SfIt~~la~~L~L~~ 38 (164)
T PF05585_consen 11 VEARALLDSGSQRSFITESLANKLNLPG 38 (164)
T ss_pred EEEEEEEecCCchhHHhHHHHHHhCCCC
Confidence 5788999999999999999999999975
No 22
>COG5550 Predicted aspartyl protease [Posttranslational modification, protein turnover, chaperones]
Probab=98.10 E-value=2.7e-05 Score=55.45 Aligned_cols=70 Identities=17% Similarity=0.155 Sum_probs=58.5
Q ss_pred CCEeeEEEecCCCc-eeEECHHHHHHcCCeE--------------------EEEEECCEEEEEEEEEecCCCCcEEechh
Q 040033 86 GNISPIVLVDSGST-HNFISDTFAKKVKNFI--------------------VNLILQGVYVIVDFNLRELEGYDVVLGTQ 144 (158)
Q Consensus 86 ~~~~v~aLiDSGat-~sfI~~~~a~~~~~~~--------------------A~i~i~g~~~~~~~~v~~~~~~dvILG~d 144 (158)
+++....|||||.+ --.+++++|.+++++. |.++++|.+...-..+.+....+ ++|++
T Consensus 23 Gd~~~~~LiDTGFtg~lvlp~~vaek~~~~~~~~~~~~~a~~~~v~t~V~~~~iki~g~e~~~~Vl~s~~~~~~-liG~~ 101 (125)
T COG5550 23 GDFVYDELIDTGFTGYLVLPPQVAEKLGLPLFSTIRIVLADGGVVKTSVALATIKIDGVEKVAFVLASDNLPEP-LIGVN 101 (125)
T ss_pred CcEEeeeEEecCCceeEEeCHHHHHhcCCCccCChhhhhhcCCEEEEEEEEEEEEECCEEEEEEEEccCCCccc-chhhh
Confidence 34455569999999 8899999999999887 38899999888888888888888 99999
Q ss_pred HhhhcCCceeeec
Q 040033 145 WLRTLEPILWDFA 157 (158)
Q Consensus 145 wL~~~~~i~idw~ 157 (158)
||+.++- .+|..
T Consensus 102 ~lk~l~~-~vn~~ 113 (125)
T COG5550 102 LLKLLGL-VVNPK 113 (125)
T ss_pred hhhhccE-EEcCC
Confidence 9998885 67654
No 23
>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=97.87 E-value=6.5e-05 Score=50.68 Aligned_cols=66 Identities=17% Similarity=-0.018 Sum_probs=49.4
Q ss_pred EEEECCEeeEEEecCCCceeEECHHHHHHcC----CeE----------------EEEEECCEEEEEEEEEecCCCCcEEe
Q 040033 82 NGRIGNISPIVLVDSGSTHNFISDTFAKKVK----NFI----------------VNLILQGVYVIVDFNLRELEGYDVVL 141 (158)
Q Consensus 82 ~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~----~~~----------------A~i~i~g~~~~~~~~v~~~~~~dvIL 141 (158)
...|+|+.+.+|+||||..++|++.-..+.- -+. -.+++.++.....+.|.+.....-||
T Consensus 2 ~~~i~g~~~~~llDTGAd~Tvi~~~~~p~~w~~~~~~~~i~GIGG~~~~~~~~~v~i~i~~~~~~g~vlv~~~~~P~nll 81 (87)
T cd05482 2 TLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVLSLPVNLW 81 (87)
T ss_pred EEEECCEEEEEEEccCCCCeEEcccccCCCCccCCCCeEEEeccceEEEEEEeeEEEEEcCCeEEEEEEEccCCCcccEE
Confidence 4678999999999999999999986554321 111 16777888888888888864445689
Q ss_pred chhHhh
Q 040033 142 GTQWLR 147 (158)
Q Consensus 142 G~dwL~ 147 (158)
|+|.|.
T Consensus 82 GRd~L~ 87 (87)
T cd05482 82 GRDILS 87 (87)
T ss_pred ccccCC
Confidence 999874
No 24
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=96.66 E-value=0.00073 Score=36.98 Aligned_cols=19 Identities=16% Similarity=0.048 Sum_probs=17.5
Q ss_pred cceeecCCCCCCCccCCcc
Q 040033 30 KVCATIATKSFPRDIGERS 48 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~~ 48 (158)
.+|+.|+++||+..+||.+
T Consensus 9 Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CEeecCCCCCccHhHCCCC
Confidence 6899999999999999974
No 25
>smart00343 ZnF_C2HC zinc finger.
Probab=95.88 E-value=0.0036 Score=32.39 Aligned_cols=18 Identities=6% Similarity=0.051 Sum_probs=16.0
Q ss_pred ceeecCCCCCCCccCCcc
Q 040033 31 VCATIATKSFPRDIGERS 48 (158)
Q Consensus 31 ~Cf~Cg~~gH~~~~C~~~ 48 (158)
.||+|++.||.+.+||..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 499999999999999853
No 26
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=95.67 E-value=0.0045 Score=36.05 Aligned_cols=18 Identities=11% Similarity=-0.040 Sum_probs=16.9
Q ss_pred cceeecCCCCCCCccCCc
Q 040033 30 KVCATIATKSFPRDIGER 47 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~ 47 (158)
..|.+|++.||...+|++
T Consensus 5 ~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 5 VRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CcCcccCCCCcchhhCCC
Confidence 689999999999999994
No 27
>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=95.21 E-value=0.051 Score=37.62 Aligned_cols=65 Identities=17% Similarity=0.254 Sum_probs=48.3
Q ss_pred EEEEEEECCE--eeEEEecCCCceeEECHHHHHHcCCeE---------E--------------EEEECCEEEEEEEEEec
Q 040033 79 LRINGRIGNI--SPIVLVDSGSTHNFISDTFAKKVKNFI---------V--------------NLILQGVYVIVDFNLRE 133 (158)
Q Consensus 79 i~~~~~i~~~--~v~aLiDSGat~sfI~~~~a~~~~~~~---------A--------------~i~i~g~~~~~~~~v~~ 133 (158)
|.+++.+... .+.-|||+||..|.|.+..++...++. + .+.++|......|+|+.
T Consensus 35 mvlqa~lp~fkcsipclidtgaq~niiteetvrahklptrpw~~sviyggvyp~kinrkt~kl~i~lngisikteflvvk 114 (137)
T PF12382_consen 35 MVLQAKLPDFKCSIPCLIDTGAQVNIITEETVRAHKLPTRPWSQSVIYGGVYPNKINRKTIKLNINLNGISIKTEFLVVK 114 (137)
T ss_pred hhhhhhCCCccccceeEEccCceeeeeehhhhhhccCCCCcchhheEeccccccccccceEEEEEEecceEEEEEEEEEE
Confidence 3344444333 346799999999999999999888876 0 67789999999999998
Q ss_pred CCCCcEEech
Q 040033 134 LEGYDVVLGT 143 (158)
Q Consensus 134 ~~~~dvILG~ 143 (158)
.-.++.-+.+
T Consensus 115 kfshpaaisf 124 (137)
T PF12382_consen 115 KFSHPAAISF 124 (137)
T ss_pred eccCcceEEE
Confidence 6655554443
No 28
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=95.08 E-value=0.0074 Score=33.74 Aligned_cols=19 Identities=5% Similarity=-0.027 Sum_probs=12.4
Q ss_pred cceeecCCCCCCCccCCcc
Q 040033 30 KVCATIATKSFPRDIGERS 48 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~~ 48 (158)
++|++|++..|.+.+|..+
T Consensus 3 ~~CprC~kg~Hwa~~C~sk 21 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSK 21 (36)
T ss_dssp -C-TTTSSSCS-TTT---T
T ss_pred ccCcccCCCcchhhhhhhh
Confidence 7899999999999999875
No 29
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=94.71 E-value=0.012 Score=44.95 Aligned_cols=21 Identities=19% Similarity=0.180 Sum_probs=17.9
Q ss_pred hhcc-cceeecCCCCCCCccCC
Q 040033 26 ERRA-KVCATIATKSFPRDIGE 46 (158)
Q Consensus 26 ~rR~-~~Cf~Cg~~gH~~~~C~ 46 (158)
.+++ ..||+||+.||.+++||
T Consensus 56 ~~~~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 56 IREENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccccccchhcccCcccccCC
Confidence 3344 88999999999999999
No 30
>PF05618 Zn_protease: Putative ATP-dependant zinc protease; InterPro: IPR008503 This family consists of several hypothetical proteins from different archaeal and bacterial species.; PDB: 2PMA_B.
Probab=94.21 E-value=0.14 Score=37.36 Aligned_cols=33 Identities=30% Similarity=0.526 Sum_probs=25.2
Q ss_pred EEEECCEEEEEEEEEecCC--CCcEEec-hhHhhhc
Q 040033 117 NLILQGVYVIVDFNLRELE--GYDVVLG-TQWLRTL 149 (158)
Q Consensus 117 ~i~i~g~~~~~~~~v~~~~--~~dvILG-~dwL~~~ 149 (158)
.+.++|..+.+.|.+.+=+ .|+|+|| ..||...
T Consensus 89 ~~~lg~~~~~~e~tL~dR~~m~yp~LlGrR~~l~~~ 124 (138)
T PF05618_consen 89 TLCLGGKTWKIEFTLTDRSNMKYPMLLGRRNFLRGR 124 (138)
T ss_dssp EEEETTEEEEEEEEEE-S--SS-SEEE-HHHHHHTT
T ss_pred EEEECCEEEEEEEEEcCCCcCcCCEEEEehHHhcCC
Confidence 7788999999999998754 7999999 9999653
No 31
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=93.89 E-value=0.024 Score=43.41 Aligned_cols=19 Identities=11% Similarity=0.034 Sum_probs=16.9
Q ss_pred cceeecCCCCCCCccC-Ccc
Q 040033 30 KVCATIATKSFPRDIG-ERS 48 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C-~~~ 48 (158)
..||+||+.||++++| |++
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~~ 117 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPSK 117 (190)
T ss_pred cccccccccCccccccCccc
Confidence 5799999999999999 655
No 32
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=93.23 E-value=0.028 Score=33.63 Aligned_cols=22 Identities=9% Similarity=0.129 Sum_probs=18.7
Q ss_pred hhcc-cceeecCCCCCCCccCCc
Q 040033 26 ERRA-KVCATIATKSFPRDIGER 47 (158)
Q Consensus 26 ~rR~-~~Cf~Cg~~gH~~~~C~~ 47 (158)
+-|- ..||+||..||....||+
T Consensus 27 YE~lp~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 27 YERLPRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ECCcChhhcCCCCcCcCHhHcCC
Confidence 3355 789999999999999985
No 33
>COG4067 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]
Probab=93.12 E-value=0.26 Score=36.62 Aligned_cols=38 Identities=32% Similarity=0.533 Sum_probs=31.1
Q ss_pred EEEECCEEEEEEEEEecCC--CCcEEechhHhhhcCCceee
Q 040033 117 NLILQGVYVIVDFNLRELE--GYDVVLGTQWLRTLEPILWD 155 (158)
Q Consensus 117 ~i~i~g~~~~~~~~v~~~~--~~dvILG~dwL~~~~~i~id 155 (158)
.+.++|....+.|.+.+=. .|+|+||.-+|..... .+|
T Consensus 113 ~l~lG~~~~~~E~tLtDR~~m~Yp~LlGrk~l~~~~~-~VD 152 (162)
T COG4067 113 TLCLGGRILPIEFTLTDRSNMRYPVLLGRKALRHFGA-VVD 152 (162)
T ss_pred EEeeCCeeeeEEEEeecccccccceEecHHHHhhCCe-EEC
Confidence 6778999999999988754 7999999999998654 444
No 34
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=91.21 E-value=0.089 Score=38.43 Aligned_cols=17 Identities=12% Similarity=0.077 Sum_probs=14.2
Q ss_pred ceeecCCCCCCCccCCc
Q 040033 31 VCATIATKSFPRDIGER 47 (158)
Q Consensus 31 ~Cf~Cg~~gH~~~~C~~ 47 (158)
+||+|++.||++++||.
