Citrus Sinensis ID: 043220

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-
Protein Sequence
FSVTDEIHNNETREVANIEGNEKKENSRSLFQVKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKSPDVALDVKWSEQIGSIMRGWKKDEN
Secondary Structure (PSIPRED)
cccccccccccHHHccccccccccccEEEEEcccccccccEEEEEEEEccEEEEEEEEcccccccHHHHHHHHccccccccccEEEEEEcccEEEcccEEEcEEEccccccEEEEEEEccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEccccccccccccHHHHcccccccEEEEEEEEcccEEEEEEEccccHHHHHHHHHHHccccccccccEEEEEEcccccccHHHHHHHHHHHHHccEEEccccccc
Coil and Loop (DISEMBL)
fsvtdeihnnetrevaniegnekkensRSLFQVKCGQLRKFCVVATKIRFHEVVILISsgstanfvsdkvaallplpmmptkpfsvriangahlkspdvaldvkWSEQIGSIMRGWKKDEN
Flexible Loop (DISEMBL)
fsvtdeihnnetrevaniegnekkensrsLFQVKCGQLRKFCVVATKIRFHEVVILissgstanfVSDKVAALLPLPMMPTKPFSVRIANGAHlkspdvaldvkwseqigsimrgwkkden
Low Complexity Region (SEG)
FSVTDEIHNNETREVANIEGNEKKENSRSLFQVKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKSPDVALDVKWSEQIGSIMRGWKKDEN
Disordered region (IsUnstruct)
*****************************LFQVKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKSPDVALDVKWSEQIGSIMR*******
Disordered Region (DISOPRED)
*SVT***********************RSLFQVKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKSPDVALDVKWSEQIGSIMRGWKKD**
Disordered Region (DISEMBL)
FSVTDEIHNNETREVANIEGNEKKENSRSLFQVKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKSPDVALDVKWSEQIGSIMRGWKKDEN
Disordered Region (DISPRO)
**********************KKENSRSLFQVKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKSPDVALDVKWSEQIGSIMRGWK****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
FSVTDEIHNNETREVANIEGNEKKENSRSLFQVKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKSPDVALDVKWSEQIGSIMRGWKKDEN
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	121
147838975	566	hypothetical protein VITISV_042364 [Viti	0.809	0.173	0.384	3e-14
147842329	522	hypothetical protein VITISV_041623 [Viti	0.619	0.143	0.431	3e-13
147784790	793	hypothetical protein VITISV_035856 [Viti	0.809	0.123	0.368	6e-13
147860462	1384	hypothetical protein VITISV_014148 [Viti	0.619	0.054	0.411	1e-12
147770944	617	hypothetical protein VITISV_013569 [Viti	0.801	0.157	0.370	5e-12
147775005	1122	hypothetical protein VITISV_013478 [Viti	0.619	0.066	0.401	5e-12
147860532	1241	hypothetical protein VITISV_034528 [Viti	0.619	0.060	0.392	1e-11
147786921	361	hypothetical protein VITISV_011230 [Viti	0.429	0.144	0.653	2e-11
147861322	499	hypothetical protein VITISV_031193 [Viti	0.776	0.188	0.38	4e-11
147772855	1308	hypothetical protein VITISV_003711 [Viti	0.900	0.083	0.328	2e-10

>gi|147838975|emb|CAN68101.1| hypothetical protein VITISV_042364 [Vitis vinifera]

 Score = 82.4 bits (202), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 48/125 (38%), Positives = 66/125 (52%), Gaps = 27/125 (21%)

Query: 21  NEKKENSRSLFQVKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMP 80
           NE+ E   S   +      K   + TKI  HEVV+LI SGST NF+S+KVA +L LP++P
Sbjct: 301 NEQTEPXISFHALTGWSTPKTMRITTKIAQHEVVVLIDSGSTHNFISEKVAYMLHLPVVP 360

Query: 81  TKPFSVRIANGAHLKSP---------------------------DVALDVKWSEQIGSIM 113
           TKPF+V++ANG  LK                             D+ L V+W EQ+G+++
Sbjct: 361 TKPFTVKVANGTPLKCQWRFEHVHVILQGIPFSLTLYSLPLTXLDLVLGVQWLEQLGTVV 420

Query: 114 RGWKK 118
             WKK
Sbjct: 421 CNWKK 425

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147842329|emb|CAN76208.1| hypothetical protein VITISV_041623 [Vitis vinifera]

 Score = 79.3 bits (194), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 44/102 (43%), Positives = 56/102 (54%), Gaps = 27/102 (26%)

Query: 44  VATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKSP------ 97
           V  KI  H+VV+LI SGST NF+SDKV ALL LP++PT PF VR+ANG  LK        
Sbjct: 322 VTAKIGTHDVVVLIDSGSTHNFISDKVVALLHLPVVPTAPFHVRVANGQPLKCQGRFDNI 381

Query: 98  ---------------------DVALDVKWSEQIGSIMRGWKK 118
                                D+ L V+W EQ+GS++  WK+
Sbjct: 382 HILLQGIPFSITFYSLPLNGLDLVLGVQWLEQLGSVVCDWKQ 423

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147784790|emb|CAN75225.1| hypothetical protein VITISV_035856 [Vitis vinifera]

 Score = 78.2 bits (191), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 46/125 (36%), Positives = 64/125 (51%), Gaps = 27/125 (21%)

Query: 21  NEKKENSRSLFQVKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMP 80
           NE+ E   S   +      K   +  KI  HEVV+LI SGST NF+S+KVA +L LP++P
Sbjct: 283 NEQIEPEISFHALTGWSTPKTMRITAKIGQHEVVVLIDSGSTHNFISEKVADMLHLPVVP 342

Query: 81  TKPFSVRIANGAHLKSP---------------------------DVALDVKWSEQIGSIM 113
           TKPF+V++ NG  LK                             D+ L V+W EQ+G+++
Sbjct: 343 TKPFTVKVVNGTPLKCQGRFEHVHVILQGIPFSLTLYSLPLTGLDLVLGVQWLEQLGTVV 402

Query: 114 RGWKK 118
             WKK
Sbjct: 403 CNWKK 407

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860462|emb|CAN82562.1| hypothetical protein VITISV_014148 [Vitis vinifera]

 Score = 77.4 bits (189), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/102 (41%), Positives = 56/102 (54%), Gaps = 27/102 (26%)

Query: 44  VATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKSP------ 97
           + TKI  HEVV+LI SGST NF+S+KV  +L LP +PT PF+V++ANG  LK        
Sbjct: 414 ITTKIGQHEVVVLIDSGSTHNFISEKVVDMLHLPXVPTDPFTVKVANGTPLKCQGRFEHV 473

Query: 98  ---------------------DVALDVKWSEQIGSIMRGWKK 118
                                D+ L V+W EQ+G+I+  WKK
Sbjct: 474 HVILQGIPFSLTLYSLPLTGLDLVLGVQWLEQLGTIVCNWKK 515

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147770944|emb|CAN69535.1| hypothetical protein VITISV_013569 [Vitis vinifera]

 Score = 75.1 bits (183), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 46/124 (37%), Positives = 63/124 (50%), Gaps = 27/124 (21%)

Query: 22  EKKENSRSLFQVKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPT 81
           E K +  S  ++    L  +    TKI  H++V+ I SGST NF+SDKVAALL L ++PT
Sbjct: 200 EAKTDIPSDPEISLHALTGWTTAKTKIGTHDIVVFIDSGSTHNFISDKVAALLHLLVVPT 259

Query: 82  KPFSVRIANGAHLK---------------------------SPDVALDVKWSEQIGSIMR 114
            PF VR+AN   LK                           S D+ L V+W EQ+GS++ 
Sbjct: 260 APFHVRVANDQPLKCQGRFHNIHILLQGIPFSITFYSLPLTSLDLVLGVQWLEQLGSVVC 319

Query: 115 GWKK 118
            WK+
Sbjct: 320 DWKR 323

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147775005|emb|CAN70471.1| hypothetical protein VITISV_013478 [Vitis vinifera]

 Score = 75.1 bits (183), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 41/102 (40%), Positives = 57/102 (55%), Gaps = 27/102 (26%)

Query: 44  VATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKSP------ 97
           +  KI  HEVV+LI SGST NF+S+KVA +L L ++PTKPF+V++ANG  LK        
Sbjct: 3   ITAKIGQHEVVVLIDSGSTHNFISEKVADMLHLSVVPTKPFTVKVANGTPLKCQGRFEHV 62

Query: 98  ---------------------DVALDVKWSEQIGSIMRGWKK 118
                                D+ L V+W EQ+G+++  WKK
Sbjct: 63  HVILQGIPFSLTLYSLPLTGLDLVLGVQWLEQLGTVVCNWKK 104

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860532|emb|CAN81876.1| hypothetical protein VITISV_034528 [Vitis vinifera]

 Score = 73.9 bits (180), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/102 (39%), Positives = 57/102 (55%), Gaps = 27/102 (26%)

Query: 44  VATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKSP------ 97
           +  KI  H+VV+LI SGST NF+S+KVA +L LP++PTKPF+V++ANG  LK        
Sbjct: 338 ITAKIGQHKVVVLIDSGSTHNFISEKVADMLHLPVVPTKPFTVKVANGTPLKCQGRFEHV 397

Query: 98  ---------------------DVALDVKWSEQIGSIMRGWKK 118
                                D+ L V+W EQ+ +++  WKK
Sbjct: 398 HVILQGIPFSLTLYSLPLTGLDLVLGVQWLEQLETVVCNWKK 439

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147786921|emb|CAN64438.1| hypothetical protein VITISV_011230 [Vitis vinifera]

 Score = 73.2 bits (178), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/52 (65%), Positives = 41/52 (78%)

Query: 44  VATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLK 95
           V  KI  H++V+LI SGST NF+SDKVAALL LP++PT PF VR+ANG  LK
Sbjct: 298 VTAKIGTHDIVVLIDSGSTHNFISDKVAALLHLPVVPTAPFHVRVANGQPLK 349

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147861322|emb|CAN83996.1| hypothetical protein VITISV_031193 [Vitis vinifera]

 Score = 72.0 bits (175), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 38/100 (38%), Positives = 61/100 (61%), Gaps = 6/100 (6%)

Query: 9   NNETREVANIEGNEKKENSRSLFQVKCGQLR--KFCV----VATKIRFHEVVILISSGST 62
           N  +R+ +     E  E  R +F  K  +L   K+      V+ K+  HE+++LI SGST
Sbjct: 35  NERSRQSSYGRSRENTERGRPMFSSKLAKLEFPKYSARTMRVSAKVGPHELIVLIDSGST 94

Query: 63  ANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKSPDVALD 102
            NF+++++A LL LPM+P +PF+V++ANG  LK  + AL+
Sbjct: 95  HNFINERIAELLQLPMVPIEPFNVKVANGDPLKCQERALN 134

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147772855|emb|CAN73669.1| hypothetical protein VITISV_003711 [Vitis vinifera]

 Score = 69.7 bits (169), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/137 (32%), Positives = 66/137 (48%), Gaps = 28/137 (20%)

Query: 10  NETREVANIEGNEK-KENSRSLFQVKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSD 68
           N TRE++ IE ++  KE   +L  +    + +   +   I  H+VV LI SGST NF+SD
Sbjct: 193 NTTREISEIEEDDNGKEPEITLHALTGWIVPRTMQIKAIIGAHDVVALIDSGSTHNFISD 252

Query: 69  KVAALLPLPMMPTKPFSVRIANGAHLKSP---------------------------DVAL 101
           +V   L L + PT PF+VR+ANG  L                              D+ L
Sbjct: 253 RVVETLRLLVKPTTPFTVRVANGERLSCKGKYEKLTVNLQGNEFHLDFFSVPLNGLDMVL 312

Query: 102 DVKWSEQIGSIMRGWKK 118
            ++W E +GS++  WKK
Sbjct: 313 GIQWLETLGSVVCDWKK 329

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00026534001 SubName- Full=Chromosome chr12 scaffold_38, whole genome shotgun sequence; (226 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	121
cd00303	92	cd00303, retropepsin_like, Retropepsins; pepsin-li	1e-08
pfam13975	72	pfam13975, gag-asp_proteas, gag-polyprotein putati	4e-05

>gnl|CDD|133136 cd00303, retropepsin_like, Retropepsins; pepsin-like aspartate proteases

 Score = 48.5 bits (116), Expect = 1e-08
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 47  KIRFHEVVILISSGSTANFVSDKVAALLPLPMMPT-KPFSVRIANGAHLKSPDVALDVKW 105
           KI    V  L+ SG++ NF+S+ +A  L LP      P  V+ ANG+ +K+  V L V  
Sbjct: 4   KINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTI 63

Query: 106 S 106
            
Sbjct: 64  G 64

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 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. Length = 92

>gnl|CDD|206145 pfam13975, gag-asp_proteas, gag-polyprotein putative aspartyl protease

 Score = 38.8 bits (91), Expect = 4e-05
 Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 51  HEVVILISSGSTANFVSDKVAALLPLPM-MPTKPFSVRIANGAHLKSPDVALDVK 104
            EV  L+ +G+T +F+S+ +AA L LP+     P  VR+A+G+  +   +  D+ 
Sbjct: 18  VEVKALVDTGATHSFISESLAARLGLPLEADQAPSRVRLADGSVREIQGLLKDLV 72

This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins. Length = 72

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	121
PF08284	135	RVP_2: Retroviral aspartyl protease; InterPro: IPR	99.93
cd05479	124	RP_DDI RP_DDI; retropepsin-like domain of DNA dama	99.85
cd05484	91	retropepsin_like_LTR_2 Retropepsins_like_LTR, peps	99.63
PF13975	72	gag-asp_proteas: gag-polyprotein putative aspartyl	99.58
TIGR02281	121	clan_AA_DTGA clan AA aspartic protease, TIGR02281	99.57
PF13650	90	Asp_protease_2: Aspartyl protease	99.44
cd05483	96	retropepsin_like_bacteria Bacterial aspartate prot	99.39
TIGR03698	107	clan_AA_DTGF clan AA aspartic protease, AF_0612 fa	99.35
COG3577	215	Predicted aspartyl protease [General function pred	99.25
PF09668	124	Asp_protease: Aspartyl protease; InterPro: IPR0191	99.23
PF00077	100	RVP: Retroviral aspartyl protease The Prosite entr	99.15
cd06095	86	RP_RTVL_H_like Retropepsin of the RTVL_H family of	99.14
cd00303	92	retropepsin_like Retropepsins; pepsin-like asparta	99.07
PF12384	177	Peptidase_A2B: Ty3 transposon peptidase; InterPro:	98.98
cd05480	103	NRIP_C NRIP_C; putative nuclear receptor interacti	98.82
PF02160	201	Peptidase_A3: Cauliflower mosaic virus peptidase (	98.5
cd06094	89	RP_Saci_like RP_Saci_like, retropepsin family. Ret	98.5
KOG0012	380	consensus DNA damage inducible protein [Replicatio	98.4
PF05585	164	DUF1758: Putative peptidase (DUF1758); InterPro: I	98.39
cd05481	93	retropepsin_like_LTR_1 Retropepsins_like_LTR; peps	98.03
COG5550	125	Predicted aspartyl protease [Posttranslational mod	97.3
cd05482	87	HIV_retropepsin_like Retropepsins, pepsin-like asp	94.63
cd05476	265	pepsin_A_like_plant Chroloplast Nucleoids DNA-bind	94.39
cd06096	326	Plasmepsin_5 Plasmepsins are a class of aspartic p	94.11
cd06097	278	Aspergillopepsin_like Aspergillopepsin_like, aspar	91.94
cd05471	283	pepsin_like Pepsin-like aspartic proteases, biloba	91.85
PF12382	137	Peptidase_A2E: Retrotransposon peptidase; InterPro	91.8
cd06098	317	phytepsin Phytepsin, a plant homolog of mammalian	89.66
cd05485	329	Cathepsin_D_like Cathepsin_D_like, pepsin family o	86.51
PF00026	317	Asp: Eukaryotic aspartyl protease The Prosite entr	84.32
PF00455	161	DeoRC: DeoR C terminal sensor domain; InterPro: IP	81.16
cd05470	109	pepsin_retropepsin_like Cellular and retroviral pe	81.0
cd05474	295	SAP_like SAPs, pepsin-like proteinases secreted fr	80.64

>PF08284 RVP_2: Retroviral aspartyl protease; InterPro: IPR013242 This region defines single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses)

Probab=99.93  E-value=4.7e-26  Score=161.33  Aligned_cols=86  Identities=24%  Similarity=0.422  Sum_probs=73.5

Q ss_pred             eecccccCeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCC-CCCeEEEecCCceecc---------------
Q 043220           33 VKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMP-TKPFSVRIANGAHLKS---------------   96 (121)
Q Consensus        33 l~g~~~~~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~-~~~~~V~va~G~~l~~---------------   96 (121)
                      -.+...|..|+.++.|+++++.+|||||||||||++++|++++++..+ ..++.|..++| .+.|               
T Consensus        13 ~~~~~~~~vi~g~~~I~~~~~~vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~~V~~~g~-~~~~~~~~~~~~~~i~g~~   91 (135)
T PF08284_consen   13 EEAEESPDVITGTFLINSIPASVLIDSGATHSFISSSFAKKLGLPLEPLPRPIVVSAPGG-SINCEGVCPDVPLSIQGHE   91 (135)
T ss_pred             hcccCCCCeEEEEEEeccEEEEEEEecCCCcEEccHHHHHhcCCEEEEccCeeEEecccc-cccccceeeeEEEEECCeE
Confidence            344567889999999999999999999999999999999999999885 46777775544 3332               


Q ss_pred             ------------ceEeecchhhhhcCCeeeecccCC
Q 043220           97 ------------PDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        97 ------------~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                                  ||+|||||||++|+| .|||.+++
T Consensus        92 ~~~dl~vl~l~~~DvILGm~WL~~~~~-~IDw~~k~  126 (135)
T PF08284_consen   92 FVVDLLVLDLGGYDVILGMDWLKKHNP-VIDWATKT  126 (135)
T ss_pred             EEeeeEEecccceeeEeccchHHhCCC-EEEccCCE
Confidence                        999999999999999 59999875

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.

