Query 045258
Match_columns 106
No_of_seqs 113 out of 486
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 11:26:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045258.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045258hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14541 TAXi_C: Xylanase inhi 99.9 3.1E-28 6.8E-33 173.5 5.9 103 1-106 9-142 (161)
2 cd05489 xylanase_inhibitor_I_l 99.9 1.2E-23 2.7E-28 167.2 9.7 104 1-106 208-341 (362)
3 PLN03146 aspartyl protease fam 99.8 1.1E-20 2.3E-25 153.4 8.7 98 1-106 288-406 (431)
4 KOG1339 Aspartyl protease [Pos 99.6 1.1E-15 2.4E-20 122.5 8.3 99 1-106 251-371 (398)
5 cd05472 cnd41_like Chloroplast 99.6 2.1E-14 4.6E-19 109.9 9.1 98 1-106 155-277 (299)
6 cd05475 nucellin_like Nucellin 99.2 6.7E-11 1.5E-15 90.0 6.6 74 21-106 176-251 (273)
7 cd05476 pepsin_A_like_plant Ch 99.2 8.3E-11 1.8E-15 88.9 6.8 88 1-105 155-242 (265)
8 cd05473 beta_secretase_like Be 99.0 6.6E-10 1.4E-14 87.7 5.8 97 1-106 195-325 (364)
9 cd05474 SAP_like SAPs, pepsin- 99.0 5.6E-10 1.2E-14 84.6 3.9 80 21-105 177-274 (295)
10 cd05478 pepsin_A Pepsin A, asp 98.9 4.4E-09 9.5E-14 81.4 5.7 78 22-105 206-297 (317)
11 cd05486 Cathespin_E Cathepsin 98.8 1E-08 2.3E-13 79.2 6.4 81 23-105 199-296 (316)
12 cd05477 gastricsin Gastricsins 98.8 1E-08 2.2E-13 79.2 5.9 93 1-105 188-297 (318)
13 cd06096 Plasmepsin_5 Plasmepsi 98.7 1.3E-08 2.9E-13 79.2 4.9 73 21-105 230-302 (326)
14 cd05490 Cathepsin_D2 Cathepsin 98.6 7.7E-08 1.7E-12 74.5 6.6 82 22-105 206-305 (325)
15 cd05485 Cathepsin_D_like Cathe 98.6 1.4E-07 3E-12 73.7 6.7 82 22-105 210-309 (329)
16 cd05487 renin_like Renin stimu 98.6 1.8E-07 3.8E-12 72.8 6.8 81 23-105 208-305 (326)
17 cd05488 Proteinase_A_fungi Fun 98.6 1.1E-07 2.4E-12 73.8 5.5 79 23-105 206-300 (320)
18 PTZ00165 aspartyl protease; Pr 98.3 1.3E-06 2.9E-11 72.6 7.0 78 22-105 327-425 (482)
19 cd06098 phytepsin Phytepsin, a 98.3 2.4E-06 5.2E-11 66.3 6.3 87 1-105 197-297 (317)
20 PTZ00147 plasmepsin-1; Provisi 97.9 1.2E-05 2.6E-10 66.5 4.2 81 22-105 332-428 (453)
21 PTZ00013 plasmepsin 4 (PM4); P 97.8 1.9E-05 4E-10 65.4 4.1 81 22-105 331-427 (450)
22 cd05471 pepsin_like Pepsin-lik 97.5 0.00011 2.4E-09 54.5 3.5 40 21-62 201-240 (283)
23 cd06097 Aspergillopepsin_like 96.8 0.0011 2.4E-08 50.3 2.8 27 22-50 198-224 (278)
24 PF00026 Asp: Eukaryotic aspar 96.2 0.0056 1.2E-07 46.3 3.6 78 24-104 201-295 (317)
25 PF13650 Asp_protease_2: Aspar 91.1 0.28 6.1E-06 30.2 3.0 22 25-46 12-33 (90)
26 cd05484 retropepsin_like_LTR_2 88.2 0.61 1.3E-05 29.7 3.0 22 25-46 14-35 (91)
27 TIGR02281 clan_AA_DTGA clan AA 83.3 1.5 3.3E-05 29.9 3.1 23 24-46 24-46 (121)
28 cd05483 retropepsin_like_bacte 82.8 1.9 4E-05 26.7 3.2 22 24-45 15-36 (96)
29 cd06095 RP_RTVL_H_like Retrope 71.8 4.9 0.00011 25.4 2.8 20 25-44 12-31 (86)
30 cd05479 RP_DDI RP_DDI; retrope 70.6 5.7 0.00012 26.9 3.1 23 24-46 29-51 (124)
31 cd05481 retropepsin_like_LTR_1 63.1 9.1 0.0002 24.9 2.8 22 24-45 12-33 (93)
32 PF09668 Asp_protease: Asparty 62.1 9.3 0.0002 26.7 2.8 20 25-44 38-57 (124)
33 PF00077 RVP: Retroviral aspar 62.0 6.1 0.00013 25.1 1.8 20 25-44 19-38 (100)
34 PHA02087 hypothetical protein 57.4 9.5 0.00021 24.6 2.0 25 4-34 53-77 (83)
35 PF13975 gag-asp_proteas: gag- 56.7 11 0.00024 23.2 2.2 23 24-46 21-43 (72)
36 COG5550 Predicted aspartyl pro 56.0 8.4 0.00018 27.2 1.7 21 26-46 30-51 (125)
37 cd05480 NRIP_C NRIP_C; putativ 36.7 42 0.00091 23.0 2.7 19 25-43 12-30 (103)
38 TIGR03698 clan_AA_DTGF clan AA 33.6 37 0.00079 22.5 2.1 23 24-46 18-41 (107)
39 cd00303 retropepsin_like Retro 33.2 42 0.0009 18.6 2.1 21 25-45 12-32 (92)
40 PF14781 BBS2_N: Ciliary BBSom 30.2 63 0.0014 23.1 2.9 26 79-104 90-115 (136)
41 COG4877 Uncharacterized protei 27.9 38 0.00083 21.0 1.3 15 35-49 12-26 (63)
42 COG3128 PiuC Uncharacterized i 24.9 1.2E+02 0.0026 23.3 3.7 38 55-93 83-127 (229)
43 COG1907 Predicted archaeal sug 22.8 44 0.00095 27.0 1.1 19 22-40 132-150 (312)
44 PF11520 Cren7: Chromatin prot 22.6 71 0.0015 19.8 1.7 25 3-27 14-39 (60)
45 COG0522 RpsD Ribosomal protein 22.5 47 0.001 25.1 1.1 16 1-16 121-136 (205)
46 PF14607 GxDLY: N-terminus of 21.4 78 0.0017 22.7 2.0 54 24-79 16-75 (147)
No 1
>PF14541 TAXi_C: Xylanase inhibitor C-terminal; PDB: 3AUP_D 3HD8_A 1T6G_A 1T6E_X 2B42_A 3VLB_A 3VLA_A.