T Consensus 2 ~C~~C~~~GH~~~~c~~ 18 (148)
T PTZ00368 2 VCYRCGGVGHQSRECPN 18 (148)
T ss_pred cCCCCCCCCcCcccCcC
Confidence 58888888888888886
No 35
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=90.86 E-value=0.092 Score=41.99 Aligned_cols=18 Identities=11% Similarity=0.110 Sum_probs=16.2
Q ss_pred cceeecCCCCCCCccCCc
Q 040033 30 KVCATIATKSFPRDIGER 47 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~ 47 (158)
..||.||+.||+.++||.
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~ 161 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPE 161 (261)
T ss_pred CccCCCCcCCcchhhCCC
Confidence 349999999999999994
No 36
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.13 E-value=0.21 Score=41.07 Aligned_cols=19 Identities=16% Similarity=0.041 Sum_probs=17.5
Q ss_pred cceeecCCCCCCCccCCcc
Q 040033 30 KVCATIATKSFPRDIGERS 48 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~~ 48 (158)
..||+||++||....||.+
T Consensus 177 Y~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 177 YVCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred eeEEecCCCCchhhcCCCC
Confidence 6799999999999999966
No 37
>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=89.34 E-value=1.4 Score=34.86 Aligned_cols=62 Identities=18% Similarity=0.272 Sum_probs=38.4
Q ss_pred eEEEecCCCceeEECHHHHHHcCCeEEEEEEC-CEEEEEE--------------EEEecC-CCCcEEechhHhhhcCCce
Q 040033 90 PIVLVDSGSTHNFISDTFAKKVKNFIVNLILQ-GVYVIVD--------------FNLREL-EGYDVVLGTQWLRTLEPIL 153 (158)
Q Consensus 90 v~aLiDSGat~sfI~~~~a~~~~~~~A~i~i~-g~~~~~~--------------~~v~~~-~~~dvILG~dwL~~~~~i~ 153 (158)
..++||||++..++.+.+.-.+ .+.++ +..+.+. +.++.. ..--.|||-.||+.+-- .
T Consensus 177 ~~ai~DTGTs~~~lp~~~~P~i-----~~~f~~~~~~~i~~~~y~~~~~~~~~C~~~~~~~~~~~~ilG~~fl~~~~~-v 250 (265)
T cd05476 177 GGTIIDSGTTLTYLPDPAYPDL-----TLHFDGGADLELPPENYFVDVGEGVVCLAILSSSSGGVSILGNIQQQNFLV-E 250 (265)
T ss_pred CcEEEeCCCcceEcCccccCCE-----EEEECCCCEEEeCcccEEEECCCCCEEEEEecCCCCCcEEEChhhcccEEE-E
Confidence 3489999999999998876222 23333 3322211 122222 34568999999998764 4
Q ss_pred eeec
Q 040033 154 WDFA 157 (158)
Q Consensus 154 idw~ 157 (158)
.|+.
T Consensus 251 FD~~ 254 (265)
T cd05476 251 YDLE 254 (265)
T ss_pred EECC
Confidence 5654
No 38
>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=89.22 E-value=1.8 Score=35.14 Aligned_cols=67 Identities=15% Similarity=0.207 Sum_probs=43.8
Q ss_pred eEEEecCCCceeEECHHHHHHcC----CeE-----------E-------EEEECCEEEEEE-------------EEEecC
Q 040033 90 PIVLVDSGSTHNFISDTFAKKVK----NFI-----------V-------NLILQGVYVIVD-------------FNLREL 134 (158)
Q Consensus 90 v~aLiDSGat~sfI~~~~a~~~~----~~~-----------A-------~i~i~g~~~~~~-------------~~v~~~ 134 (158)
..++||||++..++...+++.+- ... . .+.++|.++.+. +.+.+.
T Consensus 202 ~~~iiDSGtt~~~lP~~~~~~l~~~~~~~~~~~~~~~~~C~~~~~~p~l~~~f~g~~~~v~~~~y~~~~~~~C~~~i~~~ 281 (318)
T cd05477 202 CQAIVDTGTSLLTAPQQVMSTLMQSIGAQQDQYGQYVVNCNNIQNLPTLTFTINGVSFPLPPSAYILQNNGYCTVGIEPT 281 (318)
T ss_pred ceeeECCCCccEECCHHHHHHHHHHhCCccccCCCEEEeCCccccCCcEEEEECCEEEEECHHHeEecCCCeEEEEEEec
Confidence 36899999999999998877642 111 0 456677766642 122211
Q ss_pred ------CCCcEEechhHhhhcCCceeeec
Q 040033 135 ------EGYDVVLGTQWLRTLEPILWDFA 157 (158)
Q Consensus 135 ------~~~dvILG~dwL~~~~~i~idw~ 157 (158)
+....|||..||+.+-- ..|+.
T Consensus 282 ~~~~~~~~~~~ilG~~fl~~~y~-vfD~~ 309 (318)
T cd05477 282 YLPSQNGQPLWILGDVFLRQYYS-VYDLG 309 (318)
T ss_pred ccCCCCCCceEEEcHHHhhheEE-EEeCC
Confidence 12358999999998775 46764
No 39
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=88.93 E-value=0.17 Score=36.90 Aligned_cols=18 Identities=6% Similarity=0.064 Sum_probs=11.0
Q ss_pred cceeecCCCCCCCccCCc
Q 040033 30 KVCATIATKSFPRDIGER 47 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~ 47 (158)
..||+|++.||++++||+
T Consensus 104 ~~C~~Cg~~gH~~~~C~~ 121 (148)
T PTZ00368 104 RACYNCGGEGHISRDCPN 121 (148)
T ss_pred hhhcccCcCCcchhcCCC
Confidence 356666666666666665
No 40
>PTZ00013 plasmepsin 4 (PM4); Provisional
Probab=87.34 E-value=2 Score=37.29 Aligned_cols=26 Identities=19% Similarity=0.480 Sum_probs=21.1
Q ss_pred EEEEEC--CEeeEEEecCCCceeEECHH
Q 040033 81 INGRIG--NISPIVLVDSGSTHNFISDT 106 (158)
Q Consensus 81 ~~~~i~--~~~v~aLiDSGat~sfI~~~ 106 (158)
.++.|+ .+++.+++||||+..+|...
T Consensus 141 ~~i~IGTP~Q~f~vi~DTGSsdlWV~s~ 168 (450)
T PTZ00013 141 GEGEVGDNHQKFMLIFDTGSANLWVPSK 168 (450)
T ss_pred EEEEECCCCeEEEEEEeCCCCceEEecc
Confidence 355665 79999999999999999643
No 41
>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=86.83 E-value=0.79 Score=30.93 Aligned_cols=25 Identities=28% Similarity=0.414 Sum_probs=20.1
Q ss_pred EEEECC--EeeEEEecCCCceeEECHH
Q 040033 82 NGRIGN--ISPIVLVDSGSTHNFISDT 106 (158)
Q Consensus 82 ~~~i~~--~~v~aLiDSGat~sfI~~~ 106 (158)
++.|+. +++.++|||||+..++...
T Consensus 2 ~i~vGtP~q~~~~~~DTGSs~~Wv~~~ 28 (109)
T cd05470 2 EIGIGTPPQTFNVLLDTGSSNLWVPSV 28 (109)
T ss_pred EEEeCCCCceEEEEEeCCCCCEEEeCC
Confidence 355654 8999999999999888765
No 42
>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=86.08 E-value=2.8 Score=34.03 Aligned_cols=74 Identities=16% Similarity=0.183 Sum_probs=48.3
Q ss_pred EEECCEee------EEEecCCCceeEECHHHHHHc----CCeE-------------E-----EEEECCEEEEEE------
Q 040033 83 GRIGNISP------IVLVDSGSTHNFISDTFAKKV----KNFI-------------V-----NLILQGVYVIVD------ 128 (158)
Q Consensus 83 ~~i~~~~v------~aLiDSGat~sfI~~~~a~~~----~~~~-------------A-----~i~i~g~~~~~~------ 128 (158)
+.|+++.+ .++||||++..++......++ +... . .+.++|..|.+.
T Consensus 194 v~v~g~~~~~~~~~~~iiDTGts~~~lp~~~~~~l~~~~~~~~~~~~~~~~~C~~~~~~P~~~f~f~g~~~~i~~~~y~~ 273 (317)
T cd05478 194 VTINGQVVACSGGCQAIVDTGTSLLVGPSSDIANIQSDIGASQNQNGEMVVNCSSISSMPDVVFTINGVQYPLPPSAYIL 273 (317)
T ss_pred EEECCEEEccCCCCEEEECCCchhhhCCHHHHHHHHHHhCCccccCCcEEeCCcCcccCCcEEEEECCEEEEECHHHhee
Confidence 46777654 689999999999998877653 2211 0 455677766642
Q ss_pred -------EEEecCC-CCcEEechhHhhhcCCceeeec
Q 040033 129 -------FNLRELE-GYDVVLGTQWLRTLEPILWDFA 157 (158)
Q Consensus 129 -------~~v~~~~-~~dvILG~dwL~~~~~i~idw~ 157 (158)
+.+.+.. ....|||-.||+.+-. ..|+.
T Consensus 274 ~~~~~C~~~~~~~~~~~~~IlG~~fl~~~y~-vfD~~ 309 (317)
T cd05478 274 QDQGSCTSGFQSMGLGELWILGDVFIRQYYS-VFDRA 309 (317)
T ss_pred cCCCEEeEEEEeCCCCCeEEechHHhcceEE-EEeCC
Confidence 1122222 2458999999998775 46664
No 43
>PTZ00147 plasmepsin-1; Provisional
Probab=85.75 E-value=3.1 Score=36.11 Aligned_cols=26 Identities=15% Similarity=0.304 Sum_probs=21.6
Q ss_pred EEEEEEC--CEeeEEEecCCCceeEECH
Q 040033 80 RINGRIG--NISPIVLVDSGSTHNFISD 105 (158)
Q Consensus 80 ~~~~~i~--~~~v~aLiDSGat~sfI~~ 105 (158)
...+.|+ .+++.++|||||+..+|..
