Citrus Sinensis ID: 039270

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-
Protein Sequence
MPTTNQTTYRNSSIPVRRLSRTELQERCAKNSTKMLEISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDFAS
Secondary Structure (PSIPRED)
ccccccccccccccccccccHHHHHHHHcccccccEEEEEEEEEccccccEEEEEEEEccEEEEEEEccccccccccccEEEccEEEEEEEEEccEEEEEEEEEEccccccEEEcHHHHHHcccEEEEccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccHHHHHHccccccccEEEEEEEEcccccccEEEEEEEEccEEEEEEEEccccccHHcHHHccccccccEEEEEccEEEEEEEEEEEcccccEEEEHHHHHHcccEEEEccc
Coil and Loop (DISEMBL)
mpttnqttyrnssipvrrlsRTELQERCAKNSTKMLEISLRVISgarasetmringrignispivlvdsgstrnfmseqfystrkctnvnlILQGVSVIVdfnlrdlegydvvlgTQWLRTLEPILWDFAS
Flexible Loop (DISEMBL)
mpttnqttyrnssipvrrlsrtelqercaknstkmleislrvisgarasetmringrignispivlvdsgsTRNFMSEQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDFAS
Low Complexity Region (SEG)
MPTTNQTTYRNSSIPVRRLSRTELQERCAKNSTKMLEISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDFAS
Disordered region (IsUnstruct)
**********************************MLEISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDF**
Disordered Region (DISOPRED)
***************************************LRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDFAS
Disordered Region (DISEMBL)
*************IPVRRLSRTELQERCAKNSTKMLEISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDFAS
Disordered Region (DISPRO)
***********SSIPVRRLSRTELQERCAKNSTKMLEISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDFAS
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPTTNQTTYRNSSIPVRRLSRTELQERCAKNSTKMLEISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDFAS
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	131
218197921	402	hypothetical protein OsI_22431 [Oryza sa	0.702	0.228	0.387	1e-13
357130210	635	PREDICTED: uncharacterized protein LOC10	0.793	0.163	0.390	6e-12
242085414	1462	hypothetical protein SORBIDRAFT_08g01083	0.709	0.063	0.350	4e-11
147774273	1469	hypothetical protein VITISV_026680 [Viti	0.778	0.069	0.346	5e-11
147843077	1366	hypothetical protein VITISV_044100 [Viti	0.778	0.074	0.346	5e-11
147789424	2822	hypothetical protein VITISV_017554 [Viti	0.778	0.036	0.346	1e-10
108864287	413	retrotransposon protein, putative, uncla	0.702	0.222	0.333	1e-09
32483242	1395	OSJNBb0069N01.1 [Oryza sativa Japonica G	0.732	0.068	0.358	1e-09
62734405	575	retrotransposon protein, putative, uncla	0.702	0.16	0.333	1e-09
147842329	522	hypothetical protein VITISV_041623 [Viti	0.938	0.235	0.290	3e-09

>gi|218197921|gb|EEC80348.1| hypothetical protein OsI_22431 [Oryza sativa Indica Group]

 Score = 80.9 bits (198), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 45/116 (38%), Positives = 61/116 (52%), Gaps = 24/116 (20%)

Query: 38  ISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMS-------------------- 77
           ISL  ++G R S+TMR+   IG ++   LVDSGST  F++                    
Sbjct: 159 ISLHALTGIRTSKTMRLAVIIGGVTMSALVDSGSTHTFVATEAARRLGLSPTTKSGLNVM 218

Query: 78  ----EQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDF 129
               +Q  S+  C+ + + +     I+D  +  LEGYDVVLG QWLRTL PILWDF
Sbjct: 219 VANGDQVTSSGICSGIPIKIDSEDFIIDCYVIPLEGYDVVLGVQWLRTLGPILWDF 274

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357130210|ref|XP_003566743.1| PREDICTED: uncharacterized protein LOC100838891 [Brachypodium distachyon]

 Score = 75.5 bits (184), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 50/128 (39%), Positives = 64/128 (50%), Gaps = 24/128 (18%)

Query: 26  ERCAKNSTKMLEISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQF---YS 82
           E   K   + L+ISL  I+G R S+TM++   +G    + L+DSGST NF+SE+     S
Sbjct: 171 EVADKEEEEDLQISLLAITGVRTSDTMQLVVWVGERELLALIDSGSTHNFISEELAAHVS 230