Probab=99.95 E-value=3.1e-28 Score=173.49 Aligned_cols=103 Identities=24% Similarity=0.420 Sum_probs=85.1
Q ss_pred CeeCCEEeecCCCccccccCCCCceEEeCCCcccccChhHHHHhhCHHHHhhhc------------CCCCcccc------
Q 045258 1 MKVDDRVVPLNSTLLSIDSQGFGGTKISTVNPYTALEKSIFKAEHTWHAFGGIR------------ADHPTCFA------ 62 (106)
Q Consensus 1 IsVgg~~l~ip~~~~~~~~~G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~------------~~fd~Cy~------ 62 (106)
|+|||++|++|++.|++ ++|+||+||||||+||+|++++|++|++ ||.+++ .++++||+
T Consensus 9 Isvg~~~l~~~~~~~~~-~~~~g~~iiDSGT~~T~L~~~~y~~l~~--al~~~~~~~~~~~~~~~~~~~~~Cy~~~~~~~ 85 (161)
T PF14541_consen 9 ISVGGKRLPIPPSVFQL-SDGSGGTIIDSGTTYTYLPPPVYDALVQ--ALDAQMGAPGVSREAPPFSGFDLCYNLSSFGV 85 (161)
T ss_dssp EEETTEEE---TTCSCE-TTSTCSEEE-SSSSSEEEEHHHHHHHHH--HHHHHHHTCT--CEE---TT-S-EEEGGCS-E
T ss_pred EEECCEEecCChHHhhc-cCCCCCEEEECCCCccCCcHHHHHHHHH--HHHHHhhhcccccccccCCCCCceeecccccc
Confidence 79999999999999999 8999999999999999999999999999 999988 45899999
Q ss_pred -------------CCCCeEEEEcCCCeeEEeCCCeeeeEEEeCCCCCCceeEeeccC
Q 045258 63 -------------ENENVIWRIFDANSMVQVNEDMYCPGFVNGGSKPTTSIVIGGHQ 106 (106)
Q Consensus 63 -------------~~~g~~~~l~~~n~~v~v~~~~~CLaf~~~~~~~~~~~viGn~Q 106 (106)
+.+|++|+++++|||+...++++||||.+++......+|||++|
T Consensus 86 ~~~~~~~P~i~l~F~~ga~l~l~~~~y~~~~~~~~~Cla~~~~~~~~~~~~viG~~~ 142 (161)
T PF14541_consen 86 NRDWAKFPTITLHFEGGADLTLPPENYFVQVSPGVFCLAFVPSDADDDGVSVIGNFQ 142 (161)
T ss_dssp ETTEESS--EEEEETTSEEEEE-HHHHEEEECTTEEEESEEEETSTTSSSEEE-HHH
T ss_pred ccccccCCeEEEEEeCCcceeeeccceeeeccCCCEEEEEEccCCCCCCcEEECHHH
Confidence 34589999999999999999999999999833344568999975
No 2
>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=99.90 E-value=1.2e-23 Score=167.19 Aligned_cols=104 Identities=47% Similarity=0.775 Sum_probs=90.7
Q ss_pred CeeCCEEeecCCCccccccCCCCceEEeCCCcccccChhHHHHhhCHHHHhhhcC---------C-CCcccc--------
Q 045258 1 MKVDDRVVPLNSTLLSIDSQGFGGTKISTVNPYTALEKSIFKAEHTWHAFGGIRA---------D-HPTCFA-------- 62 (106)
Q Consensus 1 IsVgg~~l~ip~~~~~~~~~G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~~---------~-fd~Cy~-------- 62 (106)
|+||+++|++|++.++++.+|.||+||||||++|+||+++|++|++ ||.+++. . +|+||+
T Consensus 208 IsVg~~~l~~~~~~~~~~~~~~~g~iiDSGTs~t~lp~~~y~~l~~--a~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~ 285 (362)
T cd05489 208 IAVNGHAVPLNPTLSANDRLGPGGVKLSTVVPYTVLRSDIYRAFTQ--AFAKATARIPRVPAAAVFPELCYPASALGNTR 285 (362)
T ss_pred EEECCEECCCCchhccccccCCCcEEEecCCceEEECHHHHHHHHH--HHHHHhcccCcCCCCCCCcCccccCCCcCCcc
Confidence 7899999999999999888899999999999999999999999999 9998871 1 389996
Q ss_pred -----------CCC-CeEEEEcCCCeeEEeCCCeeeeEEEeCCCCCCceeEeeccC
Q 045258 63 -----------ENE-NVIWRIFDANSMVQVNEDMYCPGFVNGGSKPTTSIVIGGHQ 106 (106)
Q Consensus 63 -----------~~~-g~~~~l~~~n~~v~v~~~~~CLaf~~~~~~~~~~~viGn~Q 106 (106)
+.+ |++|.|+++|||+++++++.||+|.+++....+++||||+|
T Consensus 286 ~~~~~P~it~~f~g~g~~~~l~~~ny~~~~~~~~~Cl~f~~~~~~~~~~~IlG~~~ 341 (362)
T cd05489 286 LGYAVPAIDLVLDGGGVNWTIFGANSMVQVKGGVACLAFVDGGSEPRPAVVIGGHQ 341 (362)
T ss_pred cccccceEEEEEeCCCeEEEEcCCceEEEcCCCcEEEEEeeCCCCCCceEEEeehe
Confidence 234 69999999999999988899999998764434678999987
No 3
>PLN03146 aspartyl protease family protein; Provisional
Probab=99.83 E-value=1.1e-20 Score=153.43 Aligned_cols=98 Identities=16% Similarity=0.260 Sum_probs=85.5
Q ss_pred CeeCCEEeecCCCccccccCCCCceEEeCCCcccccChhHHHHhhCHHHHhhhc---------CCCCcccc---------
Q 045258 1 MKVDDRVVPLNSTLLSIDSQGFGGTKISTVNPYTALEKSIFKAEHTWHAFGGIR---------ADHPTCFA--------- 62 (106)
Q Consensus 1 IsVgg~~l~ip~~~~~~~~~G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~---------~~fd~Cy~--------- 62 (106)
|+||++++++|++.|+ .+|.||+||||||++|+||+++|++|++ +|++++ ..+++||+
T Consensus 288 IsVgg~~l~~~~~~~~--~~~~g~~iiDSGTt~t~Lp~~~y~~l~~--~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~P~ 363 (431)
T PLN03146 288 ISVGSKKLPYTGSSKN--GVEEGNIIIDSGTTLTLLPSDFYSELES--AVEEAIGGERVSDPQGLLSLCYSSTSDIKLPI 363 (431)
T ss_pred EEECCEECcCCccccc--cCCCCcEEEeCCccceecCHHHHHHHHH--HHHHHhccccCCCCCCCCCccccCCCCCCCCe
Confidence 7899999999998886 5678999999999999999999999999 999888 23789996
Q ss_pred ---CCCCeEEEEcCCCeeEEeCCCeeeeEEEeCCCCCCceeEeeccC
Q 045258 63 ---ENENVIWRIFDANSMVQVNEDMYCPGFVNGGSKPTTSIVIGGHQ 106 (106)
Q Consensus 63 ---~~~g~~~~l~~~n~~v~v~~~~~CLaf~~~~~~~~~~~viGn~Q 106 (106)
+++|++|.++++|||+.++++..||+|.++.+ ..||||+|
T Consensus 364 i~~~F~Ga~~~l~~~~~~~~~~~~~~Cl~~~~~~~----~~IlG~~~ 406 (431)
T PLN03146 364 ITAHFTGADVKLQPLNTFVKVSEDLVCFAMIPTSS----IAIFGNLA 406 (431)
T ss_pred EEEEECCCeeecCcceeEEEcCCCcEEEEEecCCC----ceEECeee
Confidence 24689999999999999988889999987532 36899986
No 4
>KOG1339 consensus Aspartyl protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.63 E-value=1.1e-15 Score=122.45 Aligned_cols=99 Identities=24% Similarity=0.380 Sum_probs=83.2
Q ss_pred CeeCCEEeecCCCccccccCCCCceEEeCCCcccccChhHHHHhhCHHHHhhh---c----CCCCccccCC---------
Q 045258 1 MKVDDRVVPLNSTLLSIDSQGFGGTKISTVNPYTALEKSIFKAEHTWHAFGGI---R----ADHPTCFAEN--------- 64 (106)
Q Consensus 1 IsVgg~~l~ip~~~~~~~~~G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~---~----~~fd~Cy~~~--------- 64 (106)
|+||++. +++++.+..+ .+++||||||++|+||+.+|+++++ +|.++ . ..+..||+..
T Consensus 251 I~vgg~~-~~~~~~~~~~---~~~~iiDSGTs~t~lp~~~y~~i~~--~~~~~~~~~~~~~~~~~~C~~~~~~~~~~P~i 324 (398)
T KOG1339|consen 251 ISVGGKR-PIGSSLFCTD---GGGAIIDSGTSLTYLPTSAYNALRE--AIGAEVSVVGTDGEYFVPCFSISTSGVKLPDI 324 (398)
T ss_pred EEECCcc-CCCcceEecC---CCCEEEECCcceeeccHHHHHHHHH--HHHhheeccccCCceeeecccCCCCcccCCcE
Confidence 6799999 8888888654 6899999999999999999999999 99986 4 3456999732
Q ss_pred ----C-CeEEEEcCCCeeEEeCCCee-eeEEEeCCCCCCceeEeeccC
Q 045258 65 ----E-NVIWRIFDANSMVQVNEDMY-CPGFVNGGSKPTTSIVIGGHQ 106 (106)
Q Consensus 65 ----~-g~~~~l~~~n~~v~v~~~~~-CLaf~~~~~~~~~~~viGn~Q 106 (106)
+ |+.|.++++||++.++++.. |+++..+.+.. +..|||++|
T Consensus 325 ~~~f~~g~~~~l~~~~y~~~~~~~~~~Cl~~~~~~~~~-~~~ilG~~~ 371 (398)
T KOG1339|consen 325 TFHFGGGAVFSLPPKNYLVEVSDGGGVCLAFFNGMDSG-PLWILGDVF 371 (398)
T ss_pred EEEECCCcEEEeCccceEEEECCCCCceeeEEecCCCC-ceEEEchHH
Confidence 2 89999999999999987655 99999876543 678999976
No 5
>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=99.55 E-value=2.1e-14 Score=109.88 Aligned_cols=98 Identities=21% Similarity=0.289 Sum_probs=75.3
Q ss_pred CeeCCEEeecCCCccccccCCCCceEEeCCCcccccChhHHHHhhCHHHHhhhc---------CCCCcccc---------
Q 045258 1 MKVDDRVVPLNSTLLSIDSQGFGGTKISTVNPYTALEKSIFKAEHTWHAFGGIR---------ADHPTCFA--------- 62 (106)
Q Consensus 1 IsVgg~~l~ip~~~~~~~~~G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~---------~~fd~Cy~--------- 62 (106)
|+||++.+.+++.. .+.+++||||||++|+||+++|++|.+ ++.+++ ..++.||+
