Query 039270
Match_columns 131
No_of_seqs 124 out of 480
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 08:01:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039270.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039270hhsearch_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 100.0 1.9E-28 4.1E-33 178.9 8.5 87 44-131 14-124 (135)
2 cd05479 RP_DDI RP_DDI; retrope 99.9 4.1E-22 8.8E-27 142.9 8.7 81 50-131 15-119 (124)
3 cd05484 retropepsin_like_LTR_2 99.6 8.8E-16 1.9E-20 103.9 6.9 66 53-120 2-91 (91)
4 PF09668 Asp_protease: Asparty 99.6 2E-15 4.3E-20 109.3 8.0 79 49-128 22-124 (124)
5 cd05480 NRIP_C NRIP_C; putativ 99.4 8.6E-13 1.9E-17 92.2 6.6 76 54-130 1-102 (103)
6 PF00077 RVP: Retroviral aspar 99.3 2.8E-11 6E-16 82.4 8.6 74 50-124 4-97 (100)
7 PF13650 Asp_protease_2: Aspar 99.2 5.1E-11 1.1E-15 78.4 7.1 65 54-118 1-90 (90)
8 cd00303 retropepsin_like Retro 99.2 5.3E-11 1.1E-15 74.3 6.8 66 55-120 2-92 (92)
9 cd05483 retropepsin_like_bacte 99.2 5.7E-11 1.2E-15 78.9 7.1 70 51-120 2-96 (96)
10 TIGR02281 clan_AA_DTGA clan AA 99.2 1.5E-10 3.2E-15 82.9 8.8 83 47-129 7-114 (121)
11 KOG0012 DNA damage inducible p 99.0 3.4E-10 7.4E-15 94.0 5.5 84 47-131 231-338 (380)
12 PF02160 Peptidase_A3: Caulifl 98.9 6.4E-09 1.4E-13 80.8 8.5 81 49-130 2-110 (201)
13 cd06095 RP_RTVL_H_like Retrope 98.9 6.2E-09 1.3E-13 69.9 6.7 65 55-120 2-86 (86)
14 TIGR03698 clan_AA_DTGF clan AA 98.9 9.1E-09 2E-13 72.2 7.0 69 61-131 15-104 (107)
15 PF12384 Peptidase_A2B: Ty3 tr 98.7 5.2E-08 1.1E-12 73.8 7.9 75 50-124 33-131 (177)
16 PF13975 gag-asp_proteas: gag- 98.7 1.5E-08 3.2E-13 66.3 3.5 36 46-81 3-38 (72)
17 cd05481 retropepsin_like_LTR_1 97.8 8E-05 1.7E-09 51.0 5.9 60 56-117 3-90 (93)
18 cd06094 RP_Saci_like RP_Saci_l 97.7 7.7E-05 1.7E-09 51.2 5.3 61 61-123 8-88 (89)
19 cd05482 HIV_retropepsin_like R 97.4 0.0011 2.4E-08 45.2 7.3 66 55-120 2-87 (87)
20 COG3577 Predicted aspartyl pro 97.3 0.00035 7.6E-09 54.8 4.7 88 36-127 94-206 (215)
21 PF05585 DUF1758: Putative pep 96.5 0.003 6.5E-08 46.7 3.4 21 61-81 11-31 (164)
22 COG5550 Predicted aspartyl pro 96.3 0.027 5.8E-07 40.9 7.4 79 51-131 12-114 (125)
23 PF12382 Peptidase_A2E: Retrot 92.0 0.29 6.3E-06 34.8 4.1 56 52-107 35-115 (137)
24 PF05618 Zn_protease: Putative 90.3 1.9 4.2E-05 31.5 7.3 35 88-122 87-124 (138)
25 cd05476 pepsin_A_like_plant Ch 89.6 1.3 2.9E-05 34.6 6.4 62 63-130 177-254 (265)
26 cd06097 Aspergillopepsin_like 85.7 0.63 1.4E-05 36.6 2.3 58 62-130 198-270 (278)
27 cd05477 gastricsin Gastricsins 84.5 2.7 6E-05 33.6 5.6 66 64-130 203-309 (318)
28 PF00026 Asp: Eukaryotic aspar 84.2 8.3 0.00018 30.2 8.1 25 53-77 3-29 (317)
29 cd05485 Cathepsin_D_like Cathe 82.5 4 8.6E-05 33.1 5.8 67 63-130 211-321 (329)
30 PF00026 Asp: Eukaryotic aspar 81.5 1.3 2.8E-05 34.7 2.6 67 63-130 200-308 (317)
31 PF03539 Spuma_A9PTase: Spumav 81.4 7.3 0.00016 29.4 6.3 62 58-122 1-83 (163)
32 cd05478 pepsin_A Pepsin A, asp 81.1 4.3 9.3E-05 32.5 5.5 74 56-130 194-309 (317)
33 PTZ00147 plasmepsin-1; Provisi 80.8 11 0.00023 32.7 8.1 25 53-77 141-167 (453)
34 cd05471 pepsin_like Pepsin-lik 80.4 1.4 3.1E-05 33.8 2.4 61 61-130 201-275 (283)
35 cd05474 SAP_like SAPs, pepsin- 79.4 18 0.0004 28.1 8.5 66 53-118 4-80 (295)
36 PTZ00013 plasmepsin 4 (PM4); P 78.9 11 0.00024 32.5 7.6 26 53-78 140-167 (450)
37 cd06096 Plasmepsin_5 Plasmepsi 78.6 2.7 5.9E-05 33.9 3.6 68 62-130 231-314 (326)
38 cd05474 SAP_like SAPs, pepsin- 77.1 4.7 0.0001 31.6 4.5 67 63-130 179-286 (295)
39 cd05470 pepsin_retropepsin_lik 75.6 2.7 5.9E-05 28.0 2.4 25 55-79 2-28 (109)
40 KOG3048 Molecular chaperone Pr 75.6 1.1 2.4E-05 33.5 0.5 66 12-80 6-99 (153)
41 cd05486 Cathespin_E Cathepsin 72.1 8.9 0.00019 30.7 5.0 67 63-130 199-308 (316)
42 cd06098 phytepsin Phytepsin, a 71.7 11 0.00025 30.2 5.6 67 63-130 211-309 (317)
43 COG4067 Uncharacterized protei 68.4 17 0.00037 27.5 5.5 37 88-124 111-149 (162)
44 PTZ00147 plasmepsin-1; Provisi 67.6 19 0.00042 31.1 6.4 68 62-130 332-440 (453)
45 cd05476 pepsin_A_like_plant Ch 65.7 29 0.00062 27.0 6.6 65 54-118 4-88 (265)
46 cd05488 Proteinase_A_fungi Fun 64.3 16 0.00034 29.4 5.0 67 63-130 206-312 (320)
47 cd05473 beta_secretase_like Be 62.8 46 0.00099 27.2 7.5 27 53-79 5-33 (364)
48 cd05486 Cathespin_E Cathepsin 61.6 45 0.00098 26.6 7.2 24 54-77 3-28 (316)
49 PTZ00013 plasmepsin 4 (PM4); P 60.3 14 0.0003 32.0 4.1 68 62-130 331-439 (450)
50 cd06097 Aspergillopepsin_like 58.5 11 0.00024 29.5 3.0 25 54-78 3-29 (278)
51 COG2383 Uncharacterized conser 54.1 2.3 5E-05 30.0 -1.3 18 113-130 51-68 (109)
52 cd05487 renin_like Renin stimu 46.6 23 0.00049 28.5 3.2 26 52-77 9-36 (326)
53 cd05490 Cathepsin_D2 Cathepsin 45.3 25 0.00055 28.1 3.2 25 53-77 8-34 (325)
54 cd06098 phytepsin Phytepsin, a 45.0 25 0.00055 28.2 3.2 27 52-78 11-39 (317)
55 cd05477 gastricsin Gastricsins 39.7 35 0.00075 27.2 3.2 25 54-78 6-32 (318)
56 cd06096 Plasmepsin_5 Plasmepsi 39.1 37 0.00081 27.3 3.3 26 53-78 5-32 (326)
57 cd05472 cnd41_like Chloroplast 39.0 32 0.0007 27.1 2.9 24 54-77 4-29 (299)
58 cd05488 Proteinase_A_fungi Fun 38.6 36 0.00079 27.2 3.2 27 52-78 11-39 (320)
59 KOG4584 Uncharacterized conser 38.1 21 0.00045 30.0 1.7 22 95-116 196-217 (348)
60 cd05475 nucellin_like Nucellin 37.9 36 0.00078 26.6 3.0 26 53-78 4-31 (273)
61 PF13352 DUF4100: Protein of u 37.8 26 0.00057 27.7 2.2 22 50-71 188-211 (212)
62 cd05478 pepsin_A Pepsin A, asp 37.3 39 0.00085 26.9 3.2 26 53-78 12-39 (317)
63 cd05471 pepsin_like Pepsin-lik 34.6 49 0.0011 25.2 3.2 26 54-79 3-30 (283)
64 cd05485 Cathepsin_D_like Cathe 34.1 46 0.001 26.8 3.1 27 52-78 12-40 (329)
65 PF03419 Peptidase_U4: Sporula 31.1 76 0.0016 25.5 3.9 24 50-73 156-181 (293)
66 TIGR02854 spore_II_GA sigma-E 26.9 91 0.002 25.3 3.7 24 50-73 157-182 (288)
67 PF14543 TAXi_N: Xylanase inhi 25.2 87 0.0019 22.8 3.0 25 54-78 3-29 (164)
68 PTZ00165 aspartyl protease; Pr 24.1 86 0.0019 27.4 3.2 27 52-78 121-149 (482)
69 COG1490 Dtd D-Tyr-tRNAtyr deac 23.5 1.3E+02 0.0029 22.3 3.7 12 58-69 134-145 (145)
70 KOG3217 Protein tyrosine phosp 20.9 37 0.0008 25.6 0.3 13 105-117 81-93 (159)
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=99.95 E-value=1.9e-28 Score=178.94 Aligned_cols=87 Identities=36% Similarity=0.654 Sum_probs=80.8
Q ss_pred cccccCCeEEEEEEECCeeeEEEEeCCCccccccceeE------------------------eeeeeeeeEEEECcEEEE
Q 039270 44 SGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLILQGVSVI 99 (131)
Q Consensus 44 ~g~~~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------------~~g~~~~~~~~i~g~~f~ 99 (131)
.....+..+...+.|+++++.+|||||||||||+.++| +.+.|..+++.++|+.|.
T Consensus 14 ~~~~~~~vi~g~~~I~~~~~~vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~~V~~~g~~~~~~~~~~~~~~~i~g~~~~ 93 (135)
T PF08284_consen 14 EAEESPDVITGTFLINSIPASVLIDSGATHSFISSSFAKKLGLPLEPLPRPIVVSAPGGSINCEGVCPDVPLSIQGHEFV 93 (135)
T ss_pred cccCCCCeEEEEEEeccEEEEEEEecCCCcEEccHHHHHhcCCEEEEccCeeEEecccccccccceeeeEEEEECCeEEE
Confidence 34456789999999999999999999999999999999 566789999999999999
Q ss_pred eeeEEecCCCcceeecccccccCCCeeeeecC
Q 039270 100 VDFNLRDLEGYDVVLGTQWLRTLEPILWDFAS 131 (131)
Q Consensus 100 ~df~vl~l~~~DvILG~dWL~~~~pi~idw~~ 131 (131)
.||+|+++++||+|||||||++|+| .|||.+
T Consensus 94 ~dl~vl~l~~~DvILGm~WL~~~~~-~IDw~~ 124 (135)
T PF08284_consen 94 VDLLVLDLGGYDVILGMDWLKKHNP-VIDWAT 124 (135)
T ss_pred eeeEEecccceeeEeccchHHhCCC-EEEccC
Confidence 9999999999999999999999999 799975
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=99.87 E-value=4.1e-22 Score=142.87 Aligned_cols=81 Identities=17% Similarity=0.253 Sum_probs=75.0
Q ss_pred CeEEEEEEECCeeeEEEEeCCCccccccceeE------------------------eeeeeeeeEEEECcEEEEeeeEEe
Q 039270 50 ETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLILQGVSVIVDFNLR 105 (131)
Q Consensus 50 ~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------------~~g~~~~~~~~i~g~~f~~df~vl 105 (131)
..|++.++|+|+++.+|||||||||||+++++ +.|.+..+++++++..|..+|.|+
T Consensus 15 ~~~~v~~~Ing~~~~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~~~~~Vl 94 (124)
T cd05479 15 PMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRIHLAQVKIGNLFLPCSFTVL 94 (124)
T ss_pred eEEEEEEEECCEEEEEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCCCcEEEeEEEEEEEEECCEEeeeEEEEE
Confidence 57999999999999999999999999999888 345677889999999999999999
Q ss_pred cCCCcceeecccccccCCCeeeeecC
Q 039270 106 DLEGYDVVLGTQWLRTLEPILWDFAS 131 (131)
Q Consensus 106 ~l~~~DvILG~dWL~~~~pi~idw~~ 131 (131)
++.++|+|||||||++++. .|||++
T Consensus 95 ~~~~~d~ILG~d~L~~~~~-~ID~~~ 119 (124)
T cd05479 95 EDDDVDFLIGLDMLKRHQC-VIDLKE 119 (124)
T ss_pred CCCCcCEEecHHHHHhCCe-EEECCC
Confidence 9999999999999999996 899975
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=99.63 E-value=8.8e-16 Score=103.94 Aligned_cols=66 Identities=18% Similarity=0.249 Sum_probs=60.3
Q ss_pred EEEEEECCeeeEEEEeCCCccccccceeE------------------------eeeeeeeeEEEECcEEEEeeeEEecCC
Q 039270 53 RINGRIGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLILQGVSVIVDFNLRDLE 108 (131)
Q Consensus 53 rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------------~~g~~~~~~~~i~g~~f~~df~vl~l~ 108 (131)
+++++|+|+++.+|||+||++|||+++.+ +.|++ .+.+++++..+..+|+|++..