T Consensus 141 ~~~I~IGTP~Q~f~Vi~DTGSsdlWVps 168 (453)
T PTZ00147 141 YGEAKLGDNGQKFNFIFDTGSANLWVPS 168 (453)
T ss_pred EEEEEECCCCeEEEEEEeCCCCcEEEee
Confidence 4466776 7999999999999999964
No 44
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=85.34 E-value=0.45 Score=27.34 Aligned_cols=18 Identities=11% Similarity=0.025 Sum_probs=15.6
Q ss_pred ceeecCCCCCCC--ccCCcc
Q 040033 31 VCATIATKSFPR--DIGERS 48 (158)
Q Consensus 31 ~Cf~Cg~~gH~~--~~C~~~ 48 (158)
.|-.||..||.+ +.||-+
T Consensus 3 kC~~CG~~GH~~t~k~CP~~ 22 (40)
T PF15288_consen 3 KCKNCGAFGHMRTNKRCPMY 22 (40)
T ss_pred cccccccccccccCccCCCC
Confidence 499999999998 789865
No 45
>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=84.62 E-value=2.2 Score=34.86 Aligned_cols=68 Identities=19% Similarity=0.312 Sum_probs=42.7
Q ss_pred eeEEEecCCCceeEECHHHHHHcCC--eEEEEEEC-CEEEEEE-------------EEEecCCCCcEEechhHhhhcCCc
Q 040033 89 SPIVLVDSGSTHNFISDTFAKKVKN--FIVNLILQ-GVYVIVD-------------FNLRELEGYDVVLGTQWLRTLEPI 152 (158)
Q Consensus 89 ~v~aLiDSGat~sfI~~~~a~~~~~--~~A~i~i~-g~~~~~~-------------~~v~~~~~~dvILG~dwL~~~~~i 152 (158)
...++||||++..++...+.+++.- +.-.+.++ |..+.+. +..+....--.|||-.||+.+--
T Consensus 231 ~~~aivDSGTs~~~lp~~~~~~l~~~~P~i~~~f~~g~~~~i~p~~y~~~~~~~~c~~~~~~~~~~~ILG~~flr~~y~- 309 (326)
T cd06096 231 GLGMLVDSGSTLSHFPEDLYNKINNFFPTITIIFENNLKIDWKPSSYLYKKESFWCKGGEKSVSNKPILGASFFKNKQI- 309 (326)
T ss_pred CCCEEEeCCCCcccCCHHHHHHHHhhcCcEEEEEcCCcEEEECHHHhccccCCceEEEEEecCCCceEEChHHhcCcEE-
Confidence 3458999999999999999887542 11134444 4433320 11122223357999999998774
Q ss_pred eeeec
Q 040033 153 LWDFA 157 (158)
Q Consensus 153 ~idw~ 157 (158)
..|+.
T Consensus 310 vFD~~ 314 (326)
T cd06096 310 IFDLD 314 (326)
T ss_pred EEECc
Confidence 56764
No 46
>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=84.25 E-value=4.1 Score=32.31 Aligned_cols=64 Identities=22% Similarity=0.299 Sum_probs=40.5
Q ss_pred EEEEECC--EeeEEEecCCCceeEECHHHHHHcCC--eE------EEEEECCEEEE-EEEEEecC-CCCcEEechhH
Q 040033 81 INGRIGN--ISPIVLVDSGSTHNFISDTFAKKVKN--FI------VNLILQGVYVI-VDFNLREL-EGYDVVLGTQW 145 (158)
Q Consensus 81 ~~~~i~~--~~v~aLiDSGat~sfI~~~~a~~~~~--~~------A~i~i~g~~~~-~~~~v~~~-~~~dvILG~dw 145 (158)
+++.|+. +++.+++||||+..+|.. +-..++- .. ..+.+++.... ..|.++.. ...|-|||..+
T Consensus 5 ~~i~iGtp~q~~~v~~DTgS~~~wv~~-~~~~Y~~g~~~~G~~~~D~v~~g~~~~~~~~fg~~~~~~~~~GilGLg~ 80 (295)
T cd05474 5 AELSVGTPPQKVTVLLDTGSSDLWVPD-FSISYGDGTSASGTWGTDTVSIGGATVKNLQFAVANSTSSDVGVLGIGL 80 (295)
T ss_pred EEEEECCCCcEEEEEEeCCCCcceeee-eEEEeccCCcEEEEEEEEEEEECCeEecceEEEEEecCCCCcceeeECC
Confidence 4566665 899999999999998881 1111111 11 17777776553 45655543 46888988764
No 47
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=81.40 E-value=0.76 Score=37.67 Aligned_cols=17 Identities=6% Similarity=-0.023 Sum_probs=16.3
Q ss_pred eeecCCCCCCCccCCcc
Q 040033 32 CATIATKSFPRDIGERS 48 (158)
Q Consensus 32 Cf~Cg~~gH~~~~C~~~ 48 (158)
||.||+.||.+.+||..
T Consensus 163 cyrcGkeghwskEcP~~ 179 (346)
T KOG0109|consen 163 CYRCGKEGHWSKECPVD 179 (346)
T ss_pred heeccccccccccCCcc
Confidence 99999999999999976
No 48
>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=79.30 E-value=1.6 Score=34.72 Aligned_cols=68 Identities=12% Similarity=0.080 Sum_probs=37.8
Q ss_pred eeEEEecCCCceeEECHHHHHHcCCeE--EEEEECCEEEEEEEEE-ecCC--CCcEEechhHhhhcCCceeeec
Q 040033 89 SPIVLVDSGSTHNFISDTFAKKVKNFI--VNLILQGVYVIVDFNL-RELE--GYDVVLGTQWLRTLEPILWDFA 157 (158)
Q Consensus 89 ~v~aLiDSGat~sfI~~~~a~~~~~~~--A~i~i~g~~~~~~~~v-~~~~--~~dvILG~dwL~~~~~i~idw~ 157 (158)
...++||||++..++...+++++.-.. |........+.+++.- +|-. .+..|||-.||+++-. ..||.
T Consensus 198 ~~~~iiDSGTs~~~lP~~~~~~l~~~l~g~~~~~~~~~~~~~C~~~~P~i~f~~~~ilGd~fl~~~y~-vfD~~ 270 (278)
T cd06097 198 GFSAIADTGTTLILLPDAIVEAYYSQVPGAYYDSEYGGWVFPCDTTLPDLSFAVFSILGDVFLKAQYV-VFDVG 270 (278)
T ss_pred CceEEeecCCchhcCCHHHHHHHHHhCcCCcccCCCCEEEEECCCCCCCEEEEEEEEEcchhhCceeE-EEcCC
Confidence 456999999999999987766542111 1110001111111110 0000 0157999999998875 57775
No 49
>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=79.24 E-value=2.7 Score=32.77 Aligned_cols=61 Identities=16% Similarity=0.252 Sum_probs=39.1
Q ss_pred EeeEEEecCCCceeEECHHHHHHcCCeE-EEEE------------EC-CEEEEEEEEEecCCCCcEEechhHhhhcCCce
Q 040033 88 ISPIVLVDSGSTHNFISDTFAKKVKNFI-VNLI------------LQ-GVYVIVDFNLRELEGYDVVLGTQWLRTLEPIL 153 (158)
Q Consensus 88 ~~v~aLiDSGat~sfI~~~~a~~~~~~~-A~i~------------i~-g~~~~~~~~v~~~~~~dvILG~dwL~~~~~i~ 153 (158)
....++||||++..++...++..+--.. +... .. --.+...| ..|||..||+.+-- .
T Consensus 201 ~~~~~iiDsGt~~~~lp~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~p~i~f~f--------~~ilG~~fl~~~y~-v 271 (283)
T cd05471 201 GGGGAIVDSGTSLIYLPSSVYDAILKALGAAVSSSDGGYGVDCSPCDTLPDITFTF--------LWILGDVFLRNYYT-V 271 (283)
T ss_pred CCcEEEEecCCCCEeCCHHHHHHHHHHhCCcccccCCcEEEeCcccCcCCCEEEEE--------EEEccHhhhhheEE-E
Confidence 4678999999999999999887753222 1000 00 00111222 89999999998774 4
Q ss_pred eeec
Q 040033 154 WDFA 157 (158)
Q Consensus 154 idw~ 157 (158)
.|+.
T Consensus 272 fD~~ 275 (283)
T cd05471 272 FDLD 275 (283)
T ss_pred EeCC
Confidence 5653
No 50
>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=78.01 E-value=3.7 Score=32.71 Aligned_cols=26 Identities=35% Similarity=0.528 Sum_probs=21.7
Q ss_pred EEEEEEC--CEeeEEEecCCCceeEECH
Q 040033 80 RINGRIG--NISPIVLVDSGSTHNFISD 105 (158)
Q Consensus 80 ~~~~~i~--~~~v~aLiDSGat~sfI~~ 105 (158)
.+++.|+ .+++.++|||||+..+|..
T Consensus 3 ~~~v~iGtp~q~~~~~iDTGS~~~wv~~ 30 (317)
T PF00026_consen 3 YINVTIGTPPQTFRVLIDTGSSDTWVPS 30 (317)
T ss_dssp EEEEEETTTTEEEEEEEETTBSSEEEEB
T ss_pred EEEEEECCCCeEEEEEEecccceeeece
Confidence 3567776 8999999999999998874
No 51
>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=75.84 E-value=1.2 Score=31.85 Aligned_cols=18 Identities=11% Similarity=0.054 Sum_probs=16.0
Q ss_pred cceeecCCCCCCCccCCc
Q 040033 30 KVCATIATKSFPRDIGER 47 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~ 47 (158)
+.||.||.--|-.+.|+.
T Consensus 63 ~~C~~CG~~l~~~~~C~~ 80 (124)
T PF05515_consen 63 NRCFKCGRYLHNNGNCRR 80 (124)
T ss_pred CccccccceeecCCcCCC
Confidence 999999997788899984
No 52
>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=74.04 E-value=4.3 Score=32.17 Aligned_cols=25 Identities=20% Similarity=0.287 Sum_probs=20.5
Q ss_pred EEEEECC--EeeEEEecCCCceeEECH
Q 040033 81 INGRIGN--ISPIVLVDSGSTHNFISD 105 (158)
Q Consensus 81 ~~~~i~~--~~v~aLiDSGat~sfI~~ 105 (158)
+.+.|+. +++.+++||||+..+|..
T Consensus 3 ~~i~vGtP~Q~~~v~~DTGS~~~wv~~ 29 (278)
T cd06097 3 TPVKIGTPPQTLNLDLDTGSSDLWVFS 29 (278)
T ss_pred eeEEECCCCcEEEEEEeCCCCceeEee
Confidence 4566766 899999999999999854
No 53
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=72.95 E-value=1.9 Score=26.42 Aligned_cols=22 Identities=18% Similarity=-0.043 Sum_probs=16.6
Q ss_pred hhcc--cceeecCCCCCCC----ccCCc
Q 040033 26 ERRA--KVCATIATKSFPR----DIGER 47 (158)
Q Consensus 26 ~rR~--~~Cf~Cg~~gH~~----~~C~~ 47 (158)
+-|. .-||+||-++--. ..||-
T Consensus 22 YLR~~~~YC~~Cg~~Y~d~~dL~~~CPG 49 (55)
T PF13821_consen 22 YLREEHNYCFWCGTKYDDEEDLERNCPG 49 (55)
T ss_pred HHHhhCceeeeeCCccCCHHHHHhCCCC
Confidence 3355 8899999887665 77875
No 54
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=69.85 E-value=2.1 Score=36.92 Aligned_cols=19 Identities=16% Similarity=-0.008 Sum_probs=16.9
Q ss_pred cceeecCCCCCCCccCCcc
Q 040033 30 KVCATIATKSFPRDIGERS 48 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~~ 48 (158)
.-|-|||..||+..+||+-
T Consensus 571 kGCayCgGLGHRItdCPKl 589 (610)
T KOG0341|consen 571 KGCAYCGGLGHRITDCPKL 589 (610)
T ss_pred cccccccCCCcccccCchh
Confidence 3499999999999999983
No 55
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=69.69 E-value=1.8 Score=34.52 Aligned_cols=19 Identities=5% Similarity=0.013 Sum_probs=17.5
Q ss_pred cceeecCCCCCCCccCCcc
Q 040033 30 KVCATIATKSFPRDIGERS 48 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~~ 48 (158)
..||+|++.||..++|+..