Query: 83  TRKCTNVNL---ILQG------------------VSVIVDFNLRDLEGYDVVLGTQWLRT 121
              CT   L   I  G                   S +VD     L G+DVVLGT WL+T
Sbjct: 231 APFCTGRRLRVTIANGDHVTCSGLLRHTAIAIGQESFVVDLYAIPLGGFDVVLGTHWLKT 290

Query: 122 LEPILWDF 129
           L PILWDF
Sbjct: 291 LGPILWDF 298

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242085414|ref|XP_002443132.1| hypothetical protein SORBIDRAFT_08g010830 [Sorghum bicolor] gi|241943825|gb|EES16970.1| hypothetical protein SORBIDRAFT_08g010830 [Sorghum bicolor]

 Score = 73.2 bits (178), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 41/117 (35%), Positives = 60/117 (51%), Gaps = 24/117 (20%)

Query: 39  SLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQ-------FYSTR------- 84
           SL  ++G R S+T+R+   +G++S + L DSGS+ NF+SE+          +R       
Sbjct: 314 SLHAVAGVRLSDTLRVRVMVGSVSLVALSDSGSSHNFISERAAQRTGLLVVSRPRLSAVV 373

Query: 85  ------KCTNV----NLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDFAS 131
                  C  V      ++QG S   D  +  L G+DVVLG QWL TL P+ WDF +
Sbjct: 374 ANGERIACPGVLPQAPFVIQGSSFTADLFIMPLAGFDVVLGAQWLGTLGPVTWDFTA 430

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147774273|emb|CAN76793.1| hypothetical protein VITISV_026680 [Vitis vinifera]

 Score = 72.8 bits (177), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 45/130 (34%), Positives = 63/130 (48%), Gaps = 28/130 (21%)

Query: 29  AKNSTKMLEI----SLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMS------- 77
           +K  T ++EI    S+  + G+   +TMR  G I   + ++LVD+GST NFM        
Sbjct: 335 SKEETPIVEIEPGISIHALVGSPNPKTMRFLGHICGRAVVILVDTGSTHNFMDPSVIQRA 394

Query: 78  -----------------EQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLR 120
                            +   S   C  V L +QG    +DF +  L G D+VLG QWL+
Sbjct: 395 HLPSNPTEGLSVKVANGQAVRSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIVLGVQWLQ 454

Query: 121 TLEPILWDFA 130
           TL PILWDF+
Sbjct: 455 TLGPILWDFS 464

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147843077|emb|CAN83300.1| hypothetical protein VITISV_044100 [Vitis vinifera]

 Score = 72.4 bits (176), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 45/130 (34%), Positives = 63/130 (48%), Gaps = 28/130 (21%)

Query: 29  AKNSTKMLEI----SLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMS------- 77
           +K  T ++EI    S+  + G+   +TMR  G I   + ++LVD+GST NFM        
Sbjct: 302 SKEETPIVEIEPGISIHALVGSPNPKTMRFLGHICGRAVVILVDTGSTHNFMDPSVIQRA 361

Query: 78  -----------------EQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLR 120
                            +   S   C  V L +QG    +DF +  L G D+VLG QWL+
Sbjct: 362 HLPSNPTEGLSVKVANGQAVRSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIVLGVQWLQ 421

Query: 121 TLEPILWDFA 130
           TL PILWDF+
Sbjct: 422 TLGPILWDFS 431

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147789424|emb|CAN66607.1| hypothetical protein VITISV_017554 [Vitis vinifera]

 Score = 71.2 bits (173), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 45/130 (34%), Positives = 63/130 (48%), Gaps = 28/130 (21%)

Query: 29  AKNSTKMLEI----SLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMS------- 77
           +K  T ++EI    S+  + G+   +TMR  G I   + ++LVD+GST NFM        
Sbjct: 300 SKEETPIVEIEPGISIHALVGSPNPKTMRFLGHICGRAVVILVDTGSTHNFMDPSVIQRA 359

Query: 78  -----------------EQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLR 120
                            +   S   C  V L +QG    +DF +  L G D+VLG QWL+
Sbjct: 360 HLPSNPTEGLSVKVANGQAVCSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIVLGVQWLQ 419

Query: 121 TLEPILWDFA 130
           TL PILWDF+
Sbjct: 420 TLGPILWDFS 429

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|108864287|gb|ABA92869.2| retrotransposon protein, putative, unclassified [Oryza sativa Japonica Group]