T Consensus 2 ~~~~~Ing~~i~~lvDTGA~~svis~~~~~~lg~~~~~~~~~~v~~a~G~~~~~~G~~-~~~v~~~~~~~~~~~~v~~~~ 80 (91)
T cd05484 2 TVTLLVNGKPLKFQLDTGSAITVISEKTWRKLGSPPLKPTKKRLRTATGTKLSVLGQI-LVTVKYGGKTKVLTLYVVKNE 80 (91)
T ss_pred EEEEEECCEEEEEEEcCCcceEEeCHHHHHHhCCCccccccEEEEecCCCEeeEeEEE-EEEEEECCEEEEEEEEEEECC
Confidence 57899999999999999999999999875 45566 789999999999999999998
Q ss_pred Ccceeecccccc
Q 039270 109 GYDVVLGTQWLR 120 (131)
Q Consensus 109 ~~DvILG~dWL~ 120 (131)
+|.|||+|||.
T Consensus 81 -~~~lLG~~wl~ 91 (91)
T cd05484 81 -GLNLLGRDWLD 91 (91)
T ss_pred -CCCccChhhcC
Confidence 99999999985
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=99.61 E-value=2e-15 Score=109.29 Aligned_cols=79 Identities=22% Similarity=0.321 Sum_probs=67.7
Q ss_pred CCeEEEEEEECCeeeEEEEeCCCccccccceeE------------------------eeeeeeeeEEEECcEEEEeeeEE
Q 039270 49 SETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLILQGVSVIVDFNL 104 (131)
Q Consensus 49 ~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------------~~g~~~~~~~~i~g~~f~~df~v 104 (131)
...+++.++|||+++.|+|||||.+|.|+.+++ ..|+...+++++++..+...|.|
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 457899999999999999999999999999999 45678889999999999999999
Q ss_pred ecCCCcceeecccccccCCCeeee
Q 039270 105 RDLEGYDVVLGTQWLRTLEPILWD 128 (131)
Q Consensus 105 l~l~~~DvILG~dWL~~~~pi~id 128 (131)
++-...|+|||.|||++|.- .||
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 99889999999999999998 576
No 5
>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=99.39 E-value=8.6e-13 Score=92.21 Aligned_cols=76 Identities=20% Similarity=0.231 Sum_probs=69.4
Q ss_pred EEEEECCeeeEEEEeCCCccccccceeE--------------------------eeeeeeeeEEEECcEEEEeeeEEecC
Q 039270 54 INGRIGNISPIVLVDSGSTRNFMSEQFY--------------------------STRKCTNVNLILQGVSVIVDFNLRDL 107 (131)
Q Consensus 54 v~~~I~~~~v~aLIDSGsThnFIs~~~a--------------------------~~g~~~~~~~~i~g~~f~~df~vl~l 107 (131)
+.+++||+++.|+|||||.+|.||+.++ ..|+++.+++++++..+...|.|++-
T Consensus 1 vnCk~nG~~vkAfVDsGaQ~timS~~caercgL~r~v~~~r~~g~A~gvgt~~kiiGrih~~~ikig~~~~~CSftVld~ 80 (103)
T cd05480 1 VSCQCAGKELRALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSLPTSVKVIGQIERLVLQLGQLTVECSAQVVDD 80 (103)
T ss_pred CceeECCEEEEEEEecCCchhhcCHHHHHHcChHhhhhhccccccccCCCcceeEeeEEEEEEEEeCCEEeeEEEEEEcC
Confidence 3588999999999999999999999999 34567789999999999999999998
Q ss_pred CCcceeecccccccCCCeeeeec
Q 039270 108 EGYDVVLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 108 ~~~DvILG~dWL~~~~pi~idw~ 130 (131)
...|++||.|-|++|.- .||.+
T Consensus 81 ~~~d~llGLdmLkrhqc-~IdL~ 102 (103)
T cd05480 81 NEKNFSLGLQTLKSLKC-VINLE 102 (103)
T ss_pred CCcceEeeHHHHhhcce-eeecc
Confidence 89999999999999999 68865
No 6
>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=99.28 E-value=2.8e-11 Score=82.41 Aligned_cols=74 Identities=20% Similarity=0.284 Sum_probs=62.6
Q ss_pred CeEEEEEEECCeeeEEEEeCCCccccccceeE---------------eeee-----eeeeEEEECcEEEEeeeEEecCCC
Q 039270 50 ETMRINGRIGNISPIVLVDSGSTRNFMSEQFY---------------STRK-----CTNVNLILQGVSVIVDFNLRDLEG 109 (131)
Q Consensus 50 ~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a---------------~~g~-----~~~~~~~i~g~~f~~df~vl~l~~ 109 (131)
+.-++..+++|+++.+|||+||+.++|+.+.. ..|. ...+.+++++..+...|+|.+-..
T Consensus 4 ~rp~i~v~i~g~~i~~LlDTGA~vsiI~~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~v~~~~~~~~~~~~v~~~~~ 83 (100)
T PF00077_consen 4 NRPYITVKINGKKIKALLDTGADVSIISEKDWKKLGPPPKTSITVRGAGGSSSILGSTTVEVKIGGKEFNHTFLVVPDLP 83 (100)
T ss_dssp SSSEEEEEETTEEEEEEEETTBSSEEESSGGSSSTSSEEEEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEESSTCS
T ss_pred CCceEEEeECCEEEEEEEecCCCcceecccccccccccccCCceeccCCCcceeeeEEEEEEEEECccceEEEEecCCCC
Confidence 34567899999999999999999999999877 0111 135688899999999999999877
Q ss_pred cceeecccccccCCC
Q 039270 110 YDVVLGTQWLRTLEP 124 (131)
Q Consensus 110 ~DvILG~dWL~~~~p 124 (131)
+| |||.|||++++.
T Consensus 84 ~~-ILG~D~L~~~~~ 97 (100)
T PF00077_consen 84 MN-ILGRDFLKKLNA 97 (100)
T ss_dssp SE-EEEHHHHTTTTC
T ss_pred CC-EeChhHHHHcCC
Confidence 88 999999999987
No 7
>PF13650 Asp_protease_2: Aspartyl protease
Probab=99.22 E-value=5.1e-11 Score=78.44 Aligned_cols=65 Identities=17% Similarity=0.304 Sum_probs=53.1
Q ss_pred EEEEECCeeeEEEEeCCCccccccceeE------------------eeee-----eeeeEEEECcEEE-EeeeEEec-CC
Q 039270 54 INGRIGNISPIVLVDSGSTRNFMSEQFY------------------STRK-----CTNVNLILQGVSV-IVDFNLRD-LE 108 (131)
Q Consensus 54 v~~~I~~~~v~aLIDSGsThnFIs~~~a------------------~~g~-----~~~~~~~i~g~~f-~~df~vl~-l~ 108 (131)
|.++|+|+++.+||||||++++|+.+++ ..|. ..--.+++++..+ ..++.+++ -.
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 4688999999999999999999999998 0111 1122688899888 68899999 56
Q ss_pred Ccceeecccc
Q 039270 109 GYDVVLGTQW 118 (131)
Q Consensus 109 ~~DvILG~dW 118 (131)
.+|.|||+||
T Consensus 81 ~~~~iLG~df 90 (90)
T PF13650_consen 81 PIDGILGMDF 90 (90)
T ss_pred CCEEEeCCcC
Confidence 8999999998
No 8
>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=99.21 E-value=5.3e-11 Score=74.34 Aligned_cols=66 Identities=38% Similarity=0.639 Sum_probs=55.4
Q ss_pred EEEECCeeeEEEEeCCCccccccceeE-------------------------eeeeeeeeEEEECcEEEEeeeEEecCCC
Q 039270 55 NGRIGNISPIVLVDSGSTRNFMSEQFY-------------------------STRKCTNVNLILQGVSVIVDFNLRDLEG 109 (131)
Q Consensus 55 ~~~I~~~~v~aLIDSGsThnFIs~~~a-------------------------~~g~~~~~~~~i~g~~f~~df~vl~l~~ 109 (131)
.+.+++.++.+|+|+||++++++..++ ..+.+..+.+.+++..+...|++.+...
T Consensus 2 ~~~~~~~~~~~liDtgs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~ 81 (92)
T cd00303 2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS 81 (92)
T ss_pred EEEECCEEEEEEEcCCCcccccCHHHHHHcCCCcccCCCceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcCCC
Confidence 466888999999999999999988775 0112246678888999999999999999
Q ss_pred cceeecccccc
Q 039270 110 YDVVLGTQWLR 120 (131)
Q Consensus 110 ~DvILG~dWL~ 120 (131)
+|+|||++||+
T Consensus 82 ~~~ilG~~~l~ 92 (92)
T cd00303 82 YDVILGRPWLE 92 (92)
T ss_pred cCEEecccccC
Confidence 99999999985
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=99.21 E-value=5.7e-11 Score=78.94 Aligned_cols=70 Identities=20% Similarity=0.299 Sum_probs=58.2
Q ss_pred eEEEEEEECCeeeEEEEeCCCccccccceeE-----------------eee-----eeeeeEEEECcEEEE-eeeEEecC
Q 039270 51 TMRINGRIGNISPIVLVDSGSTRNFMSEQFY-----------------STR-----KCTNVNLILQGVSVI-VDFNLRDL 107 (131)
Q Consensus 51 t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a-----------------~~g-----~~~~~~~~i~g~~f~-~df~vl~l 107 (131)
.+.+.+.|+++++.+|||+||++++|+.+++ ..| ...-..+++++..+. ..+.++++
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 5788999999999999999999999999876 011 112346788999887 68999999
Q ss_pred CC--cceeecccccc
Q 039270 108 EG--YDVVLGTQWLR 120 (131)
Q Consensus 108 ~~--~DvILG~dWL~ 120 (131)
.. .|.|||+|||+
T Consensus 82 ~~~~~~gIlG~d~l~ 96 (96)
T cd05483 82 DALGVDGLLGMDFLR 96 (96)
T ss_pred cccCCceEeChHHhC
Confidence 87 99999999985
No 10
>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family. This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Sequences in the seed alignment and those scoring above the trusted cutoff are Proteobacterial; homologs scroing between trusted and noise are found in Pyrobaculum aerophilum str. IM2 (archaeal), Pirellula sp. (Planctomycetes), and Nostoc sp. PCC 7120 (Cyanobacteria).