T Consensus 155 i~vg~~~~~~~~~~-----~~~~~~ivDSGTt~~~lp~~~~~~l~~--~l~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~ 227 (299)
T cd05472 155 ISVGGRRLPIPPAS-----FGAGGVIIDSGTVITRLPPSAYAALRD--AFRAAMAAYPRAPGFSILDTCYDLSGFRSVSV 227 (299)
T ss_pred EEECCEECCCCccc-----cCCCCeEEeCCCcceecCHHHHHHHHH--HHHHHhccCCCCCCCCCCCccCcCCCCcCCcc
Confidence 57888888766422 346789999999999999999999999 998765 13568985
Q ss_pred ------CCCCeEEEEcCCCeeEEe-CCCeeeeEEEeCCCCCCceeEeeccC
Q 045258 63 ------ENENVIWRIFDANSMVQV-NEDMYCPGFVNGGSKPTTSIVIGGHQ 106 (106)
Q Consensus 63 ------~~~g~~~~l~~~n~~v~v-~~~~~CLaf~~~~~~~~~~~viGn~Q 106 (106)
+.+|+.+++++++|++.. ..+..||+|...... .+..|||++|
T Consensus 228 P~i~f~f~~g~~~~l~~~~y~~~~~~~~~~C~~~~~~~~~-~~~~ilG~~f 277 (299)
T cd05472 228 PTVSLHFQGGADVELDASGVLYPVDDSSQVCLAFAGTSDD-GGLSIIGNVQ 277 (299)
T ss_pred CCEEEEECCCCEEEeCcccEEEEecCCCCEEEEEeCCCCC-CCCEEEchHH
Confidence 224899999999999954 346889999875422 3456899864
No 6
>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=99.17 E-value=6.7e-11 Score=90.03 Aligned_cols=74 Identities=15% Similarity=0.189 Sum_probs=57.0
Q ss_pred CCCceEEeCCCcccccChhHHHHhhCHHHHhhhcCCCCccccCC-CCeEEEEcCCCeeEEeCCCeeeeEEEeCCCC-CCc
Q 045258 21 GFGGTKISTVNPYTALEKSIFKAEHTWHAFGGIRADHPTCFAEN-ENVIWRIFDANSMVQVNEDMYCPGFVNGGSK-PTT 98 (106)
Q Consensus 21 G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~~~fd~Cy~~~-~g~~~~l~~~n~~v~v~~~~~CLaf~~~~~~-~~~ 98 (106)
+.+++||||||++|+||+++| ..++.+||.-. +++.|+++++||++...++..||++..+.+. ..+
T Consensus 176 ~~~~~ivDTGTt~t~lp~~~y------------~p~i~~~f~~~~~~~~~~l~~~~y~~~~~~~~~Cl~~~~~~~~~~~~ 243 (273)
T cd05475 176 KGLEVVFDSGSSYTYFNAQAY------------FKPLTLKFGKGWRTRLLEIPPENYLIISEKGNVCLGILNGSEIGLGN 243 (273)
T ss_pred CCceEEEECCCceEEcCCccc------------cccEEEEECCCCceeEEEeCCCceEEEcCCCCEEEEEecCCCcCCCc
Confidence 357899999999999999998 23456777421 2389999999999987777899999976432 234
Q ss_pred eeEeeccC
Q 045258 99 SIVIGGHQ 106 (106)
Q Consensus 99 ~~viGn~Q 106 (106)
..|||+.|
T Consensus 244 ~~ilG~~~ 251 (273)
T cd05475 244 TNIIGDIS 251 (273)
T ss_pred eEEECceE
Confidence 67899875
No 7
>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=99.16 E-value=8.3e-11 Score=88.94 Aligned_cols=88 Identities=22% Similarity=0.363 Sum_probs=70.8
Q ss_pred CeeCCEEeecCCCccccccCCCCceEEeCCCcccccChhHHHHhhCHHHHhhhcCCCCccccCCCCeEEEEcCCCeeEEe
Q 045258 1 MKVDDRVVPLNSTLLSIDSQGFGGTKISTVNPYTALEKSIFKAEHTWHAFGGIRADHPTCFAENENVIWRIFDANSMVQV 80 (106)
Q Consensus 1 IsVgg~~l~ip~~~~~~~~~G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~~~fd~Cy~~~~g~~~~l~~~n~~v~v 80 (106)
|+||++.+++|++.+.......+.+||||||++|+||+++| - +.-+.+.+++.+.++++||++..
T Consensus 155 i~v~~~~~~~~~~~~~~~~~~~~~ai~DTGTs~~~lp~~~~----P-----------~i~~~f~~~~~~~i~~~~y~~~~ 219 (265)
T cd05476 155 ISVGGKRLPIPPSVFAIDSDGSGGTIIDSGTTLTYLPDPAY----P-----------DLTLHFDGGADLELPPENYFVDV 219 (265)
T ss_pred EEECCEEecCCchhcccccCCCCcEEEeCCCcceEcCcccc----C-----------CEEEEECCCCEEEeCcccEEEEC
Confidence 68999999999887776666678999999999999999999 1 23344455899999999999987
Q ss_pred CCCeeeeEEEeCCCCCCceeEeecc
Q 045258 81 NEDMYCPGFVNGGSKPTTSIVIGGH 105 (106)
Q Consensus 81 ~~~~~CLaf~~~~~~~~~~~viGn~ 105 (106)
..+..|+++...+. ....|||..
T Consensus 220 ~~~~~C~~~~~~~~--~~~~ilG~~ 242 (265)
T cd05476 220 GEGVVCLAILSSSS--GGVSILGNI 242 (265)
T ss_pred CCCCEEEEEecCCC--CCcEEEChh
Confidence 77889999997642 245789975
No 8
>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=98.99 E-value=6.6e-10 Score=87.66 Aligned_cols=97 Identities=16% Similarity=0.252 Sum_probs=68.1
Q ss_pred CeeCCEEeecCCCccccccCCCCceEEeCCCcccccChhHHHHhhCHHHHhhhcC------C-----CCcccc-------
Q 045258 1 MKVDDRVVPLNSTLLSIDSQGFGGTKISTVNPYTALEKSIFKAEHTWHAFGGIRA------D-----HPTCFA------- 62 (106)
Q Consensus 1 IsVgg~~l~ip~~~~~~~~~G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~~------~-----fd~Cy~------- 62 (106)
|+||++.++++...+. ..++||||||++++||+++|+++.+ ++.++.. . ...|++
T Consensus 195 i~vg~~~~~~~~~~~~-----~~~~ivDSGTs~~~lp~~~~~~l~~--~l~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~ 267 (364)
T cd05473 195 LEVGGQSLNLDCKEYN-----YDKAIVDSGTTNLRLPVKVFNAAVD--AIKAASLIEDFPDGFWLGSQLACWQKGTTPWE 267 (364)
T ss_pred EEECCEeccccccccc-----CccEEEeCCCcceeCCHHHHHHHHH--HHHhhcccccCCccccCcceeecccccCchHh
Confidence 5788888876654332 2479999999999999999999999 9988751 1 147984
Q ss_pred --------CCC-----CeEEEEcCCCeeEEeC---CCeeeeEEEeCCCCCCceeEeeccC
Q 045258 63 --------ENE-----NVIWRIFDANSMVQVN---EDMYCPGFVNGGSKPTTSIVIGGHQ 106 (106)
Q Consensus 63 --------~~~-----g~~~~l~~~n~~v~v~---~~~~CLaf~~~~~~~~~~~viGn~Q 106 (106)
+.+ +..+.+++++|+.... .+..|++|..... ....|||+.+
T Consensus 268 ~~P~i~~~f~g~~~~~~~~l~l~p~~Y~~~~~~~~~~~~C~~~~~~~~--~~~~ILG~~f 325 (364)
T cd05473 268 IFPKISIYLRDENSSQSFRITILPQLYLRPVEDHGTQLDCYKFAISQS--TNGTVIGAVI 325 (364)
T ss_pred hCCcEEEEEccCCCCceEEEEECHHHhhhhhccCCCcceeeEEeeecC--CCceEEeeee
Confidence 111 2467889999988653 2468987654322 1246899864
No 9
>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=98.96 E-value=5.6e-10 Score=84.59 Aligned_cols=80 Identities=15% Similarity=0.108 Sum_probs=62.8
Q ss_pred CCCceEEeCCCcccccChhHHHHhhCHHHHhhhcC-----CCCcccc--------CCCCeEEEEcCCCeeEEeCC----C
Q 045258 21 GFGGTKISTVNPYTALEKSIFKAEHTWHAFGGIRA-----DHPTCFA--------ENENVIWRIFDANSMVQVNE----D 83 (106)
Q Consensus 21 G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~~-----~fd~Cy~--------~~~g~~~~l~~~n~~v~v~~----~ 83 (106)
+.++++|||||++++||+++|++|.+ +|.++.. .+..|++ .++|+.+.+|+++|++.... +
T Consensus 177 ~~~~~iiDSGt~~~~lP~~~~~~l~~--~~~~~~~~~~~~~~~~C~~~~~p~i~f~f~g~~~~i~~~~~~~~~~~~~~~~ 254 (295)
T cd05474 177 KNLPALLDSGTTLTYLPSDIVDAIAK--QLGATYDSDEGLYVVDCDAKDDGSLTFNFGGATISVPLSDLVLPASTDDGGD 254 (295)
T ss_pred CCccEEECCCCccEeCCHHHHHHHHH--HhCCEEcCCCcEEEEeCCCCCCCEEEEEECCeEEEEEHHHhEeccccCCCCC
Confidence 46899999999999999999999999 9987761 2357775 24678999999999987752 5
Q ss_pred eee-eEEEeCCCCCCceeEeecc
Q 045258 84 MYC-PGFVNGGSKPTTSIVIGGH 105 (106)
Q Consensus 84 ~~C-Laf~~~~~~~~~~~viGn~ 105 (106)
..| ++|.+... ...|||..
T Consensus 255 ~~C~~~i~~~~~---~~~iLG~~ 274 (295)
T cd05474 255 GACYLGIQPSTS---DYNILGDT 274 (295)
T ss_pred CCeEEEEEeCCC---CcEEeChH
Confidence 778 68887553 24688864
No 10
>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=98.86 E-value=4.4e-09 Score=81.37 Aligned_cols=78 Identities=13% Similarity=0.128 Sum_probs=58.8
Q ss_pred CCceEEeCCCcccccChhHHHHhhCHHHHhhhc---CCC-Ccccc---------CCCCeEEEEcCCCeeEEeCCCeeeeE
Q 045258 22 FGGTKISTVNPYTALEKSIFKAEHTWHAFGGIR---ADH-PTCFA---------ENENVIWRIFDANSMVQVNEDMYCPG 88 (106)
Q Consensus 22 ~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~---~~f-d~Cy~---------~~~g~~~~l~~~n~~v~v~~~~~CLa 88 (106)
+.+++|||||++++||+++|+++.+ ++.... ..+ -.|.+ .++|+.+.+++++|+... +..|+.