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 39/117 (33%), Positives = 56/117 (47%), Gaps = 25/117 (21%)

Query: 38  ISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFM--------------------- 76
           +SL V++G   + TMR+   I     + LVDSGST NF+                     
Sbjct: 208 VSLNVLAGLDGANTMRLPVEIAGERVVALVDSGSTHNFIHTELARHLCLHLSPVRHDLYV 267

Query: 77  ----SEQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDF 129
                ++  S  +C N+ L ++G    VD    D+   D++LGT+WL TL PILWDF
Sbjct: 268 VVANGDRLVSPGRCANLRLRIEGKLFTVDCFALDISTVDIILGTEWLSTLGPILWDF 324

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|32483242|emb|CAE02543.1| OSJNBb0069N01.1 [Oryza sativa Japonica Group] gi|38344504|emb|CAE05183.2| OSJNBa0013A04.20 [Oryza sativa Japonica Group]

 Score = 67.8 bits (164), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/120 (35%), Positives = 56/120 (46%), Gaps = 24/120 (20%)

Query: 36  LEISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFYS-------TRKCTN 88
           L ISL V +G R S+ M I   +G+     L+DSGST  F+S+   +        R   N
Sbjct: 379 LRISLHVATGVRVSDAMHIMVHLGDTDLYALIDSGSTPTFLSQDAAARVGRDPQPRSGLN 438

Query: 89  VNLI-----------------LQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDFAS 131
           V +                  + G     D  +  L GYD+VLGTQWL TL PILWDF +
Sbjct: 439 VTVANGDKVACPGVFPDMPFQIAGEEFATDVYVLTLGGYDLVLGTQWLATLGPILWDFTA 498

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|62734405|gb|AAX96514.1| retrotransposon protein, putative, unclassified [Oryza sativa Japonica Group]

 Score = 67.8 bits (164), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 39/117 (33%), Positives = 56/117 (47%), Gaps = 25/117 (21%)

Query: 38  ISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFM--------------------- 76
           +SL V++G   + TMR+   I     + LVDSGST NF+                     
Sbjct: 370 VSLNVLAGLDGANTMRLPVEIAGERVVALVDSGSTHNFIHTELARHLCLHLSPVRHDLYV 429

Query: 77  ----SEQFYSTRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDF 129
                ++  S  +C N+ L ++G    VD    D+   D++LGT+WL TL PILWDF
Sbjct: 430 VVANGDRLVSPGRCANLRLRIEGKLFTVDCFALDISTVDIILGTEWLSTLGPILWDF 486

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 66.6 bits (161), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 52/179 (29%), Positives = 81/179 (45%), Gaps = 56/179 (31%)

Query: 1   MPTTNQTTYRNSSIPVRRLSRTELQER------------------CAKNSTKMLE----- 37
           +PTT + ++      V+RLS  E+Q+R                  C +  TK  E     
Sbjct: 249 LPTTTKASH------VKRLSWEEMQKRRAQGLCFNCDEKFTSGHRCKEGDTKEAETDLPS 302

Query: 38  ---ISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQF-------------Y 81
              ISL  + G   ++TMR+  +IG    +VL+DSGST NF+S++              +
Sbjct: 303 DPEISLHALIGWTTTKTMRVTAKIGTHDVVVLIDSGSTHNFISDKVVALLHLPVVPTAPF 362

Query: 82  STR-------KCT----NVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPILWDF 129
             R       KC     N++++LQG+   + F    L G D+VLG QWL  L  ++ D+
Sbjct: 363 HVRVANGQPLKCQGRFDNIHILLQGIPFSITFYSLPLNGLDLVLGVQWLEQLGSVVCDW 421

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: GSVIVG00008595001 SubName- Full=Chromosome chr6 scaffold_202, whole genome shotgun sequence; (150 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	131
cd00303	92	cd00303, retropepsin_like, Retropepsins; pepsin-li	2e-09
pfam08284	135	pfam08284, RVP_2, Retroviral aspartyl protease	6e-05
pfam13975	72	pfam13975, gag-asp_proteas, gag-polyprotein putati	4e-04

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

 Score = 50.4 bits (121), Expect = 2e-09
 Identities = 25/92 (27%), Positives = 37/92 (40%), Gaps = 25/92 (27%)