>cd05479 RP_DDI RP_DDI; retropepsin-like domain of DNA damage inducible protein

Probab=99.85  E-value=3.3e-21  Score=134.20  Aligned_cols=82  Identities=15%  Similarity=0.083  Sum_probs=68.8

Q ss_pred             ccCeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCceecc---------------------
Q 043220           38 LRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKS---------------------   96 (121)
Q Consensus        38 ~~~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l~~---------------------   96 (121)
                      ....|++.+.|||+++.+|||||||||||++++|+|+|++.....++.+.++++....+                     
T Consensus        13 ~~~~~~v~~~Ing~~~~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~~~~~   92 (124)
T cd05479          13 KVPMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRIHLAQVKIGNLFLPCSFT   92 (124)
T ss_pred             eeeEEEEEEEECCEEEEEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCCCcEEEeEEEEEEEEECCEEeeeEEE
Confidence            45678999999999999999999999999999999999987666666666665332211                     


Q ss_pred             ------ceEeecchhhhhcCCeeeecccCC
Q 043220           97 ------PDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        97 ------~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                            +|+|||||||++++. .|||++++
T Consensus        93 Vl~~~~~d~ILG~d~L~~~~~-~ID~~~~~  121 (124)
T cd05479          93 VLEDDDVDFLIGLDMLKRHQC-VIDLKENV  121 (124)
T ss_pred             EECCCCcCEEecHHHHHhCCe-EEECCCCE
Confidence                  899999999999996 69999874

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.

>cd05484 retropepsin_like_LTR_2 Retropepsins_like_LTR, pepsin-like aspartate proteases

Probab=99.63  E-value=6.8e-16  Score=101.59  Aligned_cols=65  Identities=20%  Similarity=0.254  Sum_probs=58.7

Q ss_pred             EEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCceecc-------------------------c
Q 043220           43 VVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKS-------------------------P   97 (121)
Q Consensus        43 ~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l~~-------------------------~   97 (121)
                      .+++.|||+++.+||||||++|||+++.+++++++.......++..|+|..+.+                         +
T Consensus         2 ~~~~~Ing~~i~~lvDTGA~~svis~~~~~~lg~~~~~~~~~~v~~a~G~~~~~~G~~~~~v~~~~~~~~~~~~v~~~~~   81 (91)
T cd05484           2 TVTLLVNGKPLKFQLDTGSAITVISEKTWRKLGSPPLKPTKKRLRTATGTKLSVLGQILVTVKYGGKTKVLTLYVVKNEG   81 (91)
T ss_pred             EEEEEECCEEEEEEEcCCcceEEeCHHHHHHhCCCccccccEEEEecCCCEeeEeEEEEEEEEECCEEEEEEEEEEECCC
Confidence            578999999999999999999999999999999987666789999999987643                         8


Q ss_pred             eEeecchhhh
Q 043220           98 DVALDVKWSE  107 (121)
Q Consensus        98 dvILG~~WL~  107 (121)
                      +.|||++||.
T Consensus        82 ~~lLG~~wl~   91 (91)
T cd05484          82 LNLLGRDWLD   91 (91)
T ss_pred             CCccChhhcC
Confidence            9999999984

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

>PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease

Probab=99.58  E-value=1.2e-14  Score=92.56  Aligned_cols=61  Identities=30%  Similarity=0.433  Sum_probs=56.3

Q ss_pred             ccccCeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCC-CeEEEecCCceecc
Q 043220           36 GQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTK-PFSVRIANGAHLKS   96 (121)
Q Consensus        36 ~~~~~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~-~~~V~va~G~~l~~   96 (121)
                      ...++++++.+.|+|+.+.+|||||||||||+.++|+||+++..+.. +.+|++|||....+
T Consensus         3 ~~~~g~~~v~~~I~g~~~~alvDtGat~~fis~~~a~rLgl~~~~~~~~~~v~~a~g~~~~~   64 (72)
T PF13975_consen    3 TPDPGLMYVPVSIGGVQVKALVDTGATHNFISESLAKRLGLPLEKPPSPIRVKLANGSVIEI   64 (72)
T ss_pred             cccCCEEEEEEEECCEEEEEEEeCCCcceecCHHHHHHhCCCcccCCCCEEEEECCCCcccc
Confidence            45788999999999999999999999999999999999999988766 99999999987765

>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family

Probab=99.57  E-value=2.1e-14  Score=99.84  Aligned_cols=83  Identities=16%  Similarity=0.165  Sum_probs=70.5

Q ss_pred             ccccCeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCC-CCCeEEEecCCceecc------------------
Q 043220           36 GQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMP-TKPFSVRIANGAHLKS------------------   96 (121)
Q Consensus        36 ~~~~~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~-~~~~~V~va~G~~l~~------------------   96 (121)
                      ....+++.+.++|||+++.+|||||||+++|++++|+++++.... ..+..+..|+|.....                  
T Consensus         6 ~~~~g~~~v~~~InG~~~~flVDTGAs~t~is~~~A~~Lgl~~~~~~~~~~~~ta~G~~~~~~~~l~~l~iG~~~~~nv~   85 (121)
T TIGR02281         6 KDGDGHFYATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIKAARVTLDRVAIGGIVVNDVD   85 (121)
T ss_pred             EcCCCeEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCcccCCceEEEEeCCCcEEEEEEEeCEEEECCEEEeCcE
Confidence            356789999999999999999999999999999999999987654 4578889999974321                  


Q ss_pred             ---------ceEeecchhhhhcCCeeeeccc
Q 043220           97 ---------PDVALDVKWSEQIGSIMRGWKK  118 (121)
Q Consensus        97 ---------~dvILG~~WL~~~~p~~idw~~  118 (121)
                               .+.+|||+||.++.++.+|-.+
T Consensus        86 ~~v~~~~~~~~~LLGm~fL~~~~~~~~~~~~  116 (121)
T TIGR02281        86 AMVAEGGALSESLLGMSFLNRLSRFTVRGGK  116 (121)
T ss_pred             EEEeCCCcCCceEcCHHHHhccccEEEECCE
Confidence                     4799999999999988777543

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).

>PF13650 Asp_protease_2: Aspartyl protease

Probab=99.44  E-value=4.1e-13  Score=86.37  Aligned_cols=49  Identities=33%  Similarity=0.432  Sum_probs=43.7

Q ss_pred             EEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCC-CeEEEecCCc
Q 043220           44 VATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTK-PFSVRIANGA   92 (121)
Q Consensus        44 v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~-~~~V~va~G~   92 (121)
                      |+++|||+++.+||||||+.++|+++++++++++..... +..+..++|.
T Consensus         1 V~v~vng~~~~~liDTGa~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~g~   50 (90)
T PF13650_consen    1 VPVKVNGKPVRFLIDTGASISVISRSLAKKLGLKPRPKSVPISVSGAGGS   50 (90)
T ss_pred             CEEEECCEEEEEEEcCCCCcEEECHHHHHHcCCCCcCCceeEEEEeCCCC
Confidence            468999999999999999999999999999999877553 6788888887

>cd05483 retropepsin_like_bacteria Bacterial aspartate proteases, retropepsin-like protease family

Probab=99.39  E-value=2.4e-12  Score=83.52  Aligned_cols=68  Identities=25%  Similarity=0.344  Sum_probs=57.1

Q ss_pred             CeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCceecc-----------------------
Q 043220           40 KFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKS-----------------------   96 (121)
Q Consensus        40 ~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l~~-----------------------   96 (121)
                      +.+.+++.||++++.+||||||++++|+.+++++++++.....+..+..++|....+                       
T Consensus         1 ~~~~v~v~i~~~~~~~llDTGa~~s~i~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~ig~~~~~~~~~~v~d   80 (96)
T cd05483           1 GHFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAARVRLDSLQIGGITLRNVPAVVLP   80 (96)
T ss_pred             CcEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCccCCCcEEEEecCCCccceEEEcceEEECCcEEeccEEEEeC
Confidence            357899999999999999999999999999999998855555677888888864322                       


Q ss_pred             -----ceEeecchhhh
Q 043220           97 -----PDVALDVKWSE  107 (121)
Q Consensus        97 -----~dvILG~~WL~  107 (121)
                           .|.|||++||+
T Consensus        81 ~~~~~~~gIlG~d~l~   96 (96)
T cd05483          81 GDALGVDGLLGMDFLR   96 (96)
T ss_pred             CcccCCceEeChHHhC
Confidence                 67999999985

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.

>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family

Probab=99.35  E-value=2.8e-12  Score=87.44  Aligned_cols=67  Identities=21%  Similarity=0.340  Sum_probs=56.8

Q ss_pred             EEEEEEecCCCcccc-cCHHHHhhcCCCCCCCCCeEEEecCCceecc------------------------ceEeecchh
Q 043220           51 HEVVILISSGSTANF-VSDKVAALLPLPMMPTKPFSVRIANGAHLKS------------------------PDVALDVKW  105 (121)
Q Consensus        51 ~~v~~LIDSGAT~nF-I~~~~a~rl~l~~~~~~~~~V~va~G~~l~~------------------------~dvILG~~W  105 (121)
                      -++.+|||||||+.+ |++++|+++|++..  ....+.+|||.....                        .+++|||.|
T Consensus        15 ~~v~~LVDTGat~~~~l~~~~a~~lgl~~~--~~~~~~tA~G~~~~~~v~~~~v~igg~~~~~~v~~~~~~~~~LLG~~~   92 (107)
T TIGR03698        15 MEVRALVDTGFSGFLLVPPDIVNKLGLPEL--DQRRVYLADGREVLTDVAKASIIINGLEIDAFVESLGYVDEPLLGTEL   92 (107)
T ss_pred             eEEEEEEECCCCeEEecCHHHHHHcCCCcc--cCcEEEecCCcEEEEEEEEEEEEECCEEEEEEEEecCCCCccEecHHH
Confidence            489999999999998 99999999999764  367899999963321                        578999999


Q ss_pred             hhhcCCeeeecccCC
Q 043220          106 SEQIGSIMRGWKKDE  120 (121)
Q Consensus       106 L~~~~p~~idw~~~~  120 (121)
                      |++++. .+||++++
T Consensus        93 L~~l~l-~id~~~~~  106 (107)
T TIGR03698        93 LEGLGI-VIDYRNQG  106 (107)
T ss_pred             HhhCCE-EEehhhCc
Confidence            999986 59999875

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.

>COG3577 Predicted aspartyl protease [General function prediction only]

Probab=99.25  E-value=4.9e-11  Score=89.67  Aligned_cols=87  Identities=15%  Similarity=0.172  Sum_probs=75.3

Q ss_pred             cceEEEeeeecccccCeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCC-CCCCeEEEecCCceecc-------
Q 043220           25 ENSRSLFQVKCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMM-PTKPFSVRIANGAHLKS-------   96 (121)
Q Consensus        25 ~~~isl~Al~g~~~~~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~-~~~~~~V~va~G~~l~~-------   96 (121)
                      .-+++|++    ...+|+...+.|||+++.+|||||||.-.+++.-|+|+|+... ...++.|.+|||+..-.       
T Consensus        93 ~~~v~Lak----~~~GHF~a~~~VNGk~v~fLVDTGATsVal~~~dA~RlGid~~~l~y~~~v~TANG~~~AA~V~Ld~v  168 (215)
T COG3577          93 YQEVSLAK----SRDGHFEANGRVNGKKVDFLVDTGATSVALNEEDARRLGIDLNSLDYTITVSTANGRARAAPVTLDRV  168 (215)
T ss_pred             ceEEEEEe----cCCCcEEEEEEECCEEEEEEEecCcceeecCHHHHHHhCCCccccCCceEEEccCCccccceEEeeeE
Confidence            45788877    8889999999999999999999999999999999999999876 56899999999974321       


Q ss_pred             --------------------ceEeecchhhhhcCCeeee
Q 043220           97 --------------------PDVALDVKWSEQIGSIMRG  115 (121)
Q Consensus        97 --------------------~dvILG~~WL~~~~p~~id  115 (121)
                                          -...|||+||.+++-...+
T Consensus       169 ~IG~I~~~nV~A~V~~~g~L~~sLLGMSfL~rL~~fq~~  207 (215)
T COG3577         169 QIGGIRVKNVDAMVAEDGALDESLLGMSFLNRLSGFQVD  207 (215)
T ss_pred             EEccEEEcCchhheecCCccchhhhhHHHHhhccceEec
Confidence                                5678999999999876543

>PF09668 Asp_protease: Aspartyl protease; InterPro: IPR019103 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=99.23  E-value=1.3e-11  Score=86.60  Aligned_cols=77  Identities=17%  Similarity=0.160  Sum_probs=50.3

Q ss_pred             ccCeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeE-EEecCC-----------------ceecc---
Q 043220           38 LRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFS-VRIANG-----------------AHLKS---   96 (121)
Q Consensus        38 ~~~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~-V~va~G-----------------~~l~~---   96 (121)
                      ....+.+..+|||++++|+|||||.+|.|+.++|+|+|+.....+.+. +..+-|                 ..+.|   
T Consensus        21 ~v~mLyI~~~ing~~vkA~VDtGAQ~tims~~~a~r~gL~~lid~r~~g~a~GvG~~~i~G~Ih~~~l~ig~~~~~~s~~  100 (124)
T PF09668_consen   21 QVSMLYINCKINGVPVKAFVDTGAQSTIMSKSCAERCGLMRLIDKRFAGVAKGVGTQKILGRIHSVQLKIGGLFFPCSFT  100 (124)
T ss_dssp             -----EEEEEETTEEEEEEEETT-SS-EEEHHHHHHTTGGGGEEGGG-EE-------EEEEEEEEEEEEETTEEEEEEEE
T ss_pred             CcceEEEEEEECCEEEEEEEeCCCCccccCHHHHHHcCChhhccccccccccCCCcCceeEEEEEEEEEECCEEEEEEEE
Confidence            345678999999999999999999999999999999998632222221 111112                 12222   


Q ss_pred             ------ceEeecchhhhhcCCeeee
Q 043220           97 ------PDVALDVKWSEQIGSIMRG  115 (121)
Q Consensus        97 ------~dvILG~~WL~~~~p~~id  115 (121)
                            .|++||.|||++|..+ ||
T Consensus       101 Vle~~~~d~llGld~L~~~~c~-ID  124 (124)
T PF09668_consen  101 VLEDQDVDLLLGLDMLKRHKCC-ID  124 (124)
T ss_dssp             EETTSSSSEEEEHHHHHHTT-E-EE
T ss_pred             EeCCCCcceeeeHHHHHHhCcc-cC
Confidence                  8999999999999884 65

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.

>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

Probab=99.15  E-value=4.6e-11  Score=79.16  Aligned_cols=68  Identities=21%  Similarity=0.322  Sum_probs=55.8

Q ss_pred             eEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCceecc------------------------
Q 043220           41 FCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKS------------------------   96 (121)
Q Consensus        41 ~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l~~------------------------   96 (121)
                      .-++..+++|+++.+||||||+.++|+++...++..+  ...+..+..++|.. .+                        
T Consensus         5 rp~i~v~i~g~~i~~LlDTGA~vsiI~~~~~~~~~~~--~~~~~~v~~~~g~~-~~~~~~~~~v~~~~~~~~~~~~v~~~   81 (100)
T PF00077_consen    5 RPYITVKINGKKIKALLDTGADVSIISEKDWKKLGPP--PKTSITVRGAGGSS-SILGSTTVEVKIGGKEFNHTFLVVPD   81 (100)
T ss_dssp             SSEEEEEETTEEEEEEEETTBSSEEESSGGSSSTSSE--EEEEEEEEETTEEE-EEEEEEEEEEEETTEEEEEEEEESST
T ss_pred             CceEEEeECCEEEEEEEecCCCcceeccccccccccc--ccCCceeccCCCcc-eeeeEEEEEEEEECccceEEEEecCC
Confidence            3467889999999999999999999999998877654  45567788888865 21                        


Q ss_pred             --ceEeecchhhhhcCCe
Q 043220           97 --PDVALDVKWSEQIGSI  112 (121)
Q Consensus        97 --~dvILG~~WL~~~~p~  112 (121)
                        .| |||.|||++++..
T Consensus        82 ~~~~-ILG~D~L~~~~~~   98 (100)
T PF00077_consen   82 LPMN-ILGRDFLKKLNAV   98 (100)
T ss_dssp             CSSE-EEEHHHHTTTTCE
T ss_pred             CCCC-EeChhHHHHcCCE
Confidence              67 9999999999873

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 ....