Probab=99.19 E-value=1.5e-10 Score=82.91 Aligned_cols=83 Identities=19% Similarity=0.233 Sum_probs=67.3
Q ss_pred ccCCeEEEEEEECCeeeEEEEeCCCccccccceeE------------------eeeeeee-----eEEEECcEEEE-eee
Q 039270 47 RASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------STRKCTN-----VNLILQGVSVI-VDF 102 (131)
Q Consensus 47 ~~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------~~g~~~~-----~~~~i~g~~f~-~df 102 (131)
.....+.+.++|||+++.+|||+|||+++|+++++ ..|.... -.+++++..+. ..+
T Consensus 7 ~~~g~~~v~~~InG~~~~flVDTGAs~t~is~~~A~~Lgl~~~~~~~~~~~~ta~G~~~~~~~~l~~l~iG~~~~~nv~~ 86 (121)
T TIGR02281 7 DGDGHFYATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIKAARVTLDRVAIGGIVVNDVDA 86 (121)
T ss_pred cCCCeEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCcccCCceEEEEeCCCcEEEEEEEeCEEEECCEEEeCcEE
Confidence 34578999999999999999999999999999998 1222211 24778888877 889
Q ss_pred EEecCCC-cceeecccccccCCCeeeee
Q 039270 103 NLRDLEG-YDVVLGTQWLRTLEPILWDF 129 (131)
Q Consensus 103 ~vl~l~~-~DvILG~dWL~~~~pi~idw 129 (131)
.|+|.+. .|.+|||++|+++.++.+|-
T Consensus 87 ~v~~~~~~~~~LLGm~fL~~~~~~~~~~ 114 (121)
T TIGR02281 87 MVAEGGALSESLLGMSFLNRLSRFTVRG 114 (121)
T ss_pred EEeCCCcCCceEcCHHHHhccccEEEEC
Confidence 9999873 58999999999999877763
No 11
>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]
Probab=99.03 E-value=3.4e-10 Score=94.03 Aligned_cols=84 Identities=21% Similarity=0.303 Sum_probs=76.8
Q ss_pred ccCCeEEEEEEECCeeeEEEEeCCCccccccceeE------------------------eeeeeeeeEEEECcEEEEeee
Q 039270 47 RASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLILQGVSVIVDF 102 (131)
Q Consensus 47 ~~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------------~~g~~~~~~~~i~g~~f~~df 102 (131)
..-..++|.|+|+|++|+|+|||||..|.||..|| ..|+++.+.+++++..+.+.|
T Consensus 231 ~~v~ML~iN~~ing~~VKAfVDsGaq~timS~~Caer~gL~rlid~r~~g~a~gvg~~ki~g~Ih~~~lki~~~~l~c~f 310 (380)
T KOG0012|consen 231 TQVTMLYINCEINGVPVKAFVDSGAQTTIMSAACAERCGLNRLIDKRFQGEARGVGTEKILGRIHQAQLKIEDLYLPCSF 310 (380)
T ss_pred ccceEEEEEEEECCEEEEEEEcccchhhhhhHHHHHHhChHHHhhhhhhccccCCCcccccceeEEEEEEeccEeeccce
Confidence 34467889999999999999999999999999999 357788999999999999999
Q ss_pred EEecCCCcceeecccccccCCCeeeeecC
Q 039270 103 NLRDLEGYDVVLGTQWLRTLEPILWDFAS 131 (131)
Q Consensus 103 ~vl~l~~~DvILG~dWL~~~~pi~idw~~ 131 (131)
-|++-...|+.||.|-|++|+. .||.++
T Consensus 311 tV~d~~~~d~llGLd~Lrr~~c-cIdL~~ 338 (380)
T KOG0012|consen 311 TVLDRRDMDLLLGLDMLRRHQC-CIDLKT 338 (380)
T ss_pred EEecCCCcchhhhHHHHHhccc-eeeccc
Confidence 9999999999999999999999 598763
No 12
>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=98.92 E-value=6.4e-09 Score=80.79 Aligned_cols=81 Identities=21% Similarity=0.317 Sum_probs=65.6
Q ss_pred CCeEEEEEEE--CC---eeeEEEEeCCCccccccceeE-----------------------eeeeeeeeEEEECcEEEEe
Q 039270 49 SETMRINGRI--GN---ISPIVLVDSGSTRNFMSEQFY-----------------------STRKCTNVNLILQGVSVIV 100 (131)
Q Consensus 49 ~~t~rv~~~I--~~---~~v~aLIDSGsThnFIs~~~a-----------------------~~g~~~~~~~~i~g~~f~~ 100 (131)
|+.+++++++ .| ..+.++||+|||.+.++..+. ...+|.++.+.+.|+.|..
T Consensus 2 pNsiyI~~~i~~~gy~~~~~~~~vDTGAt~C~~~~~iiP~e~we~~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~I 81 (201)
T PF02160_consen 2 PNSIYIKVKISFPGYKKFNYHCYVDTGATICCASKKIIPEEYWEKSKKPIKVKGANGSIIQINKKAKNGKIQIADKIFRI 81 (201)
T ss_pred CccEEEEEEEEEcCceeEEEEEEEeCCCceEEecCCcCCHHHHHhCCCcEEEEEecCCceEEEEEecCceEEEccEEEec
Confidence 5666666664 44 457889999999999999988 3456788999999999997
Q ss_pred eeEEecCCCcceeecccccccCCCeeeeec
Q 039270 101 DFNLRDLEGYDVVLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 101 df~vl~l~~~DvILG~dWL~~~~pi~idw~ 130 (131)
.+.-.--.|.|+|||++||+.++|. +.|.
T Consensus 82 P~iYq~~~g~d~IlG~NF~r~y~Pf-iq~~ 110 (201)
T PF02160_consen 82 PTIYQQESGIDIILGNNFLRLYEPF-IQTE 110 (201)
T ss_pred cEEEEecCCCCEEecchHHHhcCCc-EEEc
Confidence 7654433799999999999999994 8875
No 13
>cd06095 RP_RTVL_H_like Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements. This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where
Probab=98.89 E-value=6.2e-09 Score=69.95 Aligned_cols=65 Identities=22% Similarity=0.250 Sum_probs=52.3
Q ss_pred EEEECCeeeEEEEeCCCccccccceeE--------------eeee----ee-ee-EEEECcEEEEeeeEEecCCCcceee
Q 039270 55 NGRIGNISPIVLVDSGSTRNFMSEQFY--------------STRK----CT-NV-NLILQGVSVIVDFNLRDLEGYDVVL 114 (131)
Q Consensus 55 ~~~I~~~~v~aLIDSGsThnFIs~~~a--------------~~g~----~~-~~-~~~i~g~~f~~df~vl~l~~~DvIL 114 (131)
.+.|||+++.+|||+||+++.|+.+.+ ..|. .. -. .++++++....++.+.+- ..|.||
T Consensus 2 ~v~InG~~~~fLvDTGA~~tii~~~~a~~~~~~~~~~~v~gagG~~~~~v~~~~~~v~vg~~~~~~~~~v~~~-~~~~lL 80 (86)
T cd06095 2 TITVEGVPIVFLVDTGATHSVLKSDLGPKQELSTTSVLIRGVSGQSQQPVTTYRTLVDLGGHTVSHSFLVVPN-CPDPLL 80 (86)
T ss_pred EEEECCEEEEEEEECCCCeEEECHHHhhhccCCCCcEEEEeCCCcccccEEEeeeEEEECCEEEEEEEEEEcC-CCCcEe
Confidence 578999999999999999999999877 1121 11 12 488999999999988874 469999
Q ss_pred cccccc
Q 039270 115 GTQWLR 120 (131)
Q Consensus 115 G~dWL~ 120 (131)
|||||+
T Consensus 81 G~dfL~ 86 (86)
T cd06095 81 GRDLLS 86 (86)
T ss_pred chhhcC
Confidence 999985
No 14
>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family. Members of this protein family are clan AA aspartic proteases, related to family TIGR02281. These proteins resemble retropepsins, pepsin-like proteases of retroviruses such as HIV. Members of this family are found in archaea and bacteria.
Probab=98.86 E-value=9.1e-09 Score=72.22 Aligned_cols=69 Identities=17% Similarity=0.289 Sum_probs=54.1
Q ss_pred eeeEEEEeCCCcccc-ccceeE---------------eeeee-----eeeEEEECcEEEEeeeEEecCCCcceeeccccc
Q 039270 61 ISPIVLVDSGSTRNF-MSEQFY---------------STRKC-----TNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWL 119 (131)
Q Consensus 61 ~~v~aLIDSGsThnF-Is~~~a---------------~~g~~-----~~~~~~i~g~~f~~df~vl~l~~~DvILG~dWL 119 (131)
.++.+|||||||+.. ++.+.+ .+|.. ....+.++|....+.+.+.+... +.+|||.||
T Consensus 15 ~~v~~LVDTGat~~~~l~~~~a~~lgl~~~~~~~~~tA~G~~~~~~v~~~~v~igg~~~~~~v~~~~~~~-~~LLG~~~L 93 (107)
T TIGR03698 15 MEVRALVDTGFSGFLLVPPDIVNKLGLPELDQRRVYLADGREVLTDVAKASIIINGLEIDAFVESLGYVD-EPLLGTELL 93 (107)
T ss_pred eEEEEEEECCCCeEEecCHHHHHHcCCCcccCcEEEecCCcEEEEEEEEEEEEECCEEEEEEEEecCCCC-ccEecHHHH
Confidence 378999999999998 998888 23422 34567788888766655556556 899999999
Q ss_pred ccCCCeeeeecC
Q 039270 120 RTLEPILWDFAS 131 (131)
Q Consensus 120 ~~~~pi~idw~~ 131 (131)
++++. .+||++
T Consensus 94 ~~l~l-~id~~~ 104 (107)
T TIGR03698 94 EGLGI-VIDYRN 104 (107)
T ss_pred hhCCE-EEehhh
Confidence 99997 799974
No 15
>PF12384 Peptidase_A2B: Ty3 transposon peptidase; InterPro: IPR024650 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Ty3 is a gypsy-type, retrovirus-like, element found in the budding yeast. The Ty3 aspartyl protease is required for processing of the viral polyprotein into its mature species [].
Probab=98.74 E-value=5.2e-08 Score=73.78 Aligned_cols=75 Identities=16% Similarity=0.227 Sum_probs=66.8
Q ss_pred CeEEEEEEECCeeeEEEEeCCCccccccceeE--------------ee----------eeeeeeEEEECcEEEEeeeEEe
Q 039270 50 ETMRINGRIGNISPIVLVDSGSTRNFMSEQFY--------------ST----------RKCTNVNLILQGVSVIVDFNLR 105 (131)
Q Consensus 50 ~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a--------------~~----------g~~~~~~~~i~g~~f~~df~vl 105 (131)
++..+...++|.++.+|+||||--|||+.+.+ .. .+...+++.+++..+...++|+
T Consensus 33 ~T~~v~l~~~~t~i~vLfDSGSPTSfIr~di~~kL~L~~~~app~~fRG~vs~~~~~tsEAv~ld~~i~n~~i~i~aYV~ 112 (177)
T PF12384_consen 33 KTAIVQLNCKGTPIKVLFDSGSPTSFIRSDIVEKLELPTHDAPPFRFRGFVSGESATTSEAVTLDFYIDNKLIDIAAYVT 112 (177)
T ss_pred cEEEEEEeecCcEEEEEEeCCCccceeehhhHHhhCCccccCCCEEEeeeccCCceEEEEeEEEEEEECCeEEEEEEEEe
Confidence 67888999999999999999999999999998 11 1335778999999999999999
Q ss_pred cCCCcceeecccccccCCC
Q 039270 106 DLEGYDVVLGTQWLRTLEP 124 (131)
Q Consensus 106 ~l~~~DvILG~dWL~~~~p 124 (131)
+.-++|+|+|.+.|++|..
T Consensus 113 d~m~~dlIIGnPiL~ryp~ 131 (177)
T PF12384_consen 113 DNMDHDLIIGNPILDRYPT 131 (177)
T ss_pred ccCCcceEeccHHHhhhHH
Confidence 9999999999999998864
No 16
>PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease
Probab=98.70 E-value=1.5e-08 Score=66.30 Aligned_cols=36 Identities=33% Similarity=0.491 Sum_probs=33.7
Q ss_pred cccCCeEEEEEEECCeeeEEEEeCCCccccccceeE
Q 039270 46 ARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY 81 (131)
Q Consensus 46 ~~~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a 81 (131)
...+.++++.+.|+++.+.+|||||||||||+.+++
T Consensus 3 ~~~~g~~~v~~~I~g~~~~alvDtGat~~fis~~~a 38 (72)
T PF13975_consen 3 TPDPGLMYVPVSIGGVQVKALVDTGATHNFISESLA 38 (72)
T ss_pred cccCCEEEEEEEECCEEEEEEEeCCCcceecCHHHH
Confidence 456789999999999999999999999999999999
No 17
>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=97.78 E-value=8e-05 Score=50.96 Aligned_cols=60 Identities=18% Similarity=0.244 Sum_probs=47.7
Q ss_pred EEECC-eeeEEEEeCCCccccccceeE---------------------------eeeeeeeeEEEECcEEEEeeeEEecC
Q 039270 56 GRIGN-ISPIVLVDSGSTRNFMSEQFY---------------------------STRKCTNVNLILQGVSVIVDFNLRDL 107 (131)
Q Consensus 56 ~~I~~-~~v~aLIDSGsThnFIs~~~a---------------------------~~g~~~~~~~~i~g~~f~~df~vl~l 107 (131)
..+++ +++.+++|+||+.|.|+.+.. ..|. ..+.+++++..+..+|+|++.