Query: 54  INGRIGNISPIVLVDSGSTRNFMSEQFY-------------------------STRKCTN 88
           + G+I  +    LVDSG++ NF+SE                            +      
Sbjct: 1   LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILP 60

Query: 89  VNLILQGVSVIVDFNLRDLEGYDVVLGTQWLR 120
           V + + G +  VDF + DL  YDV+LG  WL 
Sbjct: 61  VTIGIGGKTFTVDFYVLDLLSYDVILGRPWLE 92

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|116868 pfam08284, RVP_2, Retroviral aspartyl protease

 Score = 39.7 bits (93), Expect = 6e-05
 Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 24/86 (27%)

Query: 58  IGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLIL 93
           + +I   VL DSG++ +F+S+ F                         +T +C +VN+ +
Sbjct: 28  VNSIPATVLFDSGASHSFISQAFVGRHGLPLEALRTPMLVHSPGGDMTATHRCPSVNIEI 87

Query: 94  QGVSVIVDFNLRDLEGYDVVLGTQWL 119
           QGV    +  L D +  DV+LG  WL
Sbjct: 88  QGVDFPANLILLDSKDLDVILGMDWL 113

Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases. Length = 135

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

 Score = 36.1 bits (84), Expect = 4e-04
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 51 TMRINGRIGNISPIVLVDSGSTRNFMSEQFYS 82
           + +   IG +    LVD+G+T +F+SE   +
Sbjct: 8  LVTVEVSIGGVEVKALVDTGATHSFISESLAA 39

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	131
PF08284	135	RVP_2: Retroviral aspartyl protease; InterPro: IPR	99.95
cd05479	124	RP_DDI RP_DDI; retropepsin-like domain of DNA dama	99.87
cd05484	91	retropepsin_like_LTR_2 Retropepsins_like_LTR, peps	99.63
PF09668	124	Asp_protease: Aspartyl protease; InterPro: IPR0191	99.61
cd05480	103	NRIP_C NRIP_C; putative nuclear receptor interacti	99.39
PF00077	100	RVP: Retroviral aspartyl protease The Prosite entr	99.28
PF13650	90	Asp_protease_2: Aspartyl protease	99.22
cd00303	92	retropepsin_like Retropepsins; pepsin-like asparta	99.21
cd05483	96	retropepsin_like_bacteria Bacterial aspartate prot	99.21
TIGR02281	121	clan_AA_DTGA clan AA aspartic protease, TIGR02281	99.19
KOG0012	380	consensus DNA damage inducible protein [Replicatio	99.03
PF02160	201	Peptidase_A3: Cauliflower mosaic virus peptidase (	98.92
cd06095	86	RP_RTVL_H_like Retropepsin of the RTVL_H family of	98.89
TIGR03698	107	clan_AA_DTGF clan AA aspartic protease, AF_0612 fa	98.86
PF12384	177	Peptidase_A2B: Ty3 transposon peptidase; InterPro:	98.74
PF13975	72	gag-asp_proteas: gag-polyprotein putative aspartyl	98.7
cd05481	93	retropepsin_like_LTR_1 Retropepsins_like_LTR; peps	97.78
cd06094	89	RP_Saci_like RP_Saci_like, retropepsin family. Ret	97.73
cd05482	87	HIV_retropepsin_like Retropepsins, pepsin-like asp	97.4
COG3577	215	Predicted aspartyl protease [General function pred	97.33
PF05585	164	DUF1758: Putative peptidase (DUF1758); InterPro: I	96.48
COG5550	125	Predicted aspartyl protease [Posttranslational mod	96.3
PF12382	137	Peptidase_A2E: Retrotransposon peptidase; InterPro	92.02
PF05618	138	Zn_protease: Putative ATP-dependant zinc protease;	90.34
cd05476	265	pepsin_A_like_plant Chroloplast Nucleoids DNA-bind	89.65
cd06097	278	Aspergillopepsin_like Aspergillopepsin_like, aspar	85.67
cd05477	318	gastricsin Gastricsins, asparate proteases produce	84.45
PF00026	317	Asp: Eukaryotic aspartyl protease The Prosite entr	84.21
cd05485	329	Cathepsin_D_like Cathepsin_D_like, pepsin family o	82.49
PF00026	317	Asp: Eukaryotic aspartyl protease The Prosite entr	81.47
PF03539	163	Spuma_A9PTase: Spumavirus aspartic protease (A9);	81.41
cd05478	317	pepsin_A Pepsin A, aspartic protease produced in g	81.06
PTZ00147	453	plasmepsin-1; Provisional	80.82
cd05471	283	pepsin_like Pepsin-like aspartic proteases, biloba	80.4