T Consensus 93 ~~c~~C~~~gH~~~~c~~~ 111 (261)
T KOG4400|consen 93 AACFNCGEGGHIERDCPEA 111 (261)
T ss_pred hhhhhCCCCccchhhCCcc
Confidence 6799999999999999976
No 56
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=69.64 E-value=2.2 Score=25.87 Aligned_cols=16 Identities=6% Similarity=-0.070 Sum_probs=13.6
Q ss_pred cceeecCCCCCCCccC
Q 040033 30 KVCATIATKSFPRDIG 45 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C 45 (158)
..||+|++.||..-.|
T Consensus 49 ~fC~~C~~~~H~~~~C 64 (64)
T smart00647 49 SFCFRCKVPWHSPVSC 64 (64)
T ss_pred eECCCCCCcCCCCCCC
Confidence 6699999999987665
No 57
>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=68.48 E-value=2.6 Score=30.33 Aligned_cols=18 Identities=6% Similarity=-0.114 Sum_probs=16.2
Q ss_pred cceeecCCCCCCCccCCcc
Q 040033 30 KVCATIATKSFPRDIGERS 48 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~~ 48 (158)
..|+.|+ ..|+..+||.+
T Consensus 107 v~CR~Ck-GdH~T~~CPyK 124 (128)
T PF12353_consen 107 VKCRICK-GDHWTSKCPYK 124 (128)
T ss_pred EEeCCCC-CCcccccCCcc
Confidence 6699996 99999999986
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=68.48 E-value=16 Score=27.10 Aligned_cols=63 Identities=19% Similarity=0.225 Sum_probs=38.3
Q ss_pred ECCEeeEEEecCCCceeEECHHHHHHcC-CeE-------------E---EEEECCEEEEEEEEEecCCCCcEEe----ch
Q 040033 85 IGNISPIVLVDSGSTHNFISDTFAKKVK-NFI-------------V---NLILQGVYVIVDFNLRELEGYDVVL----GT 143 (158)
Q Consensus 85 i~~~~v~aLiDSGat~sfI~~~~a~~~~-~~~-------------A---~i~i~g~~~~~~~~v~~~~~~dvIL----G~ 143 (158)
|.|..+.+--||||+.+.|...|...-. +.. + .++++|+.....++--++ |.|| -.
T Consensus 1 ikg~~l~~~wDsga~ITCiP~~fl~~E~Pi~~~~i~Tihg~~~~~vYYl~fKi~grkv~aEVi~s~~---dy~li~p~di 77 (163)
T PF03539_consen 1 IKGTKLKGHWDSGAQITCIPESFLEEEQPIGKTLIKTIHGEKEQDVYYLTFKINGRKVEAEVIASPY---DYILISPSDI 77 (163)
T ss_dssp ETTEEEEEEE-TT-SSEEEEGGGTTT---SEEEEEE-SS-EEEEEEEEEEEEESS-EEEEEEEEESS---SSEEE-TTT-
T ss_pred CCCceeeEEecCCCeEEEccHHHhCccccccceEEEEecCceeccEEEEEEEEcCeEEEEEEecCcc---ceEEEccccc
Confidence 4577889999999999999998865321 111 1 778899877766665553 3333 24
Q ss_pred hHhhhcC
Q 040033 144 QWLRTLE 150 (158)
Q Consensus 144 dwL~~~~ 150 (158)
+|+.+..
T Consensus 78 Pw~~~~p 84 (163)
T PF03539_consen 78 PWYKKKP 84 (163)
T ss_dssp HHHHS--
T ss_pred ccccCCC
Confidence 7887654
No 59
>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=67.26 E-value=6.7 Score=31.37 Aligned_cols=21 Identities=19% Similarity=0.246 Sum_probs=17.7
Q ss_pred EEEecCCCceeEECHHHHHHc
Q 040033 91 IVLVDSGSTHNFISDTFAKKV 111 (158)
Q Consensus 91 ~aLiDSGat~sfI~~~~a~~~ 111 (158)
.++||||++..++.+.+.+.+
T Consensus 173 ~~ivDSGTt~~~lp~~~~~~l 193 (299)
T cd05472 173 GVIIDSGTVITRLPPSAYAAL 193 (299)
T ss_pred CeEEeCCCcceecCHHHHHHH
Confidence 589999999999998776643
No 60
>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=65.86 E-value=11 Score=30.68 Aligned_cols=26 Identities=23% Similarity=0.256 Sum_probs=21.1
Q ss_pred EEEEEEC--CEeeEEEecCCCceeEECH
Q 040033 80 RINGRIG--NISPIVLVDSGSTHNFISD 105 (158)
Q Consensus 80 ~~~~~i~--~~~v~aLiDSGat~sfI~~ 105 (158)
...+.|+ .+++.++|||||+..+|..
T Consensus 12 ~~~i~iGtP~Q~~~v~~DTGSs~lWv~~ 39 (317)
T cd06098 12 FGEIGIGTPPQKFTVIFDTGSSNLWVPS 39 (317)
T ss_pred EEEEEECCCCeEEEEEECCCccceEEec
Confidence 4456666 6899999999999998864
No 61
>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=65.84 E-value=1.7 Score=26.37 Aligned_cols=16 Identities=6% Similarity=-0.020 Sum_probs=13.0
Q ss_pred cceeecCCCCCCCccC
Q 040033 30 KVCATIATKSFPRDIG 45 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C 45 (158)
..||.|+++||....|
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 62
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=63.96 E-value=3.4 Score=36.18 Aligned_cols=19 Identities=11% Similarity=0.004 Sum_probs=14.3
Q ss_pred cceeecCCCCCCCccCCcc
Q 040033 30 KVCATIATKSFPRDIGERS 48 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~~ 48 (158)
++|++||..||.+.+|+.+
T Consensus 286 n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 286 NVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccCCcccccccCCCc
Confidence 4788888888888888754
No 63
>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=62.55 E-value=12 Score=30.39 Aligned_cols=25 Identities=24% Similarity=0.294 Sum_probs=20.5
Q ss_pred EEEEEC--CEeeEEEecCCCceeEECH
Q 040033 81 INGRIG--NISPIVLVDSGSTHNFISD 105 (158)
Q Consensus 81 ~~~~i~--~~~v~aLiDSGat~sfI~~ 105 (158)
..+.|+ .+++.++|||||+..+|..
T Consensus 11 ~~i~iGtP~q~~~v~~DTGSs~~Wv~~ 37 (326)
T cd05487 11 GEIGIGTPPQTFKVVFDTGSSNLWVPS 37 (326)
T ss_pred EEEEECCCCcEEEEEEeCCccceEEcc
Confidence 455665 7899999999999999953
No 64
>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=62.39 E-value=12 Score=30.24 Aligned_cols=25 Identities=24% Similarity=0.283 Sum_probs=20.1
Q ss_pred EEEEEEC--CEeeEEEecCCCceeEEC
Q 040033 80 RINGRIG--NISPIVLVDSGSTHNFIS 104 (158)
Q Consensus 80 ~~~~~i~--~~~v~aLiDSGat~sfI~ 104 (158)
..++.|+ .+++.++|||||+..+|.
T Consensus 8 ~~~i~iGtP~q~~~v~~DTGSs~~Wv~ 34 (325)
T cd05490 8 YGEIGIGTPPQTFTVVFDTGSSNLWVP 34 (325)
T ss_pred EEEEEECCCCcEEEEEEeCCCccEEEE
Confidence 3456665 488999999999999984
No 65
>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=62.14 E-value=9.9 Score=29.92 Aligned_cols=65 Identities=20% Similarity=0.210 Sum_probs=38.3
Q ss_pred EEEEEC--CEeeEEEecCCCceeEECH-HHHHHcC--CeE------EEEEECCE--EE-EEEEEEecC------CCCcEE
Q 040033 81 INGRIG--NISPIVLVDSGSTHNFISD-TFAKKVK--NFI------VNLILQGV--YV-IVDFNLREL------EGYDVV 140 (158)
Q Consensus 81 ~~~~i~--~~~v~aLiDSGat~sfI~~-~~a~~~~--~~~------A~i~i~g~--~~-~~~~~v~~~------~~~dvI 140 (158)
+.+.|+ .+.+.+++||||+..++.. .+...++ -.. ..+.+++. .. ...|.++.. ...|-|
T Consensus 4 ~~i~iGtP~q~~~v~~DTGSs~~wv~~~~~~~~Y~dg~~~~G~~~~D~v~~g~~~~~~~~~~Fg~~~~~~~~~~~~~~GI 83 (265)
T cd05476 4 VTLSIGTPPQPFSLIVDTGSDLTWTQCCSYEYSYGDGSSTSGVLATETFTFGDSSVSVPNVAFGCGTDNEGGSFGGADGI 83 (265)
T ss_pred EEEecCCCCcceEEEecCCCCCEEEcCCceEeEeCCCceeeeeEEEEEEEecCCCCccCCEEEEecccccCCccCCCCEE
Confidence 445565 6899999999999998853 1111111 000 16667665 22 234555443 258899
Q ss_pred echhH
Q 040033 141 LGTQW 145 (158)
Q Consensus 141 LG~dw 145 (158)
||..+
T Consensus 84 lGLg~ 88 (265)
T cd05476 84 LGLGR 88 (265)
T ss_pred EECCC
Confidence 99865
No 66
>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=61.17 E-value=14 Score=29.91 Aligned_cols=25 Identities=28% Similarity=0.391 Sum_probs=20.4
Q ss_pred EEEEEC--CEeeEEEecCCCceeEECH
Q 040033 81 INGRIG--NISPIVLVDSGSTHNFISD 105 (158)
Q Consensus 81 ~~~~i~--~~~v~aLiDSGat~sfI~~ 105 (158)
.++.|+ .+++.++|||||+..++..
T Consensus 6 ~~i~iGtP~q~~~v~~DTGS~~~wv~~ 32 (318)
T cd05477 6 GEISIGTPPQNFLVLFDTGSSNLWVPS 32 (318)
T ss_pred EEEEECCCCcEEEEEEeCCCccEEEcc
Confidence 455666 4899999999999999964
No 67
>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=60.54 E-value=12 Score=30.32 Aligned_cols=74 Identities=16% Similarity=0.300 Sum_probs=47.8
Q ss_pred EEECCEe-------eEEEecCCCceeEECHHHHHHcCCeE-----E-----EEEECCEEEEEE---EE------------
Q 040033 83 GRIGNIS-------PIVLVDSGSTHNFISDTFAKKVKNFI-----V-----NLILQGVYVIVD---FN------------ 130 (158)
Q Consensus 83 ~~i~~~~-------v~aLiDSGat~sfI~~~~a~~~~~~~-----A-----~i~i~g~~~~~~---~~------------ 130 (158)
+.|+++. ..++||||++..++..++++.+.... . .+.++|..+.+. +.