T Consensus 3 ~~i~g~~~v~~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~~~G~-~~~~v~~~~~~~~~~f~Vvd~ 81 (93)
T cd05481 3 MKINGKQSVKFQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIPVEGG-VKLKCRYRNPKYNLTFQVVKE 81 (93)
T ss_pred eEeCCceeEEEEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEeeeeEE-EEEEEEECCcEEEEEEEEECC
Confidence 45778 999999999999999998875 2344 478889999999999999996
Q ss_pred CCcceeeccc
Q 039270 108 EGYDVVLGTQ 117 (131)
Q Consensus 108 ~~~DvILG~d 117 (131)
... -|||.+
T Consensus 82 ~~~-~lLG~~ 90 (93)
T cd05481 82 EGP-PLLGAK 90 (93)
T ss_pred CCC-ceEccc
Confidence 643 345643
No 18
>cd06094 RP_Saci_like RP_Saci_like, retropepsin family. Retropepsin on retrotransposons with long terminal repeats (LTR) including Saci-1, -2 and -3 of Schistosoma mansoni. Retropepsins are related to fungal and mammalian pepsins. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified
Probab=97.73 E-value=7.7e-05 Score=51.24 Aligned_cols=61 Identities=18% Similarity=0.250 Sum_probs=46.6
Q ss_pred eeeEEEEeCCCccccccceeE-------------eee------eeeeeEEEECc-EEEEeeeEEecCCCcceeecccccc
Q 039270 61 ISPIVLVDSGSTRNFMSEQFY-------------STR------KCTNVNLILQG-VSVIVDFNLRDLEGYDVVLGTQWLR 120 (131)
Q Consensus 61 ~~v~aLIDSGsThnFIs~~~a-------------~~g------~~~~~~~~i~g-~~f~~df~vl~l~~~DvILG~dWL~ 120 (131)
-.+..|||+||.+|.|..... .+| -...+.+.++. +.|.-.|.|-+.. .-|||.|+|+
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 357899999999999987766 111 12455667775 4899999997775 4799999999
Q ss_pred cCC
Q 039270 121 TLE 123 (131)
Q Consensus 121 ~~~ 123 (131)
+|+
T Consensus 86 ~~~ 88 (89)
T cd06094 86 HYG 88 (89)
T ss_pred HcC
Confidence 986
No 19
>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=97.40 E-value=0.0011 Score=45.22 Aligned_cols=66 Identities=15% Similarity=0.093 Sum_probs=51.1
Q ss_pred EEEECCeeeEEEEeCCCccccccceeE--------------------eeeeeeeeEEEECcEEEEeeeEEecCCCcceee
Q 039270 55 NGRIGNISPIVLVDSGSTRNFMSEQFY--------------------STRKCTNVNLILQGVSVIVDFNLRDLEGYDVVL 114 (131)
Q Consensus 55 ~~~I~~~~v~aLIDSGsThnFIs~~~a--------------------~~g~~~~~~~~i~g~~f~~df~vl~l~~~DvIL 114 (131)
..+++|+.+.+|+|+||-++.|...-. -..++..+.+++.++.....+.+.+..-..-|+
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 467899999999999999999986553 111345788999999888889998873445678
Q ss_pred cccccc
Q 039270 115 GTQWLR 120 (131)
Q Consensus 115 G~dWL~ 120 (131)
|.|-|+
T Consensus 82 GRd~L~ 87 (87)
T cd05482 82 GRDILS 87 (87)
T ss_pred ccccCC
Confidence 988763
No 20
>COG3577 Predicted aspartyl protease [General function prediction only]
Probab=97.33 E-value=0.00035 Score=54.75 Aligned_cols=88 Identities=23% Similarity=0.288 Sum_probs=64.7
Q ss_pred eeeehhhhcccccCCeEEEEEEECCeeeEEEEeCCCccccccceeE------------------eeeeeeee-----EEE
Q 039270 36 LEISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------STRKCTNV-----NLI 92 (131)
Q Consensus 36 ~~iSl~Al~g~~~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------~~g~~~~~-----~~~ 92 (131)
.+++|+ ......+...+.|||+++..|||+|||.--++++-| .+|+...- +++
T Consensus 94 ~~v~La----k~~~GHF~a~~~VNGk~v~fLVDTGATsVal~~~dA~RlGid~~~l~y~~~v~TANG~~~AA~V~Ld~v~ 169 (215)
T COG3577 94 QEVSLA----KSRDGHFEANGRVNGKKVDFLVDTGATSVALNEEDARRLGIDLNSLDYTITVSTANGRARAAPVTLDRVQ 169 (215)
T ss_pred eEEEEE----ecCCCcEEEEEEECCEEEEEEEecCcceeecCHHHHHHhCCCccccCCceEEEccCCccccceEEeeeEE
Confidence 355553 234578999999999999999999999988877777 34444332 456
Q ss_pred ECcEEEE-eeeEEecCC-CcceeecccccccCCCeee
Q 039270 93 LQGVSVI-VDFNLRDLE-GYDVVLGTQWLRTLEPILW 127 (131)
Q Consensus 93 i~g~~f~-~df~vl~l~-~~DvILG~dWL~~~~pi~i 127 (131)
|++..+. .+.+|++-+ .-...|||.+|.+++-...
T Consensus 170 IG~I~~~nV~A~V~~~g~L~~sLLGMSfL~rL~~fq~ 206 (215)
T COG3577 170 IGGIRVKNVDAMVAEDGALDESLLGMSFLNRLSGFQV 206 (215)
T ss_pred EccEEEcCchhheecCCccchhhhhHHHHhhccceEe
Confidence 6777665 777888776 4567899999998876433
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=96.48 E-value=0.003 Score=46.69 Aligned_cols=21 Identities=38% Similarity=0.683 Sum_probs=19.4
Q ss_pred eeeEEEEeCCCccccccceeE
Q 039270 61 ISPIVLVDSGSTRNFMSEQFY 81 (131)
Q Consensus 61 ~~v~aLIDSGsThnFIs~~~a 81 (131)
+.+.+|+||||..|||+++++
T Consensus 11 ~~~~~LlDsGSq~SfIt~~la 31 (164)
T PF05585_consen 11 VEARALLDSGSQRSFITESLA 31 (164)
T ss_pred EEEEEEEecCCchhHHhHHHH
Confidence 467899999999999999999
No 22
>COG5550 Predicted aspartyl protease [Posttranslational modification, protein turnover, chaperones]
Probab=96.30 E-value=0.027 Score=40.94 Aligned_cols=79 Identities=18% Similarity=0.182 Sum_probs=53.7
Q ss_pred eEEEEEEE---CCeeeEEEEeCCCcc-ccccceeE---------------eeee-----eeeeEEEECcEEEEeeeEEec
Q 039270 51 TMRINGRI---GNISPIVLVDSGSTR-NFMSEQFY---------------STRK-----CTNVNLILQGVSVIVDFNLRD 106 (131)
Q Consensus 51 t~rv~~~I---~~~~v~aLIDSGsTh-nFIs~~~a---------------~~g~-----~~~~~~~i~g~~f~~df~vl~ 106 (131)
++.+.... +..-...|||+|.|. --++++++ ..|. .....++++|.+..+-..+.+
T Consensus 12 ~v~~~f~~~~~Gd~~~~~LiDTGFtg~lvlp~~vaek~~~~~~~~~~~~~a~~~~v~t~V~~~~iki~g~e~~~~Vl~s~ 91 (125)
T COG5550 12 TVPVTFRLPGQGDFVYDELIDTGFTGYLVLPPQVAEKLGLPLFSTIRIVLADGGVVKTSVALATIKIDGVEKVAFVLASD 91 (125)
T ss_pred eEEEEEEecCCCcEEeeeEEecCCceeEEeCHHHHHhcCCCccCChhhhhhcCCEEEEEEEEEEEEECCEEEEEEEEccC
Confidence 34444444 333344599999983 44555555 2222 345578889998888888888
Q ss_pred CCCcceeecccccccCCCeeeeecC
Q 039270 107 LEGYDVVLGTQWLRTLEPILWDFAS 131 (131)
Q Consensus 107 l~~~DvILG~dWL~~~~pi~idw~~ 131 (131)
....+ ++|++||+..+- .+|.++
T Consensus 92 ~~~~~-liG~~~lk~l~~-~vn~~~ 114 (125)
T COG5550 92 NLPEP-LIGVNLLKLLGL-VVNPKT 114 (125)
T ss_pred CCccc-chhhhhhhhccE-EEcCCc
Confidence 88788 899999999887 677653
No 23
>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=92.02 E-value=0.29 Score=34.81 Aligned_cols=56 Identities=25% Similarity=0.445 Sum_probs=40.2
Q ss_pred EEEEEEECCe--eeEEEEeCCCccccccceeE-----------------------eeeeeeeeEEEECcEEEEeeeEEec
Q 039270 52 MRINGRIGNI--SPIVLVDSGSTRNFMSEQFY-----------------------STRKCTNVNLILQGVSVIVDFNLRD 106 (131)
Q Consensus 52 ~rv~~~I~~~--~v~aLIDSGsThnFIs~~~a-----------------------~~g~~~~~~~~i~g~~f~~df~vl~ 106 (131)
|.+.+.+... .+..|||+||..|.|.++.+ .+.+...+.+.++|......|+|+.
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 4444444332 35689999999999999887 1223345678889999999999876
Q ss_pred C
Q 039270 107 L 107 (131)
Q Consensus 107 l 107 (131)
-
T Consensus 115 k 115 (137)
T PF12382_consen 115 K 115 (137)
T ss_pred e
Confidence 3
No 24
>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=90.34 E-value=1.9 Score=31.53 Aligned_cols=35 Identities=31% Similarity=0.556 Sum_probs=26.3
Q ss_pred eeEEEECcEEEEeeeEEecCC--Ccceeec-ccccccC
Q 039270 88 NVNLILQGVSVIVDFNLRDLE--GYDVVLG-TQWLRTL 122 (131)
Q Consensus 88 ~~~~~i~g~~f~~df~vl~l~--~~DvILG-~dWL~~~ 122 (131)
...+.++|..+.+.|-+.+=. .|.++|| -.||+..
T Consensus 87 ~~~~~lg~~~~~~e~tL~dR~~m~yp~LlGrR~~l~~~ 124 (138)
T PF05618_consen 87 ETTLCLGGKTWKIEFTLTDRSNMKYPMLLGRRNFLRGR 124 (138)
T ss_dssp EEEEEETTEEEEEEEEEE-S--SS-SEEE-HHHHHHTT
T ss_pred EEEEEECCEEEEEEEEEcCCCcCcCCEEEEehHHhcCC
Confidence 567889999999999988854 7999999 9998754
No 25
>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=89.65 E-value=1.3 Score=34.57 Aligned_cols=62 Identities=18% Similarity=0.343 Sum_probs=39.7
Q ss_pred eEEEEeCCCccccccceeEeeeeeeeeEEEEC-cEEEEee--------------eEEecC-CCcceeecccccccCCCee
Q 039270 63 PIVLVDSGSTRNFMSEQFYSTRKCTNVNLILQ-GVSVIVD--------------FNLRDL-EGYDVVLGTQWLRTLEPIL 126 (131)
Q Consensus 63 v~aLIDSGsThnFIs~~~a~~g~~~~~~~~i~-g~~f~~d--------------f~vl~l-~~~DvILG~dWL~~~~pi~ 126 (131)
..++||||++-.++.++.. +.+.+.++ +..+... +-++.. ..--.|||..||+.+-- .
T Consensus 177 ~~ai~DTGTs~~~lp~~~~-----P~i~~~f~~~~~~~i~~~~y~~~~~~~~~C~~~~~~~~~~~~ilG~~fl~~~~~-v 250 (265)
T cd05476 177 GGTIIDSGTTLTYLPDPAY-----PDLTLHFDGGADLELPPENYFVDVGEGVVCLAILSSSSGGVSILGNIQQQNFLV-E 250 (265)
T ss_pred CcEEEeCCCcceEcCcccc-----CCEEEEECCCCEEEeCcccEEEECCCCCEEEEEecCCCCCcEEEChhhcccEEE-E
Confidence 3489999999998887765 55555555 4333211 111222 23458999999998876 3
Q ss_pred eeec
Q 039270 127 WDFA 130 (131)
Q Consensus 127 idw~ 130 (131)
.|++
T Consensus 251 FD~~ 254 (265)
T cd05476 251 YDLE 254 (265)
T ss_pred EECC
Confidence 6654
No 26
>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=85.67 E-value=0.63 Score=36.62 Aligned_cols=58 Identities=17% Similarity=0.260 Sum_probs=35.2
Q ss_pred eeEEEEeCCCccccccceeE------eeee---------eeeeEEEECcEEEEeeeEEecCCCcceeecccccccCCCee
Q 039270 62 SPIVLVDSGSTRNFMSEQFY------STRK---------CTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPIL 126 (131)
Q Consensus 62 ~v~aLIDSGsThnFIs~~~a------~~g~---------~~~~~~~i~g~~f~~df~vl~l~~~DvILG~dWL~~~~pi~ 126 (131)
...++||||++-.++..+.+ ..|. ...|.-.+-...|.. ..|||-.+|+++-. .