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

Probab=99.95  E-value=1.9e-28  Score=178.94  Aligned_cols=87  Identities=36%  Similarity=0.654  Sum_probs=80.8

Q ss_pred             cccccCCeEEEEEEECCeeeEEEEeCCCccccccceeE------------------------eeeeeeeeEEEECcEEEE
Q 039270           44 SGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLILQGVSVI   99 (131)
Q Consensus        44 ~g~~~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------------~~g~~~~~~~~i~g~~f~   99 (131)
                      .....+..+...+.|+++++.+|||||||||||+.++|                        +.+.|..+++.++|+.|.
T Consensus        14 ~~~~~~~vi~g~~~I~~~~~~vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~~V~~~g~~~~~~~~~~~~~~~i~g~~~~   93 (135)
T PF08284_consen   14 EAEESPDVITGTFLINSIPASVLIDSGATHSFISSSFAKKLGLPLEPLPRPIVVSAPGGSINCEGVCPDVPLSIQGHEFV   93 (135)
T ss_pred             cccCCCCeEEEEEEeccEEEEEEEecCCCcEEccHHHHHhcCCEEEEccCeeEEecccccccccceeeeEEEEECCeEEE
Confidence            34456789999999999999999999999999999999                        566789999999999999


Q ss_pred             eeeEEecCCCcceeecccccccCCCeeeeecC
Q 039270          100 VDFNLRDLEGYDVVLGTQWLRTLEPILWDFAS  131 (131)
Q Consensus       100 ~df~vl~l~~~DvILG~dWL~~~~pi~idw~~  131 (131)
                      .||+|+++++||+|||||||++|+| .|||.+
T Consensus        94 ~dl~vl~l~~~DvILGm~WL~~~~~-~IDw~~  124 (135)
T PF08284_consen   94 VDLLVLDLGGYDVILGMDWLKKHNP-VIDWAT  124 (135)
T ss_pred             eeeEEecccceeeEeccchHHhCCC-EEEccC
Confidence            9999999999999999999999999 799975

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=99.87  E-value=4.1e-22  Score=142.87  Aligned_cols=81  Identities=17%  Similarity=0.253  Sum_probs=75.0

Q ss_pred             CeEEEEEEECCeeeEEEEeCCCccccccceeE------------------------eeeeeeeeEEEECcEEEEeeeEEe
Q 039270           50 ETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLILQGVSVIVDFNLR  105 (131)
Q Consensus        50 ~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------------~~g~~~~~~~~i~g~~f~~df~vl  105 (131)
                      ..|++.++|+|+++.+|||||||||||+++++                        +.|.+..+++++++..|..+|.|+
T Consensus        15 ~~~~v~~~Ing~~~~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~~~~~Vl   94 (124)
T cd05479          15 PMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRIHLAQVKIGNLFLPCSFTVL   94 (124)
T ss_pred             eEEEEEEEECCEEEEEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCCCcEEEeEEEEEEEEECCEEeeeEEEEE
Confidence            57999999999999999999999999999888                        345677889999999999999999


Q ss_pred             cCCCcceeecccccccCCCeeeeecC
Q 039270          106 DLEGYDVVLGTQWLRTLEPILWDFAS  131 (131)
Q Consensus       106 ~l~~~DvILG~dWL~~~~pi~idw~~  131 (131)
                      ++.++|+|||||||++++. .|||++
T Consensus        95 ~~~~~d~ILG~d~L~~~~~-~ID~~~  119 (124)
T cd05479          95 EDDDVDFLIGLDMLKRHQC-VIDLKE  119 (124)
T ss_pred             CCCCcCEEecHHHHHhCCe-EEECCC
Confidence            9999999999999999996 899975

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=8.8e-16  Score=103.94  Aligned_cols=66  Identities=18%  Similarity=0.249  Sum_probs=60.3