>cd06095 RP_RTVL_H_like Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements

Probab=99.14  E-value=1.1e-10  Score=76.19  Aligned_cols=61  Identities=18%  Similarity=0.294  Sum_probs=49.6

Q ss_pred             EEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCce---ecc----------------------ce
Q 043220           44 VATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAH---LKS----------------------PD   98 (121)
Q Consensus        44 v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~---l~~----------------------~d   98 (121)
                      +++.|||+++.+|+||||+++.|++..++++   .....+..+..++|..   +..                      .+
T Consensus         1 ~~v~InG~~~~fLvDTGA~~tii~~~~a~~~---~~~~~~~~v~gagG~~~~~v~~~~~~v~vg~~~~~~~~~v~~~~~~   77 (86)
T cd06095           1 VTITVEGVPIVFLVDTGATHSVLKSDLGPKQ---ELSTTSVLIRGVSGQSQQPVTTYRTLVDLGGHTVSHSFLVVPNCPD   77 (86)
T ss_pred             CEEEECCEEEEEEEECCCCeEEECHHHhhhc---cCCCCcEEEEeCCCcccccEEEeeeEEEECCEEEEEEEEEEcCCCC
Confidence            4678999999999999999999999999997   2334677888888863   210                      78


Q ss_pred             Eeecchhhh
Q 043220           99 VALDVKWSE  107 (121)
Q Consensus        99 vILG~~WL~  107 (121)
                      .|||||||.
T Consensus        78 ~lLG~dfL~   86 (86)
T cd06095          78 PLLGRDLLS   86 (86)
T ss_pred             cEechhhcC
Confidence            899999984

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

>cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases

Probab=99.07  E-value=7.5e-10  Score=67.60  Aligned_cols=63  Identities=40%  Similarity=0.557  Sum_probs=48.6

Q ss_pred             EEEECCEEEEEEecCCCcccccCHHHHhhcCC-CCCCCCCeEEEecCCceec---------------------------c
Q 043220           45 ATKIRFHEVVILISSGSTANFVSDKVAALLPL-PMMPTKPFSVRIANGAHLK---------------------------S   96 (121)
Q Consensus        45 ~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l-~~~~~~~~~V~va~G~~l~---------------------------~   96 (121)
                      .+.++++++.+|+|+||++++++..++.++++ ......+..+..++|....                           .
T Consensus         2 ~~~~~~~~~~~liDtgs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   81 (92)
T cd00303           2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS   81 (92)
T ss_pred             EEEECCEEEEEEEcCCCcccccCHHHHHHcCCCcccCCCceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcCCC
Confidence            45678899999999999999999999999987 4444455666666553211                           1


Q ss_pred             ceEeecchhhh
Q 043220           97 PDVALDVKWSE  107 (121)
Q Consensus        97 ~dvILG~~WL~  107 (121)
                      +|+|||++||.
T Consensus        82 ~~~ilG~~~l~   92 (92)
T cd00303          82 YDVILGRPWLE   92 (92)
T ss_pred             cCEEecccccC
Confidence            88999999984

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

>PF12384 Peptidase_A2B: Ty3 transposon peptidase; InterPro: IPR024650 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=98.98  E-value=2.1e-09  Score=78.58  Aligned_cols=87  Identities=17%  Similarity=0.252  Sum_probs=70.0

Q ss_pred             cceEEEeeeec-c---cccCeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCce-ecc---
Q 043220           25 ENSRSLFQVKC-G---QLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAH-LKS---   96 (121)
Q Consensus        25 ~~~isl~Al~g-~---~~~~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~-l~~---   96 (121)
                      .+.+.+.-+.- .   ...++..+...++|.++.+|+||||..+||+..++++|+++.....|++++.+.+.. ..|   
T Consensus        14 ~~~~~~~PIV~~~~~Pevg~T~~v~l~~~~t~i~vLfDSGSPTSfIr~di~~kL~L~~~~app~~fRG~vs~~~~~tsEA   93 (177)
T PF12384_consen   14 KSSITTCPIVHYIAIPEVGKTAIVQLNCKGTPIKVLFDSGSPTSFIRSDIVEKLELPTHDAPPFRFRGFVSGESATTSEA   93 (177)
T ss_pred             cceeeeeeeEEEeeccccCcEEEEEEeecCcEEEEEEeCCCccceeehhhHHhhCCccccCCCEEEeeeccCCceEEEEe
Confidence            45555555443 2   344688999999999999999999999999999999999999999998887664431 112   


Q ss_pred             -----------------------ceEeecchhhhhcCC
Q 043220           97 -----------------------PDVALDVKWSEQIGS  111 (121)
Q Consensus        97 -----------------------~dvILG~~WL~~~~p  111 (121)
                                             +|+|+|.+.|+++..
T Consensus        94 v~ld~~i~n~~i~i~aYV~d~m~~dlIIGnPiL~ryp~  131 (177)
T PF12384_consen   94 VTLDFYIDNKLIDIAAYVTDNMDHDLIIGNPILDRYPT  131 (177)
T ss_pred             EEEEEEECCeEEEEEEEEeccCCcceEeccHHHhhhHH
Confidence                                   999999999999854

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 [].

>cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein

Probab=98.82  E-value=6e-09  Score=70.49  Aligned_cols=71  Identities=11%  Similarity=0.148  Sum_probs=53.3

Q ss_pred             EEEECCEEEEEEecCCCcccccCHHHHhhcCCCCC-CCCCe--------------------EEEecCCceecc-------
Q 043220           45 ATKIRFHEVVILISSGSTANFVSDKVAALLPLPMM-PTKPF--------------------SVRIANGAHLKS-------   96 (121)
Q Consensus        45 ~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~-~~~~~--------------------~V~va~G~~l~~-------   96 (121)
                      ..++||++++|+|||||-+|.||+.+|+|.|+.-. ...++                    .+++++ ..+.|       
T Consensus         2 nCk~nG~~vkAfVDsGaQ~timS~~caercgL~r~v~~~r~~g~A~gvgt~~kiiGrih~~~ikig~-~~~~CSftVld~   80 (103)
T cd05480           2 SCQCAGKELRALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSLPTSVKVIGQIERLVLQLGQ-LTVECSAQVVDD   80 (103)
T ss_pred             ceeECCEEEEEEEecCCchhhcCHHHHHHcChHhhhhhccccccccCCCcceeEeeEEEEEEEEeCC-EEeeEEEEEEcC
Confidence            46899999999999999999999999999998632 11111                    111211 23334       


Q ss_pred             --ceEeecchhhhhcCCeeeecc
Q 043220           97 --PDVALDVKWSEQIGSIMRGWK  117 (121)
Q Consensus        97 --~dvILG~~WL~~~~p~~idw~  117 (121)
                        .|++||-|-|++|.. .||.+
T Consensus        81 ~~~d~llGLdmLkrhqc-~IdL~  102 (103)
T cd05480          81 NEKNFSLGLQTLKSLKC-VINLE  102 (103)
T ss_pred             CCcceEeeHHHHhhcce-eeecc
Confidence              999999999999998 48865

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.

>PF02160 Peptidase_A3: Cauliflower mosaic virus peptidase (A3); InterPro: IPR000588 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=98.50  E-value=2.9e-07  Score=69.29  Aligned_cols=75  Identities=17%  Similarity=0.145  Sum_probs=53.6

Q ss_pred             EEEEEEECC---EEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCceec----c------------------
Q 043220           42 CVVATKIRF---HEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLK----S------------------   96 (121)
Q Consensus        42 ~~v~g~i~~---~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l~----~------------------   96 (121)
                      ++++..+.|   ..+.++||||||.+.++....=.-.. .....++.|+.||+....    |                  
T Consensus         7 I~~~i~~~gy~~~~~~~~vDTGAt~C~~~~~iiP~e~w-e~~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~IP~iY   85 (201)
T PF02160_consen    7 IKVKISFPGYKKFNYHCYVDTGATICCASKKIIPEEYW-EKSKKPIKVKGANGSIIQINKKAKNGKIQIADKIFRIPTIY   85 (201)
T ss_pred             EEEEEEEcCceeEEEEEEEeCCCceEEecCCcCCHHHH-HhCCCcEEEEEecCCceEEEEEecCceEEEccEEEeccEEE
Confidence            344445555   45788999999999988766421110 123457899999987432    1                  


Q ss_pred             -----ceEeecchhhhhcCCeeeeccc
Q 043220           97 -----PDVALDVKWSEQIGSIMRGWKK  118 (121)
Q Consensus        97 -----~dvILG~~WL~~~~p~~idw~~  118 (121)
                           .|+|||++|++.+.|. +.|..
T Consensus        86 q~~~g~d~IlG~NF~r~y~Pf-iq~~~  111 (201)
T PF02160_consen   86 QQESGIDIILGNNFLRLYEPF-IQTED  111 (201)
T ss_pred             EecCCCCEEecchHHHhcCCc-EEEcc
Confidence                 9999999999999997 88864

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

>cd06094 RP_Saci_like RP_Saci_like, retropepsin family

Probab=98.50  E-value=1.2e-07  Score=62.89  Aligned_cols=55  Identities=16%  Similarity=0.414  Sum_probs=45.8

Q ss_pred             EEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCceecc-------------------------ceEeecchhh
Q 043220           52 EVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKS-------------------------PDVALDVKWS  106 (121)
Q Consensus        52 ~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l~~-------------------------~dvILG~~WL  106 (121)
                      .+.+||||||.+|.|.+...++.    ....++.++.|||+.+.+                         ...|||.|+|
T Consensus         9 ~~~fLVDTGA~vSviP~~~~~~~----~~~~~~~l~AANgt~I~tyG~~~l~ldlGlrr~~~w~FvvAdv~~pIlGaDfL   84 (89)
T cd06094           9 GLRFLVDTGAAVSVLPASSTKKS----LKPSPLTLQAANGTPIATYGTRSLTLDLGLRRPFAWNFVVADVPHPILGADFL   84 (89)
T ss_pred             CcEEEEeCCCceEeecccccccc----ccCCceEEEeCCCCeEeeeeeEEEEEEcCCCcEEeEEEEEcCCCcceecHHHH
Confidence            46799999999999998887763    345678999999998754                         5569999999


Q ss_pred             hhcC
Q 043220          107 EQIG  110 (121)
Q Consensus       107 ~~~~  110 (121)
                      ++|+
T Consensus        85 ~~~~   88 (89)
T cd06094          85 QHYG   88 (89)
T ss_pred             HHcC
Confidence            9986

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

>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]

Probab=98.40  E-value=2.5e-07  Score=74.65  Aligned_cols=82  Identities=17%  Similarity=0.133  Sum_probs=60.9

Q ss_pred             cccCeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCe-EEEecCC-----------------ceecc--
Q 043220           37 QLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPF-SVRIANG-----------------AHLKS--   96 (121)
Q Consensus        37 ~~~~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~-~V~va~G-----------------~~l~~--   96 (121)
                      .....+.|..+|||++|+|+|||||-.|-||..+|+|.|+.-...+.+ -+.-+.|                 ..+.|  
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            344456789999999999999999999999999999999864322111 1111111                 12234  


Q ss_pred             -------ceEeecchhhhhcCCeeeecccC
Q 043220           97 -------PDVALDVKWSEQIGSIMRGWKKD  119 (121)
Q Consensus        97 -------~dvILG~~WL~~~~p~~idw~~~  119 (121)
                             .|+.||-+-|++|.. .||.++.
T Consensus       311 tV~d~~~~d~llGLd~Lrr~~c-cIdL~~~  339 (380)
T KOG0012|consen  311 TVLDRRDMDLLLGLDMLRRHQC-CIDLKTN  339 (380)
T ss_pred             EEecCCCcchhhhHHHHHhccc-eeecccC
Confidence                   899999999999999 4998764

>PF05585 DUF1758: Putative peptidase (DUF1758); InterPro: IPR008737 This is a family of nematode proteins of unknown function []

Probab=98.39  E-value=5.6e-07  Score=64.88  Aligned_cols=32  Identities=34%  Similarity=0.478  Sum_probs=28.1

Q ss_pred             EEEEEEecCCCcccccCHHHHhhcCCCCCCCC
Q 043220           51 HEVVILISSGSTANFVSDKVAALLPLPMMPTK   82 (121)
Q Consensus        51 ~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~   82 (121)
                      +.+.+|+||||..|||.+++|++|+|+.....
T Consensus        11 ~~~~~LlDsGSq~SfIt~~la~~L~L~~~~~~   42 (164)
T PF05585_consen   11 VEARALLDSGSQRSFITESLANKLNLPGTGEK   42 (164)
T ss_pred             EEEEEEEecCCchhHHhHHHHHHhCCCCCCce
Confidence            56789999999999999999999999876543

However, it seems likely that these proteins act as aspartic peptidases.

>cd05481 retropepsin_like_LTR_1 Retropepsins_like_LTR; pepsin-like aspartate protease from retrotransposons with long terminal repeats

Probab=98.03  E-value=1.1e-05  Score=53.54  Aligned_cols=50  Identities=20%  Similarity=0.282  Sum_probs=42.9

Q ss_pred             EEECC-EEEEEEecCCCcccccCHHHHhhcC---CCCCCCCCeEEEecCCceec
Q 043220           46 TKIRF-HEVVILISSGSTANFVSDKVAALLP---LPMMPTKPFSVRIANGAHLK   95 (121)
Q Consensus        46 g~i~~-~~v~~LIDSGAT~nFI~~~~a~rl~---l~~~~~~~~~V~va~G~~l~   95 (121)
                      ..+++ +++.+++|+||+.|.|+.+..++++   .+.-.+.++.+..+||..+.
T Consensus         3 ~~i~g~~~v~~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~   56 (93)
T cd05481           3 MKINGKQSVKFQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIP   56 (93)
T ss_pred             eEeCCceeEEEEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEee
Confidence            46788 9999999999999999999999998   45555667999999998764

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

>COG5550 Predicted aspartyl protease [Posttranslational modification, protein turnover, chaperones]

Probab=97.30  E-value=0.00077  Score=47.26  Aligned_cols=76  Identities=24%  Similarity=0.291  Sum_probs=50.2

Q ss_pred             CeEEEEEEE--CC-EEEEEEecCCCc-ccccCHHHHhhcCCCCCCCCCeEEEecCCceecc-------------------
Q 043220           40 KFCVVATKI--RF-HEVVILISSGST-ANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKS-------------------   96 (121)
Q Consensus        40 ~~~~v~g~i--~~-~~v~~LIDSGAT-~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l~~-------------------   96 (121)
                      .++.++...  +| +.-..|||||.| -..+++++|.+++++...+  .++..++|+++++                   
T Consensus        11 ~~v~~~f~~~~~Gd~~~~~LiDTGFtg~lvlp~~vaek~~~~~~~~--~~~~~a~~~~v~t~V~~~~iki~g~e~~~~Vl   88 (125)
T COG5550          11 VTVPVTFRLPGQGDFVYDELIDTGFTGYLVLPPQVAEKLGLPLFST--IRIVLADGGVVKTSVALATIKIDGVEKVAFVL   88 (125)
T ss_pred             eeEEEEEEecCCCcEEeeeEEecCCceeEEeCHHHHHhcCCCccCC--hhhhhhcCCEEEEEEEEEEEEECCEEEEEEEE
Confidence            455555555  33 333449999999 7889999999999876533  2333444443322                   


Q ss_pred             -----ceEeecchhhhhcCCeeeeccc
Q 043220           97 -----PDVALDVKWSEQIGSIMRGWKK  118 (121)
Q Consensus        97 -----~dvILG~~WL~~~~p~~idw~~  118 (121)
                           .-.++|++||+.++- .+|.++
T Consensus        89 ~s~~~~~~liG~~~lk~l~~-~vn~~~  114 (125)
T COG5550          89 ASDNLPEPLIGVNLLKLLGL-VVNPKT  114 (125)
T ss_pred             ccCCCcccchhhhhhhhccE-EEcCCc
Confidence                 223999999999876 477653

>cd05482 HIV_retropepsin_like Retropepsins, pepsin-like aspartate proteases

Probab=94.63  E-value=0.038  Score=36.41  Aligned_cols=25  Identities=12%  Similarity=0.189  Sum_probs=22.6