T Consensus 206 ~~~~iiDTGts~~~lp~~~~~~l~~--~~~~~~~~~~~~~~~C~~~~~~P~~~f~f~g~~~~i~~~~y~~~~--~~~C~~ 281 (317)
T cd05478 206 GCQAIVDTGTSLLVGPSSDIANIQS--DIGASQNQNGEMVVNCSSISSMPDVVFTINGVQYPLPPSAYILQD--QGSCTS 281 (317)
T ss_pred CCEEEECCCchhhhCCHHHHHHHHH--HhCCccccCCcEEeCCcCcccCCcEEEEECCEEEEECHHHheecC--CCEEeE
Confidence 4589999999999999999999999 886654 122 26775 247899999999999865 467985
Q ss_pred -EEeCCCCCCceeEeecc
Q 045258 89 -FVNGGSKPTTSIVIGGH 105 (106)
Q Consensus 89 -f~~~~~~~~~~~viGn~ 105 (106)
|.+.+. ....|||+.
T Consensus 282 ~~~~~~~--~~~~IlG~~ 297 (317)
T cd05478 282 GFQSMGL--GELWILGDV 297 (317)
T ss_pred EEEeCCC--CCeEEechH
Confidence 665433 234689974
No 11
>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=98.81 E-value=1e-08 Score=79.23 Aligned_cols=81 Identities=11% Similarity=0.160 Sum_probs=58.4
Q ss_pred CceEEeCCCcccccChhHHHHhhCHHHHhhhc--CCC-Ccccc---------CCCCeEEEEcCCCeeEEe--CCCeeee-
Q 045258 23 GGTKISTVNPYTALEKSIFKAEHTWHAFGGIR--ADH-PTCFA---------ENENVIWRIFDANSMVQV--NEDMYCP- 87 (106)
Q Consensus 23 GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~--~~f-d~Cy~---------~~~g~~~~l~~~n~~v~v--~~~~~CL- 87 (106)
.++||||||++++||+++|+++.+ ++.+.. ..+ -.|.+ .++|+.+++++++|++.. ..+..|+
T Consensus 199 ~~aiiDTGTs~~~lP~~~~~~l~~--~~~~~~~~~~~~~~C~~~~~~p~i~f~f~g~~~~l~~~~y~~~~~~~~~~~C~~ 276 (316)
T cd05486 199 CQAIVDTGTSLITGPSGDIKQLQN--YIGATATDGEYGVDCSTLSLMPSVTFTINGIPYSLSPQAYTLEDQSDGGGYCSS 276 (316)
T ss_pred CEEEECCCcchhhcCHHHHHHHHH--HhCCcccCCcEEEeccccccCCCEEEEECCEEEEeCHHHeEEecccCCCCEEee
Confidence 579999999999999999999988 775432 112 26874 247899999999999875 2346797
Q ss_pred EEEeCC--CCCCceeEeecc
Q 045258 88 GFVNGG--SKPTTSIVIGGH 105 (106)
Q Consensus 88 af~~~~--~~~~~~~viGn~ 105 (106)
+|.... .......|||+.
T Consensus 277 ~~~~~~~~~~~~~~~ILGd~ 296 (316)
T cd05486 277 GFQGLDIPPPAGPLWILGDV 296 (316)
T ss_pred EEEECCCCCCCCCeEEEchH
Confidence 566532 112345689974
No 12
>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=98.79 E-value=1e-08 Score=79.20 Aligned_cols=93 Identities=11% Similarity=0.162 Sum_probs=65.3
Q ss_pred CeeCCEEeecCCCccccccCCCCceEEeCCCcccccChhHHHHhhCHHHHhhhcCC----CCcccc---------CCCCe
Q 045258 1 MKVDDRVVPLNSTLLSIDSQGFGGTKISTVNPYTALEKSIFKAEHTWHAFGGIRAD----HPTCFA---------ENENV 67 (106)
Q Consensus 1 IsVgg~~l~ip~~~~~~~~~G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~~~----fd~Cy~---------~~~g~ 67 (106)
|+||++++++.. ...++||||||++++||+++|+++.+ ++.++... .-.|.+ .++|+
T Consensus 188 i~v~g~~~~~~~--------~~~~~iiDSGtt~~~lP~~~~~~l~~--~~~~~~~~~~~~~~~C~~~~~~p~l~~~f~g~ 257 (318)
T cd05477 188 FQINGQATGWCS--------QGCQAIVDTGTSLLTAPQQVMSTLMQ--SIGAQQDQYGQYVVNCNNIQNLPTLTFTINGV 257 (318)
T ss_pred EEECCEEecccC--------CCceeeECCCCccEECCHHHHHHHHH--HhCCccccCCCEEEeCCccccCCcEEEEECCE
Confidence 356666654322 13579999999999999999999999 99776511 234765 24689
Q ss_pred EEEEcCCCeeEEeCCCeeee-EEEeCC---CCCCceeEeecc
Q 045258 68 IWRIFDANSMVQVNEDMYCP-GFVNGG---SKPTTSIVIGGH 105 (106)
Q Consensus 68 ~~~l~~~n~~v~v~~~~~CL-af~~~~---~~~~~~~viGn~ 105 (106)
++.+++++|+... ...|+ +|.+.. ..+.+..|||+.
T Consensus 258 ~~~v~~~~y~~~~--~~~C~~~i~~~~~~~~~~~~~~ilG~~ 297 (318)
T cd05477 258 SFPLPPSAYILQN--NGYCTVGIEPTYLPSQNGQPLWILGDV 297 (318)
T ss_pred EEEECHHHeEecC--CCeEEEEEEecccCCCCCCceEEEcHH
Confidence 9999999998864 35695 786531 122345789974
No 13
>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=98.74 E-value=1.3e-08 Score=79.21 Aligned_cols=73 Identities=7% Similarity=0.034 Sum_probs=55.6
Q ss_pred CCCceEEeCCCcccccChhHHHHhhCHHHHhhhcCCCCccccCCCCeEEEEcCCCeeEEeCCCeeeeEEEeCCCCCCcee
Q 045258 21 GFGGTKISTVNPYTALEKSIFKAEHTWHAFGGIRADHPTCFAENENVIWRIFDANSMVQVNEDMYCPGFVNGGSKPTTSI 100 (106)
Q Consensus 21 G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~~~fd~Cy~~~~g~~~~l~~~n~~v~v~~~~~CLaf~~~~~~~~~~~ 100 (106)
...++||||||++|+||+++|++|++ ++ +. .=|.+.+|+.+.+++++|++...+...|+++.... ...
T Consensus 230 ~~~~aivDSGTs~~~lp~~~~~~l~~--~~----P~--i~~~f~~g~~~~i~p~~y~~~~~~~~c~~~~~~~~----~~~ 297 (326)
T cd06096 230 KGLGMLVDSGSTLSHFPEDLYNKINN--FF----PT--ITIIFENNLKIDWKPSSYLYKKESFWCKGGEKSVS----NKP 297 (326)
T ss_pred cCCCEEEeCCCCcccCCHHHHHHHHh--hc----Cc--EEEEEcCCcEEEECHHHhccccCCceEEEEEecCC----Cce
Confidence 45789999999999999999999999 77 11 22223448999999999999876656677766432 246
Q ss_pred Eeecc
Q 045258 101 VIGGH 105 (106)
Q Consensus 101 viGn~ 105 (106)
|||+.
T Consensus 298 ILG~~ 302 (326)
T cd06096 298 ILGAS 302 (326)
T ss_pred EEChH
Confidence 89874
No 14
>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=98.64 E-value=7.7e-08 Score=74.54 Aligned_cols=82 Identities=11% Similarity=0.135 Sum_probs=59.9
Q ss_pred CCceEEeCCCcccccChhHHHHhhCHHHHhhhc----CCCCcccc---------CCCCeEEEEcCCCeeEEeCC--Ceee
Q 045258 22 FGGTKISTVNPYTALEKSIFKAEHTWHAFGGIR----ADHPTCFA---------ENENVIWRIFDANSMVQVNE--DMYC 86 (106)
Q Consensus 22 ~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~----~~fd~Cy~---------~~~g~~~~l~~~n~~v~v~~--~~~C 86 (106)
..++||||||++++||+++|+++.+ ++.+.- .-.-.|.+ .++|+.+.+++++|++.... ...|
T Consensus 206 ~~~aiiDSGTt~~~~p~~~~~~l~~--~~~~~~~~~~~~~~~C~~~~~~P~i~f~fgg~~~~l~~~~y~~~~~~~~~~~C 283 (325)
T cd05490 206 GCEAIVDTGTSLITGPVEEVRALQK--AIGAVPLIQGEYMIDCEKIPTLPVISFSLGGKVYPLTGEDYILKVSQRGTTIC 283 (325)
T ss_pred CCEEEECCCCccccCCHHHHHHHHH--HhCCccccCCCEEecccccccCCCEEEEECCEEEEEChHHeEEeccCCCCCEE
Confidence 4689999999999999999999999 885432 11346875 24789999999999997653 3679
Q ss_pred eE-EEeCCC--CCCceeEeecc
Q 045258 87 PG-FVNGGS--KPTTSIVIGGH 105 (106)
Q Consensus 87 La-f~~~~~--~~~~~~viGn~ 105 (106)
++ |..... ......|||+.