T Consensus 198 ~~~~iiDSGTs~~~lP~~~~~~l~~~l~g~~~~~~~~~~~~~C~~~~P~i~f~~----------~~ilGd~fl~~~y~-v 266 (278)
T cd06097 198 GFSAIADTGTTLILLPDAIVEAYYSQVPGAYYDSEYGGWVFPCDTTLPDLSFAV----------FSILGDVFLKAQYV-V 266 (278)
T ss_pred CceEEeecCCchhcCCHHHHHHHHHhCcCCcccCCCCEEEEECCCCCCCEEEEE----------EEEEcchhhCceeE-E
Confidence 45699999999999887665 1011 011111111111111 57999999999887 4
Q ss_pred eeec
Q 039270 127 WDFA 130 (131)
Q Consensus 127 idw~ 130 (131)
.||.
T Consensus 267 fD~~ 270 (278)
T cd06097 267 FDVG 270 (278)
T ss_pred EcCC
Confidence 7774
No 27
>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=84.45 E-value=2.7 Score=33.62 Aligned_cols=66 Identities=18% Similarity=0.290 Sum_probs=43.8
Q ss_pred EEEEeCCCccccccceeE--------------------eee--eeeeeEEEECcEEEEeee-------------EEecC-
Q 039270 64 IVLVDSGSTRNFMSEQFY--------------------STR--KCTNVNLILQGVSVIVDF-------------NLRDL- 107 (131)
Q Consensus 64 ~aLIDSGsThnFIs~~~a--------------------~~g--~~~~~~~~i~g~~f~~df-------------~vl~l- 107 (131)
.++||||++..++..... |.. ..+.+.+.++|..+...- -+.+.
T Consensus 203 ~~iiDSGtt~~~lP~~~~~~l~~~~~~~~~~~~~~~~~C~~~~~~p~l~~~f~g~~~~v~~~~y~~~~~~~C~~~i~~~~ 282 (318)
T cd05477 203 QAIVDTGTSLLTAPQQVMSTLMQSIGAQQDQYGQYVVNCNNIQNLPTLTFTINGVSFPLPPSAYILQNNGYCTVGIEPTY 282 (318)
T ss_pred eeeECCCCccEECCHHHHHHHHHHhCCccccCCCEEEeCCccccCCcEEEEECCEEEEECHHHeEecCCCeEEEEEEecc
Confidence 589999999988887766 221 124677778887765331 11111
Q ss_pred -----CCcceeecccccccCCCeeeeec
Q 039270 108 -----EGYDVVLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 108 -----~~~DvILG~dWL~~~~pi~idw~ 130 (131)
+....|||..+|+.+-. ..|+.
T Consensus 283 ~~~~~~~~~~ilG~~fl~~~y~-vfD~~ 309 (318)
T cd05477 283 LPSQNGQPLWILGDVFLRQYYS-VYDLG 309 (318)
T ss_pred cCCCCCCceEEEcHHHhhheEE-EEeCC
Confidence 22458999999999877 46764
No 28
>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=84.21 E-value=8.3 Score=30.16 Aligned_cols=25 Identities=36% Similarity=0.513 Sum_probs=20.9
Q ss_pred EEEEEEC--CeeeEEEEeCCCcccccc
Q 039270 53 RINGRIG--NISPIVLVDSGSTRNFMS 77 (131)
Q Consensus 53 rv~~~I~--~~~v~aLIDSGsThnFIs 77 (131)
.+...|+ .+++.++||+||+..++.
T Consensus 3 ~~~v~iGtp~q~~~~~iDTGS~~~wv~ 29 (317)
T PF00026_consen 3 YINVTIGTPPQTFRVLIDTGSSDTWVP 29 (317)
T ss_dssp EEEEEETTTTEEEEEEEETTBSSEEEE
T ss_pred EEEEEECCCCeEEEEEEecccceeeec
Confidence 3567787 799999999999988876
No 29
>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=82.49 E-value=4 Score=33.09 Aligned_cols=67 Identities=13% Similarity=0.181 Sum_probs=43.5
Q ss_pred eEEEEeCCCccccccceeE--------------------eee--eeeeeEEEECcEEEEee---eE----------E---
Q 039270 63 PIVLVDSGSTRNFMSEQFY--------------------STR--KCTNVNLILQGVSVIVD---FN----------L--- 104 (131)
Q Consensus 63 v~aLIDSGsThnFIs~~~a--------------------~~g--~~~~~~~~i~g~~f~~d---f~----------v--- 104 (131)
..++||||++..++..+.. |.. ..+.+.+.+++..|... +. +
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 3699999999988877655 221 23567777777766432 11 1
Q ss_pred -ec-----CCCcceeecccccccCCCeeeeec
Q 039270 105 -RD-----LEGYDVVLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 105 -l~-----l~~~DvILG~dWL~~~~pi~idw~ 130 (131)
.. -.+...|||..+|+.+-. ..||+
T Consensus 291 ~~~~~~~~~~~~~~IlG~~fl~~~y~-vFD~~ 321 (329)
T cd05485 291 FMGIDIPPPAGPLWILGDVFIGKYYT-EFDLG 321 (329)
T ss_pred EEECcCCCCCCCeEEEchHHhccceE-EEeCC
Confidence 10 112348999999999887 47764
No 30
>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=81.47 E-value=1.3 Score=34.74 Aligned_cols=67 Identities=15% Similarity=0.454 Sum_probs=45.1
Q ss_pred eEEEEeCCCccccccceeE-------------------eeee--eeeeEEEECcEEEEee-----------------eEE
Q 039270 63 PIVLVDSGSTRNFMSEQFY-------------------STRK--CTNVNLILQGVSVIVD-----------------FNL 104 (131)
Q Consensus 63 v~aLIDSGsThnFIs~~~a-------------------~~g~--~~~~~~~i~g~~f~~d-----------------f~v 104 (131)
..++||||++..++..+.. |... .+.+.+.+++..+... +.+
T Consensus 200 ~~~~~Dtgt~~i~lp~~~~~~i~~~l~~~~~~~~~~~~c~~~~~~p~l~f~~~~~~~~i~~~~~~~~~~~~~~~~C~~~i 279 (317)
T PF00026_consen 200 QQAILDTGTSYIYLPRSIFDAIIKALGGSYSDGVYSVPCNSTDSLPDLTFTFGGVTFTIPPSDYIFKIEDGNGGYCYLGI 279 (317)
T ss_dssp EEEEEETTBSSEEEEHHHHHHHHHHHTTEEECSEEEEETTGGGGSEEEEEEETTEEEEEEHHHHEEEESSTTSSEEEESE
T ss_pred eeeecccccccccccchhhHHHHhhhcccccceeEEEecccccccceEEEeeCCEEEEecchHhcccccccccceeEeee
Confidence 5799999999988887766 2211 3556677776655321 222
Q ss_pred ec----CCCcceeecccccccCCCeeeeec
Q 039270 105 RD----LEGYDVVLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 105 l~----l~~~DvILG~dWL~~~~pi~idw~ 130 (131)
.+ -.....|||+.||+++-. ..|++
T Consensus 280 ~~~~~~~~~~~~iLG~~fl~~~y~-vfD~~ 308 (317)
T PF00026_consen 280 QPMDSSDDSDDWILGSPFLRNYYV-VFDYE 308 (317)
T ss_dssp EEESSTTSSSEEEEEHHHHTTEEE-EEETT
T ss_pred ecccccccCCceEecHHHhhceEE-EEeCC
Confidence 22 346789999999999877 46664
No 31
>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=81.41 E-value=7.3 Score=29.40 Aligned_cols=62 Identities=19% Similarity=0.282 Sum_probs=39.8
Q ss_pred ECCeeeEEEEeCCCccccccceeE-------------eee----eeeeeEEEECcEEEEeeeEEecCCCcceee----cc
Q 039270 58 IGNISPIVLVDSGSTRNFMSEQFY-------------STR----KCTNVNLILQGVSVIVDFNLRDLEGYDVVL----GT 116 (131)
Q Consensus 58 I~~~~v~aLIDSGsThnFIs~~~a-------------~~g----~~~~~~~~i~g~~f~~df~vl~l~~~DvIL----G~ 116 (131)
|.|..+.+.-||||+..+|-..|. ..| ..-=+.++++|+...+.+..-+ ||.|| -+
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 IKGTKLKGHWDSGAQITCIPESFLEEEQPIGKTLIKTIHGEKEQDVYYLTFKINGRKVEAEVIASP---YDYILISPSDI 77 (163)
T ss_dssp ETTEEEEEEE-TT-SSEEEEGGGTTT---SEEEEEE-SS-EEEEEEEEEEEEESS-EEEEEEEEES---SSSEEE-TTT-
T ss_pred CCCceeeEEecCCCeEEEccHHHhCccccccceEEEEecCceeccEEEEEEEEcCeEEEEEEecCc---cceEEEccccc
Confidence 457788899999999999988887 112 2223678889988887777666 44444 34
Q ss_pred cccccC
Q 039270 117 QWLRTL 122 (131)
Q Consensus 117 dWL~~~ 122 (131)
+|+.+.
T Consensus 78 Pw~~~~ 83 (163)
T PF03539_consen 78 PWYKKK 83 (163)
T ss_dssp HHHHS-
T ss_pred ccccCC
Confidence 787654
No 32
>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=81.06 E-value=4.3 Score=32.54 Aligned_cols=74 Identities=18% Similarity=0.230 Sum_probs=48.6
Q ss_pred EEECCeee------EEEEeCCCccccccceeE--------------------eee--eeeeeEEEECcEEEEeee-----
Q 039270 56 GRIGNISP------IVLVDSGSTRNFMSEQFY--------------------STR--KCTNVNLILQGVSVIVDF----- 102 (131)
Q Consensus 56 ~~I~~~~v------~aLIDSGsThnFIs~~~a--------------------~~g--~~~~~~~~i~g~~f~~df----- 102 (131)
..|+++.+ .++||||++..++..... |.. ..+.+.+.++|..|....
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 45676654 589999999988886655 322 235667778887765331
Q ss_pred --------EEecCC-CcceeecccccccCCCeeeeec
Q 039270 103 --------NLRDLE-GYDVVLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 103 --------~vl~l~-~~DvILG~dWL~~~~pi~idw~ 130 (131)
.+.+.+ .-..|||-.+|+.+-. ..|+.
T Consensus 274 ~~~~~C~~~~~~~~~~~~~IlG~~fl~~~y~-vfD~~ 309 (317)
T cd05478 274 QDQGSCTSGFQSMGLGELWILGDVFIRQYYS-VFDRA 309 (317)
T ss_pred cCCCEEeEEEEeCCCCCeEEechHHhcceEE-EEeCC
Confidence 122222 2458999999998877 36664
No 33
>PTZ00147 plasmepsin-1; Provisional
Probab=80.82 E-value=11 Score=32.69 Aligned_cols=25 Identities=16% Similarity=0.278 Sum_probs=21.1
Q ss_pred EEEEEEC--CeeeEEEEeCCCcccccc
Q 039270 53 RINGRIG--NISPIVLVDSGSTRNFMS 77 (131)
Q Consensus 53 rv~~~I~--~~~v~aLIDSGsThnFIs 77 (131)
.....|+ .+++.+++|+||+..++.
T Consensus 141 ~~~I~IGTP~Q~f~Vi~DTGSsdlWVp 167 (453)
T PTZ00147 141 YGEAKLGDNGQKFNFIFDTGSANLWVP 167 (453)
T ss_pred EEEEEECCCCeEEEEEEeCCCCcEEEe
Confidence 3567787 688999999999999885
No 34
>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=80.40 E-value=1.4 Score=33.77 Aligned_cols=61 Identities=18% Similarity=0.268 Sum_probs=36.5
Q ss_pred eeeEEEEeCCCccccccceeE------eeeeee--------eeEEEECcEEEEeeeEEecCCCcceeecccccccCCCee
Q 039270 61 ISPIVLVDSGSTRNFMSEQFY------STRKCT--------NVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPIL 126 (131)
Q Consensus 61 ~~v~aLIDSGsThnFIs~~~a------~~g~~~--------~~~~~i~g~~f~~df~vl~l~~~DvILG~dWL~~~~pi~ 126 (131)
....++||||++-.++...+. ....+. .+.-...--.+...| ..|||..+|+.+-. .
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 457899999999999988877 111110 000000011122222 89999999999877 4
Q ss_pred eeec
Q 039270 127 WDFA 130 (131)
Q Consensus 127 idw~ 130 (131)
.|+.