Q ss_pred             EEEECCEEEEEEecCCCcccccCHH
Q 043220           45 ATKIRFHEVVILISSGSTANFVSDK   69 (121)
Q Consensus        45 ~g~i~~~~v~~LIDSGAT~nFI~~~   69 (121)
                      +.+|+|+.+.+|+||||-++.|...
T Consensus         2 ~~~i~g~~~~~llDTGAd~Tvi~~~   26 (87)
T cd05482           2 TLYINGKLFEGLLDTGADVSIIAEN   26 (87)
T ss_pred             EEEECCEEEEEEEccCCCCeEEccc
Confidence            4678999999999999999999973

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

>cd05476 pepsin_A_like_plant Chroloplast Nucleoids DNA-binding Protease and Nucellin, pepsin-like aspartic proteases from plants

Probab=94.39  E-value=0.087  Score=40.19  Aligned_cols=56  Identities=14%  Similarity=0.157  Sum_probs=38.2

Q ss_pred             EEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCc---------------eecc---------ceEeecchhhhhc
Q 043220           54 VILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGA---------------HLKS---------PDVALDVKWSEQI  109 (121)
Q Consensus        54 ~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~---------------~l~~---------~dvILG~~WL~~~  109 (121)
                      .++||||+|..++.+.+.-          ++.+..++|.               ...|         .-.|||-.||+.+
T Consensus       178 ~ai~DTGTs~~~lp~~~~P----------~i~~~f~~~~~~~i~~~~y~~~~~~~~~C~~~~~~~~~~~~ilG~~fl~~~  247 (265)
T cd05476         178 GTIIDSGTTLTYLPDPAYP----------DLTLHFDGGADLELPPENYFVDVGEGVVCLAILSSSSGGVSILGNIQQQNF  247 (265)
T ss_pred             cEEEeCCCcceEcCccccC----------CEEEEECCCCEEEeCcccEEEECCCCCEEEEEecCCCCCcEEEChhhcccE
Confidence            4899999999999987762          2223232221               1123         3479999999999


Q ss_pred             CCeeeecccCC
Q 043220          110 GSIMRGWKKDE  120 (121)
Q Consensus       110 ~p~~idw~~~~  120 (121)
                      -.+ .|+.++|
T Consensus       248 ~~v-FD~~~~~  257 (265)
T cd05476         248 LVE-YDLENSR  257 (265)
T ss_pred             EEE-EECCCCE
Confidence            885 8887764

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

>cd06096 Plasmepsin_5 Plasmepsins are a class of aspartic proteinases produced by the plasmodium parasite

Probab=94.11  E-value=0.08  Score=41.69  Aligned_cols=65  Identities=12%  Similarity=0.168  Sum_probs=47.5

Q ss_pred             EEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCceec--------------c--------ceEeecchhhhhc
Q 043220           52 EVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLK--------------S--------PDVALDVKWSEQI  109 (121)
Q Consensus        52 ~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l~--------------~--------~dvILG~~WL~~~  109 (121)
                      ...++||||.|..++.+.+.+++.-.+   +.+.+...+|..+.              |        --.|||-.||+.+
T Consensus       231 ~~~aivDSGTs~~~lp~~~~~~l~~~~---P~i~~~f~~g~~~~i~p~~y~~~~~~~~c~~~~~~~~~~~ILG~~flr~~  307 (326)
T cd06096         231 GLGMLVDSGSTLSHFPEDLYNKINNFF---PTITIIFENNLKIDWKPSSYLYKKESFWCKGGEKSVSNKPILGASFFKNK  307 (326)
T ss_pred             CCCEEEeCCCCcccCCHHHHHHHHhhc---CcEEEEEcCCcEEEECHHHhccccCCceEEEEEecCCCceEEChHHhcCc
Confidence            345899999999999999998864322   35666666554432              1        2369999999999


Q ss_pred             CCeeeecccCC
Q 043220          110 GSIMRGWKKDE  120 (121)
Q Consensus       110 ~p~~idw~~~~  120 (121)
                      -.+ .|+.++|
T Consensus       308 y~v-FD~~~~r  317 (326)
T cd06096         308 QII-FDLDNNR  317 (326)
T ss_pred             EEE-EECcCCE
Confidence            875 8887764

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

>cd06097 Aspergillopepsin_like Aspergillopepsin_like, aspartic proteases of fungal origin

Probab=91.94  E-value=0.46  Score=36.36  Aligned_cols=65  Identities=8%  Similarity=-0.027  Sum_probs=41.5

Q ss_pred             EEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCc-eecc----------ceEeecchhhhhcCCeeeecccCC
Q 043220           52 EVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGA-HLKS----------PDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        52 ~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~-~l~~----------~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                      ...++||||++..++...+++++.-.+...   ......|. .+.|          ...|||-.+|+++-.+ .||.++|
T Consensus       198 ~~~~iiDSGTs~~~lP~~~~~~l~~~l~g~---~~~~~~~~~~~~C~~~~P~i~f~~~~ilGd~fl~~~y~v-fD~~~~~  273 (278)
T cd06097         198 GFSAIADTGTTLILLPDAIVEAYYSQVPGA---YYDSEYGGWVFPCDTTLPDLSFAVFSILGDVFLKAQYVV-FDVGGPK  273 (278)
T ss_pred             CceEEeecCCchhcCCHHHHHHHHHhCcCC---cccCCCCEEEEECCCCCCCEEEEEEEEEcchhhCceeEE-EcCCCce
Confidence            356899999999999988776652111000   00001111 2333          2569999999999885 9998765

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-

>cd05471 pepsin_like Pepsin-like aspartic proteases, bilobal enzymes that cleave bonds in peptides at acidic pH

Probab=91.85  E-value=0.32  Score=36.51  Aligned_cols=66  Identities=8%  Similarity=0.011  Sum_probs=42.2

Q ss_pred             EEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCceecc------------ceEeecchhhhhcCCeeeeccc
Q 043220           51 HEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLKS------------PDVALDVKWSEQIGSIMRGWKK  118 (121)
Q Consensus        51 ~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l~~------------~dvILG~~WL~~~~p~~idw~~  118 (121)
                      ....++||||++..++...+...+--.+......   .-......|            +..|||..||+.+-.+ .|+.+
T Consensus       201 ~~~~~iiDsGt~~~~lp~~~~~~l~~~~~~~~~~---~~~~~~~~~~~~~~~p~i~f~f~~ilG~~fl~~~y~v-fD~~~  276 (283)
T cd05471         201 GGGGAIVDSGTSLIYLPSSVYDAILKALGAAVSS---SDGGYGVDCSPCDTLPDITFTFLWILGDVFLRNYYTV-FDLDN  276 (283)
T ss_pred             CCcEEEEecCCCCEeCCHHHHHHHHHHhCCcccc---cCCcEEEeCcccCcCCCEEEEEEEEccHhhhhheEEE-EeCCC
Confidence            3568999999999999999888763222111000   000000111            5799999999999885 78776


Q ss_pred             CC
Q 043220          119 DE  120 (121)
Q Consensus       119 ~~  120 (121)
                      ++
T Consensus       277 ~~  278 (283)
T cd05471         277 NR  278 (283)
T ss_pred             CE
Confidence            53

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

>PF12382 Peptidase_A2E: Retrotransposon peptidase; InterPro: IPR024648 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=91.80  E-value=0.18  Score=34.58  Aligned_cols=40  Identities=23%  Similarity=0.384  Sum_probs=31.4

Q ss_pred             EEEEEEECCE--EEEEEecCCCcccccCHHHHhhcCCCCCCC
Q 043220           42 CVVATKIRFH--EVVILISSGSTANFVSDKVAALLPLPMMPT   81 (121)
Q Consensus        42 ~~v~g~i~~~--~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~   81 (121)
                      |.+.+.+-..  .+..|||+||..|.|.++.++.+.+|.++.
T Consensus        35 mvlqa~lp~fkcsipclidtgaq~niiteetvrahklptrpw   76 (137)
T PF12382_consen   35 MVLQAKLPDFKCSIPCLIDTGAQVNIITEETVRAHKLPTRPW   76 (137)
T ss_pred             hhhhhhCCCccccceeEEccCceeeeeehhhhhhccCCCCcc
Confidence            4444444332  467899999999999999999999998764

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.

>cd06098 phytepsin Phytepsin, a plant homolog of mammalian lysosomal pepsins

Probab=89.66  E-value=1.8  Score=33.87  Aligned_cols=74  Identities=12%  Similarity=0.063  Sum_probs=47.8

Q ss_pred             EEECCEE-------EEEEecCCCcccccCHHHHhhcCC--CCC---CCCCeEEEecC----------------Cceecc-
Q 043220           46 TKIRFHE-------VVILISSGSTANFVSDKVAALLPL--PMM---PTKPFSVRIAN----------------GAHLKS-   96 (121)
Q Consensus        46 g~i~~~~-------v~~LIDSGAT~nFI~~~~a~rl~l--~~~---~~~~~~V~va~----------------G~~l~~-   96 (121)
                      ..|+++.       ..++||||++..++.+.+++++..  +..   ..+.+....++                +....| 
T Consensus       197 i~v~g~~~~~~~~~~~aivDTGTs~~~lP~~~~~~i~~~~~C~~~~~~P~i~f~f~g~~~~l~~~~yi~~~~~~~~~~C~  276 (317)
T cd06098         197 VLIGGKSTGFCAGGCAAIADSGTSLLAGPTTIVTQINSAVDCNSLSSMPNVSFTIGGKTFELTPEQYILKVGEGAAAQCI  276 (317)
T ss_pred             EEECCEEeeecCCCcEEEEecCCcceeCCHHHHHhhhccCCccccccCCcEEEEECCEEEEEChHHeEEeecCCCCCEEe
Confidence            4666654       358999999999999999987642  221   11233333321                111134 


Q ss_pred             -------------ceEeecchhhhhcCCeeeecccCC
Q 043220           97 -------------PDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        97 -------------~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                                   ...|||-.||+.+-.+ .|+.++|
T Consensus       277 ~~~~~~~~~~~~~~~~IlGd~Flr~~y~V-fD~~~~~  312 (317)
T cd06098         277 SGFTALDVPPPRGPLWILGDVFMGAYHTV-FDYGNLR  312 (317)
T ss_pred             ceEEECCCCCCCCCeEEechHHhcccEEE-EeCCCCE
Confidence                         1359999999999885 8888764

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

>cd05485 Cathepsin_D_like Cathepsin_D_like, pepsin family of proteinases

Probab=86.51  E-value=3.3  Score=32.64  Aligned_cols=22  Identities=5%  Similarity=-0.191  Sum_probs=18.6

Q ss_pred             eEeecchhhhhcCCeeeecccCC
Q 043220           98 DVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        98 dvILG~~WL~~~~p~~idw~~~~  120 (121)
                      ..|||..||+.+-.+ .||+++|
T Consensus       303 ~~IlG~~fl~~~y~v-FD~~~~~  324 (329)
T cd05485         303 LWILGDVFIGKYYTE-FDLGNNR  324 (329)
T ss_pred             eEEEchHHhccceEE-EeCCCCE
Confidence            379999999999885 8998765

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

>PF00026 Asp: Eukaryotic aspartyl protease The Prosite entry also includes Pfam:PF00077

Probab=84.32  E-value=0.35  Score=37.03  Aligned_cols=67  Identities=7%  Similarity=0.167  Sum_probs=44.0

Q ss_pred             EEEEEecCCCcccccCHHHHhhc----CC---------CCCC---CCCeEEEecCCcee-----------------cc--
Q 043220           52 EVVILISSGSTANFVSDKVAALL----PL---------PMMP---TKPFSVRIANGAHL-----------------KS--   96 (121)
Q Consensus        52 ~v~~LIDSGAT~nFI~~~~a~rl----~l---------~~~~---~~~~~V~va~G~~l-----------------~~--   96 (121)
                      ...++||||++..++...+..++    +.         +...   ..++..... |..+                 .|  
T Consensus       199 ~~~~~~Dtgt~~i~lp~~~~~~i~~~l~~~~~~~~~~~~c~~~~~~p~l~f~~~-~~~~~i~~~~~~~~~~~~~~~~C~~  277 (317)
T PF00026_consen  199 GQQAILDTGTSYIYLPRSIFDAIIKALGGSYSDGVYSVPCNSTDSLPDLTFTFG-GVTFTIPPSDYIFKIEDGNGGYCYL  277 (317)
T ss_dssp             EEEEEEETTBSSEEEEHHHHHHHHHHHTTEEECSEEEEETTGGGGSEEEEEEET-TEEEEEEHHHHEEEESSTTSSEEEE
T ss_pred             ceeeecccccccccccchhhHHHHhhhcccccceeEEEecccccccceEEEeeC-CEEEEecchHhcccccccccceeEe
Confidence            35799999999999999987754    11         1111   122333333 2211                 13  


Q ss_pred             -----------ceEeecchhhhhcCCeeeecccCC
Q 043220           97 -----------PDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        97 -----------~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                                 ...|||++||+.+-.+ +|+.++|
T Consensus       278 ~i~~~~~~~~~~~~iLG~~fl~~~y~v-fD~~~~~  311 (317)
T PF00026_consen  278 GIQPMDSSDDSDDWILGSPFLRNYYVV-FDYENNR  311 (317)
T ss_dssp             SEEEESSTTSSSEEEEEHHHHTTEEEE-EETTTTE
T ss_pred             eeecccccccCCceEecHHHhhceEEE-EeCCCCE
Confidence                       5889999999999875 8887764

; 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 ....

>PF00455 DeoRC: DeoR C terminal sensor domain; InterPro: IPR014036 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=81.16  E-value=1.1  Score=32.20  Aligned_cols=63  Identities=13%  Similarity=0.050  Sum_probs=44.8

Q ss_pred             EEEecCCCcccccCHHHHhhcCCCCCC-----------CCCeEEEecCCceeccceEeecchhhhhcCCeeeec
Q 043220           54 VILISSGSTANFVSDKVAALLPLPMMP-----------TKPFSVRIANGAHLKSPDVALDVKWSEQIGSIMRGW  116 (121)
Q Consensus        54 ~~LIDSGAT~nFI~~~~a~rl~l~~~~-----------~~~~~V~va~G~~l~~~dvILG~~WL~~~~p~~idw  116 (121)
                      .+.||+|+|.-.+.+.+..+.++.+..           .+...|.+.+|..........|..-+.....+.+|+
T Consensus        22 ~Ifld~GtT~~~la~~L~~~~~ltVvTnsl~ia~~l~~~~~~~vi~~GG~~~~~~~~~~G~~a~~~l~~~~~d~   95 (161)
T PF00455_consen   22 TIFLDSGTTTLELAKYLPDKKNLTVVTNSLPIANELSENPNIEVILLGGEVNPKSLSFVGPIALEALRQFRFDK   95 (161)
T ss_pred             EEEEECchHHHHHHHHhhcCCceEEEECCHHHHHHHHhcCceEEEEeCCEEEcCCCcEECchHHHHHHhhccce
Confidence            378999999999999999997766543           236788889998776666666655555444444443

This family of prokaryotic regulators is named after Escherichia coli deoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerization domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].