T Consensus 284 ~~~~~~~~~~~~~~~~~ilGd~ 305 (325)
T cd05490 284 LSGFMGLDIPPPAGPLWILGDV 305 (325)
T ss_pred eeEEEECCCCCCCCceEEEChH
Confidence 85 654321 12345689975
No 15
>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=98.59 E-value=1.4e-07 Score=73.71 Aligned_cols=82 Identities=12% Similarity=0.114 Sum_probs=59.4
Q ss_pred CCceEEeCCCcccccChhHHHHhhCHHHHhhhc---CCC-Ccccc---------CCCCeEEEEcCCCeeEEeCC--Ceee
Q 045258 22 FGGTKISTVNPYTALEKSIFKAEHTWHAFGGIR---ADH-PTCFA---------ENENVIWRIFDANSMVQVNE--DMYC 86 (106)
Q Consensus 22 ~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~---~~f-d~Cy~---------~~~g~~~~l~~~n~~v~v~~--~~~C 86 (106)
..++||||||++++||+++|+++.+ ++...- ..+ -.|.. .++|+.+.+++++|++++.. ...|
T Consensus 210 ~~~~iiDSGtt~~~lP~~~~~~l~~--~~~~~~~~~~~~~~~C~~~~~~p~i~f~fgg~~~~i~~~~yi~~~~~~~~~~C 287 (329)
T cd05485 210 GCQAIADTGTSLIAGPVDEIEKLNN--AIGAKPIIGGEYMVNCSAIPSLPDITFVLGGKSFSLTGKDYVLKVTQMGQTIC 287 (329)
T ss_pred CcEEEEccCCcceeCCHHHHHHHHH--HhCCccccCCcEEEeccccccCCcEEEEECCEEeEEChHHeEEEecCCCCCEE
Confidence 4579999999999999999999999 876432 112 36764 24789999999999998753 4679
Q ss_pred eE-EEeCC--CCCCceeEeecc
Q 045258 87 PG-FVNGG--SKPTTSIVIGGH 105 (106)
Q Consensus 87 La-f~~~~--~~~~~~~viGn~ 105 (106)
+. |.... ....+..|||..
T Consensus 288 ~~~~~~~~~~~~~~~~~IlG~~ 309 (329)
T cd05485 288 LSGFMGIDIPPPAGPLWILGDV 309 (329)
T ss_pred eeeEEECcCCCCCCCeEEEchH
Confidence 85 66532 112235689974
No 16
>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=98.57 E-value=1.8e-07 Score=72.77 Aligned_cols=81 Identities=15% Similarity=0.178 Sum_probs=59.6
Q ss_pred CceEEeCCCcccccChhHHHHhhCHHHHhhhcC--C-CCcccc---------CCCCeEEEEcCCCeeEEeCC--Ceeee-
Q 045258 23 GGTKISTVNPYTALEKSIFKAEHTWHAFGGIRA--D-HPTCFA---------ENENVIWRIFDANSMVQVNE--DMYCP- 87 (106)
Q Consensus 23 GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~~--~-fd~Cy~---------~~~g~~~~l~~~n~~v~v~~--~~~CL- 87 (106)
..++|||||++++||+++|+++.+ ++..+.. . .-.|.+ .++|..+.+++++|++...+ +..|+
T Consensus 208 ~~aiiDSGts~~~lP~~~~~~l~~--~~~~~~~~~~y~~~C~~~~~~P~i~f~fgg~~~~v~~~~yi~~~~~~~~~~C~~ 285 (326)
T cd05487 208 CTAVVDTGASFISGPTSSISKLME--ALGAKERLGDYVVKCNEVPTLPDISFHLGGKEYTLSSSDYVLQDSDFSDKLCTV 285 (326)
T ss_pred CEEEECCCccchhCcHHHHHHHHH--HhCCcccCCCEEEeccccCCCCCEEEEECCEEEEeCHHHhEEeccCCCCCEEEE
Confidence 479999999999999999999999 8865431 1 235765 24789999999999987654 46796
Q ss_pred EEEeCCC--CCCceeEeecc
Q 045258 88 GFVNGGS--KPTTSIVIGGH 105 (106)
Q Consensus 88 af~~~~~--~~~~~~viGn~ 105 (106)
+|..... ......|||+.
T Consensus 286 ~~~~~~~~~~~~~~~ilG~~ 305 (326)
T cd05487 286 AFHAMDIPPPTGPLWVLGAT 305 (326)
T ss_pred EEEeCCCCCCCCCeEEEehH
Confidence 7876431 11245789964
No 17
>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=98.56 E-value=1.1e-07 Score=73.78 Aligned_cols=79 Identities=14% Similarity=0.190 Sum_probs=56.2
Q ss_pred CceEEeCCCcccccChhHHHHhhCHHHHhhhc---CCC-Ccccc---------CCCCeEEEEcCCCeeEEeCCCeeeeEE
Q 045258 23 GGTKISTVNPYTALEKSIFKAEHTWHAFGGIR---ADH-PTCFA---------ENENVIWRIFDANSMVQVNEDMYCPGF 89 (106)
Q Consensus 23 GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~---~~f-d~Cy~---------~~~g~~~~l~~~n~~v~v~~~~~CLaf 89 (106)
.+++|||||++++||+++|+++.+ ++.+.. ..+ -.|.+ .++|+++.++++||++... -.|+..
T Consensus 206 ~~~ivDSGtt~~~lp~~~~~~l~~--~~~~~~~~~~~~~~~C~~~~~~P~i~f~f~g~~~~i~~~~y~~~~~--g~C~~~ 281 (320)
T cd05488 206 TGAAIDTGTSLIALPSDLAEMLNA--EIGAKKSWNGQYTVDCSKVDSLPDLTFNFDGYNFTLGPFDYTLEVS--GSCISA 281 (320)
T ss_pred CeEEEcCCcccccCCHHHHHHHHH--HhCCccccCCcEEeeccccccCCCEEEEECCEEEEECHHHheecCC--CeEEEE
Confidence 579999999999999999999998 886543 111 14765 2468999999999998543 369865
Q ss_pred EeCCC---CCCceeEeecc
Q 045258 90 VNGGS---KPTTSIVIGGH 105 (106)
Q Consensus 90 ~~~~~---~~~~~~viGn~ 105 (106)
..+.+ ......|||+.
T Consensus 282 ~~~~~~~~~~~~~~ilG~~ 300 (320)
T cd05488 282 FTGMDFPEPVGPLAIVGDA 300 (320)
T ss_pred EEECcCCCCCCCeEEEchH
Confidence 53221 11235689974
No 18
>PTZ00165 aspartyl protease; Provisional
Probab=98.35 E-value=1.3e-06 Score=72.62 Aligned_cols=78 Identities=12% Similarity=0.148 Sum_probs=57.1
Q ss_pred CCceEEeCCCcccccChhHHHHhhCHHHHhhhcCCCCccccC---------CCC-----eEEEEcCCCeeEEe---C-CC
Q 045258 22 FGGTKISTVNPYTALEKSIFKAEHTWHAFGGIRADHPTCFAE---------NEN-----VIWRIFDANSMVQV---N-ED 83 (106)
Q Consensus 22 ~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~~~fd~Cy~~---------~~g-----~~~~l~~~n~~v~v---~-~~ 83 (106)
...+||||||+++++|+++|+++.+ ++... ..|.+. .+| +.+.+++++|++.+ . .+
T Consensus 327 ~~~aIiDTGTSli~lP~~~~~~i~~--~i~~~----~~C~~~~~lP~itf~f~g~~g~~v~~~l~p~dYi~~~~~~~~~~ 400 (482)
T PTZ00165 327 KCKAAIDTGSSLITGPSSVINPLLE--KIPLE----EDCSNKDSLPRISFVLEDVNGRKIKFDMDPEDYVIEEGDSEEQE 400 (482)
T ss_pred ceEEEEcCCCccEeCCHHHHHHHHH--HcCCc----ccccccccCCceEEEECCCCCceEEEEEchHHeeeecccCCCCC
Confidence 3579999999999999999999999 77543 478751 222 48899999999975 2 34
Q ss_pred eee-eEEEeCCC--CCCceeEeecc
Q 045258 84 MYC-PGFVNGGS--KPTTSIVIGGH 105 (106)
Q Consensus 84 ~~C-Laf~~~~~--~~~~~~viGn~ 105 (106)
..| ++|...+. ..++..|||+.