T Consensus 197 i~v~g~~~~~~~~~~~aivDTGTs~~~lP~~~~~~i~~~~~C~~~~~~P~i~f~f~g~~~~l~~~~yi~~~~~~~~~~C~ 276 (317)
T cd06098 197 VLIGGKSTGFCAGGCAAIADSGTSLLAGPTTIVTQINSAVDCNSLSSMPNVSFTIGGKTFELTPEQYILKVGEGAAAQCI 276 (317)
T ss_pred EEECCEEeeecCCCcEEEEecCCcceeCCHHHHHhhhccCCccccccCCcEEEEECCEEEEEChHHeEEeecCCCCCEEe
Confidence 3566654 46999999999999999988765322 0 456677666542 11
Q ss_pred --Ee--cC---CCCcEEechhHhhhcCCceeeec
Q 040033 131 --LR--EL---EGYDVVLGTQWLRTLEPILWDFA 157 (158)
Q Consensus 131 --v~--~~---~~~dvILG~dwL~~~~~i~idw~ 157 (158)
+. +. .+...|||-.||+.+-- -.|+.
T Consensus 277 ~~~~~~~~~~~~~~~~IlGd~Flr~~y~-VfD~~ 309 (317)
T cd06098 277 SGFTALDVPPPRGPLWILGDVFMGAYHT-VFDYG 309 (317)
T ss_pred ceEEECCCCCCCCCeEEechHHhcccEE-EEeCC
Confidence 11 11 12246999999998765 45664
No 68
>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=59.74 E-value=14 Score=29.29 Aligned_cols=24 Identities=21% Similarity=0.368 Sum_probs=19.6
Q ss_pred EEEEEC--CEeeEEEecCCCceeEEC
Q 040033 81 INGRIG--NISPIVLVDSGSTHNFIS 104 (158)
Q Consensus 81 ~~~~i~--~~~v~aLiDSGat~sfI~ 104 (158)
+.+.|+ .+.+.+++||||+..+|.
T Consensus 5 ~~i~iGtP~q~~~v~~DTGS~~~Wv~ 30 (273)
T cd05475 5 VTINIGNPPKPYFLDIDTGSDLTWLQ 30 (273)
T ss_pred EEEEcCCCCeeEEEEEccCCCceEEe
Confidence 345555 688999999999999994
No 69
>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=59.63 E-value=12 Score=30.60 Aligned_cols=67 Identities=13% Similarity=0.131 Sum_probs=42.4
Q ss_pred eEEEecCCCceeEECHHHHHHc----CCeE-----------E-------EEEECCEEEEEE---EE--------------
Q 040033 90 PIVLVDSGSTHNFISDTFAKKV----KNFI-----------V-------NLILQGVYVIVD---FN-------------- 130 (158)
Q Consensus 90 v~aLiDSGat~sfI~~~~a~~~----~~~~-----------A-------~i~i~g~~~~~~---~~-------------- 130 (158)
..++||||++..++...+++.+ +... . .+.++|..|.+. +.
T Consensus 211 ~~~iiDSGtt~~~lP~~~~~~l~~~~~~~~~~~~~~~~~C~~~~~~p~i~f~fgg~~~~i~~~~yi~~~~~~~~~~C~~~ 290 (329)
T cd05485 211 CQAIADTGTSLIAGPVDEIEKLNNAIGAKPIIGGEYMVNCSAIPSLPDITFVLGGKSFSLTGKDYVLKVTQMGQTICLSG 290 (329)
T ss_pred cEEEEccCCcceeCCHHHHHHHHHHhCCccccCCcEEEeccccccCCcEEEEECCEEeEEChHHeEEEecCCCCCEEeee
Confidence 3699999999999999876654 2110 0 445667666542 11
Q ss_pred Eec-----CCCCcEEechhHhhhcCCceeeec
Q 040033 131 LRE-----LEGYDVVLGTQWLRTLEPILWDFA 157 (158)
Q Consensus 131 v~~-----~~~~dvILG~dwL~~~~~i~idw~ 157 (158)
+.. ..+...|||..||+.+-. ..||.
T Consensus 291 ~~~~~~~~~~~~~~IlG~~fl~~~y~-vFD~~ 321 (329)
T cd05485 291 FMGIDIPPPAGPLWILGDVFIGKYYT-EFDLG 321 (329)
T ss_pred EEECcCCCCCCCeEEEchHHhccceE-EEeCC
Confidence 111 112348999999998775 46765
No 70
>COG2383 Uncharacterized conserved protein [Function unknown]
Probab=59.40 E-value=2.7 Score=29.02 Aligned_cols=18 Identities=22% Similarity=0.470 Sum_probs=16.1
Q ss_pred EechhHhhhcCCceeeec
Q 040033 140 VLGTQWLRTLEPILWDFA 157 (158)
Q Consensus 140 ILG~dwL~~~~~i~idw~ 157 (158)
||+.-||++++-|+|||.
T Consensus 51 ilsl~~La~~GVItin~~ 68 (109)
T COG2383 51 ILSLFWLAQYGVITINWE 68 (109)
T ss_pred HHHHHHHHHcCeEEEcHH
Confidence 577799999999999995
No 71
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=59.09 E-value=4.7 Score=30.80 Aligned_cols=18 Identities=6% Similarity=0.051 Sum_probs=16.6
Q ss_pred cceeecCCCCCCCccCCc
Q 040033 30 KVCATIATKSFPRDIGER 47 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~ 47 (158)
+.|++||+.||..+.|.+
T Consensus 101 ~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 101 GFCYRCGERGHIGRNCKD 118 (195)
T ss_pred cccccCCCcccccccccc
Confidence 669999999999999987
No 72
>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=58.29 E-value=11 Score=31.10 Aligned_cols=20 Identities=25% Similarity=0.257 Sum_probs=17.4
Q ss_pred EEEecCCCceeEECHHHHHH
Q 040033 91 IVLVDSGSTHNFISDTFAKK 110 (158)
Q Consensus 91 ~aLiDSGat~sfI~~~~a~~ 110 (158)
.++||||++..++.......
T Consensus 213 ~~ivDSGTs~~~lp~~~~~~ 232 (364)
T cd05473 213 KAIVDSGTTNLRLPVKVFNA 232 (364)
T ss_pred cEEEeCCCcceeCCHHHHHH
Confidence 48999999999999887664
No 73
>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=57.80 E-value=9.8 Score=30.77 Aligned_cols=29 Identities=17% Similarity=0.142 Sum_probs=21.6
Q ss_pred EEECCEe------eEEEecCCCceeEECHHHHHHc
Q 040033 83 GRIGNIS------PIVLVDSGSTHNFISDTFAKKV 111 (158)
Q Consensus 83 ~~i~~~~------v~aLiDSGat~sfI~~~~a~~~ 111 (158)
+.|+++. ..++||||++..++....++.+
T Consensus 186 i~v~g~~~~~~~~~~aiiDTGTs~~~lP~~~~~~l 220 (316)
T cd05486 186 IQVGGTVIFCSDGCQAIVDTGTSLITGPSGDIKQL 220 (316)
T ss_pred EEEecceEecCCCCEEEECCCcchhhcCHHHHHHH
Confidence 3556543 3699999999999998866544
No 74
>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=57.46 E-value=15 Score=29.61 Aligned_cols=24 Identities=25% Similarity=0.403 Sum_probs=19.3
Q ss_pred EEEEC--CEeeEEEecCCCceeEECH
Q 040033 82 NGRIG--NISPIVLVDSGSTHNFISD 105 (158)
Q Consensus 82 ~~~i~--~~~v~aLiDSGat~sfI~~ 105 (158)
++.|+ .+++.++|||||+..+|..
T Consensus 4 ~i~iGtP~Q~~~v~~DTGSs~~Wv~s 29 (316)
T cd05486 4 QISIGTPPQNFTVIFDTGSSNLWVPS 29 (316)
T ss_pred EEEECCCCcEEEEEEcCCCccEEEec
Confidence 44554 6889999999999999853
No 75
>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=57.20 E-value=17 Score=29.36 Aligned_cols=26 Identities=23% Similarity=0.284 Sum_probs=20.7
Q ss_pred EEEEEEC--CEeeEEEecCCCceeEECH
Q 040033 80 RINGRIG--NISPIVLVDSGSTHNFISD 105 (158)
Q Consensus 80 ~~~~~i~--~~~v~aLiDSGat~sfI~~ 105 (158)
...+.|+ .+++.++|||||+..+|..
T Consensus 12 ~~~i~vGtp~q~~~v~~DTGS~~~wv~~ 39 (317)
T cd05478 12 YGTISIGTPPQDFTVIFDTGSSNLWVPS 39 (317)
T ss_pred EEEEEeCCCCcEEEEEEeCCCccEEEec
Confidence 3455665 6889999999999999964
No 76
>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=56.36 E-value=16 Score=30.21 Aligned_cols=25 Identities=32% Similarity=0.384 Sum_probs=20.1
Q ss_pred EEEEEC--CEeeEEEecCCCceeEECH
Q 040033 81 INGRIG--NISPIVLVDSGSTHNFISD 105 (158)
Q Consensus 81 ~~~~i~--~~~v~aLiDSGat~sfI~~ 105 (158)
+++.|+ .+++.++|||||+..+|..
T Consensus 6 ~~i~iGtP~Q~~~v~~DTGSs~lWv~~ 32 (364)
T cd05473 6 IEMLIGTPPQKLNILVDTGSSNFAVAA 32 (364)
T ss_pred EEEEecCCCceEEEEEecCCcceEEEc
Confidence 455665 5899999999999998864
No 77
>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=56.31 E-value=18 Score=29.39 Aligned_cols=25 Identities=24% Similarity=0.262 Sum_probs=19.7
Q ss_pred EEEEEC--CEeeEEEecCCCceeEECH
Q 040033 81 INGRIG--NISPIVLVDSGSTHNFISD 105 (158)
Q Consensus 81 ~~~~i~--~~~v~aLiDSGat~sfI~~ 105 (158)
+.+.|+ .+++.++|||||+..+|..