Q ss_pred             EEEEEECCeeeEEEEeCCCccccccceeE------------------------eeeeeeeeEEEECcEEEEeeeEEecCC
Q 039270           53 RINGRIGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLILQGVSVIVDFNLRDLE  108 (131)
Q Consensus        53 rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------------~~g~~~~~~~~i~g~~f~~df~vl~l~  108 (131)
                      +++++|+|+++.+|||+||++|||+++.+                        +.|++ .+.+++++..+..+|+|++..
T Consensus         2 ~~~~~Ing~~i~~lvDTGA~~svis~~~~~~lg~~~~~~~~~~v~~a~G~~~~~~G~~-~~~v~~~~~~~~~~~~v~~~~   80 (91)
T cd05484           2 TVTLLVNGKPLKFQLDTGSAITVISEKTWRKLGSPPLKPTKKRLRTATGTKLSVLGQI-LVTVKYGGKTKVLTLYVVKNE   80 (91)
T ss_pred             EEEEEECCEEEEEEEcCCcceEEeCHHHHHHhCCCccccccEEEEecCCCEeeEeEEE-EEEEEECCEEEEEEEEEEECC
Confidence            57899999999999999999999999875                        45566 789999999999999999998


Q ss_pred             Ccceeecccccc
Q 039270          109 GYDVVLGTQWLR  120 (131)
Q Consensus       109 ~~DvILG~dWL~  120 (131)
                       +|.|||+|||.
T Consensus        81 -~~~lLG~~wl~   91 (91)
T cd05484          81 -GLNLLGRDWLD   91 (91)
T ss_pred             -CCCccChhhcC
Confidence             99999999985

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

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

Probab=99.61  E-value=2e-15  Score=109.29  Aligned_cols=79  Identities=22%  Similarity=0.321  Sum_probs=67.7

Q ss_pred             CCeEEEEEEECCeeeEEEEeCCCccccccceeE------------------------eeeeeeeeEEEECcEEEEeeeEE
Q 039270           49 SETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLILQGVSVIVDFNL  104 (131)
Q Consensus        49 ~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------------~~g~~~~~~~~i~g~~f~~df~v  104 (131)
                      ...+++.++|||+++.|+|||||.+|.|+.+++                        ..|+...+++++++..+...|.|
T Consensus        22 v~mLyI~~~ing~~vkA~VDtGAQ~tims~~~a~r~gL~~lid~r~~g~a~GvG~~~i~G~Ih~~~l~ig~~~~~~s~~V  101 (124)
T PF09668_consen   22 VSMLYINCKINGVPVKAFVDTGAQSTIMSKSCAERCGLMRLIDKRFAGVAKGVGTQKILGRIHSVQLKIGGLFFPCSFTV  101 (124)
T ss_dssp             ----EEEEEETTEEEEEEEETT-SS-EEEHHHHHHTTGGGGEEGGG-EE-------EEEEEEEEEEEEETTEEEEEEEEE
T ss_pred             cceEEEEEEECCEEEEEEEeCCCCccccCHHHHHHcCChhhccccccccccCCCcCceeEEEEEEEEEECCEEEEEEEEE
Confidence            457899999999999999999999999999999                        45678889999999999999999


Q ss_pred             ecCCCcceeecccccccCCCeeee
Q 039270          105 RDLEGYDVVLGTQWLRTLEPILWD  128 (131)
Q Consensus       105 l~l~~~DvILG~dWL~~~~pi~id  128 (131)
                      ++-...|+|||.|||++|.- .||
T Consensus       102 le~~~~d~llGld~L~~~~c-~ID  124 (124)
T PF09668_consen  102 LEDQDVDLLLGLDMLKRHKC-CID  124 (124)
T ss_dssp             ETTSSSSEEEEHHHHHHTT--EEE
T ss_pred             eCCCCcceeeeHHHHHHhCc-ccC
Confidence            99889999999999999998 576

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.

>cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein

Probab=99.39  E-value=8.6e-13  Score=92.21  Aligned_cols=76  Identities=20%  Similarity=0.231  Sum_probs=69.4