T Consensus 401 ~~C~~g~~~~d~~~~~g~~~ILGd~ 425 (482)
T PTZ00165 401 HQCVIGIIPMDVPAPRGPLFVLGNN 425 (482)
T ss_pred CeEEEEEEECCCCCCCCceEEEchh
Confidence 689 47876432 12366789974
No 19
>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=98.26 E-value=2.4e-06 Score=66.29 Aligned_cols=87 Identities=11% Similarity=0.145 Sum_probs=59.4
Q ss_pred CeeCCEEeecCCCccccccCCCCceEEeCCCcccccChhHHHHhhCHHHHhhhcCCCCcccc---------CCCCeEEEE
Q 045258 1 MKVDDRVVPLNSTLLSIDSQGFGGTKISTVNPYTALEKSIFKAEHTWHAFGGIRADHPTCFA---------ENENVIWRI 71 (106)
Q Consensus 1 IsVgg~~l~ip~~~~~~~~~G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~~~fd~Cy~---------~~~g~~~~l 71 (106)
|+|||+.+++++ ....+||||||++++||+++++++.. . -.|++ .++|+.+.+
T Consensus 197 i~v~g~~~~~~~--------~~~~aivDTGTs~~~lP~~~~~~i~~--~--------~~C~~~~~~P~i~f~f~g~~~~l 258 (317)
T cd06098 197 VLIGGKSTGFCA--------GGCAAIADSGTSLLAGPTTIVTQINS--A--------VDCNSLSSMPNVSFTIGGKTFEL 258 (317)
T ss_pred EEECCEEeeecC--------CCcEEEEecCCcceeCCHHHHHhhhc--c--------CCccccccCCcEEEEECCEEEEE
Confidence 456666655432 13479999999999999998877653 2 25775 247899999
Q ss_pred cCCCeeEEeCC--CeeeeE-EEeCC--CCCCceeEeecc
Q 045258 72 FDANSMVQVNE--DMYCPG-FVNGG--SKPTTSIVIGGH 105 (106)
Q Consensus 72 ~~~n~~v~v~~--~~~CLa-f~~~~--~~~~~~~viGn~ 105 (106)
++++|++...+ ...|+. |.... ....+..|||..
T Consensus 259 ~~~~yi~~~~~~~~~~C~~~~~~~~~~~~~~~~~IlGd~ 297 (317)
T cd06098 259 TPEQYILKVGEGAAAQCISGFTALDVPPPRGPLWILGDV 297 (317)
T ss_pred ChHHeEEeecCCCCCEEeceEEECCCCCCCCCeEEechH
Confidence 99999987754 357975 65422 112345688864
No 20
>PTZ00147 plasmepsin-1; Provisional
Probab=97.91 E-value=1.2e-05 Score=66.48 Aligned_cols=81 Identities=6% Similarity=0.170 Sum_probs=58.8
Q ss_pred CCceEEeCCCcccccChhHHHHhhCHHHHhhhc---CC--CCcccc--------CCCCeEEEEcCCCeeEEeCC--Ceee
Q 045258 22 FGGTKISTVNPYTALEKSIFKAEHTWHAFGGIR---AD--HPTCFA--------ENENVIWRIFDANSMVQVNE--DMYC 86 (106)
Q Consensus 22 ~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~---~~--fd~Cy~--------~~~g~~~~l~~~n~~v~v~~--~~~C 86 (106)
..++||||||++++||+++|+++.+ ++.... .+ ...|++ ..+|+.+.+++++|+....+ ...|
T Consensus 332 ~~~aIiDSGTsli~lP~~~~~ai~~--~l~~~~~~~~~~y~~~C~~~~lP~~~f~f~g~~~~L~p~~yi~~~~~~~~~~C 409 (453)
T PTZ00147 332 KANVIVDSGTSVITVPTEFLNKFVE--SLDVFKVPFLPLYVTTCNNTKLPTLEFRSPNKVYTLEPEYYLQPIEDIGSALC 409 (453)
T ss_pred ceeEEECCCCchhcCCHHHHHHHHH--HhCCeecCCCCeEEEeCCCCCCCeEEEEECCEEEEECHHHheeccccCCCcEE
Confidence 4679999999999999999999999 885432 11 257985 24688999999999876533 3579
Q ss_pred e-EEEeCCCCCCceeEeecc
Q 045258 87 P-GFVNGGSKPTTSIVIGGH 105 (106)
Q Consensus 87 L-af~~~~~~~~~~~viGn~ 105 (106)
+ +|++.... ....|||+.
T Consensus 410 ~~~i~~~~~~-~~~~ILGd~ 428 (453)
T PTZ00147 410 MLNIIPIDLE-KNTFILGDP 428 (453)
T ss_pred EEEEEECCCC-CCCEEECHH
Confidence 7 57764322 234689864
No 21
>PTZ00013 plasmepsin 4 (PM4); Provisional
Probab=97.83 E-value=1.9e-05 Score=65.36 Aligned_cols=81 Identities=10% Similarity=0.148 Sum_probs=57.4
Q ss_pred CCceEEeCCCcccccChhHHHHhhCHHHHhhhc---CC--CCcccc--------CCCCeEEEEcCCCeeEEeC--CCeee
Q 045258 22 FGGTKISTVNPYTALEKSIFKAEHTWHAFGGIR---AD--HPTCFA--------ENENVIWRIFDANSMVQVN--EDMYC 86 (106)
Q Consensus 22 ~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~---~~--fd~Cy~--------~~~g~~~~l~~~n~~v~v~--~~~~C 86 (106)
..+++|||||++++||+++++++.+ ++.... .+ ...|++ ..+|..+++++++|+.+.. ++..|
T Consensus 331 ~~~aIlDSGTSli~lP~~~~~~i~~--~l~~~~~~~~~~y~~~C~~~~lP~i~F~~~g~~~~L~p~~Yi~~~~~~~~~~C 408 (450)
T PTZ00013 331 KANVIVDSGTTTITAPSEFLNKFFA--NLNVIKVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYMNPLLDVDDTLC 408 (450)
T ss_pred ccceEECCCCccccCCHHHHHHHHH--HhCCeecCCCCeEEeecCCCCCCeEEEEECCEEEEECHHHheehhccCCCCee
Confidence 4579999999999999999999888 764332 11 247875 1457899999999997643 34679
Q ss_pred e-EEEeCCCCCCceeEeecc
Q 045258 87 P-GFVNGGSKPTTSIVIGGH 105 (106)
Q Consensus 87 L-af~~~~~~~~~~~viGn~ 105 (106)
+ ++.+.... ....|||..
T Consensus 409 ~~~i~~~~~~-~~~~ILGd~ 427 (450)
T PTZ00013 409 MITMLPVDID-DNTFILGDP 427 (450)
T ss_pred EEEEEECCCC-CCCEEECHH
Confidence 6 66653322 234688864
No 22
>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=97.48 E-value=0.00011 Score=54.47 Aligned_cols=40 Identities=20% Similarity=0.312 Sum_probs=33.0
Q ss_pred CCCceEEeCCCcccccChhHHHHhhCHHHHhhhcCCCCcccc
Q 045258 21 GFGGTKISTVNPYTALEKSIFKAEHTWHAFGGIRADHPTCFA 62 (106)
Q Consensus 21 G~GG~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~~~fd~Cy~ 62 (106)
...+++|||||++++||+++|+++.+ ++.++....+.|+.
T Consensus 201 ~~~~~iiDsGt~~~~lp~~~~~~l~~--~~~~~~~~~~~~~~ 240 (283)
T cd05471 201 GGGGAIVDSGTSLIYLPSSVYDAILK--ALGAAVSSSDGGYG 240 (283)
T ss_pred CCcEEEEecCCCCEeCCHHHHHHHHH--HhCCcccccCCcEE
Confidence 46799999999999999999999999 99888743334443
No 23
>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=96.77 E-value=0.0011 Score=50.30 Aligned_cols=27 Identities=15% Similarity=-0.053 Sum_probs=24.7
Q ss_pred CCceEEeCCCcccccChhHHHHhhCHHHH
Q 045258 22 FGGTKISTVNPYTALEKSIFKAEHTWHAF 50 (106)
Q Consensus 22 ~GG~iiDSgt~~T~L~~~~Y~~l~~~~af 50 (106)
+..++|||||++++||+++|+++.+ ++
T Consensus 198 ~~~~iiDSGTs~~~lP~~~~~~l~~--~l 224 (278)
T cd06097 198 GFSAIADTGTTLILLPDAIVEAYYS--QV 224 (278)
T ss_pred CceEEeecCCchhcCCHHHHHHHHH--hC
Confidence 4679999999999999999999988 77
No 24
>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=96.21 E-value=0.0056 Score=46.25 Aligned_cols=78 Identities=22% Similarity=0.307 Sum_probs=55.4
Q ss_pred ceEEeCCCcccccChhHHHHhhCHHHHhhhcC-------------CCCccccCCCCeEEEEcCCCeeEEeCCC--eeeeE
Q 045258 24 GTKISTVNPYTALEKSIFKAEHTWHAFGGIRA-------------DHPTCFAENENVIWRIFDANSMVQVNED--MYCPG 88 (106)
Q Consensus 24 G~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~~-------------~fd~Cy~~~~g~~~~l~~~n~~v~v~~~--~~CLa 88 (106)
.++||||+++.+||..+|+.+.+ ++..... ..++.|. .++..+.+++.+|+...... ..|..
T Consensus 201 ~~~~Dtgt~~i~lp~~~~~~i~~--~l~~~~~~~~~~~~c~~~~~~p~l~f~-~~~~~~~i~~~~~~~~~~~~~~~~C~~ 277 (317)
T PF00026_consen 201 QAILDTGTSYIYLPRSIFDAIIK--ALGGSYSDGVYSVPCNSTDSLPDLTFT-FGGVTFTIPPSDYIFKIEDGNGGYCYL 277 (317)
T ss_dssp EEEEETTBSSEEEEHHHHHHHHH--HHTTEEECSEEEEETTGGGGSEEEEEE-ETTEEEEEEHHHHEEEESSTTSSEEEE
T ss_pred eeecccccccccccchhhHHHHh--hhcccccceeEEEecccccccceEEEe-eCCEEEEecchHhcccccccccceeEe
Confidence 58999999999999999999999 8876641 1133333 45889999999999987653 37855
Q ss_pred -EEeCC-CCCCceeEeec
Q 045258 89 -FVNGG-SKPTTSIVIGG 104 (106)
Q Consensus 89 -f~~~~-~~~~~~~viGn 104 (106)
|.... .......|||.