>cd05470 pepsin_retropepsin_like Cellular and retroviral pepsin-like aspartate proteases

Probab=81.00  E-value=1.7  Score=28.25  Aligned_cols=27  Identities=19%  Similarity=0.258  Sum_probs=21.5

Q ss_pred             EEEECC--EEEEEEecCCCcccccCHHHH
Q 043220           45 ATKIRF--HEVVILISSGSTANFVSDKVA   71 (121)
Q Consensus        45 ~g~i~~--~~v~~LIDSGAT~nFI~~~~a   71 (121)
                      ...|+.  +++.+++|+||+..++...-+
T Consensus         2 ~i~vGtP~q~~~~~~DTGSs~~Wv~~~~c   30 (109)
T cd05470           2 EIGIGTPPQTFNVLLDTGSSNLWVPSVDC   30 (109)
T ss_pred             EEEeCCCCceEEEEEeCCCCCEEEeCCCC
Confidence            355665  889999999999999887644

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

>cd05474 SAP_like SAPs, pepsin-like proteinases secreted from pathogens to degrade host proteins

Probab=80.64  E-value=4.2  Score=30.97  Aligned_cols=25  Identities=20%  Similarity=0.400  Sum_probs=21.4

Q ss_pred             EEEEEECC--EEEEEEecCCCcccccC
Q 043220           43 VVATKIRF--HEVVILISSGSTANFVS   67 (121)
Q Consensus        43 ~v~g~i~~--~~v~~LIDSGAT~nFI~   67 (121)
                      .+...|+.  +++.+++||||+..++.
T Consensus         4 ~~~i~iGtp~q~~~v~~DTgS~~~wv~   30 (295)
T cd05474           4 SAELSVGTPPQKVTVLLDTGSSDLWVP   30 (295)
T ss_pred             EEEEEECCCCcEEEEEEeCCCCcceee
Confidence            45667776  88999999999999998

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	121
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	99.75
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	99.61
3slz_A	132	GAG-Pro-POL polyprotein; beta sheet and dimer, pro	98.38
1fmb_A	104	EIAV protease; hydrolase (acid proteinase), RNA-di	97.96
3ec0_A	99	Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1	97.37
2hs1_A	99	HIV-1 protease; ultra-high resolution active site	97.15
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	96.66
2hah_A	116	Protease, retropepsin; retroviral, aspartyl, hydro	94.61
3sqf_A	114	Protease; folded monomer, retropepsin, D-type retr	93.69
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	93.39
2rsp_A	124	RSV protease; hydrolase(aspartyl proteinase); 2.00	91.4
3liy_A	116	Protease; hydrolase, hydrolase-hydrolase inhibitor	87.34
1lya_A	97	Cathepsin D; lysosomal aspartic protease; HET: NAG	85.42
1j71_A	334	Candidapepsin, aspartic proteinase; candida tropic	85.17
3fv3_A	339	SAPP1P-secreted aspartic protease 1; secreted aspa	84.25
2jys_A	107	Protease/reverse transcriptase; retroviral proteas	81.83

>3s8i_A Protein DDI1 homolog 1; protease, structural genomics, structural genomics consortiu retropepsin-like domain, protein turnover, hydrolase; 1.70A {Homo sapiens}

Probab=99.75  E-value=8.4e-19  Score=124.85  Aligned_cols=83  Identities=13%  Similarity=0.121  Sum_probs=61.6

Q ss_pred             cccCeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEE--ecCCc----------------eecc--
Q 043220           37 QLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVR--IANGA----------------HLKS--   96 (121)
Q Consensus        37 ~~~~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~--va~G~----------------~l~~--   96 (121)
                      ....++.+.+.|||+++.+||||||+++||++++|+|+|++......+...  .+++.                ...|  
T Consensus        20 ~~~~~l~v~~~Ing~~v~~LVDTGAs~s~Is~~~A~rlGL~~~~~~~~~~~a~g~G~~~~~g~v~~~~I~Ig~~~~~~~~   99 (148)
T 3s8i_A           20 GQVTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIIGRVHLAQIQIEGDFLQCSF   99 (148)
T ss_dssp             --CCCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHTTCGGGEEGGGCEECCC---CEEEEEEEEEEEEETTEEEEEEE
T ss_pred             cccCEEEEEEEECCEEEEEEEeCCCCcEeeCHHHHHHcCCccccCcceeEEEEcCCccEEEEEEEEEEEEECCEEEEEEE
Confidence            456788999999999999999999999999999999999975321111111  11111                1111  


Q ss_pred             -------ceEeecchhhhhcCCeeeecccCC
Q 043220           97 -------PDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        97 -------~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                             +|+|||||||++++. .|||++++
T Consensus       100 ~Vle~~~~d~LLGmD~L~~~~~-~ID~~~~~  129 (148)
T 3s8i_A          100 SILEDQPMDMLLGLDMLRRHQC-SIDLKKNV  129 (148)
T ss_dssp             EEETTCSSSEEECHHHHHHTTC-EEETTTTE
T ss_pred             EEeCCCCcCeeccHHHHHhCCE-EEEcCCCE
Confidence                   899999999999997 59999864

>2i1a_A DNA damage-inducible protein DDI1; acid protease fold, dimer, retroviral protease domain, protein turnover; HET: DNA; 2.30A {Saccharomyces cerevisiae}

Probab=99.61  E-value=5.3e-16  Score=108.88  Aligned_cols=83  Identities=16%  Similarity=0.151  Sum_probs=61.1

Q ss_pred             cccCeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeE--EEecCCc----------------eec---
Q 043220           37 QLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFS--VRIANGA----------------HLK---   95 (121)
Q Consensus        37 ~~~~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~--V~va~G~----------------~l~---   95 (121)
                      ...+++.+.+.|||+++.+||||||++++|++++|++++++......+.  +...+|.                ...   
T Consensus        22 ~~~~~~~v~v~InG~~~~~LvDTGAs~s~is~~~a~~lgl~~~~~~~~~~~a~g~g~~~~~~~~~~~~i~ig~~~~~~~~  101 (148)
T 2i1a_A           22 TQVPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGKIIGRIHQAQVKIETQYIPCSF  101 (148)
T ss_dssp             -CCCCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHHTGGGGCBCCCC-----------CEEEEEEEEEETTEEEEEEE
T ss_pred             cccceEEEEEEECCEEEEEEEECCCCccccCHHHHHHcCCCccCCcceEEEEecCCCcccccEEEEEEEEECCEEeceeE
Confidence            3567899999999999999999999999999999999998643222221  1111111                100   


Q ss_pred             -----cceEeecchhhhhcCCeeeecccCC
Q 043220           96 -----SPDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        96 -----~~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                           .+|+|||||||++++. .|||++++
T Consensus       102 ~vl~~~~d~iLG~d~L~~~~~-~ID~~~~~  130 (148)
T 2i1a_A          102 TVLDTDIDVLIGLDMLKRHLA-CVDLKENV  130 (148)
T ss_dssp             EEECSSCSEEECHHHHHHTTC-EEETTTTE
T ss_pred             EEecCCCCeEecHHHHhhCCE-EEECCCCE
Confidence                 1789999999999988 69998764

>3slz_A GAG-Pro-POL polyprotein; beta sheet and dimer, protease, peptide inhibitor, TL-3 PEPS virus, hydrolase-hydrolase inhibitor complex; HET: 3TL; 1.40A {Dg-75 murine leukemia virus} PDB: 3nr6_A* 3sm1_A* 3sm2_A* 4exh_A*

Probab=98.38  E-value=1.9e-07  Score=65.19  Aligned_cols=77  Identities=13%  Similarity=0.139  Sum_probs=53.6

Q ss_pred             ecccccCeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCcee-----------------c-
Q 043220           34 KCGQLRKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHL-----------------K-   95 (121)
Q Consensus        34 ~g~~~~~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l-----------------~-   95 (121)
                      .|....+.-.+.++|+|+++.+|+|+||+.+.++..-+.     . ..+|..+..++|...                 . 
T Consensus        15 ~~~d~~~RP~v~i~I~G~~~~~LlDTGAd~tVl~~~~~p-----~-~~~p~~I~GiGG~i~vr~~~~i~IeI~g~~~~~~   88 (132)
T 3slz_A           15 QGQEPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGP-----L-SDKSAWVQGATGGKRYRWTTDRKVHLATGKVTHS   88 (132)
T ss_dssp             ---CCCCSSEEEEEETTEEEEEEECTTCSSCEECSCCCS-----E-EEEEEEEECSSCEEEEEEECCEEEEETTEEEEEC
T ss_pred             cCCCccCCCEEEEEECCEEEEEEEeCCCCeEEEccccCC-----C-CCCceEEEccCCEEEEEEEeeeEEEECCeeecce
Confidence            445566677788999999999999999999999875333     1 123445555555322                 0 


Q ss_pred             ------cceEeecchhhhhcCCeeeecc
Q 043220           96 ------SPDVALDVKWSEQIGSIMRGWK  117 (121)
Q Consensus        96 ------~~dvILG~~WL~~~~p~~idw~  117 (121)
                            +..-|||+|||.+++.. +++.
T Consensus        89 ~lV~~~tPvnLLGrd~Ltqlg~t-L~fp  115 (132)
T 3slz_A           89 FLHVPDCPYPLLGRDLLTKLKAQ-IHFE  115 (132)
T ss_dssp             CEECTTSSSCEECHHHHHHHTCE-EEEE
T ss_pred             EEEECCCCccEECHhhHhhCCcE-EECC
Confidence                  14468999999999984 7764

>1fmb_A EIAV protease; hydrolase (acid proteinase), RNA-directed DNA polymerase, AS protease, endonuclease, polyprotein; HET: HYB; 1.80A {Equine infectious anemia virus} SCOP: b.50.1.1 PDB: 2fmb_A*

Probab=97.96  E-value=1.4e-05  Score=53.51  Aligned_cols=74  Identities=14%  Similarity=0.103  Sum_probs=52.9

Q ss_pred             eEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCc---------------eec-------cce
Q 043220           41 FCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGA---------------HLK-------SPD   98 (121)
Q Consensus        41 ~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~---------------~l~-------~~d   98 (121)
                      ...++.+|+|+.+.+|+||||-.+.++.+...++++|-.+.+|..+.-.+|.               +..       +..
T Consensus         8 RP~v~v~I~Gq~~e~LLDTGAD~TVl~~~~w~~i~lp~~~w~p~~i~GiGG~i~v~~~~i~i~i~g~~~~gtvlv~~tp~   87 (104)
T 1fmb_A            8 RPTTIVLINDTPLNVLLDTGADTSVLTTAHYNRLKYRGRKYQGTGIGGVGGNVETFSTPVTIKKKGRHIKTRMLVADIPV   87 (104)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHCSSCCCCEECCCEEETTEEECCEEEEEEEEETTEEEEEEEEEESCSS
T ss_pred             CCEEEEEECCEEEEEEeccCCCcEEEccccCcccCCCCccCCccEEEeCCCeEEeeEeeeEEEECCeEEEEEEEECCCCC
Confidence            4457899999999999999999999999999988887752222222222221               110       145


Q ss_pred             EeecchhhhhcCCeeee
Q 043220           99 VALDVKWSEQIGSIMRG  115 (121)
Q Consensus        99 vILG~~WL~~~~p~~id  115 (121)
                      =|+|-|||.+.+.. +|
T Consensus        88 niiGRd~L~qlg~t-Ln  103 (104)
T 1fmb_A           88 TILGRDILQDLGAK-LV  103 (104)
T ss_dssp             CEECHHHHHHTTCC-CC
T ss_pred             CEecHhHHhhcCcE-Ee
Confidence            68999999999874 44

>3ec0_A Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1.18A {Human immunodeficiency virus type 2} SCOP: b.50.1.1 PDB: 1hii_A* 1hsi_A 1hsh_A* 1idb_A* 1jld_A* 2mip_A 1ida_A* 3ebz_A* 3ecg_A* 3s45_A* 4upj_A* 1ivq_A* 1ivp_A 2hpf_A 3upj_A* 2hpe_A* 5upj_A* 6upj_A* 1sip_A 1tcw_A* ...

Probab=97.37  E-value=0.00094  Score=44.19  Aligned_cols=66  Identities=18%  Similarity=0.175  Sum_probs=44.0

Q ss_pred             EEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCceec-----------c-------------ce
Q 043220           43 VVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLK-----------S-------------PD   98 (121)
Q Consensus        43 ~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l~-----------~-------------~d   98 (121)
                      .++.+|+|+.+.+|+||||-++.+.     ...+|-.- +|. ...+.|..++           |             .-
T Consensus        10 ~vti~I~Gq~~e~LLDTGAD~TVl~-----~~~~Pg~w-~pk-~igGiGG~i~v~qy~~i~iei~g~~~~gtvlV~~tPv   82 (99)
T 3ec0_A           10 VVTAYIEGQPVEVLLDTGADDSIVA-----GIELGNNY-SPK-IVGGIGGFINTKEYKNVEIEVLNKKVRATIMTGDTPI   82 (99)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEES-----SCCCCSCC-EEE-EEEETTEEEEEEEEEEEEEEETTEEEEEEEEEECCSS
T ss_pred             eEEEEECCEEEEEEEecCCCceEEc-----CcccCCCC-Cce-EEEecCCcEeeeEEeeEEEEECCeEEEEEEEeCCCCc
Confidence            5779999999999999999999995     23343221 121 2333333211           1             44


Q ss_pred             EeecchhhhhcCCeeeec
Q 043220           99 VALDVKWSEQIGSIMRGW  116 (121)
Q Consensus        99 vILG~~WL~~~~p~~idw  116 (121)
                      =|+|-|+|.+.|.. ++|
T Consensus        83 niiGRnlLtqlG~t-Lnf   99 (99)
T 3ec0_A           83 NIFGRNILTALGMS-LNL   99 (99)
T ss_dssp             CEECHHHHHHHTCE-EEC
T ss_pred             CeeehhhHhhcCcE-EeC
Confidence            58999999999983 553

>2hs1_A HIV-1 protease; ultra-high resolution active site surface binding site, HYDR; HET: 017; 0.84A {Human immunodeficiency virus 1} PDB: 3nu4_A* 3tl9_A* 3tkw_A* 3tkg_A* 3ndu_A* 3ndt_A* 3k4v_A* 3a2o_A* 1fgc_C* 2a1e_A* 2aod_A* 2aoi_A* 2aoj_A* 2hb3_A* 2ien_A* 1sdt_A* 2z4o_A* 2zye_A* 2nmw_A* 3b7v_A* ...

Probab=97.15  E-value=0.0022  Score=42.35  Aligned_cols=67  Identities=22%  Similarity=0.285  Sum_probs=44.2

Q ss_pred             EEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCceec-----------c-------------c
Q 043220           42 CVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHLK-----------S-------------P   97 (121)
Q Consensus        42 ~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l~-----------~-------------~   97 (121)
                      -.++.+|+|+.+.+|+||||-++.++.     ..+|-. .+|. ...+.|..++           |             .
T Consensus         9 P~vtvkI~Gq~~eaLLDTGAD~TVl~~-----~~~p~~-wkpk-~igGiGG~i~v~qy~qi~iei~g~~~~gtvlV~~tP   81 (99)
T 2hs1_A            9 PLVTIKIGGQLKEALLDTGADDTIIEE-----MSLPGR-WKPK-MIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTP   81 (99)
T ss_dssp             CEEEEEETTEEEEEEECTTCSSEEESC-----CSSCCC-CEEE-EEEETTEEEEEEEEEEEEEEETTEEEEEEEEESCCS
T ss_pred             CEEEEEECCEEEEEEeccCCCcEEEec-----ccCCCC-CCCc-EEEeCCCcEeeeEeccEEEEEeCCEEEEEEEeCCCc
Confidence            347799999999999999999999984     233322 1222 2233332211           1             3


Q ss_pred             eEeecchhhhhcCCeeeec
Q 043220           98 DVALDVKWSEQIGSIMRGW  116 (121)
Q Consensus        98 dvILG~~WL~~~~p~~idw  116 (121)
                      -=|+|-|||.+.|.. +++
T Consensus        82 vniiGRd~Ltqlg~t-Lnf   99 (99)
T 2hs1_A           82 VNIIGRNLLTQIGAT-LNF   99 (99)
T ss_dssp             SCEECHHHHTTTTCE-EEC
T ss_pred             cCchhHhHHHHcCCE-EeC
Confidence            348999999999884 553

>3ka2_A [L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydrolase-hydrolase inhibitor complex; HET: YCM 2NC; 1.40A {Synthetic} PDB: 3fsm_A* 3gi0_A* 2o40_A* 3hzc_A* 3hlo_A* 3iaw_A* 3nxe_A* 3nxn_A* 4epj_A 4ep2_A 4ep3_A 4eq0_A 4eqj_A 1hvc_A* 1g6l_A 2whh_A* 1lv1_A* 3dox_A 3kt5_A 3kt2_A ...