T Consensus 6 ~~i~vGtP~Q~~~v~~DTGS~~~wv~~ 32 (326)
T cd06096 6 IDIFIGNPPQKQSLILDTGSSSLSFPC 32 (326)
T ss_pred EEEEecCCCeEEEEEEeCCCCceEEec
Confidence 455555 5899999999999988754
No 78
>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=56.26 E-value=11 Score=30.09 Aligned_cols=65 Identities=20% Similarity=0.245 Sum_probs=37.1
Q ss_pred EEEEEC--CEeeEEEecCCCceeEECHH----HHHHcCCe--E----E--EEEECCE-EEE-EEEEEecCC-----CCcE
Q 040033 81 INGRIG--NISPIVLVDSGSTHNFISDT----FAKKVKNF--I----V--NLILQGV-YVI-VDFNLRELE-----GYDV 139 (158)
Q Consensus 81 ~~~~i~--~~~v~aLiDSGat~sfI~~~----~a~~~~~~--~----A--~i~i~g~-~~~-~~~~v~~~~-----~~dv 139 (158)
..+.|+ .+++.+++||||+..+|.-. +..+++-- . + .+.+++. ... ..|.+.... ..|-
T Consensus 4 ~~i~iGtP~q~~~v~~DTGSs~~Wv~c~~c~~~~i~Yg~Gs~~~G~~~~D~v~ig~~~~~~~~~Fg~~~~~~~~~~~~~G 83 (299)
T cd05472 4 VTVGLGTPARDQTVIVDTGSDLTWVQCQPCCLYQVSYGDGSYTTGDLATDTLTLGSSDVVPGFAFGCGHDNEGLFGGAAG 83 (299)
T ss_pred EEEecCCCCcceEEEecCCCCcccccCCCCCeeeeEeCCCceEEEEEEEEEEEeCCCCccCCEEEECCccCCCccCCCCE
Confidence 345555 58999999999999988321 11111100 0 1 6667664 322 345444321 5788
Q ss_pred EechhH
Q 040033 140 VLGTQW 145 (158)
Q Consensus 140 ILG~dw 145 (158)
|||+.+
T Consensus 84 ilGLg~ 89 (299)
T cd05472 84 LLGLGR 89 (299)
T ss_pred EEECCC
Confidence 999864
No 79
>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=55.72 E-value=18 Score=29.26 Aligned_cols=27 Identities=19% Similarity=0.308 Sum_probs=21.4
Q ss_pred EEEEEEEC--CEeeEEEecCCCceeEECH
Q 040033 79 LRINGRIG--NISPIVLVDSGSTHNFISD 105 (158)
Q Consensus 79 i~~~~~i~--~~~v~aLiDSGat~sfI~~ 105 (158)
...++.|+ .+++.++|||||+..+|..
T Consensus 11 Y~~~i~iGtp~q~~~v~~DTGSs~~wv~~ 39 (320)
T cd05488 11 YFTDITLGTPPQKFKVILDTGSSNLWVPS 39 (320)
T ss_pred EEEEEEECCCCcEEEEEEecCCcceEEEc
Confidence 34456666 5899999999999998854
No 80
>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=55.57 E-value=19 Score=29.36 Aligned_cols=27 Identities=26% Similarity=0.231 Sum_probs=21.6
Q ss_pred EEEEEEC--CEeeEEEecCCCceeEECHH
Q 040033 80 RINGRIG--NISPIVLVDSGSTHNFISDT 106 (158)
Q Consensus 80 ~~~~~i~--~~~v~aLiDSGat~sfI~~~ 106 (158)
...+.|+ .+++.++|||||+..++...
T Consensus 13 ~~~i~vGtP~q~~~v~~DTGSs~~Wv~~~ 41 (329)
T cd05485 13 YGVITIGTPPQSFKVVFDTGSSNLWVPSK 41 (329)
T ss_pred EEEEEECCCCcEEEEEEcCCCccEEEecC
Confidence 4466776 58999999999999988753
No 81
>PF14543 TAXi_N: Xylanase inhibitor N-terminal; PDB: 3HD8_A 3VLB_A 3VLA_A 3AUP_D 1T6G_A 1T6E_X 2B42_A.
Probab=51.70 E-value=24 Score=25.88 Aligned_cols=23 Identities=26% Similarity=0.462 Sum_probs=16.9
Q ss_pred EEEEECC--EeeEEEecCCCceeEE
Q 040033 81 INGRIGN--ISPIVLVDSGSTHNFI 103 (158)
Q Consensus 81 ~~~~i~~--~~v~aLiDSGat~sfI 103 (158)
+.+.|+. +++.++||||+...++
T Consensus 3 ~~~~iGtP~~~~~lvvDtgs~l~W~ 27 (164)
T PF14543_consen 3 VSVSIGTPPQPFSLVVDTGSDLTWV 27 (164)
T ss_dssp EEEECTCTTEEEEEEEETT-SSEEE
T ss_pred EEEEeCCCCceEEEEEECCCCceEE
Confidence 3445543 7899999999999987
No 82
>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=51.17 E-value=22 Score=27.53 Aligned_cols=26 Identities=23% Similarity=0.289 Sum_probs=19.6
Q ss_pred EEEEC--CEeeEEEecCCCceeEECHHH
Q 040033 82 NGRIG--NISPIVLVDSGSTHNFISDTF 107 (158)
Q Consensus 82 ~~~i~--~~~v~aLiDSGat~sfI~~~~ 107 (158)
.+.|+ .+++.++|||||+..+|...-
T Consensus 4 ~i~iGtp~q~~~l~~DTGS~~~wv~~~~ 31 (283)
T cd05471 4 EITIGTPPQKFSVIFDTGSSLLWVPSSN 31 (283)
T ss_pred EEEECCCCcEEEEEEeCCCCCEEEecCC
Confidence 34454 368999999999999886553
No 83
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=49.90 E-value=11 Score=32.90 Aligned_cols=19 Identities=11% Similarity=0.069 Sum_probs=17.2
Q ss_pred cceeecCCCCCCCccCCcc
Q 040033 30 KVCATIATKSFPRDIGERS 48 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~~ 48 (158)
--||+|+..-|--++|+++
T Consensus 129 ~~CFNC~g~~hsLrdC~rp 147 (485)
T KOG2673|consen 129 DPCFNCGGTPHSLRDCPRP 147 (485)
T ss_pred ccccccCCCCCccccCCCc
Confidence 4589999999999999987
No 84
>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=46.72 E-value=29 Score=29.03 Aligned_cols=20 Identities=5% Similarity=-0.014 Sum_probs=16.5
Q ss_pred EEEecCCCceeEECHHHHHH
Q 040033 91 IVLVDSGSTHNFISDTFAKK 110 (158)
Q Consensus 91 ~aLiDSGat~sfI~~~~a~~ 110 (158)
.++||||++.+++...+.+.
T Consensus 231 g~iiDSGTs~t~lp~~~y~~ 250 (362)
T cd05489 231 GVKLSTVVPYTVLRSDIYRA 250 (362)
T ss_pred cEEEecCCceEEECHHHHHH
Confidence 48999999999988876554
No 85
>PLN03146 aspartyl protease family protein; Provisional
Probab=46.46 E-value=23 Score=30.32 Aligned_cols=19 Identities=26% Similarity=0.578 Sum_probs=16.3
Q ss_pred EEEecCCCceeEECHHHHH
Q 040033 91 IVLVDSGSTHNFISDTFAK 109 (158)
Q Consensus 91 ~aLiDSGat~sfI~~~~a~ 109 (158)
.++||||++.+++.+...+
T Consensus 309 ~~iiDSGTt~t~Lp~~~y~ 327 (431)
T PLN03146 309 NIIIDSGTTLTLLPSDFYS 327 (431)
T ss_pred cEEEeCCccceecCHHHHH
Confidence 4799999999999998543
No 86
>PTZ00165 aspartyl protease; Provisional
Probab=44.14 E-value=34 Score=29.97 Aligned_cols=28 Identities=25% Similarity=0.339 Sum_probs=22.2
Q ss_pred EEEEEEECC--EeeEEEecCCCceeEECHH
Q 040033 79 LRINGRIGN--ISPIVLVDSGSTHNFISDT 106 (158)
Q Consensus 79 i~~~~~i~~--~~v~aLiDSGat~sfI~~~ 106 (158)
....+.|+. +++.+++||||+..+|...
T Consensus 121 Y~~~I~IGTPpQ~f~Vv~DTGSS~lWVps~ 150 (482)
T PTZ00165 121 YFGEIQVGTPPKSFVVVFDTGSSNLWIPSK 150 (482)
T ss_pred EEEEEEeCCCCceEEEEEeCCCCCEEEEch
Confidence 345667765 8999999999999998643
No 87
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=43.63 E-value=5.8 Score=34.51 Aligned_cols=19 Identities=11% Similarity=0.097 Sum_probs=17.2
Q ss_pred cccceeecCCCCCCCccCC
Q 040033 28 RAKVCATIATKSFPRDIGE 46 (158)
Q Consensus 28 R~~~Cf~Cg~~gH~~~~C~ 46 (158)
|.|.|-+||.-+|....|=
T Consensus 111 RKGACeNCGAmtHk~KDCm 129 (529)
T KOG2560|consen 111 RKGACENCGAMTHKVKDCM 129 (529)
T ss_pred hhhhhhhhhhhhcchHHHh
Confidence 4599999999999999994
No 88
>PF14541 TAXi_C: Xylanase inhibitor C-terminal; PDB: 3AUP_D 3HD8_A 1T6G_A 1T6E_X 2B42_A 3VLB_A 3VLA_A.
Probab=42.07 E-value=22 Score=25.88 Aligned_cols=23 Identities=22% Similarity=0.368 Sum_probs=17.3
Q ss_pred eeEEEecCCCceeEECHHHHHHc
Q 040033 89 SPIVLVDSGSTHNFISDTFAKKV 111 (158)
Q Consensus 89 ~v~aLiDSGat~sfI~~~~a~~~ 111 (158)
.-.++||||++.+++.+.+...+
T Consensus 29 ~g~~iiDSGT~~T~L~~~~y~~l 51 (161)
T PF14541_consen 29 SGGTIIDSGTTYTYLPPPVYDAL 51 (161)
T ss_dssp TCSEEE-SSSSSEEEEHHHHHHH
T ss_pred CCCEEEECCCCccCCcHHHHHHH
Confidence 44578999999999998865543
No 89
>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=41.91 E-value=31 Score=28.02 Aligned_cols=22 Identities=18% Similarity=0.156 Sum_probs=17.8
Q ss_pred eEEEecCCCceeEECHHHHHHc
Q 040033 90 PIVLVDSGSTHNFISDTFAKKV 111 (158)
Q Consensus 90 v~aLiDSGat~sfI~~~~a~~~ 111 (158)
..++||||++..++....++++
T Consensus 208 ~~aiiDSGts~~~lP~~~~~~l 229 (326)
T cd05487 208 CTAVVDTGASFISGPTSSISKL 229 (326)
T ss_pred CEEEECCCccchhCcHHHHHHH
Confidence 3689999999999998865543
No 90
>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=41.61 E-value=19 Score=29.17 Aligned_cols=22 Identities=14% Similarity=0.042 Sum_probs=18.8
Q ss_pred eEEEecCCCceeEECHHHHHHc
Q 040033 90 PIVLVDSGSTHNFISDTFAKKV 111 (158)
Q Consensus 90 v~aLiDSGat~sfI~~~~a~~~ 111 (158)
..++||||++..++....+..+
T Consensus 207 ~~aiiDSGTt~~~~p~~~~~~l 228 (325)
T cd05490 207 CEAIVDTGTSLITGPVEEVRAL 228 (325)
T ss_pred CEEEECCCCccccCCHHHHHHH
Confidence 5799999999999998877654
No 91
>PLN03146 aspartyl protease family protein; Provisional
Probab=40.89 E-value=35 Score=29.25 Aligned_cols=26 Identities=23% Similarity=0.377 Sum_probs=20.5
Q ss_pred EEEEEEEC--CEeeEEEecCCCceeEEC
Q 040033 79 LRINGRIG--NISPIVLVDSGSTHNFIS 104 (158)
Q Consensus 79 i~~~~~i~--~~~v~aLiDSGat~sfI~ 104 (158)
..+.+.|+ .+++.+++||||+..+|.