T Consensus 272 fD~~ 275 (283)
T cd05471 272 FDLD 275 (283)
T ss_pred EeCC
Confidence 6653
No 35
>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=79.45 E-value=18 Score=28.15 Aligned_cols=66 Identities=18% Similarity=0.253 Sum_probs=42.7
Q ss_pred EEEEEECC--eeeEEEEeCCCccccccceeE-------eeeeeeeeEEEECcEEEE-eeeEEec-CCCcceeecccc
Q 039270 53 RINGRIGN--ISPIVLVDSGSTRNFMSEQFY-------STRKCTNVNLILQGVSVI-VDFNLRD-LEGYDVVLGTQW 118 (131)
Q Consensus 53 rv~~~I~~--~~v~aLIDSGsThnFIs~~~a-------~~g~~~~~~~~i~g~~f~-~df~vl~-l~~~DvILG~dW 118 (131)
.++..|+. +++.+++|+||+..+|..--. ..|....=.+.+++.... ..|-+.. ....|-|||.-+
T Consensus 4 ~~~i~iGtp~q~~~v~~DTgS~~~wv~~~~~~Y~~g~~~~G~~~~D~v~~g~~~~~~~~fg~~~~~~~~~GilGLg~ 80 (295)
T cd05474 4 SAELSVGTPPQKVTVLLDTGSSDLWVPDFSISYGDGTSASGTWGTDTVSIGGATVKNLQFAVANSTSSDVGVLGIGL 80 (295)
T ss_pred EEEEEECCCCcEEEEEEeCCCCcceeeeeEEEeccCCcEEEEEEEEEEEECCeEecceEEEEEecCCCCcceeeECC
Confidence 35677777 889999999999988873222 334444445666666543 2343333 356889998765
No 36
>PTZ00013 plasmepsin 4 (PM4); Provisional
Probab=78.90 E-value=11 Score=32.54 Aligned_cols=26 Identities=19% Similarity=0.422 Sum_probs=21.0
Q ss_pred EEEEEEC--CeeeEEEEeCCCccccccc
Q 039270 53 RINGRIG--NISPIVLVDSGSTRNFMSE 78 (131)
Q Consensus 53 rv~~~I~--~~~v~aLIDSGsThnFIs~ 78 (131)
.....|+ .+++.+++|+||+.-++..
T Consensus 140 y~~i~IGTP~Q~f~vi~DTGSsdlWV~s 167 (450)
T PTZ00013 140 YGEGEVGDNHQKFMLIFDTGSANLWVPS 167 (450)
T ss_pred EEEEEECCCCeEEEEEEeCCCCceEEec
Confidence 3466776 6889999999999998853
No 37
>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=78.57 E-value=2.7 Score=33.94 Aligned_cols=68 Identities=19% Similarity=0.321 Sum_probs=42.6
Q ss_pred eeEEEEeCCCccccccceeE--eeeeeeeeEEEEC-cEEEEee-------------eEEecCCCcceeecccccccCCCe
Q 039270 62 SPIVLVDSGSTRNFMSEQFY--STRKCTNVNLILQ-GVSVIVD-------------FNLRDLEGYDVVLGTQWLRTLEPI 125 (131)
Q Consensus 62 ~v~aLIDSGsThnFIs~~~a--~~g~~~~~~~~i~-g~~f~~d-------------f~vl~l~~~DvILG~dWL~~~~pi 125 (131)
...++||||++..++.++.. .....+.+.+.++ |..+... +.......--.|||-.||+.+--
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 34589999999999998776 1222266666665 4444311 11111112247999999999877
Q ss_pred eeeec
Q 039270 126 LWDFA 130 (131)
Q Consensus 126 ~idw~ 130 (131)
..|+.
T Consensus 310 vFD~~ 314 (326)
T cd06096 310 IFDLD 314 (326)
T ss_pred EEECc
Confidence 46654
No 38
>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=77.14 E-value=4.7 Score=31.56 Aligned_cols=67 Identities=19% Similarity=0.353 Sum_probs=43.5
Q ss_pred eEEEEeCCCccccccceeE---------------------eeeee-eeeEEEECcEEEEee-------------------
Q 039270 63 PIVLVDSGSTRNFMSEQFY---------------------STRKC-TNVNLILQGVSVIVD------------------- 101 (131)
Q Consensus 63 v~aLIDSGsThnFIs~~~a---------------------~~g~~-~~~~~~i~g~~f~~d------------------- 101 (131)
..++||||++..++..+.. |...- +.+.+.++|..+...
T Consensus 179 ~~~iiDSGt~~~~lP~~~~~~l~~~~~~~~~~~~~~~~~~C~~~~~p~i~f~f~g~~~~i~~~~~~~~~~~~~~~~~~C~ 258 (295)
T cd05474 179 LPALLDSGTTLTYLPSDIVDAIAKQLGATYDSDEGLYVVDCDAKDDGSLTFNFGGATISVPLSDLVLPASTDDGGDGACY 258 (295)
T ss_pred ccEEECCCCccEeCCHHHHHHHHHHhCCEEcCCCcEEEEeCCCCCCCEEEEEECCeEEEEEHHHhEeccccCCCCCCCeE
Confidence 5789999999998887776 22111 467777787655322
Q ss_pred eEEecCCCcceeecccccccCCCeeeeec
Q 039270 102 FNLRDLEGYDVVLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 102 f~vl~l~~~DvILG~dWL~~~~pi~idw~ 130 (131)
+.+.+...-..|||..+|+.+-. ..|+.
T Consensus 259 ~~i~~~~~~~~iLG~~fl~~~y~-vfD~~ 286 (295)
T cd05474 259 LGIQPSTSDYNILGDTFLRSAYV-VYDLD 286 (295)
T ss_pred EEEEeCCCCcEEeChHHhhcEEE-EEECC
Confidence 12222222358999999998876 36653
No 39
>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=75.65 E-value=2.7 Score=28.00 Aligned_cols=25 Identities=28% Similarity=0.359 Sum_probs=20.0
Q ss_pred EEEECC--eeeEEEEeCCCccccccce
Q 039270 55 NGRIGN--ISPIVLVDSGSTRNFMSEQ 79 (131)
Q Consensus 55 ~~~I~~--~~v~aLIDSGsThnFIs~~ 79 (131)
++.|+. +++.+++|+||+..++..+
T Consensus 2 ~i~vGtP~q~~~~~~DTGSs~~Wv~~~ 28 (109)
T cd05470 2 EIGIGTPPQTFNVLLDTGSSNLWVPSV 28 (109)
T ss_pred EEEeCCCCceEEEEEeCCCCCEEEeCC
Confidence 456765 8899999999998887654
No 40
>KOG3048 consensus Molecular chaperone Prefoldin, subunit 5 [Posttranslational modification, protein turnover, chaperones]
Probab=75.61 E-value=1.1 Score=33.52 Aligned_cols=66 Identities=23% Similarity=0.438 Sum_probs=42.7
Q ss_pred CCCCcccCChHHHH---HHHhcCcccceeeehhhhcccc-------------------------cCCeEEEEEEECCeee
Q 039270 12 SSIPVRRLSRTELQ---ERCAKNSTKMLEISLRVISGAR-------------------------ASETMRINGRIGNISP 63 (131)
Q Consensus 12 ~~~~~~~~~~~e~~---~~~~~~~~~~~~iSl~Al~g~~-------------------------~~~t~rv~~~I~~~~v 63 (131)
..++.-.++++.+. +.++.+ -+..+=||++|.|.. ....|+|.|++.. +-
T Consensus 6 ~~idltkLsleQL~~lk~q~dqE-l~~lq~Sl~~L~~aq~k~~~~~~aln~~~~~~eGk~~LVPLTsSlYVPGkl~d-~~ 83 (153)
T KOG3048|consen 6 KGIDLTKLSLEQLGALKKQFDQE-LNFLQDSLNALKGAQTKYEESIAALNDVQAANEGKKLLVPLTSSLYVPGKLSD-NS 83 (153)
T ss_pred cCCChhhCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCeEEEecccceeccceecc-cc
Confidence 45677788888754 344443 233344566655542 2256888899877 67
Q ss_pred EEEEeCCCcccccccee
Q 039270 64 IVLVDSGSTRNFMSEQF 80 (131)
Q Consensus 64 ~aLIDSGsThnFIs~~~ 80 (131)
..|||.| |..||-...
T Consensus 84 k~lVDIG-TGYyVEK~~ 99 (153)
T KOG3048|consen 84 KFLVDIG-TGYYVEKDA 99 (153)
T ss_pred ceeEecc-CceEEeech
Confidence 8999999 787875543
No 41
>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=72.13 E-value=8.9 Score=30.67 Aligned_cols=67 Identities=16% Similarity=0.268 Sum_probs=41.7
Q ss_pred eEEEEeCCCccccccceeE-------------------eee--eeeeeEEEECcEEEEee---eE----------E----
Q 039270 63 PIVLVDSGSTRNFMSEQFY-------------------STR--KCTNVNLILQGVSVIVD---FN----------L---- 104 (131)
Q Consensus 63 v~aLIDSGsThnFIs~~~a-------------------~~g--~~~~~~~~i~g~~f~~d---f~----------v---- 104 (131)
..++||||++..++..+.. |.. ..+.+.+.++|..+... +. +
T Consensus 199 ~~aiiDTGTs~~~lP~~~~~~l~~~~~~~~~~~~~~~~C~~~~~~p~i~f~f~g~~~~l~~~~y~~~~~~~~~~~C~~~~ 278 (316)
T cd05486 199 CQAIVDTGTSLITGPSGDIKQLQNYIGATATDGEYGVDCSTLSLMPSVTFTINGIPYSLSPQAYTLEDQSDGGGYCSSGF 278 (316)
T ss_pred CEEEECCCcchhhcCHHHHHHHHHHhCCcccCCcEEEeccccccCCCEEEEECCEEEEeCHHHeEEecccCCCCEEeeEE
Confidence 3599999999888776543 332 23567777888765431 11 1
Q ss_pred ecC-----CCcceeecccccccCCCeeeeec
Q 039270 105 RDL-----EGYDVVLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 105 l~l-----~~~DvILG~dWL~~~~pi~idw~ 130 (131)
..+ .+-..|||-.+|+++-. ..|+.
T Consensus 279 ~~~~~~~~~~~~~ILGd~flr~~y~-vfD~~ 308 (316)
T cd05486 279 QGLDIPPPAGPLWILGDVFIRQYYS-VFDRG 308 (316)
T ss_pred EECCCCCCCCCeEEEchHHhcceEE-EEeCC
Confidence 111 12237999999998877 36654
No 42
>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=71.67 E-value=11 Score=30.16 Aligned_cols=67 Identities=16% Similarity=0.282 Sum_probs=43.8
Q ss_pred eEEEEeCCCccccccceeE--------eee--eeeeeEEEECcEEEEeee--EEe-----------------cC---CCc
Q 039270 63 PIVLVDSGSTRNFMSEQFY--------STR--KCTNVNLILQGVSVIVDF--NLR-----------------DL---EGY 110 (131)
Q Consensus 63 v~aLIDSGsThnFIs~~~a--------~~g--~~~~~~~~i~g~~f~~df--~vl-----------------~l---~~~ 110 (131)
..++||||++..++..+++ |.. ..+.+.+.++|..+.... +++ +. .+-
T Consensus 211 ~~aivDTGTs~~~lP~~~~~~i~~~~~C~~~~~~P~i~f~f~g~~~~l~~~~yi~~~~~~~~~~C~~~~~~~~~~~~~~~ 290 (317)
T cd06098 211 CAAIADSGTSLLAGPTTIVTQINSAVDCNSLSSMPNVSFTIGGKTFELTPEQYILKVGEGAAAQCISGFTALDVPPPRGP 290 (317)
T ss_pred cEEEEecCCcceeCCHHHHHhhhccCCccccccCCcEEEEECCEEEEEChHHeEEeecCCCCCEEeceEEECCCCCCCCC
Confidence 3589999999888877655 543 356777888877654421 111 11 122
Q ss_pred ceeecccccccCCCeeeeec
Q 039270 111 DVVLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 111 DvILG~dWL~~~~pi~idw~ 130 (131)
..|||-.+|+.+-.+ .|+.