Probab=96.66  E-value=0.0067  Score=44.83  Aligned_cols=69  Identities=19%  Similarity=0.175  Sum_probs=47.5

Q ss_pred             eEEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCcee-----------------c-------c
Q 043220           41 FCVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGAHL-----------------K-------S   96 (121)
Q Consensus        41 ~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~~l-----------------~-------~   96 (121)
                      ...++.+|+|+.+.+|+||||.++.+.     ..++|-. .+|..+ .+-|..+                 .       +
T Consensus         8 RP~vtv~I~Gq~~e~LLDTGAD~TVl~-----~~~lpg~-w~pk~i-gGIGG~i~vrqy~~i~iei~g~~~~gtvlVg~t   80 (203)
T 3ka2_A            8 RPLVTIRIGGQLKEALLDTGADDTVIE-----ELNLPGX-WKPKLI-GGIAGFIKVRQYDQIPVEIXGHKAIGTVLVGPT   80 (203)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEC-----SCCCSSC-EEEEEE-EETTEEEEEEEEEEEEEEETTEEEEEEEEESCC
T ss_pred             CCeEEEEECCEEEEEEEecCCCceEEe-----cccCCCC-CCceEE-EEccCcEEEEEEcceeEEEcCeEEEEEEeeCCC
Confidence            346789999999999999999999998     3555542 122222 2222211                 1       1


Q ss_pred             ceEeecchhhhhcCCeeeecc
Q 043220           97 PDVALDVKWSEQIGSIMRGWK  117 (121)
Q Consensus        97 ~dvILG~~WL~~~~p~~idw~  117 (121)
                      ..=|+|-|.|.+.+. .+++.
T Consensus        81 PvnIiGRd~LtqlG~-tLnf~  100 (203)
T 3ka2_A           81 PVNIIGRNLLTQIGX-TLNFX  100 (203)
T ss_dssp             SSCEECHHHHTTTTC-EEEGG
T ss_pred             CcCccchhhhhhcCc-eEEec
Confidence            555899999999998 47775

>2hah_A Protease, retropepsin; retroviral, aspartyl, hydrolase-hydrolase complex; HET: 3TL; 1.70A {Feline immunodeficiency virus} PDB: 3ogp_A* 3ogq_A* 2fiv_A* 6fiv_A* 3fiv_A* 5fiv_A* 4fiv_A* 1fiv_A* 1b11_A*

Probab=94.61  E-value=0.035  Score=37.51  Aligned_cols=28  Identities=7%  Similarity=0.140  Sum_probs=24.4

Q ss_pred             CeEEEEEEECCEEEEEEecCCCcccccCHH
Q 043220           40 KFCVVATKIRFHEVVILISSGSTANFVSDK   69 (121)
Q Consensus        40 ~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~   69 (121)
                      +.+.  .+|+|+.+.+|+||||-.+.|...
T Consensus        14 rP~v--ikI~Gq~~eaLLDTGAD~TVi~~~   41 (116)
T 2hah_A           14 PEIL--IFVNGYPIKFLLDTGADITVLNRR   41 (116)
T ss_dssp             CEEE--EEETTEEEEEEECTTCSSCEEEGG
T ss_pred             CCEE--EEECCEEEEEEecCCCCcEEEccc
Confidence            4444  999999999999999999999863

>3sqf_A Protease; folded monomer, retropepsin, D-type retrovirus; 1.63A {Mason-pfizer monkey virus} SCOP: b.50.1.1 PDB: 1nso_A

Probab=93.69  E-value=0.068  Score=36.04  Aligned_cols=26  Identities=12%  Similarity=0.101  Sum_probs=23.3

Q ss_pred             EEEEEECCEEEEEEecCCCcccccCH
Q 043220           43 VVATKIRFHEVVILISSGSTANFVSD   68 (121)
Q Consensus        43 ~v~g~i~~~~v~~LIDSGAT~nFI~~   68 (121)
                      .++.+|+|+.+.+|+||||-.+.|..
T Consensus        11 ~vti~I~Gq~~eaLLDTGADdTVi~~   36 (114)
T 3sqf_A           11 SLTLWLDDKMFTGLINTGADVTIIKL   36 (114)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEEEG
T ss_pred             eEEEEECCEEEEEEEccCCCceEEec
Confidence            46689999999999999999999974

>3ka2_A [L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydrolase-hydrolase inhibitor complex; HET: YCM 2NC; 1.40A {Synthetic} PDB: 3fsm_A* 3gi0_A* 2o40_A* 3hzc_A* 3hlo_A* 3iaw_A* 3nxe_A* 3nxn_A* 4epj_A 4ep2_A 4ep3_A 4eq0_A 4eqj_A 1hvc_A* 1g6l_A 2whh_A* 1lv1_A* 3dox_A 3kt5_A 3kt2_A ...

Probab=93.39  E-value=0.41  Score=35.19  Aligned_cols=26  Identities=15%  Similarity=0.216  Sum_probs=23.7

Q ss_pred             EEEEEEECCEEEEEEecCCCcccccC
Q 043220           42 CVVATKIRFHEVVILISSGSTANFVS   67 (121)
Q Consensus        42 ~~v~g~i~~~~v~~LIDSGAT~nFI~   67 (121)
                      -.++.+|+|+.+.+|+|+||-++.+.
T Consensus       113 P~~~iki~Gq~~e~LlDTGAD~TVl~  138 (203)
T 3ka2_A          113 PLVTIRIGGQLKEALLDTGADDTVIE  138 (203)
T ss_dssp             CEEEEEETTEEEEEEECTTCSSCEEC
T ss_pred             CcEEEEECCEEEeeeecccCCceeee
Confidence            45789999999999999999999995

>2rsp_A RSV protease; hydrolase(aspartyl proteinase); 2.00A {Rous sarcoma virus} SCOP: b.50.1.1 PDB: 1mvp_A 1bai_A*

Probab=91.40  E-value=0.11  Score=35.45  Aligned_cols=21  Identities=24%  Similarity=0.374  Sum_probs=19.6

Q ss_pred             ECCEEEEEEecCCCcccccCH
Q 043220           48 IRFHEVVILISSGSTANFVSD   68 (121)
Q Consensus        48 i~~~~v~~LIDSGAT~nFI~~   68 (121)
                      |+|+.+.+|+||||-++.+..
T Consensus        27 i~gq~~eaLLDTGAD~TVl~~   47 (124)
T 2rsp_A           27 QRSVYITALLDSGADITIISE   47 (124)
T ss_dssp             CSEEEEEEEECTTCSSCEEET
T ss_pred             CCCEEEEEEecCCCCcEEEec
Confidence            899999999999999999974

>3liy_A Protease; hydrolase, hydrolase-hydrolase inhibitor complex; HET: STA; 1.86A {Human t-lymphotropic virus 1} PDB: 2b7f_A* 3liq_A* 3lit_A* 3liv_A* 3lix_A* 3lin_A*

Probab=87.34  E-value=0.43  Score=32.16  Aligned_cols=26  Identities=12%  Similarity=0.312  Sum_probs=23.0

Q ss_pred             EEEEEEC-----CEEEEEEecCCCcccccCH
Q 043220           43 VVATKIR-----FHEVVILISSGSTANFVSD   68 (121)
Q Consensus        43 ~v~g~i~-----~~~v~~LIDSGAT~nFI~~   68 (121)
                      .++.+|+     |+.+.+|+|+||-.+.+..
T Consensus        12 lvtikI~~~~~~Gq~~eaLLDTGADdTVl~~   42 (116)
T 3liy_A           12 VIKAQVDTQTSHPKTIEALLDTGADMTVIPI   42 (116)
T ss_dssp             EEEEEEECSSSCCEEEEEEECTTBSSCEEEG
T ss_pred             eEEEEEccccCCCeEeEEEeccCCCccEEec
Confidence            4678888     9999999999999999874

>1lya_A Cathepsin D; lysosomal aspartic protease; HET: NAG BMA MAN; 2.50A {Homo sapiens} SCOP: b.50.1.2 PDB: 1lyb_A* 1lyw_A*

Probab=85.42  E-value=1.1  Score=28.44  Aligned_cols=29  Identities=14%  Similarity=0.125  Sum_probs=24.3

Q ss_pred             CeEEEEEEEC--CEEEEEEecCCCcccccCH
Q 043220           40 KFCVVATKIR--FHEVVILISSGSTANFVSD   68 (121)
Q Consensus        40 ~~~~v~g~i~--~~~v~~LIDSGAT~nFI~~   68 (121)
                      ....+...|+  .+++.++||+||+..++..
T Consensus        13 ~~Y~~~i~iGTP~Q~~~v~~DTGSs~lWv~~   43 (97)
T 1lya_A           13 AQYYGEIGIGTPPQCFTVVFDTGSSNLWVPS   43 (97)
T ss_dssp             TEEEEEEEETTTTEEEEEEEETTCCCEEEEB
T ss_pred             CeEEEEEEECCCCeEEEEEEeCCCCceEEeE
Confidence            3466778888  7999999999999999864

>1j71_A Candidapepsin, aspartic proteinase; candida tropicalis aspartic protease, SAPT1, hydrolase; 1.80A {Candida tropicalis} SCOP: b.50.1.2

Probab=85.17  E-value=6  Score=29.82  Aligned_cols=74  Identities=9%  Similarity=0.081  Sum_probs=47.6

Q ss_pred             EEECCEE----EEEEecCCCcccccCHHHHhhc----C------------CCCCCCCCeEEEecCCcee-----------
Q 043220           46 TKIRFHE----VVILISSGSTANFVSDKVAALL----P------------LPMMPTKPFSVRIANGAHL-----------   94 (121)
Q Consensus        46 g~i~~~~----v~~LIDSGAT~nFI~~~~a~rl----~------------l~~~~~~~~~V~va~G~~l-----------   94 (121)
                      ..++++.    ..++||||++..++.+...+++    +            .+......+.....+|..+           
T Consensus       202 i~v~g~~~~~~~~~iiDSGTt~~~lP~~~~~~l~~~~~~~~~~~~~~~~~~~C~~~p~i~f~f~~g~~~~i~~~~y~~~~  281 (334)
T 1j71_A          202 INFDGTSVSTNADVVLDSGTTITYFSQSTADKFARIVGATWDSRNEIYRLPSCDLSGDAVFNFDQGVKITVPLSELILKD  281 (334)
T ss_dssp             EEETTEEEEEEEEEEECTTCSSEEECHHHHHHHHHHHTCEEETTTTEEECSSSCCCSEEEEEESTTCEEEEEGGGGEEEC
T ss_pred             EEECCEeccCCccEEEeCCCCcEecCHHHHHHHHHHcCCcccCCCceEEEEcCCCCCceEEEEcCCcEEEECHHHheeec
Confidence            3566654    3589999999999999887653    2            1111122345555555432           


Q ss_pred             ----cc-------ceEeecchhhhhcCCeeeecccCC
Q 043220           95 ----KS-------PDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        95 ----~~-------~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                          .|       -..|||-.||+.+-.+ .|+.++|
T Consensus       282 ~~~~~C~~~i~~~~~~iLG~~fl~~~y~v-fD~~~~~  317 (334)
T 1j71_A          282 SDSSICYFGISRNDANILGDNFLRRAYIV-YDLDDKT  317 (334)
T ss_dssp             SSSSCEEESEEECTTCEECHHHHTTEEEE-EETTTTE
T ss_pred             CCCCeeEEEEeECCCcEEChHhhccEEEE-EECCCCE
Confidence                14       3479999999998774 7876653

>3fv3_A SAPP1P-secreted aspartic protease 1; secreted aspartic protease, virulence factor, H; HET: STA; 1.85A {Candida parapsilosis} SCOP: b.50.1.0 PDB: 3tne_A*

Probab=84.25  E-value=2.2  Score=32.18  Aligned_cols=73  Identities=16%  Similarity=0.204  Sum_probs=47.9

Q ss_pred             EECCEE----EEEEecCCCcccccCHHHHhhc----CCCC--------------C--CCCCeEEEecCCceec-------
Q 043220           47 KIRFHE----VVILISSGSTANFVSDKVAALL----PLPM--------------M--PTKPFSVRIANGAHLK-------   95 (121)
Q Consensus        47 ~i~~~~----v~~LIDSGAT~nFI~~~~a~rl----~l~~--------------~--~~~~~~V~va~G~~l~-------   95 (121)
                      .++++.    ..++||||.+..++....++++    +...              .  ....+....++|..+.       
T Consensus       205 ~v~g~~~~~~~~~iiDSGtt~~~lP~~~~~~i~~~~~~~~~~~~~~~~~~~~~C~~~~~p~i~f~f~~g~~~~v~~~~~~  284 (339)
T 3fv3_A          205 NLKGSSFSFGDGALLDSGTTLTYFPSDFAAQLADKAGARLVQVARDQYLYFIDCNTDTSGTTVFNFGNGAKITVPNTEYV  284 (339)
T ss_dssp             EESSCEEEEEEEEEECTTBSSEEECHHHHHHHHHHHTCEEEEEETTEEEEEECTTCCCCSEEEEEETTSCEEEEEGGGGE
T ss_pred             EECCEeecCCccEEEeCCCCCEecCHHHHHHHHHHcCCEEccccccCceEEEecCCCCCCcEEEEECCCCEEEECHHHhe
Confidence            455544    3589999999999999887764    2111              1  1233556666664331       


Q ss_pred             -------c-------ceEeecchhhhhcCCeeeecccCC
Q 043220           96 -------S-------PDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        96 -------~-------~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                             |       -..|||..||+.+-.+ .|+.++|
T Consensus       285 ~~~~~~~C~~~i~~~~~~ilG~~fl~~~y~v-fD~~~~~  322 (339)
T 3fv3_A          285 YQNGDGTCLWGIQPSDDTILGDNFLRHAYLL-YNLDANT  322 (339)
T ss_dssp             EECSSSCEEESEEECSSCEECHHHHTTEEEE-EETTTTE
T ss_pred             eeCCCCeEEEEEEeCCcEEeChHHHhCEEEE-EECCCCE
Confidence                   3       2369999999998774 8887654

>2jys_A Protease/reverse transcriptase; retroviral protease, hydrolase; NMR {Simian foamy virus type 1}

Probab=81.83  E-value=3.3  Score=27.04  Aligned_cols=30  Identities=17%  Similarity=0.162  Sum_probs=27.3

Q ss_pred             EEEEECCEEEEEEecCCCcccccCHHHHhh
Q 043220           44 VATKIRFHEVVILISSGSTANFVSDKVAAL   73 (121)
Q Consensus        44 v~g~i~~~~v~~LIDSGAT~nFI~~~~a~r   73 (121)
                      +.+.|.|..+..--||||+...|.+.+...
T Consensus        10 L~vEiKg~kLkg~WDsGA~ITCiP~~fL~~   39 (107)
T 2jys_A           10 LEAEIKGTKLKAHWDSGATITCVPEAFLED   39 (107)
T ss_dssp             EEEEETTEEEEEEECTTCSSEEEEGGGTTT
T ss_pred             eeEEEeCcEEEEEecCCCeEEEcchHHhcc
Confidence            678899999999999999999999988765

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	121
d2fmba_	104	EIAV protease {Equine infectious anemia virus [Tax	97.78
d4fiva_	113	Feline immunodeficiency virus (FIV) protease {Feli	96.19
d1nsoa_	107	Mason-Pfizer monkey virus protease {Simian retrovi	96.15
d2nmza1	99	Human immunodeficiency virus type 1 protease {Huma	95.43
d1hvca_	203	Human immunodeficiency virus type 1 protease {Huma	93.35
d3ecga1	99	Human immunodeficiency virus type 2 (HIV-2) protea	92.01
d1t6ex_	381	Xylanase inhibitor TAXI-I {Wheat (Triticum aestivu	91.3
d1eaga_	342	Acid protease {Yeast (Candida albicans) [TaxId: 54	91.18
d2bjua1	329	Plasmepsin (a hemoglobin-degrading enzyme) {Plasmo	90.34
d1j71a_	334	Acid protease {Yeast (Candida tropicalis) [TaxId:	90.1
d1izea_	323	Acid protease {Fungus (Aspergillus oryzae) [TaxId:	90.06
d1bxoa_	323	Acid protease {Fungus (Penicillium janthinellum),	89.87
d1miqa_	373	Plasmepsin (a hemoglobin-degrading enzyme) {Plasmo	89.27
d1am5a_	324	Pepsin(ogen) {Atlantic cod (Gadus morhua) [TaxId:	88.76
d1wkra_	340	Acid protease {Irpex lacteus (Polyporus tulipifera	88.49
d2apra_	325	Acid protease {Bread mold (Rhizopus chinensis) [Ta	87.92
d1smra_	335	Chymosin (synonym: renin) {Mouse (Mus musculus) [T	86.57
d2rspa_	124	Rous sarcoma virus protease {Rous sarcoma virus, s	85.02
d3cmsa_	323	Chymosin (synonym: renin) {Cow (Bos taurus) [TaxId	83.28
d1oewa_	330	Endothiapepsin {Chestnut blight fungus (Endothia p	82.61
d2qp8a1	387	beta-secretase (memapsin) {Human (Homo sapiens) [T	82.04
d1dpja_	329	Acid protease {Baker's yeast (Saccharomyces cerevi	81.75

>d2fmba_ b.50.1.1 (A:) EIAV protease {Equine infectious anemia virus [TaxId: 11665]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Retroviral protease (retropepsin)
domain: EIAV protease
species: Equine infectious anemia virus [TaxId: 11665]

Probab=97.78  E-value=2.2e-05  Score=50.79  Aligned_cols=37  Identities=14%  Similarity=0.126  Sum_probs=30.8

Q ss_pred             cCeEEEEEEECCEEEEEEecCCCcccccCHHHHhhcC
Q 043220           39 RKFCVVATKIRFHEVVILISSGSTANFVSDKVAALLP   75 (121)
Q Consensus        39 ~~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~   75 (121)
                      -+.-.++.+|+|+++.+|+||||.++.|+..--.+..
T Consensus         6 ~~RP~~~i~I~Gq~v~~LLDTGAD~TVI~~~~~p~~~   42 (104)
T d2fmba_           6 EKRPTTIVLINDTPLNVLLDTGADTSVLTTAHYNRLK   42 (104)
T ss_dssp             SSCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHCS
T ss_pred             ccCeEEEEEECCEEEEEEEeCCCCeEEEcccccCccC
Confidence            3445688999999999999999999999987766543

>d4fiva_ b.50.1.1 (A:) Feline immunodeficiency virus (FIV) protease {Feline immunodeficiency virus [TaxId: 11673]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Retroviral protease (retropepsin)
domain: Feline immunodeficiency virus (FIV) protease
species: Feline immunodeficiency virus [TaxId: 11673]

Probab=96.19  E-value=0.0021  Score=41.73  Aligned_cols=30  Identities=10%  Similarity=0.149  Sum_probs=25.8