T Consensus 85 Y~v~i~iGTPpq~~~vi~DTGS~l~Wv~ 112 (431)
T PLN03146 85 YLMNISIGTPPVPILAIADTGSDLIWTQ 112 (431)
T ss_pred EEEEEEcCCCCceEEEEECCCCCcceEc
Confidence 44566665 578999999999999884
No 92
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=38.15 E-value=11 Score=34.98 Aligned_cols=19 Identities=11% Similarity=0.085 Sum_probs=16.6
Q ss_pred cceeecCCCCCCCccCCcc
Q 040033 30 KVCATIATKSFPRDIGERS 48 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~~ 48 (158)
..||.||+.||...+|...
T Consensus 261 ~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 261 RRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred ccchhhcccCCcHhhcCCc
Confidence 4499999999999999754
No 93
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=37.12 E-value=19 Score=31.76 Aligned_cols=34 Identities=15% Similarity=0.201 Sum_probs=26.0
Q ss_pred CCCCCCHHHHHhh----cc---cceeecCCCCCCCccCCcc
Q 040033 15 PVRGLSRAELQER----RA---KVCATIATKSFPRDIGERS 48 (158)
Q Consensus 15 ~~~~ls~~e~~~r----R~---~~Cf~Cg~~gH~~~~C~~~ 48 (158)
..+++...|+..+ |. ..|-.||..||....||.+
T Consensus 240 ~l~~~Qlrela~lNgt~r~~d~~~c~~cg~~~H~q~~cp~r 280 (554)
T KOG0119|consen 240 DLKRLQLRELARLNGTLRDDDNRACRNCGSTGHKQYDCPGR 280 (554)
T ss_pred cccHHHHHHHHHhCCCCCccccccccccCCCccccccCCcc
Confidence 3556666676554 33 4799999999999999987
No 94
>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=36.61 E-value=28 Score=28.13 Aligned_cols=67 Identities=13% Similarity=0.282 Sum_probs=42.3
Q ss_pred eEEEecCCCceeEECHHHHHHcC----CeE-------------E-----EEEECCEEEEEE---E----------EEec-
Q 040033 90 PIVLVDSGSTHNFISDTFAKKVK----NFI-------------V-----NLILQGVYVIVD---F----------NLRE- 133 (158)
Q Consensus 90 v~aLiDSGat~sfI~~~~a~~~~----~~~-------------A-----~i~i~g~~~~~~---~----------~v~~- 133 (158)
..++||||++..++...+++.+. ... . .+.++|..+.+. + .+..
T Consensus 206 ~~~ivDSGtt~~~lp~~~~~~l~~~~~~~~~~~~~~~~~C~~~~~~P~i~f~f~g~~~~i~~~~y~~~~~g~C~~~~~~~ 285 (320)
T cd05488 206 TGAAIDTGTSLIALPSDLAEMLNAEIGAKKSWNGQYTVDCSKVDSLPDLTFNFDGYNFTLGPFDYTLEVSGSCISAFTGM 285 (320)
T ss_pred CeEEEcCCcccccCCHHHHHHHHHHhCCccccCCcEEeeccccccCCCEEEEECCEEEEECHHHheecCCCeEEEEEEEC
Confidence 46899999999999998876532 111 0 455667666542 1 1111
Q ss_pred -C---CCCcEEechhHhhhcCCceeeec
Q 040033 134 -L---EGYDVVLGTQWLRTLEPILWDFA 157 (158)
Q Consensus 134 -~---~~~dvILG~dwL~~~~~i~idw~ 157 (158)
+ .+...|||..||+.+-- ..|+.
T Consensus 286 ~~~~~~~~~~ilG~~fl~~~y~-vfD~~ 312 (320)
T cd05488 286 DFPEPVGPLAIVGDAFLRKYYS-VYDLG 312 (320)
T ss_pred cCCCCCCCeEEEchHHhhheEE-EEeCC
Confidence 1 12358999999987664 46654
No 95
>KOG4584 consensus Uncharacterized conserved protein [General function prediction only]
Probab=35.72 E-value=24 Score=29.33 Aligned_cols=22 Identities=27% Similarity=0.446 Sum_probs=18.2
Q ss_pred CEEEEEEEEEecCCCCcEEech
Q 040033 122 GVYVIVDFNLRELEGYDVVLGT 143 (158)
Q Consensus 122 g~~~~~~~~v~~~~~~dvILG~ 143 (158)
+.++...+.-++.+++|+|||+
T Consensus 196 ~~p~K~~lif~DNSG~DvILGi 217 (348)
T KOG4584|consen 196 GKPHKCALIFVDNSGFDVILGI 217 (348)
T ss_pred CCCcceEEEEecCCCcceeeee
Confidence 4566777788899999999998
No 96
>PTZ00147 plasmepsin-1; Provisional
Probab=35.59 E-value=53 Score=28.54 Aligned_cols=22 Identities=32% Similarity=0.454 Sum_probs=18.9
Q ss_pred eeEEEecCCCceeEECHHHHHH
Q 040033 89 SPIVLVDSGSTHNFISDTFAKK 110 (158)
Q Consensus 89 ~v~aLiDSGat~sfI~~~~a~~ 110 (158)
...++||||++..++....+..
T Consensus 332 ~~~aIiDSGTsli~lP~~~~~a 353 (453)
T PTZ00147 332 KANVIVDSGTSVITVPTEFLNK 353 (453)
T ss_pred ceeEEECCCCchhcCCHHHHHH
Confidence 4679999999999999987764
No 97
>PTZ00165 aspartyl protease; Provisional
Probab=34.78 E-value=53 Score=28.75 Aligned_cols=23 Identities=13% Similarity=0.085 Sum_probs=19.2
Q ss_pred eeEEEecCCCceeEECHHHHHHc
Q 040033 89 SPIVLVDSGSTHNFISDTFAKKV 111 (158)
Q Consensus 89 ~v~aLiDSGat~sfI~~~~a~~~ 111 (158)
...|+||||++..++...+++.+
T Consensus 327 ~~~aIiDTGTSli~lP~~~~~~i 349 (482)
T PTZ00165 327 KCKAAIDTGSSLITGPSSVINPL 349 (482)
T ss_pred ceEEEEcCCCccEeCCHHHHHHH
Confidence 35689999999999999886654
No 98
>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=34.64 E-value=30 Score=27.32 Aligned_cols=69 Identities=17% Similarity=0.310 Sum_probs=44.3
Q ss_pred EeeEEEecCCCceeEECHHHHHHc----CCeE-----------------E-EEEECCEEEEEE-----------------
Q 040033 88 ISPIVLVDSGSTHNFISDTFAKKV----KNFI-----------------V-NLILQGVYVIVD----------------- 128 (158)
Q Consensus 88 ~~v~aLiDSGat~sfI~~~~a~~~----~~~~-----------------A-~i~i~g~~~~~~----------------- 128 (158)
....++||||++..++...+...+ +... + .+.++|.++.+.
T Consensus 177 ~~~~~iiDSGt~~~~lP~~~~~~l~~~~~~~~~~~~~~~~~~C~~~~~p~i~f~f~g~~~~i~~~~~~~~~~~~~~~~~~ 256 (295)
T cd05474 177 KNLPALLDSGTTLTYLPSDIVDAIAKQLGATYDSDEGLYVVDCDAKDDGSLTFNFGGATISVPLSDLVLPASTDDGGDGA 256 (295)
T ss_pred CCccEEECCCCccEeCCHHHHHHHHHHhCCEEcCCCcEEEEeCCCCCCCEEEEEECCeEEEEEHHHhEeccccCCCCCCC
Confidence 345899999999999999987764 2211 0 345566555432
Q ss_pred --EEEecCCCCcEEechhHhhhcCCceeeec
Q 040033 129 --FNLRELEGYDVVLGTQWLRTLEPILWDFA 157 (158)
Q Consensus 129 --~~v~~~~~~dvILG~dwL~~~~~i~idw~ 157 (158)
+.+.+......|||..||+.+-- ..|+.
T Consensus 257 C~~~i~~~~~~~~iLG~~fl~~~y~-vfD~~ 286 (295)
T cd05474 257 CYLGIQPSTSDYNILGDTFLRSAYV-VYDLD 286 (295)
T ss_pred eEEEEEeCCCCcEEeChHHhhcEEE-EEECC
Confidence 12222222468999999998764 46654
No 99
>TIGR02854 spore_II_GA sigma-E processing peptidase SpoIIGA. Members of this protein family are the stage II sporulation protein SpoIIGA. This protein acts as an activating protease for Sigma-E, one of several specialized sigma factors of the sporulation process in Bacillus subtilis and related endospore-forming bacteria.