T Consensus 278 ~i~~~~~~~~~~~~iLG~ 295 (317)
T PF00026_consen 278 GIQPMDSSDDSDDWILGS 295 (317)
T ss_dssp SEEEESSTTSSSEEEEEH
T ss_pred eeecccccccCCceEecH
Confidence 44421 12234567884
No 25
>PF13650 Asp_protease_2: Aspartyl protease
Probab=91.08 E-value=0.28 Score=30.22 Aligned_cols=22 Identities=18% Similarity=0.095 Sum_probs=20.1
Q ss_pred eEEeCCCcccccChhHHHHhhC
Q 045258 25 TKISTVNPYTALEKSIFKAEHT 46 (106)
Q Consensus 25 ~iiDSgt~~T~L~~~~Y~~l~~ 46 (106)
.+||||.+.+.+.+..++.+.-
T Consensus 12 ~liDTGa~~~~i~~~~~~~l~~ 33 (90)
T PF13650_consen 12 FLIDTGASISVISRSLAKKLGL 33 (90)
T ss_pred EEEcCCCCcEEECHHHHHHcCC
Confidence 8999999999999999988765
No 26
>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=88.22 E-value=0.61 Score=29.73 Aligned_cols=22 Identities=9% Similarity=0.181 Sum_probs=19.8
Q ss_pred eEEeCCCcccccChhHHHHhhC
Q 045258 25 TKISTVNPYTALEKSIFKAEHT 46 (106)
Q Consensus 25 ~iiDSgt~~T~L~~~~Y~~l~~ 46 (106)
..||||.+.|.+.+..|+.+-.
T Consensus 14 ~lvDTGA~~svis~~~~~~lg~ 35 (91)
T cd05484 14 FQLDTGSAITVISEKTWRKLGS 35 (91)
T ss_pred EEEcCCcceEEeCHHHHHHhCC
Confidence 7899999999999999987665
No 27
>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=83.33 E-value=1.5 Score=29.91 Aligned_cols=23 Identities=13% Similarity=-0.093 Sum_probs=19.4
Q ss_pred ceEEeCCCcccccChhHHHHhhC
Q 045258 24 GTKISTVNPYTALEKSIFKAEHT 46 (106)
Q Consensus 24 G~iiDSgt~~T~L~~~~Y~~l~~ 46 (106)
-.+||||.+.|.+++..-+++--
T Consensus 24 ~flVDTGAs~t~is~~~A~~Lgl 46 (121)
T TIGR02281 24 RFLVDTGATSVALNEEDAQRLGL 46 (121)
T ss_pred EEEEECCCCcEEcCHHHHHHcCC
Confidence 48999999999999988777633
No 28
>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=82.80 E-value=1.9 Score=26.68 Aligned_cols=22 Identities=9% Similarity=-0.008 Sum_probs=18.6
Q ss_pred ceEEeCCCcccccChhHHHHhh
Q 045258 24 GTKISTVNPYTALEKSIFKAEH 45 (106)
Q Consensus 24 G~iiDSgt~~T~L~~~~Y~~l~ 45 (106)
-.+||||.+.|.+.....+.+.
T Consensus 15 ~~llDTGa~~s~i~~~~~~~l~ 36 (96)
T cd05483 15 RFLLDTGASTTVISEELAERLG 36 (96)
T ss_pred EEEEECCCCcEEcCHHHHHHcC
Confidence 3899999999999998777653
No 29
>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=71.84 E-value=4.9 Score=25.42 Aligned_cols=20 Identities=10% Similarity=0.032 Sum_probs=17.7
Q ss_pred eEEeCCCcccccChhHHHHh
Q 045258 25 TKISTVNPYTALEKSIFKAE 44 (106)
Q Consensus 25 ~iiDSgt~~T~L~~~~Y~~l 44 (106)
.++|||...|.|.+...+.+
T Consensus 12 fLvDTGA~~tii~~~~a~~~ 31 (86)
T cd06095 12 FLVDTGATHSVLKSDLGPKQ 31 (86)
T ss_pred EEEECCCCeEEECHHHhhhc
Confidence 79999999999998887664
No 30
>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=70.61 E-value=5.7 Score=26.92 Aligned_cols=23 Identities=9% Similarity=-0.026 Sum_probs=19.0
Q ss_pred ceEEeCCCcccccChhHHHHhhC
Q 045258 24 GTKISTVNPYTALEKSIFKAEHT 46 (106)
Q Consensus 24 G~iiDSgt~~T~L~~~~Y~~l~~ 46 (106)
=.+||||.+.|++.+...+.+--
T Consensus 29 ~~LvDTGAs~s~Is~~~a~~lgl 51 (124)
T cd05479 29 KAFVDSGAQMTIMSKACAEKCGL 51 (124)
T ss_pred EEEEeCCCceEEeCHHHHHHcCC
Confidence 37999999999999988776443
No 31
>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=63.07 E-value=9.1 Score=24.88 Aligned_cols=22 Identities=14% Similarity=0.051 Sum_probs=20.0
Q ss_pred ceEEeCCCcccccChhHHHHhh
Q 045258 24 GTKISTVNPYTALEKSIFKAEH 45 (106)
Q Consensus 24 G~iiDSgt~~T~L~~~~Y~~l~ 45 (106)
-..+|||...+.||...|+.+-
T Consensus 12 ~~~vDtGA~vnllp~~~~~~l~ 33 (93)
T cd05481 12 KFQLDTGATCNVLPLRWLKSLT 33 (93)
T ss_pred EEEEecCCEEEeccHHHHhhhc
Confidence 3789999999999999999886
No 32
>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=62.08 E-value=9.3 Score=26.69 Aligned_cols=20 Identities=20% Similarity=0.036 Sum_probs=16.5
Q ss_pred eEEeCCCcccccChhHHHHh
Q 045258 25 TKISTVNPYTALEKSIFKAE 44 (106)
Q Consensus 25 ~iiDSgt~~T~L~~~~Y~~l 44 (106)
..||||...|.+..+..+.+
T Consensus 38 A~VDtGAQ~tims~~~a~r~ 57 (124)
T PF09668_consen 38 AFVDTGAQSTIMSKSCAERC 57 (124)
T ss_dssp EEEETT-SS-EEEHHHHHHT
T ss_pred EEEeCCCCccccCHHHHHHc
Confidence 78999999999999999884
No 33
>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=61.98 E-value=6.1 Score=25.08 Aligned_cols=20 Identities=10% Similarity=0.064 Sum_probs=16.7
Q ss_pred eEEeCCCcccccChhHHHHh
Q 045258 25 TKISTVNPYTALEKSIFKAE 44 (106)
Q Consensus 25 ~iiDSgt~~T~L~~~~Y~~l 44 (106)
..||||...|.+++..+...
T Consensus 19 ~LlDTGA~vsiI~~~~~~~~ 38 (100)
T PF00077_consen 19 ALLDTGADVSIISEKDWKKL 38 (100)
T ss_dssp EEEETTBSSEEESSGGSSST
T ss_pred EEEecCCCcceecccccccc
Confidence 78999999999998765444
No 34
>PHA02087 hypothetical protein
Probab=57.44 E-value=9.5 Score=24.62 Aligned_cols=25 Identities=20% Similarity=0.364 Sum_probs=17.8
Q ss_pred CCEEeecCCCccccccCCCCceEEeCCCccc
Q 045258 4 DDRVVPLNSTLLSIDSQGFGGTKISTVNPYT 34 (106)
Q Consensus 4 gg~~l~ip~~~~~~~~~G~GG~iiDSgt~~T 34 (106)
+|+.+.+|.+ +|.||+++|---.|-
T Consensus 53 dg~~ielpe~------~ggggi~fddeem~~ 77 (83)
T PHA02087 53 DGVKIELPES------EGGGGITFDDEEMFH 77 (83)
T ss_pred CCcEEECCcc------cCCCceeeccHHHHH
Confidence 5777788864 688999998654443
No 35
>PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease
Probab=56.73 E-value=11 Score=23.16 Aligned_cols=23 Identities=13% Similarity=0.002 Sum_probs=20.5
Q ss_pred ceEEeCCCcccccChhHHHHhhC
Q 045258 24 GTKISTVNPYTALEKSIFKAEHT 46 (106)
Q Consensus 24 G~iiDSgt~~T~L~~~~Y~~l~~ 46 (106)
...||||.+.+++++...+.+.-
T Consensus 21 ~alvDtGat~~fis~~~a~rLgl 43 (72)
T PF13975_consen 21 KALVDTGATHNFISESLAKRLGL 43 (72)
T ss_pred EEEEeCCCcceecCHHHHHHhCC
Confidence 48999999999999999988755
No 36
>COG5550 Predicted aspartyl protease [Posttranslational modification, protein turnover, chaperones]
Probab=56.04 E-value=8.4 Score=27.23 Aligned_cols=21 Identities=19% Similarity=0.072 Sum_probs=19.0
Q ss_pred EEeCCCc-ccccChhHHHHhhC
Q 045258 26 KISTVNP-YTALEKSIFKAEHT 46 (106)
Q Consensus 26 iiDSgt~-~T~L~~~~Y~~l~~ 46 (106)
.||||.+ |+.||+.+|+++-.