Q ss_pred             CeEEEEEEECCEEEEEEecCCCcccccCHH
Q 043220           40 KFCVVATKIRFHEVVILISSGSTANFVSDK   69 (121)
Q Consensus        40 ~~~~v~g~i~~~~v~~LIDSGAT~nFI~~~   69 (121)
                      +.-+++.+|+|+++.+|+||||-++.|+..
T Consensus         9 ~RP~v~v~I~Gq~v~~LLDTGAD~TVi~~~   38 (113)
T d4fiva_           9 KRPEILIFVNGYPIKFLLDTGADITILNRR   38 (113)
T ss_dssp             SCCEEEEEETTEEEEEEECTTCSSCEEEGG
T ss_pred             cCCeEEEEECCEEEEEEEcCCCCcEEEecc
Confidence            344678889999999999999999999764

>d1nsoa_ b.50.1.1 (A:) Mason-Pfizer monkey virus protease {Simian retrovirus 1, SRV-1 [TaxId: 11942]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Retroviral protease (retropepsin)
domain: Mason-Pfizer monkey virus protease
species: Simian retrovirus 1, SRV-1 [TaxId: 11942]

Probab=96.15  E-value=0.0017  Score=41.78  Aligned_cols=28  Identities=11%  Similarity=0.074  Sum_probs=24.5

Q ss_pred             EEEEEECCEEEEEEecCCCcccccCHHH
Q 043220           43 VVATKIRFHEVVILISSGSTANFVSDKV   70 (121)
Q Consensus        43 ~v~g~i~~~~v~~LIDSGAT~nFI~~~~   70 (121)
                      .++.+|+|+++.+|+||||.++.|...-
T Consensus        11 ~~~v~I~G~~v~~LLDTGAD~TVI~~~~   38 (107)
T d1nsoa_          11 SLTLWLDDKMFTGLINTGADVTIIKLED   38 (107)
T ss_dssp             CEEEEETTEEEEECCCSSCSSCBCCGGG
T ss_pred             EEEEEECCEEEEeeecCCCCcEEEeccc
Confidence            3567899999999999999999998754

>d2nmza1 b.50.1.1 (A:1-99) Human immunodeficiency virus type 1 protease {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Retroviral protease (retropepsin)
domain: Human immunodeficiency virus type 1 protease
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=95.43  E-value=0.014  Score=36.80  Aligned_cols=67  Identities=19%  Similarity=0.232  Sum_probs=43.1

Q ss_pred             EEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCC-----------------ceecc-----ce-E
Q 043220           43 VVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANG-----------------AHLKS-----PD-V   99 (121)
Q Consensus        43 ~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G-----------------~~l~~-----~d-v   99 (121)
                      .++.+|+|+.+.+|+|+||-.+.+.     ..+++-+ .+|-.+.--+|                 ..+.+     .. =
T Consensus        10 ~vtvkIgGq~~eaLLDTGADdTVle-----ei~lpg~-WkPk~IgGIGGfikVrqYd~i~iei~g~k~~gtVLVgpTPvN   83 (99)
T d2nmza1          10 LVTIKIGGQLKEALLDTGADDTVIE-----EMSLPGR-WKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPAN   83 (99)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEEE-----SCCCCSC-CEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEESCSSC
T ss_pred             eEEEEECCEEEEEeeccCCCceEEe-----cccCCCC-CCceEEEeccceEEEEEeCceEEEECCcEEEEEEEECCCCcc
Confidence            5789999999999999999998884     3555532 22222222222                 11111     33 3


Q ss_pred             eecchhhhhcCCeeeec
Q 043220          100 ALDVKWSEQIGSIMRGW  116 (121)
Q Consensus       100 ILG~~WL~~~~p~~idw  116 (121)
                      |+|-+-|.+.|. ..||
T Consensus        84 IiGRN~Ltq~Gc-tLnf   99 (99)
T d2nmza1          84 IIGRNLLTQIGA-TLNF   99 (99)
T ss_dssp             EECHHHHTTTTC-EEEC
T ss_pred             EEcccchhhcCc-eecC
Confidence            889999999988 3554

>d1hvca_ b.50.1.1 (A:) Human immunodeficiency virus type 1 protease {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Retroviral protease (retropepsin)
domain: Human immunodeficiency virus type 1 protease
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=93.35  E-value=0.039  Score=38.78  Aligned_cols=68  Identities=19%  Similarity=0.214  Sum_probs=45.3

Q ss_pred             EEEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCc-ee----------------c------cce
Q 043220           42 CVVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGA-HL----------------K------SPD   98 (121)
Q Consensus        42 ~~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~-~l----------------~------~~d   98 (121)
                      -.++.+|+|+.+.+|+|+||-++.+.     ..+++-+ .+|..+.-.+|- ++                .      |.-
T Consensus         9 P~VtVkIgGQ~~eaLLDTGADDTVLe-----~inLpG~-WkPkiIGGIGGfIkVrqY~~V~IeI~gkk~~gTVLVgPTPv   82 (203)
T d1hvca_           9 PLVTIRIGGQLKEALLDTGADDTVLE-----EMNLPGK-WKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPV   82 (203)
T ss_dssp             CEEEEESSSCEEEEEECTTCSSEEEE-----CCCCSSC-EEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEESCSS
T ss_pred             CeEEEEECCEEEEEEecCCCCceEEe-----cccCCCC-CcccEEEecCceEEEEEeCCEEEEECCcEEEEEEEECCCCc
Confidence            35889999999999999999999983     3455432 223333333331 11                1      133


Q ss_pred             EeecchhhhhcCCeeeec
Q 043220           99 VALDVKWSEQIGSIMRGW  116 (121)
Q Consensus        99 vILG~~WL~~~~p~~idw  116 (121)
                      =|||-+-|.+.+. .+++
T Consensus        83 NIIGRNlLtqlG~-tLnF   99 (203)
T d1hvca_          83 NIIGRNLLTQIGC-TLNF   99 (203)
T ss_dssp             CEECHHHHGGGTC-EEEC
T ss_pred             cccchhhhhhhhh-eeec
Confidence            4899999999988 4665

>d3ecga1 b.50.1.1 (A:1-99) Human immunodeficiency virus type 2 (HIV-2) protease {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Retroviral protease (retropepsin)
domain: Human immunodeficiency virus type 2 (HIV-2) protease
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=92.01  E-value=0.16  Score=31.68  Aligned_cols=64  Identities=22%  Similarity=0.190  Sum_probs=41.5

Q ss_pred             EEEEEECCEEEEEEecCCCcccccCHHHHhhcCCCCCCCCCeEEEecCCc-eec---------c-------------ceE
Q 043220           43 VVATKIRFHEVVILISSGSTANFVSDKVAALLPLPMMPTKPFSVRIANGA-HLK---------S-------------PDV   99 (121)
Q Consensus        43 ~v~g~i~~~~v~~LIDSGAT~nFI~~~~a~rl~l~~~~~~~~~V~va~G~-~l~---------~-------------~dv   99 (121)
                      .++.+|+|+...+|+|+||-.+.+.     ..+++-+ .+|-.+---+|- +++         |             .-=
T Consensus        10 ~vtvkIgGq~~eaLLDTGADdTVle-----~i~lpg~-WkPk~iGGIGGfikVrqYd~i~Ieicg~k~~gtVLvgpTPvN   83 (99)
T d3ecga1          10 VVTAYIEGQPVEVLLDTGADDSIVA-----GIELGNN-YSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTGDTPIN   83 (99)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEEC-----SCCCCSC-CEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEECCSSC
T ss_pred             eEEEEECCEEeeeecccCCCceeee-----ccCCCCC-CcceEEEEeeeeEEEEEeCcEEEEECCcEEEEEEEeCCCCce
Confidence            5788999999999999999998883     4555432 233322222221 111         1             333


Q ss_pred             eecchhhhhcCCe
Q 043220          100 ALDVKWSEQIGSI  112 (121)
Q Consensus       100 ILG~~WL~~~~p~  112 (121)
                      |+|-+-|.|.|..
T Consensus        84 IiGRNlLtqlGct   96 (99)
T d3ecga1          84 IFGRNILTALGMS   96 (99)
T ss_dssp             EECHHHHHHTTCE
T ss_pred             EEccchhhhhCcc
Confidence            8899999998873

>d1t6ex_ b.50.1.2 (X:) Xylanase inhibitor TAXI-I {Wheat (Triticum aestivum) [TaxId: 4565]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Xylanase inhibitor TAXI-I
species: Wheat (Triticum aestivum) [TaxId: 4565]

Probab=91.30  E-value=0.1  Score=38.02  Aligned_cols=20  Identities=15%  Similarity=0.180  Sum_probs=17.1

Q ss_pred             EEecCCCcccccCHHHHhhc
Q 043220           55 ILISSGSTANFVSDKVAALL   74 (121)
Q Consensus        55 ~LIDSGAT~nFI~~~~a~rl   74 (121)
                      +++|||.+..++...++..+
T Consensus       232 ~i~DTGtt~~~lp~~~~~~i  251 (381)
T d1t6ex_         232 VMLSTRLPYVLLRPDVYRPL  251 (381)
T ss_dssp             EEECSSCSSEEECHHHHHHH
T ss_pred             eEEecCCceEECCHHHHHHH
Confidence            79999999999998776653

>d1eaga_ b.50.1.2 (A:) Acid protease {Yeast (Candida albicans) [TaxId: 5476]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Yeast (Candida albicans) [TaxId: 5476]

Probab=91.18  E-value=0.099  Score=37.63  Aligned_cols=74  Identities=14%  Similarity=0.172  Sum_probs=47.9

Q ss_pred             EEECCEE-----EEEEecCCCcccccCHHHHhhcC----CC--------------CCCCCCeEEEecCCceec-------
Q 043220           46 TKIRFHE-----VVILISSGSTANFVSDKVAALLP----LP--------------MMPTKPFSVRIANGAHLK-------   95 (121)
Q Consensus        46 g~i~~~~-----v~~LIDSGAT~nFI~~~~a~rl~----l~--------------~~~~~~~~V~va~G~~l~-------   95 (121)
                      ..++++.     ..++||||++..++...+.+++.    ..              ......+.+..++|..+.       
T Consensus       201 i~vgg~~~~~~~~~~iiDSGts~~~lp~~~~~~l~~~l~~~~~~~~~~~~~~~~~c~~~p~i~f~f~~~~~~~i~~~~y~  280 (342)
T d1eaga_         201 VEVSGKTINTDNVDVLLDSGTTITYLQQDLADQIIKAFNGKLTQDSNGNSFYEVDCNLSGDVVFNFSKNAKISVPASEFA  280 (342)
T ss_dssp             EEETTEEEEEEEEEEEECTTCSSEEECHHHHHHHHHHTTCEEEECTTSCEEEEEESCCCSEEEEECSTTCEEEEEGGGGE
T ss_pred             EEECCEEecccccccccccCCccccCCHHHHHHHHHHhCccccccCCCCceeccccccCCCEEEEECCCEEEEEChHHeE
Confidence            3455543     45899999999999999988752    11              111123455555555332       


Q ss_pred             -------------c------ce-EeecchhhhhcCCeeeecccCC
Q 043220           96 -------------S------PD-VALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        96 -------------~------~d-vILG~~WL~~~~p~~idw~~~~  120 (121)
                                   |      .| .|||..||+.+-.+ .|+.++|
T Consensus       281 ~~~~~~~~~~~~~~~~~~~~~~~~ILG~~fl~~~y~v-fD~~~~~  324 (342)
T d1eaga_         281 ASLQGDDGQPYDKCQLLFDVNDANILGDNFLRSAYIV-YDLDDNE  324 (342)
T ss_dssp             EEC---CCSCTTEEEECEEECTTCEECHHHHTTEEEE-EETTTTE
T ss_pred             EEecCCCCceeeEEEEccCCCCCcEECHHhhCcEEEE-EECCCCE
Confidence                         1      12 27999999999875 8887654

>d2bjua1 b.50.1.2 (A:1-329) Plasmepsin (a hemoglobin-degrading enzyme) {Plasmodium falciparum, plasmepsin II [TaxId: 5833]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Plasmepsin (a hemoglobin-degrading enzyme)
species: Plasmodium falciparum, plasmepsin II [TaxId: 5833]

Probab=90.34  E-value=0.21  Score=35.20  Aligned_cols=24  Identities=17%  Similarity=0.246  Sum_probs=21.4

Q ss_pred             EEEEEEecCCCcccccCHHHHhhc
Q 043220           51 HEVVILISSGSTANFVSDKVAALL   74 (121)
Q Consensus        51 ~~v~~LIDSGAT~nFI~~~~a~rl   74 (121)
                      ....++||||++..++...+++++
T Consensus       207 ~~~~~~iDSGt~~~~lp~~~~~~l  230 (329)
T d2bjua1         207 EKANCIVDSGTSAITVPTDFLNKM  230 (329)
T ss_dssp             EEEEEEECTTCCSEEECHHHHHHH
T ss_pred             cCCcccccccccceeCCHHHHHHH
Confidence            356789999999999999999886

>d1j71a_ b.50.1.2 (A:) Acid protease {Yeast (Candida tropicalis) [TaxId: 5482]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Yeast (Candida tropicalis) [TaxId: 5482]

Probab=90.10  E-value=0.17  Score=36.61  Aligned_cols=73  Identities=12%  Similarity=0.156  Sum_probs=48.9

Q ss_pred             EECCEE----EEEEecCCCcccccCHHHHhhc----C-----------CC-CCCCCCeEEEecCCceec-----------
Q 043220           47 KIRFHE----VVILISSGSTANFVSDKVAALL----P-----------LP-MMPTKPFSVRIANGAHLK-----------   95 (121)
Q Consensus        47 ~i~~~~----v~~LIDSGAT~nFI~~~~a~rl----~-----------l~-~~~~~~~~V~va~G~~l~-----------   95 (121)
                      .++++.    ..++||||++..++.+.+.+++    +           ++ ......+.+...+|..+.           
T Consensus       203 ~v~g~~~~~~~~aiiDSGt~~~~lp~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~p~i~f~f~~g~~~~i~~~~y~~~~~  282 (334)
T d1j71a_         203 NFDGTSVSTNADVVLDSGTTITYFSQSTADKFARIVGATWDSRNEIYRLPSCDLSGDAVFNFDQGVKITVPLSELILKDS  282 (334)
T ss_dssp             EETTEEEEEEEEEEECTTCSSEEECHHHHHHHHHHHTCEEETTTTEEECSSSCCCSEEEEEESTTCEEEEEGGGGEEECS
T ss_pred             EECCEEecccccccccCCCcceeccHHHHHHHHHHhCCEEcCCCCeeeccccccCCCceEEeCCCEEEEEChHHeEEecC
Confidence            556654    3489999999999999998774    1           11 111234556666665442           


Q ss_pred             ----c-------ceEeecchhhhhcCCeeeecccCC
Q 043220           96 ----S-------PDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        96 ----~-------~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                          |       -..|||..||+.+-.+ .|..++|
T Consensus       283 ~~~~C~~~i~~~~~~ILG~~fl~~~y~v-fD~~n~~  317 (334)
T d1j71a_         283 DSSICYFGISRNDANILGDNFLRRAYIV-YDLDDKT  317 (334)
T ss_dssp             SSSCEEESEEECTTCEECHHHHTTEEEE-EETTTTE
T ss_pred             CCCEEEEEecCCCCcEECHHhhCcEEEE-EECCCCE
Confidence                2       2358999999998775 8877654

>d1izea_ b.50.1.2 (A:) Acid protease {Fungus (Aspergillus oryzae) [TaxId: 5062]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Fungus (Aspergillus oryzae) [TaxId: 5062]

Probab=90.06  E-value=0.11  Score=36.92  Aligned_cols=23  Identities=13%  Similarity=0.291  Sum_probs=19.9

Q ss_pred             EEEEEecCCCcccccCHHHHhhc
Q 043220           52 EVVILISSGSTANFVSDKVAALL   74 (121)
Q Consensus        52 ~v~~LIDSGAT~nFI~~~~a~rl   74 (121)
                      ...++||||.+..++...+.+.+
T Consensus       208 ~~~~ivDSGts~~~lp~~~~~~~  230 (323)
T d1izea_         208 SITGIADTGTTLLLLDDSIVDAY  230 (323)
T ss_dssp             CEEEEECTTCCSEEECHHHHHHH
T ss_pred             CceEEeccCCccccCCHHHHHHH
Confidence            35689999999999999988765

>d1bxoa_ b.50.1.2 (A:) Acid protease {Fungus (Penicillium janthinellum), penicillopepsin [TaxId: 5079]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Fungus (Penicillium janthinellum), penicillopepsin [TaxId: 5079]

Probab=89.87  E-value=0.25  Score=34.84  Aligned_cols=67  Identities=13%  Similarity=0.069  Sum_probs=44.8