Probab=33.87 E-value=59 Score=26.40 Aligned_cols=35 Identities=9% Similarity=0.087 Sum_probs=24.1
Q ss_pred ceEEEEEEECCE--eeEEEecCCCc---------eeEECHHHHHHc
Q 040033 77 ETLRINGRIGNI--SPIVLVDSGST---------HNFISDTFAKKV 111 (158)
Q Consensus 77 ~~i~~~~~i~~~--~v~aLiDSGat---------~sfI~~~~a~~~ 111 (158)
....+.+.++|+ .+++|+|||.. +..++.+.++++
T Consensus 157 ~~~~v~i~~~g~~~~~~alvDTGN~L~DPlT~~PV~Ive~~~~~~~ 202 (288)
T TIGR02854 157 QIYELEICLDGKKVTIKGFLDTGNQLRDPLTKLPVIVVEYDSLKSI 202 (288)
T ss_pred eEEEEEEEECCEEEEEEEEEecCCcccCCCCCCCEEEEEHHHhhhh
Confidence 344566677776 57899999964 567776666554
No 100
>PF03419 Peptidase_U4: Sporulation factor SpoIIGA This family belongs to family U4 of the peptidase classification.; InterPro: IPR005081 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belong to the MEROPS peptidase family U4 (SpoIIGA peptidase family, clan U-). Sporulation in bacteria such as Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The sigma E factor, which is encoded within the spoIIG operon, is a cell-specific regulatory protein that directs gene transcription in the mother cell. Sigma E is synthesised as an inactive proprotein pro-sigma E, which is converted to the mature factor by the putative processing enzyme SpoIIGA []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0030436 asexual sporulation
Probab=33.37 E-value=65 Score=26.03 Aligned_cols=34 Identities=18% Similarity=0.198 Sum_probs=25.2
Q ss_pred eEEEEEEECCE--eeEEEecCCCc---------eeEECHHHHHHc
Q 040033 78 TLRINGRIGNI--SPIVLVDSGST---------HNFISDTFAKKV 111 (158)
Q Consensus 78 ~i~~~~~i~~~--~v~aLiDSGat---------~sfI~~~~a~~~ 111 (158)
...+++.++++ .+++|+|||.. +.+++.+.++++
T Consensus 157 ~~~v~i~~~~~~~~~~allDTGN~L~DPitg~PV~Vve~~~~~~~ 201 (293)
T PF03419_consen 157 LYPVTIEIGGKKIELKALLDTGNQLRDPITGRPVIVVEYEALEKL 201 (293)
T ss_pred EEEEEEEECCEEEEEEEEEECCCcccCCCCCCcEEEEEHHHHHhh
Confidence 34566677776 56899999874 568888887777
No 101
>PTZ00013 plasmepsin 4 (PM4); Provisional
Probab=31.69 E-value=31 Score=29.93 Aligned_cols=23 Identities=35% Similarity=0.426 Sum_probs=18.8
Q ss_pred eeEEEecCCCceeEECHHHHHHc
Q 040033 89 SPIVLVDSGSTHNFISDTFAKKV 111 (158)
Q Consensus 89 ~v~aLiDSGat~sfI~~~~a~~~ 111 (158)
...|+||||++..++....++++
T Consensus 331 ~~~aIlDSGTSli~lP~~~~~~i 353 (450)
T PTZ00013 331 KANVIVDSGTTTITAPSEFLNKF 353 (450)
T ss_pred ccceEECCCCccccCCHHHHHHH
Confidence 35699999999999998876543
No 102
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=30.25 E-value=24 Score=22.21 Aligned_cols=13 Identities=8% Similarity=0.077 Sum_probs=9.1
Q ss_pred cceeecCCC-CCCC
Q 040033 30 KVCATIATK-SFPR 42 (158)
Q Consensus 30 ~~Cf~Cg~~-gH~~ 42 (158)
..||.||+. ||.-
T Consensus 5 iRCFsCGkvi~~~w 18 (63)
T COG1644 5 VRCFSCGKVIGHKW 18 (63)
T ss_pred eEeecCCCCHHHHH
Confidence 359999986 5543
No 103
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=28.41 E-value=26 Score=21.99 Aligned_cols=8 Identities=25% Similarity=0.314 Sum_probs=6.5
Q ss_pred ceeecCCC
Q 040033 31 VCATIATK 38 (158)
Q Consensus 31 ~Cf~Cg~~ 38 (158)
.||.||+-
T Consensus 6 RCFtCGKv 13 (69)
T KOG3497|consen 6 RCFTCGKV 13 (69)
T ss_pred Eeeecccc
Confidence 59999874
No 104
>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=28.10 E-value=54 Score=25.88 Aligned_cols=68 Identities=15% Similarity=0.377 Sum_probs=45.1
Q ss_pred eeEEEecCCCceeEECHHHHHHc----CCeE-----------------EEEEECCEEEEE-----------------EEE
Q 040033 89 SPIVLVDSGSTHNFISDTFAKKV----KNFI-----------------VNLILQGVYVIV-----------------DFN 130 (158)
Q Consensus 89 ~v~aLiDSGat~sfI~~~~a~~~----~~~~-----------------A~i~i~g~~~~~-----------------~~~ 130 (158)
...++||||++..++...+...+ +... -.+.+++.++.+ -+.
T Consensus 199 ~~~~~~Dtgt~~i~lp~~~~~~i~~~l~~~~~~~~~~~~c~~~~~~p~l~f~~~~~~~~i~~~~~~~~~~~~~~~~C~~~ 278 (317)
T PF00026_consen 199 GQQAILDTGTSYIYLPRSIFDAIIKALGGSYSDGVYSVPCNSTDSLPDLTFTFGGVTFTIPPSDYIFKIEDGNGGYCYLG 278 (317)
T ss_dssp EEEEEEETTBSSEEEEHHHHHHHHHHHTTEEECSEEEEETTGGGGSEEEEEEETTEEEEEEHHHHEEEESSTTSSEEEES
T ss_pred ceeeecccccccccccchhhHHHHhhhcccccceeEEEecccccccceEEEeeCCEEEEecchHhcccccccccceeEee
Confidence 35799999999999999876654 3221 045556655542 111
Q ss_pred Eec----CCCCcEEechhHhhhcCCceeeec
Q 040033 131 LRE----LEGYDVVLGTQWLRTLEPILWDFA 157 (158)
Q Consensus 131 v~~----~~~~dvILG~dwL~~~~~i~idw~ 157 (158)
+.+ ......|||+.||+++-- ..|+.
T Consensus 279 i~~~~~~~~~~~~iLG~~fl~~~y~-vfD~~ 308 (317)
T PF00026_consen 279 IQPMDSSDDSDDWILGSPFLRNYYV-VFDYE 308 (317)
T ss_dssp EEEESSTTSSSEEEEEHHHHTTEEE-EEETT
T ss_pred eecccccccCCceEecHHHhhceEE-EEeCC
Confidence 222 346789999999998764 56654
No 105
>PF13395 HNH_4: HNH endonuclease
Probab=26.29 E-value=24 Score=21.10 Aligned_cols=9 Identities=11% Similarity=0.158 Sum_probs=6.3
Q ss_pred eeecCCCCC
Q 040033 32 CATIATKSF 40 (158)
Q Consensus 32 Cf~Cg~~gH 40 (158)
|||||++-.
T Consensus 1 C~Y~g~~i~ 9 (54)
T PF13395_consen 1 CPYCGKPIS 9 (54)
T ss_pred CCCCCCCCC
Confidence 888887643
No 106
>smart00400 ZnF_CHCC zinc finger.
Probab=25.65 E-value=34 Score=20.34 Aligned_cols=11 Identities=9% Similarity=-0.028 Sum_probs=8.4
Q ss_pred cceeecCCCCC
Q 040033 30 KVCATIATKSF 40 (158)
Q Consensus 30 ~~Cf~Cg~~gH 40 (158)
--||.||+.|-
T Consensus 24 ~~Cf~cg~gGd 34 (55)
T smart00400 24 FHCFGCGAGGN 34 (55)
T ss_pred EEEeCCCCCCC
Confidence 56999987764
No 107
>PF11880 DUF3400: Domain of unknown function (DUF3400); InterPro: IPR021817 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 50 amino acids in length. This domain is found associated with PF02754 from PFAM, PF02913 from PFAM, PF01565 from PFAM.
Probab=25.57 E-value=60 Score=19.01 Aligned_cols=23 Identities=22% Similarity=0.540 Sum_probs=15.4
Q ss_pred EEEEEEEecCCCCcEEechhHhhhc
Q 040033 125 VIVDFNLRELEGYDVVLGTQWLRTL 149 (158)
Q Consensus 125 ~~~~~~v~~~~~~dvILG~dwL~~~ 149 (158)
...|.+|+++- .-+||-+|+..+
T Consensus 9 ~~aDYIVVEmA--~~lLGe~W~~~~ 31 (45)
T PF11880_consen 9 LEADYIVVEMA--RHLLGENWQQDY 31 (45)
T ss_pred CccceehHHHH--HHHhhhhHHHHH
Confidence 34566777663 447999998764
No 108
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=25.01 E-value=49 Score=21.42 Aligned_cols=19 Identities=11% Similarity=-0.099 Sum_probs=13.7
Q ss_pred cceeecCCCCCCCccCCcc
Q 040033 30 KVCATIATKSFPRDIGERS 48 (158)
Q Consensus 30 ~~Cf~Cg~~gH~~~~C~~~ 48 (158)
..|+.|++++--.-+|-.+
T Consensus 37 ~~C~~C~~~~Ga~i~C~~~ 55 (90)
T PF13771_consen 37 LKCSICKKKGGACIGCSHP 55 (90)
T ss_pred CCCcCCCCCCCeEEEEeCC
Confidence 8899999993355556554
No 109
>PHA00689 hypothetical protein
Probab=24.87 E-value=18 Score=21.81 Aligned_cols=18 Identities=28% Similarity=0.350 Sum_probs=12.1
Q ss_pred HHhhcccceeecCCCCCC
Q 040033 24 LQERRAKVCATIATKSFP 41 (158)
Q Consensus 24 ~~~rR~~~Cf~Cg~~gH~ 41 (158)
-++-|...|-+||+.|-+
T Consensus 12 dqepravtckrcgktglr 29 (62)
T PHA00689 12 DQEPRAVTCKRCGKTGLR 29 (62)
T ss_pred ccCcceeehhhccccCce
Confidence 345566779899887643
No 110
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=24.56 E-value=24 Score=19.41 Aligned_cols=23 Identities=9% Similarity=0.251 Sum_probs=13.9
Q ss_pred CCCHHHHHhhcc-cceeecCCCCC
Q 040033 18 GLSRAELQERRA-KVCATIATKSF 40 (158)
Q Consensus 18 ~ls~~e~~~rR~-~~Cf~Cg~~gH 40 (158)
.+.++++..... ..|-+|+..|+
T Consensus 13 ~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 13 EIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred eCCHHHCCCCCcEEECCCCCCEeC
Confidence 344444444444 77888887664
No 111
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=23.79 E-value=31 Score=22.26 Aligned_cols=9 Identities=22% Similarity=0.217 Sum_probs=7.1
Q ss_pred cceeecCCC
Q 040033 30 KVCATIATK 38 (158)
Q Consensus 30 ~~Cf~Cg~~ 38 (158)
..||.||+.
T Consensus 5 VRCFTCGkv 13 (71)
T PLN00032 5 VRCFTCGKV 13 (71)
T ss_pred eeecCCCCC
Confidence 359999975
No 112
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=23.11 E-value=31 Score=21.68 Aligned_cols=9 Identities=22% Similarity=0.217 Sum_probs=7.1
Q ss_pred cceeecCCC
Q 040033 30 KVCATIATK 38 (158)
Q Consensus 30 ~~Cf~Cg~~ 38 (158)
..||.||+.
T Consensus 5 vRCFTCGkv 13 (62)
T PRK04016 5 VRCFTCGKV 13 (62)
T ss_pred eEecCCCCC
Confidence 359999975
No 113
>PF04746 DUF575: Protein of unknown function (DUF575); InterPro: IPR006835 This represents a conserved region found in a number of Chlamydophila pneumoniae proteins.
Probab=22.80 E-value=45 Score=22.71 Aligned_cols=12 Identities=33% Similarity=0.913 Sum_probs=9.7
Q ss_pred cEEechhHhhhc
Q 040033 138 DVVLGTQWLRTL 149 (158)
Q Consensus 138 dvILG~dwL~~~ 149 (158)
.++.|++||-..
T Consensus 28 hiv~GieWLvS~ 39 (101)
T PF04746_consen 28 HIVMGIEWLVSR 39 (101)
T ss_pred eEEeehHHHHHH
Confidence 578999999754
No 114
>KOG1339 consensus Aspartyl protease [Posttranslational modification, protein turnover, chaperones]
Probab=20.77 E-value=97 Score=26.06 Aligned_cols=22 Identities=23% Similarity=0.203 Sum_probs=18.1
Q ss_pred CEeeEEEecCCCceeEECHHHH
Q 040033 87 NISPIVLVDSGSTHNFISDTFA 108 (158)
Q Consensus 87 ~~~v~aLiDSGat~sfI~~~~a 108 (158)
.+++.+++||||+..+|.-.-.
T Consensus 57 pq~f~v~~DTGS~~lWV~c~~c 78 (398)
T KOG1339|consen 57 PQSFTVVLDTGSDLLWVPCAPC 78 (398)
T ss_pred CeeeEEEEeCCCCceeeccccc
Confidence 5789999999999998877443
Done!