T Consensus 30 LiDTGFtg~lvlp~~vaek~~~ 51 (125)
T COG5550 30 LIDTGFTGYLVLPPQVAEKLGL 51 (125)
T ss_pred EEecCCceeEEeCHHHHHhcCC
Confidence 6999999 99999999998765
No 37
>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=36.69 E-value=42 Score=22.97 Aligned_cols=19 Identities=11% Similarity=0.193 Sum_probs=16.4
Q ss_pred eEEeCCCcccccChhHHHH
Q 045258 25 TKISTVNPYTALEKSIFKA 43 (106)
Q Consensus 25 ~iiDSgt~~T~L~~~~Y~~ 43 (106)
..||||..+|.+.+.--+.
T Consensus 12 AfVDsGaQ~timS~~caer 30 (103)
T cd05480 12 ALVDTGCQYNLISAACLDR 30 (103)
T ss_pred EEEecCCchhhcCHHHHHH
Confidence 6899999999999877655
No 38
>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=33.65 E-value=37 Score=22.52 Aligned_cols=23 Identities=9% Similarity=-0.136 Sum_probs=18.9
Q ss_pred ceEEeCCCcccc-cChhHHHHhhC
Q 045258 24 GTKISTVNPYTA-LEKSIFKAEHT 46 (106)
Q Consensus 24 G~iiDSgt~~T~-L~~~~Y~~l~~ 46 (106)
-.+||||.+... |+...++.+-=
T Consensus 18 ~~LVDTGat~~~~l~~~~a~~lgl 41 (107)
T TIGR03698 18 RALVDTGFSGFLLVPPDIVNKLGL 41 (107)
T ss_pred EEEEECCCCeEEecCHHHHHHcCC
Confidence 489999999776 99998888644
No 39
>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=33.22 E-value=42 Score=18.60 Aligned_cols=21 Identities=10% Similarity=0.050 Sum_probs=18.0
Q ss_pred eEEeCCCcccccChhHHHHhh
Q 045258 25 TKISTVNPYTALEKSIFKAEH 45 (106)
Q Consensus 25 ~iiDSgt~~T~L~~~~Y~~l~ 45 (106)
.++|+|.+.+.+..+.++...
T Consensus 12 ~liDtgs~~~~~~~~~~~~~~ 32 (92)
T cd00303 12 ALVDSGASVNFISESLAKKLG 32 (92)
T ss_pred EEEcCCCcccccCHHHHHHcC
Confidence 689999999999999887653
No 40
>PF14781 BBS2_N: Ciliary BBSome complex subunit 2, N-terminal
Probab=30.19 E-value=63 Score=23.09 Aligned_cols=26 Identities=19% Similarity=0.392 Sum_probs=20.6
Q ss_pred EeCCCeeeeEEEeCCCCCCceeEeec
Q 045258 79 QVNEDMYCPGFVNGGSKPTTSIVIGG 104 (106)
Q Consensus 79 ~v~~~~~CLaf~~~~~~~~~~~viGn 104 (106)
++.+++-|+.+..-++...|.+|+|+
T Consensus 90 e~~DGvn~i~~g~~~~~~~~l~ivGG 115 (136)
T PF14781_consen 90 EVPDGVNAIVIGKLGDIPSPLVIVGG 115 (136)
T ss_pred hCccceeEEEEEecCCCCCcEEEECc
Confidence 45678999999887776778888885
No 41
>COG4877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.91 E-value=38 Score=21.03 Aligned_cols=15 Identities=33% Similarity=0.634 Sum_probs=13.0
Q ss_pred ccChhHHHHhhCHHH
Q 045258 35 ALEKSIFKAEHTWHA 49 (106)
Q Consensus 35 ~L~~~~Y~~l~~~~a 49 (106)
+|++.+|+++++|.+
T Consensus 12 Rl~paiy~Aia~wA~ 26 (63)
T COG4877 12 RLEPAIYAAIAQWAE 26 (63)
T ss_pred ecCHHHHHHHHHHHH
Confidence 688999999999864
No 42
>COG3128 PiuC Uncharacterized iron-regulated protein [Function unknown]
Probab=24.88 E-value=1.2e+02 Score=23.28 Aligned_cols=38 Identities=11% Similarity=0.273 Sum_probs=28.4
Q ss_pred CCCCcccc-------CCCCeEEEEcCCCeeEEeCCCeeeeEEEeCC
Q 045258 55 ADHPTCFA-------ENENVIWRIFDANSMVQVNEDMYCPGFVNGG 93 (106)
Q Consensus 55 ~~fd~Cy~-------~~~g~~~~l~~~n~~v~v~~~~~CLaf~~~~ 93 (106)
.|.=.||. +-+|+...+.+++-+ .++.+..|--|.+..
T Consensus 83 ~P~Fn~Y~eg~~f~fHvDgavr~~hp~~~~-~lrtdls~tlfl~DP 127 (229)
T COG3128 83 PPLFNRYQEGDFFGFHVDGAVRSIHPGSGF-RLRTDLSCTLFLSDP 127 (229)
T ss_pred CchhhhccCCCcccccccCcccccCCCCCc-eeEeeeeeeeecCCc
Confidence 44557887 346888888888887 677778999998754
No 43
>COG1907 Predicted archaeal sugar kinases [General function prediction only]
Probab=22.81 E-value=44 Score=27.04 Aligned_cols=19 Identities=21% Similarity=0.378 Sum_probs=15.4
Q ss_pred CCceEEeCCCcccccChhH
Q 045258 22 FGGTKISTVNPYTALEKSI 40 (106)
Q Consensus 22 ~GG~iiDSgt~~T~L~~~~ 40 (106)
.||.|+|.|.+..++|.++
T Consensus 132 ~GGFIVDGGh~~~f~ps~~ 150 (312)
T COG1907 132 YGGFIVDGGHSFGFLPSSA 150 (312)
T ss_pred ECCEEEECCcccCcccCCC
Confidence 4799999999999776443
No 44
>PF11520 Cren7: Chromatin protein Cren7; InterPro: IPR020906 Cren7 is a chromatin protein found in Crenarchaeota and has a higher affinity for double-stranded DNA than for single-stranded DNA. The protein contains negative DNA supercoils and is associated with genomic DNA in vivo. Cren7 interacts with duplex DNA through a beta-sheet and a long flexible loop. Its binding to double-stranded DNA is without sequence specificity. There is approximately 1 Cren7 molecule for 12 bp of DNA. The function of Cren7 has not been completely determined but it is thought that the protein may have a role similar to that of archaeal proteins in Euryarchaea [].; GO: 0003690 double-stranded DNA binding, 0005737 cytoplasm; PDB: 3KXT_A 3LWH_A 3LWI_A 2JTM_A.
Probab=22.62 E-value=71 Score=19.81 Aligned_cols=25 Identities=16% Similarity=0.207 Sum_probs=14.9
Q ss_pred eCCEEee-cCCCccccccCCCCceEE
Q 045258 3 VDDRVVP-LNSTLLSIDSQGFGGTKI 27 (106)
Q Consensus 3 Vgg~~l~-ip~~~~~~~~~G~GG~ii 27 (106)
.+|+.+. .|..+|.++..|.-|++|
T Consensus 14 ~~Gke~~L~P~KvW~L~PkGrkGV~i 39 (60)
T PF11520_consen 14 YGGKEYELKPIKVWVLQPKGRKGVKI 39 (60)
T ss_dssp -TS-EEEE--SEEEEE--TTS--EEE
T ss_pred CCCeEEEeeeeEEEEEcCCCCCceEE
Confidence 4688777 688999999999999988
No 45
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=22.51 E-value=47 Score=25.09 Aligned_cols=16 Identities=31% Similarity=0.407 Sum_probs=13.2
Q ss_pred CeeCCEEeecCCCccc
Q 045258 1 MKVDDRVVPLNSTLLS 16 (106)
Q Consensus 1 IsVgg~~l~ip~~~~~ 16 (106)
|.|||+++.||+=...
T Consensus 121 I~VnGk~V~iPSy~V~ 136 (205)
T COG0522 121 ILVNGKRVNIPSYLVS 136 (205)
T ss_pred EEECCEEeccCcEEec
Confidence 6899999999985544
No 46
>PF14607 GxDLY: N-terminus of Esterase_SGNH_hydro-type
Probab=21.37 E-value=78 Score=22.71 Aligned_cols=54 Identities=20% Similarity=0.196 Sum_probs=35.8
Q ss_pred ceEEeCCCcccccChhHHHHhhCHHHHhhhc---CCCCccccCCC---CeEEEEcCCCeeEE
Q 045258 24 GTKISTVNPYTALEKSIFKAEHTWHAFGGIR---ADHPTCFAENE---NVIWRIFDANSMVQ 79 (106)
Q Consensus 24 G~iiDSgt~~T~L~~~~Y~~l~~~~af~~~~---~~fd~Cy~~~~---g~~~~l~~~n~~v~ 79 (106)
-..-++..+|.+||...|..+++ .+.... +++-..|.-.. -+.|.+.....|--
T Consensus 16 k~w~~~~~~Y~RLp~~~~~~v~~--~Vw~Ls~~SAGl~IrF~TnS~~I~vr~~~~~~~~m~h 75 (147)
T PF14607_consen 16 KAWPDTEGPYHRLPTRAEGKVRK--PVWNLSRNSAGLAIRFRTNSPEIAVRWTVTGNLSMPH 75 (147)
T ss_pred cccccCCCccccCChhhcccCCH--HHHhhhcCCCccEEEEEeCCCcEEEEEEECCCCCCCC
Confidence 34446789999999999999999 876654 45555554111 25666666655543
Done!