Q ss_pred             EEEEEecCCCcccccCHHHHhhcCCCCCC-----------------CCCeEEEecCCcee----------------cc--
Q 043220           52 EVVILISSGSTANFVSDKVAALLPLPMMP-----------------TKPFSVRIANGAHL----------------KS--   96 (121)
Q Consensus        52 ~v~~LIDSGAT~nFI~~~~a~rl~l~~~~-----------------~~~~~V~va~G~~l----------------~~--   96 (121)
                      ...++||||++..++...++.++--.+..                 .+.+..... |..+                .|  
T Consensus       207 ~~~aiiDSGTs~~~lp~~~~~~l~~~i~~~~~~~~~~~~~~~c~~~~p~itf~f~-g~~~~i~~~~~~~~~~~~~~~C~~  285 (323)
T d1bxoa_         207 GFSGIADTGTTLLLLDDSVVSQYYSQVSGAQQDSNAGGYVFDCSTNLPDFSVSIS-GYTATVPGSLINYGPSGDGSTCLG  285 (323)
T ss_dssp             EEEEEECTTCSSEEECHHHHHHHHTTSTTCEEETTTTEEEECTTCCCCCEEEEET-TEEEEECHHHHEEEECSSSSCEEE
T ss_pred             CcceEEecccccccCCHHHHHHHHHHhCCccccCCCCcEEEeccCCCCcEEEEEC-CEEEEEChHHeEEEEcCCCCEEEE
Confidence            46799999999999999999886211110                 123444442 3222                12  


Q ss_pred             -------ce-EeecchhhhhcCCeeeecccCC
Q 043220           97 -------PD-VALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        97 -------~d-vILG~~WL~~~~p~~idw~~~~  120 (121)
                             .+ .|||-.||+.+-.+ +|+.++|
T Consensus       286 ~i~~~~~~~~~ILG~~flr~~y~v-fD~~~~~  316 (323)
T d1bxoa_         286 GIQSNSGIGFSIFGDIFLKSQYVV-FDSDGPQ  316 (323)
T ss_dssp             SEEECTTCSSEEECHHHHTTEEEE-EETTTTE
T ss_pred             EEECCCCCCcEEECHHHhCCEEEE-EECCCCE
Confidence                   33 58999999999885 8987764

>d1miqa_ b.50.1.2 (A:) Plasmepsin (a hemoglobin-degrading enzyme) {Plasmodium vivax [TaxId: 5855]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Plasmepsin (a hemoglobin-degrading enzyme)
species: Plasmodium vivax [TaxId: 5855]

Probab=89.27  E-value=0.83  Score=32.85  Aligned_cols=33  Identities=9%  Similarity=0.140  Sum_probs=24.7

Q ss_pred             EEEEEEECCE---EEEEEecCCCcccccCHHHHhhc
Q 043220           42 CVVATKIRFH---EVVILISSGSTANFVSDKVAALL   74 (121)
Q Consensus        42 ~~v~g~i~~~---~v~~LIDSGAT~nFI~~~~a~rl   74 (121)
                      +.+.+.+++.   ...++||||++..++.....+++
T Consensus       241 i~l~~~~~~~~~~~~~~iiDTGTs~~~lP~~~~~~l  276 (373)
T d1miqa_         241 IDLDVHFGKQTMEKANVIVDSGTTTITAPSEFLNKF  276 (373)
T ss_dssp             EEEEEEETTEEEEEEEEEECTTBSSEEECHHHHHHH
T ss_pred             EEEEEEECcEecCCcceEeccCCceeccCHHHHHHH
Confidence            4445555553   45699999999999999887764

>d1am5a_ b.50.1.2 (A:) Pepsin(ogen) {Atlantic cod (Gadus morhua) [TaxId: 8049]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Pepsin(ogen)
species: Atlantic cod (Gadus morhua) [TaxId: 8049]

Probab=88.76  E-value=0.28  Score=34.58  Aligned_cols=67  Identities=9%  Similarity=0.079  Sum_probs=43.2

Q ss_pred             EEEEEecCCCcccccCHHHHhhc----CCC------------CCCCCCeEEEecCCceec-------------c------
Q 043220           52 EVVILISSGSTANFVSDKVAALL----PLP------------MMPTKPFSVRIANGAHLK-------------S------   96 (121)
Q Consensus        52 ~v~~LIDSGAT~nFI~~~~a~rl----~l~------------~~~~~~~~V~va~G~~l~-------------~------   96 (121)
                      ...++||||++..++...+..++    +..            ....+.+.+.. +|..+.             |      
T Consensus       208 ~~~~iiDsGts~~~lp~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~P~i~f~f-~g~~~~l~~~~y~~~~~~~c~~~i~~  286 (324)
T d1am5a_         208 GCQAIVDTGTSKIVAPVSALANIMKDIGASENQGEMMGNCASVQSLPDITFTI-NGVKQPLPPSAYIEGDQAFCTSGLGS  286 (324)
T ss_dssp             CEEEEECTTCSSEEECTTTHHHHHHHHTCEECCCCEECCTTSSSSSCCEEEEE-TTEEEEECHHHHEEESSSCEEECEEE
T ss_pred             CcceeeccCcccccCCHHHHHHHHHHhCCcccCCcccccccccccCCceEEEE-CCEEEEECHHHhEecCCCeEEEEEEe
Confidence            45789999999999999887653    211            11122355555 333221             1      


Q ss_pred             --------ceEeecchhhhhcCCeeeecccCC
Q 043220           97 --------PDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        97 --------~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                              .-.|||..||+.+-.+ .|..++|
T Consensus       287 ~~~~~~~~~~~ILG~~fl~~~y~v-fD~~~~~  317 (324)
T d1am5a_         287 SGVPSNTSELWIFGDVFLRNYYTI-YDRTNNK  317 (324)
T ss_dssp             CCSCCSSSCEEEECHHHHHHEEEE-EETTTTE
T ss_pred             cCcCCCCCCCEEECHHhhcCEEEE-EECCCCE
Confidence                    2258999999999875 7877654

>d1wkra_ b.50.1.2 (A:) Acid protease {Irpex lacteus (Polyporus tulipiferae), Polyporopepsin [TaxId: 5319]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Irpex lacteus (Polyporus tulipiferae), Polyporopepsin [TaxId: 5319]

Probab=88.49  E-value=0.26  Score=35.35  Aligned_cols=22  Identities=14%  Similarity=0.285  Sum_probs=18.5

Q ss_pred             EEEEecCCCcccccCHHHHhhc
Q 043220           53 VVILISSGSTANFVSDKVAALL   74 (121)
Q Consensus        53 v~~LIDSGAT~nFI~~~~a~rl   74 (121)
                      ..++||||++..++...+..++
T Consensus       207 ~~aiiDSGtt~~~lP~~~~~~l  228 (340)
T d1wkra_         207 TAGIVDTGTTLTLIASDAFAKY  228 (340)
T ss_dssp             EEEEECTTBCSEEECHHHHHHH
T ss_pred             cceEEecCCccEeccHHHHHHH
Confidence            4589999999999999877654

>d2apra_ b.50.1.2 (A:) Acid protease {Bread mold (Rhizopus chinensis) [TaxId: 4843]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Bread mold (Rhizopus chinensis) [TaxId: 4843]

Probab=87.92  E-value=0.28  Score=34.99  Aligned_cols=72  Identities=15%  Similarity=0.143  Sum_probs=45.8

Q ss_pred             EECCEE----EEEEecCCCcccccCHHHHhhc----CCC----------CC--CCCCeEEEecCCcee------------
Q 043220           47 KIRFHE----VVILISSGSTANFVSDKVAALL----PLP----------MM--PTKPFSVRIANGAHL------------   94 (121)
Q Consensus        47 ~i~~~~----v~~LIDSGAT~nFI~~~~a~rl----~l~----------~~--~~~~~~V~va~G~~l------------   94 (121)
                      .+++..    ..++||||++..++...+.+++    +..          ..  ...++.... +|..+            
T Consensus       203 ~i~~~~~~~~~~~iiDSGt~~~~lp~~~~~~l~~~~~~~~~~~~~~~~~C~~~~~p~i~f~f-~g~~~~i~~~~y~~~~~  281 (325)
T d2apra_         203 TVGTSTVASSFDGILDTGTTLLILPNNIAASVARAYGASDNGDGTYTISCDTSAFKPLVFSI-NGASFQVSPDSLVFEEF  281 (325)
T ss_dssp             EETTEEEECCEEEEECTTCSSEEEEHHHHHHHHHHHTCEECSSSCEEECSCGGGCCCEEEEE-TTEEEEECGGGGEEEEE
T ss_pred             EECCEeecceeeeeccCCCccccCCHHHHHHHHHHhCCcccCCCceeecccCCCCCcEEEEE-CCEEEEEChHHeEEecC
Confidence            455544    3689999999999999887754    211          11  112344444 23322            


Q ss_pred             --cc---------ceEeecchhhhhcCCeeeecccCC
Q 043220           95 --KS---------PDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        95 --~~---------~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                        .|         .-.|||..||+.+-.+ .|..++|
T Consensus       282 ~~~C~~~i~~~~~~~~iLG~~flr~~y~v-fD~~~~~  317 (325)
T d2apra_         282 QGQCIAGFGYGNWGFAIIGDTFLKNNYVV-FNQGVPE  317 (325)
T ss_dssp             TTEEEESEEEESSSSEEECHHHHTTEEEE-EETTTTE
T ss_pred             CCEEEEEEccCCCCCEEECHHHhCcEEEE-EECCCCE
Confidence              12         3369999999998775 7877654

>d1smra_ b.50.1.2 (A:) Chymosin (synonym: renin) {Mouse (Mus musculus) [TaxId: 10090]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Chymosin (synonym: renin)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.57  E-value=0.28  Score=34.84  Aligned_cols=23  Identities=13%  Similarity=0.212  Sum_probs=20.3

Q ss_pred             EEEEEecCCCcccccCHHHHhhc
Q 043220           52 EVVILISSGSTANFVSDKVAALL   74 (121)
Q Consensus        52 ~v~~LIDSGAT~nFI~~~~a~rl   74 (121)
                      ...++||||++..++...+.+++
T Consensus       214 ~~~~iiDSGtt~~~lp~~~~~~l  236 (335)
T d1smra_         214 GCEVVVDTGSSFISAPTSSLKLI  236 (335)
T ss_dssp             CEEEEECTTBSSEEECHHHHHHH
T ss_pred             CceEEEeCCCCcccCCHHHHHHH
Confidence            35689999999999999998875

>d2rspa_ b.50.1.1 (A:) Rous sarcoma virus protease {Rous sarcoma virus, strain pr-C [TaxId: 11886]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Retroviral protease (retropepsin)
domain: Rous sarcoma virus protease
species: Rous sarcoma virus, strain pr-C [TaxId: 11886]

Probab=85.02  E-value=0.12  Score=33.53  Aligned_cols=23  Identities=26%  Similarity=0.406  Sum_probs=19.6

Q ss_pred             EECCEEEEEEecCCCcccccCHH
Q 043220           47 KIRFHEVVILISSGSTANFVSDK   69 (121)
Q Consensus        47 ~i~~~~v~~LIDSGAT~nFI~~~   69 (121)
                      +++|+.+.+|+||||-.+.|+..
T Consensus        26 k~~g~~i~~LLDTGAD~TVI~~~   48 (124)
T d2rspa_          26 KQRSVYITALLDSGADITIISEE   48 (124)
T ss_dssp             SCSEEEEEEEECTTCSSCEEETT
T ss_pred             eeCCEEEEEEEcCCCCeEEEcCC
Confidence            34668899999999999999765

>d3cmsa_ b.50.1.2 (A:) Chymosin (synonym: renin) {Cow (Bos taurus) [TaxId: 9913]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Chymosin (synonym: renin)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=83.28  E-value=1.1  Score=31.09  Aligned_cols=67  Identities=7%  Similarity=0.008  Sum_probs=44.0

Q ss_pred             EEEEEecCCCcccccCHHHHhhcC----------------CCCC-CCCCeEEEecCCceec-------------c-----
Q 043220           52 EVVILISSGSTANFVSDKVAALLP----------------LPMM-PTKPFSVRIANGAHLK-------------S-----   96 (121)
Q Consensus        52 ~v~~LIDSGAT~nFI~~~~a~rl~----------------l~~~-~~~~~~V~va~G~~l~-------------~-----   96 (121)
                      ...++||||.+..++...+.+++-                +... ..+.+.+... |..+.             |     
T Consensus       210 ~~~~iiDSGtt~~~lp~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~i~f~f~-g~~~~l~~~~y~~~~~~~c~~~i~  288 (323)
T d3cmsa_         210 GCQAILDTGTSKLVGPSSDILNIQQAIGATQNQYGEFDIDCDNLSYMPTVVFEIN-GKMYPLTPSAYTSQDQGFCTSGFQ  288 (323)
T ss_dssp             CEEEEECTTCCSEEECHHHHHHHHHHHTCEEETTTEEEECTTCTTTSCCEEEEET-TEEEEECHHHHEEEETTEEEESEE
T ss_pred             CeeEEEecCcceEEecHHHHHHHHHHhCceeccCCceeEeccccCCCCeEEEEEC-CEEEEECHHHeEEcCCCEEEEEEE
Confidence            357899999999999999988541                1011 1123444443 33221             2     


Q ss_pred             -----ceEeecchhhhhcCCeeeecccCC
Q 043220           97 -----PDVALDVKWSEQIGSIMRGWKKDE  120 (121)
Q Consensus        97 -----~dvILG~~WL~~~~p~~idw~~~~  120 (121)
                           ...|||..||+.+-.+ .|+.+.+
T Consensus       289 ~~~~~~~~iLG~~~l~~~yvv-fD~~~~~  316 (323)
T d3cmsa_         289 SENHSQKWILGDVFIREYYSV-FDRANNL  316 (323)
T ss_dssp             EC---CCEEECHHHHTTEEEE-EETTTTE
T ss_pred             eCCCCCCEEEcHHhhCcEEEE-EECCCCE
Confidence                 3479999999998875 8887653

>d1oewa_ b.50.1.2 (A:) Endothiapepsin {Chestnut blight fungus (Endothia parasitica) [TaxId: 5116]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Endothiapepsin
species: Chestnut blight fungus (Endothia parasitica) [TaxId: 5116]

Probab=82.61  E-value=0.5  Score=33.80  Aligned_cols=23  Identities=13%  Similarity=0.245  Sum_probs=20.0

Q ss_pred             EEEEEecCCCcccccCHHHHhhc
Q 043220           52 EVVILISSGSTANFVSDKVAALL   74 (121)
Q Consensus        52 ~v~~LIDSGAT~nFI~~~~a~rl   74 (121)
                      ...++||||++..++...+.+.+
T Consensus       213 ~~~~iiDSGts~~~lp~~~~~~i  235 (330)
T d1oewa_         213 SIDGIADTGTTLLYLPATVVSAY  235 (330)
T ss_dssp             EEEEEECTTCCSEEECHHHHHHH
T ss_pred             CcceeeccccccccCCHHHHHHH
Confidence            45689999999999999888875

>d2qp8a1 b.50.1.2 (A:60-446) beta-secretase (memapsin) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: beta-secretase (memapsin)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.04  E-value=0.078  Score=39.02  Aligned_cols=30  Identities=20%  Similarity=0.215  Sum_probs=24.1

Q ss_pred             EEEECCEEE----------EEEecCCCcccccCHHHHhhc
Q 043220           45 ATKIRFHEV----------VILISSGSTANFVSDKVAALL   74 (121)
Q Consensus        45 ~g~i~~~~v----------~~LIDSGAT~nFI~~~~a~rl   74 (121)
                      ...++++.+          .++||||++..++...+.+++
T Consensus       207 ~i~v~g~~~~~~~~~~~~~~aiiDSGts~i~lp~~~~~~l  246 (387)
T d2qp8a1         207 RVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAA  246 (387)
T ss_dssp             EEEETTEECCCCGGGGGSSCEEECTTCCSEEEEHHHHHHH
T ss_pred             EEEECCEecccccccCCccceEEecCCCeEeCCHHHHHHH
Confidence            446777765          489999999999999987754

>d1dpja_ b.50.1.2 (A:) Acid protease {Baker's yeast (Saccharomyces cerevisiae), proteinase A [TaxId: 4932]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Baker's yeast (Saccharomyces cerevisiae), proteinase A [TaxId: 4932]

Probab=81.75  E-value=0.46  Score=33.48  Aligned_cols=28  Identities=11%  Similarity=0.090  Sum_probs=22.3

Q ss_pred             EECCEE-----EEEEecCCCcccccCHHHHhhc
Q 043220           47 KIRFHE-----VVILISSGSTANFVSDKVAALL   74 (121)
Q Consensus        47 ~i~~~~-----v~~LIDSGAT~nFI~~~~a~rl   74 (121)
                      .+++..     ..++||||++..++...+.+++
T Consensus       202 ~v~~~~~~~~~~~~iiDSGts~~~lp~~~~~~l  234 (329)
T d1dpja_         202 GLGDEYAELESHGAAIDTGTSLITLPSGLAEMI  234 (329)
T ss_dssp             EETTEEEECSSCEEEECTTCSCEEECHHHHHHH
T ss_pred             EECCeEeeeeecccccCcccceeeCCHHHHHHH
Confidence            555544     3579999999999999998875