T Consensus 291 ~~IlGd~Flr~~y~V-fD~~ 309 (317)
T cd06098 291 LWILGDVFMGAYHTV-FDYG 309 (317)
T ss_pred eEEechHHhcccEEE-EeCC
Confidence 469999999988773 6653
No 43
>COG4067 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]
Probab=68.45 E-value=17 Score=27.50 Aligned_cols=37 Identities=32% Similarity=0.539 Sum_probs=30.5
Q ss_pred eeEEEECcEEEEeeeEEecCC--CcceeecccccccCCC
Q 039270 88 NVNLILQGVSVIVDFNLRDLE--GYDVVLGTQWLRTLEP 124 (131)
Q Consensus 88 ~~~~~i~g~~f~~df~vl~l~--~~DvILG~dWL~~~~p 124 (131)
.+.+.++|....+.|-+.+=. .|.++||--.|+...-
T Consensus 111 ~~~l~lG~~~~~~E~tLtDR~~m~Yp~LlGrk~l~~~~~ 149 (162)
T COG4067 111 RLTLCLGGRILPIEFTLTDRSNMRYPVLLGRKALRHFGA 149 (162)
T ss_pred EEEEeeCCeeeeEEEEeecccccccceEecHHHHhhCCe
Confidence 457778899888888888854 7999999999998555
No 44
>PTZ00147 plasmepsin-1; Provisional
Probab=67.64 E-value=19 Score=31.09 Aligned_cols=68 Identities=21% Similarity=0.365 Sum_probs=41.9
Q ss_pred eeEEEEeCCCccccccceeE---------------------ee-eeeeeeEEEECcEEEEee---------------e--
Q 039270 62 SPIVLVDSGSTRNFMSEQFY---------------------ST-RKCTNVNLILQGVSVIVD---------------F-- 102 (131)
Q Consensus 62 ~v~aLIDSGsThnFIs~~~a---------------------~~-g~~~~~~~~i~g~~f~~d---------------f-- 102 (131)
...++||||.+..++..+.. |. ...+.+.+.++|..+... +
T Consensus 332 ~~~aIiDSGTsli~lP~~~~~ai~~~l~~~~~~~~~~y~~~C~~~~lP~~~f~f~g~~~~L~p~~yi~~~~~~~~~~C~~ 411 (453)
T PTZ00147 332 KANVIVDSGTSVITVPTEFLNKFVESLDVFKVPFLPLYVTTCNNTKLPTLEFRSPNKVYTLEPEYYLQPIEDIGSALCML 411 (453)
T ss_pred ceeEEECCCCchhcCCHHHHHHHHHHhCCeecCCCCeEEEeCCCCCCCeEEEEECCEEEEECHHHheeccccCCCcEEEE
Confidence 35699999999988877655 22 122456666666654311 1
Q ss_pred EEec--CCCcceeecccccccCCCeeeeec
Q 039270 103 NLRD--LEGYDVVLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 103 ~vl~--l~~~DvILG~dWL~~~~pi~idw~ 130 (131)
-+.+ ...-..|||-.+|+++-. ..|+.
T Consensus 412 ~i~~~~~~~~~~ILGd~FLr~~Yt-VFD~~ 440 (453)
T PTZ00147 412 NIIPIDLEKNTFILGDPFMRKYFT-VFDYD 440 (453)
T ss_pred EEEECCCCCCCEEECHHHhccEEE-EEECC
Confidence 1222 222347999999998877 36653
No 45
>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=65.75 E-value=29 Score=26.98 Aligned_cols=65 Identities=22% Similarity=0.275 Sum_probs=38.4
Q ss_pred EEEEEC--CeeeEEEEeCCCccccccc-eeE--------eeeeeeeeEEEECcE--EE-EeeeEEec------CCCccee
Q 039270 54 INGRIG--NISPIVLVDSGSTRNFMSE-QFY--------STRKCTNVNLILQGV--SV-IVDFNLRD------LEGYDVV 113 (131)
Q Consensus 54 v~~~I~--~~~v~aLIDSGsThnFIs~-~~a--------~~g~~~~~~~~i~g~--~f-~~df~vl~------l~~~DvI 113 (131)
+...|+ .+++.+++|+||++.++.. .+. +.|....=.+.+++. .. ...|-+.. ...+|-|
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 455666 5788999999999988852 111 334444345566655 21 12232222 2358899
Q ss_pred ecccc
Q 039270 114 LGTQW 118 (131)
Q Consensus 114 LG~dW 118 (131)
||+-+
T Consensus 84 lGLg~ 88 (265)
T cd05476 84 LGLGR 88 (265)
T ss_pred EECCC
Confidence 99865
No 46
>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=64.28 E-value=16 Score=29.36 Aligned_cols=67 Identities=12% Similarity=0.298 Sum_probs=42.6
Q ss_pred eEEEEeCCCccccccceeE--------------------eee--eeeeeEEEECcEEEEeee-------------EEec-
Q 039270 63 PIVLVDSGSTRNFMSEQFY--------------------STR--KCTNVNLILQGVSVIVDF-------------NLRD- 106 (131)
Q Consensus 63 v~aLIDSGsThnFIs~~~a--------------------~~g--~~~~~~~~i~g~~f~~df-------------~vl~- 106 (131)
..++||||+|-.++..+++ |.. ..+.+.+.++|..+...- .+..
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 4689999999998877765 221 124577778877664321 1111
Q ss_pred -C---CCcceeecccccccCCCeeeeec
Q 039270 107 -L---EGYDVVLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 107 -l---~~~DvILG~dWL~~~~pi~idw~ 130 (131)
+ .+...|||..+|+.+-. ..|+.
T Consensus 286 ~~~~~~~~~~ilG~~fl~~~y~-vfD~~ 312 (320)
T cd05488 286 DFPEPVGPLAIVGDAFLRKYYS-VYDLG 312 (320)
T ss_pred cCCCCCCCeEEEchHHhhheEE-EEeCC
Confidence 1 12358999999988766 36653
No 47
>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=62.78 E-value=46 Score=27.21 Aligned_cols=27 Identities=30% Similarity=0.305 Sum_probs=21.0
Q ss_pred EEEEEEC--CeeeEEEEeCCCccccccce
Q 039270 53 RINGRIG--NISPIVLVDSGSTRNFMSEQ 79 (131)
Q Consensus 53 rv~~~I~--~~~v~aLIDSGsThnFIs~~ 79 (131)
.+...|+ .+++.+++|+||+.-++...
T Consensus 5 ~~~i~iGtP~Q~~~v~~DTGSs~lWv~~~ 33 (364)
T cd05473 5 YIEMLIGTPPQKLNILVDTGSSNFAVAAA 33 (364)
T ss_pred EEEEEecCCCceEEEEEecCCcceEEEcC
Confidence 3566676 47899999999998887543
No 48
>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=61.63 E-value=45 Score=26.58 Aligned_cols=24 Identities=25% Similarity=0.300 Sum_probs=19.0
Q ss_pred EEEEEC--CeeeEEEEeCCCcccccc
Q 039270 54 INGRIG--NISPIVLVDSGSTRNFMS 77 (131)
Q Consensus 54 v~~~I~--~~~v~aLIDSGsThnFIs 77 (131)
.+..|+ .+++.+++|+||+.-++.
T Consensus 3 ~~i~iGtP~Q~~~v~~DTGSs~~Wv~ 28 (316)
T cd05486 3 GQISIGTPPQNFTVIFDTGSSNLWVP 28 (316)
T ss_pred EEEEECCCCcEEEEEEcCCCccEEEe
Confidence 345566 478899999999998885
No 49
>PTZ00013 plasmepsin 4 (PM4); Provisional
Probab=60.26 E-value=14 Score=32.01 Aligned_cols=68 Identities=16% Similarity=0.369 Sum_probs=42.2
Q ss_pred eeEEEEeCCCccccccceeE---------------------ee-eeeeeeEEEECcEEEEee-----------------e
Q 039270 62 SPIVLVDSGSTRNFMSEQFY---------------------ST-RKCTNVNLILQGVSVIVD-----------------F 102 (131)
Q Consensus 62 ~v~aLIDSGsThnFIs~~~a---------------------~~-g~~~~~~~~i~g~~f~~d-----------------f 102 (131)
...++||||+|..++..+.+ |. ...+.+.+.++|..+... +
T Consensus 331 ~~~aIlDSGTSli~lP~~~~~~i~~~l~~~~~~~~~~y~~~C~~~~lP~i~F~~~g~~~~L~p~~Yi~~~~~~~~~~C~~ 410 (450)
T PTZ00013 331 KANVIVDSGTTTITAPSEFLNKFFANLNVIKVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYMNPLLDVDDTLCMI 410 (450)
T ss_pred ccceEECCCCccccCCHHHHHHHHHHhCCeecCCCCeEEeecCCCCCCeEEEEECCEEEEECHHHheehhccCCCCeeEE
Confidence 34599999999999887655 21 112456666777554321 1
Q ss_pred EEecC--CCcceeecccccccCCCeeeeec
Q 039270 103 NLRDL--EGYDVVLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 103 ~vl~l--~~~DvILG~dWL~~~~pi~idw~ 130 (131)
.+.+. ++-..|||-.||+++-. ..|+.
T Consensus 411 ~i~~~~~~~~~~ILGd~FLr~~Y~-VFD~~ 439 (450)
T PTZ00013 411 TMLPVDIDDNTFILGDPFMRKYFT-VFDYD 439 (450)
T ss_pred EEEECCCCCCCEEECHHHhccEEE-EEECC
Confidence 22222 22347999999998877 36653
No 50
>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=58.45 E-value=11 Score=29.51 Aligned_cols=25 Identities=20% Similarity=0.254 Sum_probs=20.5
Q ss_pred EEEEECC--eeeEEEEeCCCccccccc
Q 039270 54 INGRIGN--ISPIVLVDSGSTRNFMSE 78 (131)
Q Consensus 54 v~~~I~~--~~v~aLIDSGsThnFIs~ 78 (131)
+...|+. +++.+++|+||+.-++..
T Consensus 3 ~~i~vGtP~Q~~~v~~DTGS~~~wv~~ 29 (278)
T cd06097 3 TPVKIGTPPQTLNLDLDTGSSDLWVFS 29 (278)
T ss_pred eeEEECCCCcEEEEEEeCCCCceeEee
Confidence 4567777 889999999999988853
No 51
>COG2383 Uncharacterized conserved protein [Function unknown]
Probab=54.09 E-value=2.3 Score=30.02 Aligned_cols=18 Identities=22% Similarity=0.470 Sum_probs=16.3
Q ss_pred eecccccccCCCeeeeec
Q 039270 113 VLGTQWLRTLEPILWDFA 130 (131)
Q Consensus 113 ILG~dWL~~~~pi~idw~ 130 (131)
||+..||.+++-|.|||.
T Consensus 51 ilsl~~La~~GVItin~~ 68 (109)
T COG2383 51 ILSLFWLAQYGVITINWE 68 (109)
T ss_pred HHHHHHHHHcCeEEEcHH
Confidence 677899999999999995
No 52
>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=46.57 E-value=23 Score=28.50 Aligned_cols=26 Identities=23% Similarity=0.220 Sum_probs=21.3
Q ss_pred EEEEEEEC--CeeeEEEEeCCCcccccc
Q 039270 52 MRINGRIG--NISPIVLVDSGSTRNFMS 77 (131)
Q Consensus 52 ~rv~~~I~--~~~v~aLIDSGsThnFIs 77 (131)
-.+...|+ .+++.+++|+||+..+|.
T Consensus 9 y~~~i~iGtP~q~~~v~~DTGSs~~Wv~ 36 (326)
T cd05487 9 YYGEIGIGTPPQTFKVVFDTGSSNLWVP 36 (326)
T ss_pred EEEEEEECCCCcEEEEEEeCCccceEEc
Confidence 34567777 688999999999999995
No 53
>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=45.31 E-value=25 Score=28.12 Aligned_cols=25 Identities=24% Similarity=0.270 Sum_probs=20.5
Q ss_pred EEEEEECC--eeeEEEEeCCCcccccc
Q 039270 53 RINGRIGN--ISPIVLVDSGSTRNFMS 77 (131)
Q Consensus 53 rv~~~I~~--~~v~aLIDSGsThnFIs 77 (131)
.++..|+. +++.+++|+||+..++.
T Consensus 8 ~~~i~iGtP~q~~~v~~DTGSs~~Wv~ 34 (325)
T cd05490 8 YGEIGIGTPPQTFTVVFDTGSSNLWVP 34 (325)
T ss_pred EEEEEECCCCcEEEEEEeCCCccEEEE
Confidence 45677775 78999999999998884
No 54
>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=44.97 E-value=25 Score=28.15 Aligned_cols=27 Identities=22% Similarity=0.210 Sum_probs=21.4
Q ss_pred EEEEEEEC--CeeeEEEEeCCCccccccc
Q 039270 52 MRINGRIG--NISPIVLVDSGSTRNFMSE 78 (131)
Q Consensus 52 ~rv~~~I~--~~~v~aLIDSGsThnFIs~ 78 (131)
-.+...|+ .+++.+++|+||+.-++..
T Consensus 11 Y~~~i~iGtP~Q~~~v~~DTGSs~lWv~~ 39 (317)
T cd06098 11 YFGEIGIGTPPQKFTVIFDTGSSNLWVPS 39 (317)
T ss_pred EEEEEEECCCCeEEEEEECCCccceEEec
Confidence 34567787 5889999999999888754
No 55
>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=39.74 E-value=35 Score=27.22 Aligned_cols=25 Identities=28% Similarity=0.373 Sum_probs=20.5
Q ss_pred EEEEECC--eeeEEEEeCCCccccccc
Q 039270 54 INGRIGN--ISPIVLVDSGSTRNFMSE 78 (131)
Q Consensus 54 v~~~I~~--~~v~aLIDSGsThnFIs~ 78 (131)
.+..|+. +++.++||+||+.-++..
T Consensus 6 ~~i~iGtP~q~~~v~~DTGS~~~wv~~ 32 (318)
T cd05477 6 GEISIGTPPQNFLVLFDTGSSNLWVPS 32 (318)
T ss_pred EEEEECCCCcEEEEEEeCCCccEEEcc
Confidence 4566775 889999999999998864
No 56
>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=39.10 E-value=37 Score=27.28 Aligned_cols=26 Identities=23% Similarity=0.221 Sum_probs=20.3
Q ss_pred EEEEEEC--CeeeEEEEeCCCccccccc
Q 039270 53 RINGRIG--NISPIVLVDSGSTRNFMSE 78 (131)
Q Consensus 53 rv~~~I~--~~~v~aLIDSGsThnFIs~ 78 (131)
.+...|+ .+++.+++|+||+..++..
T Consensus 5 ~~~i~vGtP~Q~~~v~~DTGS~~~wv~~ 32 (326)
T cd06096 5 FIDIFIGNPPQKQSLILDTGSSSLSFPC 32 (326)
T ss_pred EEEEEecCCCeEEEEEEeCCCCceEEec
Confidence 3566676 4888999999999888754
No 57
>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=39.00 E-value=32 Score=27.11 Aligned_cols=24 Identities=25% Similarity=0.473 Sum_probs=19.3
Q ss_pred EEEEEC--CeeeEEEEeCCCcccccc
Q 039270 54 INGRIG--NISPIVLVDSGSTRNFMS 77 (131)
Q Consensus 54 v~~~I~--~~~v~aLIDSGsThnFIs 77 (131)
+...|+ .+++.+++|+||+..++.
T Consensus 4 ~~i~iGtP~q~~~v~~DTGSs~~Wv~ 29 (299)
T cd05472 4 VTVGLGTPARDQTVIVDTGSDLTWVQ 29 (299)
T ss_pred EEEecCCCCcceEEEecCCCCccccc
Confidence 455666 478999999999999884
No 58
>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=38.59 E-value=36 Score=27.24 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=21.7
Q ss_pred EEEEEEECC--eeeEEEEeCCCccccccc
Q 039270 52 MRINGRIGN--ISPIVLVDSGSTRNFMSE 78 (131)
Q Consensus 52 ~rv~~~I~~--~~v~aLIDSGsThnFIs~ 78 (131)
......|+. +++.+++|+||+.-+|..
T Consensus 11 Y~~~i~iGtp~q~~~v~~DTGSs~~wv~~ 39 (320)
T cd05488 11 YFTDITLGTPPQKFKVILDTGSSNLWVPS 39 (320)
T ss_pred EEEEEEECCCCcEEEEEEecCCcceEEEc
Confidence 456777874 889999999999888843
No 59
>KOG4584 consensus Uncharacterized conserved protein [General function prediction only]
Probab=38.15 E-value=21 Score=30.01 Aligned_cols=22 Identities=32% Similarity=0.530 Sum_probs=18.1
Q ss_pred cEEEEeeeEEecCCCcceeecc
Q 039270 95 GVSVIVDFNLRDLEGYDVVLGT 116 (131)
Q Consensus 95 g~~f~~df~vl~l~~~DvILG~ 116 (131)
+.+++.-+.-.+..|+|+|||+
T Consensus 196 ~~p~K~~lif~DNSG~DvILGi 217 (348)
T KOG4584|consen 196 GKPHKCALIFVDNSGFDVILGI 217 (348)
T ss_pred CCCcceEEEEecCCCcceeeee
Confidence 4566777777888999999998
No 60
>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=37.86 E-value=36 Score=26.64 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=20.5
Q ss_pred EEEEEEC--CeeeEEEEeCCCccccccc
Q 039270 53 RINGRIG--NISPIVLVDSGSTRNFMSE 78 (131)
Q Consensus 53 rv~~~I~--~~~v~aLIDSGsThnFIs~ 78 (131)
.+...|+ .+++.+++|+||++-++..
T Consensus 4 ~~~i~iGtP~q~~~v~~DTGS~~~Wv~c 31 (273)
T cd05475 4 YVTINIGNPPKPYFLDIDTGSDLTWLQC 31 (273)
T ss_pred EEEEEcCCCCeeEEEEEccCCCceEEeC
Confidence 3455666 5788999999999999853
No 61
>PF13352 DUF4100: Protein of unknown function (DUF4100)
Probab=37.78 E-value=26 Score=27.65 Aligned_cols=22 Identities=32% Similarity=0.440 Sum_probs=18.3
Q ss_pred CeEEEEEEECC--eeeEEEEeCCC
Q 039270 50 ETMRINGRIGN--ISPIVLVDSGS 71 (131)
Q Consensus 50 ~t~rv~~~I~~--~~v~aLIDSGs 71 (131)
.|..+.+++++ .|++||||-||
T Consensus 188 atte~lVk~gd~~epivalvdhgs 211 (212)
T PF13352_consen 188 ATTETLVKVGDIEEPIVALVDHGS 211 (212)
T ss_pred hhhccEEEecccccceEEEecCCC
Confidence 46777888877 58999999997
No 62
>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=37.35 E-value=39 Score=26.95 Aligned_cols=26 Identities=23% Similarity=0.249 Sum_probs=20.8
Q ss_pred EEEEEEC--CeeeEEEEeCCCccccccc
Q 039270 53 RINGRIG--NISPIVLVDSGSTRNFMSE 78 (131)
Q Consensus 53 rv~~~I~--~~~v~aLIDSGsThnFIs~ 78 (131)
.....|+ .+++.+++|+||+..++..
T Consensus 12 ~~~i~vGtp~q~~~v~~DTGS~~~wv~~ 39 (317)
T cd05478 12 YGTISIGTPPQDFTVIFDTGSSNLWVPS 39 (317)
T ss_pred EEEEEeCCCCcEEEEEEeCCCccEEEec
Confidence 3566777 4789999999999998853
No 63
>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=34.58 E-value=49 Score=25.17 Aligned_cols=26 Identities=23% Similarity=0.245 Sum_probs=19.3
Q ss_pred EEEEECC--eeeEEEEeCCCccccccce
Q 039270 54 INGRIGN--ISPIVLVDSGSTRNFMSEQ 79 (131)
Q Consensus 54 v~~~I~~--~~v~aLIDSGsThnFIs~~ 79 (131)
+...|+. +++.+++|+||+..++...
T Consensus 3 ~~i~iGtp~q~~~l~~DTGS~~~wv~~~ 30 (283)
T cd05471 3 GEITIGTPPQKFSVIFDTGSSLLWVPSS 30 (283)
T ss_pred EEEEECCCCcEEEEEEeCCCCCEEEecC
Confidence 3455655 5889999999998877544
No 64
>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=34.13 E-value=46 Score=26.84 Aligned_cols=27 Identities=26% Similarity=0.194 Sum_probs=21.7
Q ss_pred EEEEEEEC--CeeeEEEEeCCCccccccc
Q 039270 52 MRINGRIG--NISPIVLVDSGSTRNFMSE 78 (131)
Q Consensus 52 ~rv~~~I~--~~~v~aLIDSGsThnFIs~ 78 (131)
-.+...|+ .+++.+++|+||+.-++..
T Consensus 12 Y~~~i~vGtP~q~~~v~~DTGSs~~Wv~~ 40 (329)
T cd05485 12 YYGVITIGTPPQSFKVVFDTGSSNLWVPS 40 (329)
T ss_pred EEEEEEECCCCcEEEEEEcCCCccEEEec
Confidence 44577787 4889999999999888764
No 65
>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=31.07 E-value=76 Score=25.50 Aligned_cols=24 Identities=21% Similarity=0.230 Sum_probs=17.8
Q ss_pred CeEEEEEEECCee--eEEEEeCCCcc
Q 039270 50 ETMRINGRIGNIS--PIVLVDSGSTR 73 (131)
Q Consensus 50 ~t~rv~~~I~~~~--v~aLIDSGsTh 73 (131)
....++..++++. +.+|+|||...
T Consensus 156 ~~~~v~i~~~~~~~~~~allDTGN~L 181 (293)
T PF03419_consen 156 YLYPVTIEIGGKKIELKALLDTGNQL 181 (293)
T ss_pred EEEEEEEEECCEEEEEEEEEECCCcc
Confidence 3456777788864 68999999754
No 66
>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=26.93 E-value=91 Score=25.27 Aligned_cols=24 Identities=8% Similarity=0.098 Sum_probs=17.7
Q ss_pred CeEEEEEEECCee--eEEEEeCCCcc
Q 039270 50 ETMRINGRIGNIS--PIVLVDSGSTR 73 (131)
Q Consensus 50 ~t~rv~~~I~~~~--v~aLIDSGsTh 73 (131)
....++..++|+. +.+|+|||...
T Consensus 157 ~~~~v~i~~~g~~~~~~alvDTGN~L 182 (288)
T TIGR02854 157 QIYELEICLDGKKVTIKGFLDTGNQL 182 (288)
T ss_pred eEEEEEEEECCEEEEEEEEEecCCcc
Confidence 4556777788864 68999999754
No 67
>PF14543 TAXi_N: Xylanase inhibitor N-terminal; PDB: 3HD8_A 3VLB_A 3VLA_A 3AUP_D 1T6G_A 1T6E_X 2B42_A.
Probab=25.24 E-value=87 Score=22.81 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=18.3
Q ss_pred EEEEECC--eeeEEEEeCCCccccccc
Q 039270 54 INGRIGN--ISPIVLVDSGSTRNFMSE 78 (131)
Q Consensus 54 v~~~I~~--~~v~aLIDSGsThnFIs~ 78 (131)
++..|+. +++.+.||+|+...++.-
T Consensus 3 ~~~~iGtP~~~~~lvvDtgs~l~W~~C 29 (164)
T PF14543_consen 3 VSVSIGTPPQPFSLVVDTGSDLTWVQC 29 (164)
T ss_dssp EEEECTCTTEEEEEEEETT-SSEEEET
T ss_pred EEEEeCCCCceEEEEEECCCCceEEcC
Confidence 4556655 688999999999888644
No 68
>PTZ00165 aspartyl protease; Provisional
Probab=24.14 E-value=86 Score=27.36 Aligned_cols=27 Identities=22% Similarity=0.315 Sum_probs=21.7
Q ss_pred EEEEEEECC--eeeEEEEeCCCccccccc
Q 039270 52 MRINGRIGN--ISPIVLVDSGSTRNFMSE 78 (131)
Q Consensus 52 ~rv~~~I~~--~~v~aLIDSGsThnFIs~ 78 (131)
-.....|+. +++.+++|+||+.-++..
T Consensus 121 Y~~~I~IGTPpQ~f~Vv~DTGSS~lWVps 149 (482)
T PTZ00165 121 YFGEIQVGTPPKSFVVVFDTGSSNLWIPS 149 (482)
T ss_pred EEEEEEeCCCCceEEEEEeCCCCCEEEEc
Confidence 345677877 889999999999988853
No 69
>COG1490 Dtd D-Tyr-tRNAtyr deacylase [Translation, ribosomal structure and biogenesis]
Probab=23.47 E-value=1.3e+02 Score=22.35 Aligned_cols=12 Identities=25% Similarity=0.418 Sum_probs=10.5
Q ss_pred ECCeeeEEEEeC
Q 039270 58 IGNISPIVLVDS 69 (131)
Q Consensus 58 I~~~~v~aLIDS 69 (131)
+|.-|+++++||
T Consensus 134 vNdGPVTi~lds 145 (145)
T COG1490 134 VNDGPVTILLDS 145 (145)
T ss_pred ecCCCeEEEEeC
Confidence 678899999996
No 70
>KOG3217 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=20.88 E-value=37 Score=25.61 Aligned_cols=13 Identities=23% Similarity=0.583 Sum_probs=10.7
Q ss_pred ecCCCcceeeccc
Q 039270 105 RDLEGYDVVLGTQ 117 (131)
Q Consensus 105 l~l~~~DvILG~d 117 (131)
=++..||.|||||
T Consensus 81 ~DF~~FDYI~~MD 93 (159)
T KOG3217|consen 81 SDFREFDYILAMD 93 (159)
T ss_pred hHhhhcceeEEec
Confidence 3567899999997
Done!