Q ss_pred             EEEEECCeeeEEEEeCCCccccccceeE--------------------------eeeeeeeeEEEECcEEEEeeeEEecC
Q 039270           54 INGRIGNISPIVLVDSGSTRNFMSEQFY--------------------------STRKCTNVNLILQGVSVIVDFNLRDL  107 (131)
Q Consensus        54 v~~~I~~~~v~aLIDSGsThnFIs~~~a--------------------------~~g~~~~~~~~i~g~~f~~df~vl~l  107 (131)
                      +.+++||+++.|+|||||.+|.||+.++                          ..|+++.+++++++..+...|.|++-
T Consensus         1 vnCk~nG~~vkAfVDsGaQ~timS~~caercgL~r~v~~~r~~g~A~gvgt~~kiiGrih~~~ikig~~~~~CSftVld~   80 (103)
T cd05480           1 VSCQCAGKELRALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSLPTSVKVIGQIERLVLQLGQLTVECSAQVVDD   80 (103)
T ss_pred             CceeECCEEEEEEEecCCchhhcCHHHHHHcChHhhhhhccccccccCCCcceeEeeEEEEEEEEeCCEEeeEEEEEEcC
Confidence            3588999999999999999999999999                          34567789999999999999999998


Q ss_pred             CCcceeecccccccCCCeeeeec
Q 039270          108 EGYDVVLGTQWLRTLEPILWDFA  130 (131)
Q Consensus       108 ~~~DvILG~dWL~~~~pi~idw~  130 (131)
                      ...|++||.|-|++|.- .||.+
T Consensus        81 ~~~d~llGLdmLkrhqc-~IdL~  102 (103)
T cd05480          81 NEKNFSLGLQTLKSLKC-VINLE  102 (103)
T ss_pred             CCcceEeeHHHHhhcce-eeecc
Confidence            89999999999999999 68865

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.

>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=99.28  E-value=2.8e-11  Score=82.41  Aligned_cols=74  Identities=20%  Similarity=0.284  Sum_probs=62.6

Q ss_pred             CeEEEEEEECCeeeEEEEeCCCccccccceeE---------------eeee-----eeeeEEEECcEEEEeeeEEecCCC
Q 039270           50 ETMRINGRIGNISPIVLVDSGSTRNFMSEQFY---------------STRK-----CTNVNLILQGVSVIVDFNLRDLEG  109 (131)
Q Consensus        50 ~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a---------------~~g~-----~~~~~~~i~g~~f~~df~vl~l~~  109 (131)
                      +.-++..+++|+++.+|||+||+.++|+.+..               ..|.     ...+.+++++..+...|+|.+-..
T Consensus         4 ~rp~i~v~i~g~~i~~LlDTGA~vsiI~~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~v~~~~~~~~~~~~v~~~~~   83 (100)
T PF00077_consen    4 NRPYITVKINGKKIKALLDTGADVSIISEKDWKKLGPPPKTSITVRGAGGSSSILGSTTVEVKIGGKEFNHTFLVVPDLP   83 (100)
T ss_dssp             SSSEEEEEETTEEEEEEEETTBSSEEESSGGSSSTSSEEEEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEESSTCS
T ss_pred             CCceEEEeECCEEEEEEEecCCCcceecccccccccccccCCceeccCCCcceeeeEEEEEEEEECccceEEEEecCCCC
Confidence            34567899999999999999999999999877               0111     135688899999999999999877


Q ss_pred             cceeecccccccCCC
Q 039270          110 YDVVLGTQWLRTLEP  124 (131)
Q Consensus       110 ~DvILG~dWL~~~~p  124 (131)
                      +| |||.|||++++.
T Consensus        84 ~~-ILG~D~L~~~~~   97 (100)
T PF00077_consen   84 MN-ILGRDFLKKLNA   97 (100)
T ss_dssp             SE-EEEHHHHTTTTC
T ss_pred             CC-EeChhHHHHcCC
Confidence            88 999999999987

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 ....

>PF13650 Asp_protease_2: Aspartyl protease

Probab=99.22  E-value=5.1e-11  Score=78.44  Aligned_cols=65  Identities=17%  Similarity=0.304  Sum_probs=53.1

Q ss_pred             EEEEECCeeeEEEEeCCCccccccceeE------------------eeee-----eeeeEEEECcEEE-EeeeEEec-CC
Q 039270           54 INGRIGNISPIVLVDSGSTRNFMSEQFY------------------STRK-----CTNVNLILQGVSV-IVDFNLRD-LE  108 (131)
Q Consensus        54 v~~~I~~~~v~aLIDSGsThnFIs~~~a------------------~~g~-----~~~~~~~i~g~~f-~~df~vl~-l~  108 (131)
                      |.++|+|+++.+||||||++++|+.+++                  ..|.     ..--.+++++..+ ..++.+++ -.
T Consensus         1 V~v~vng~~~~~liDTGa~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~~~~i~ig~~~~~~~~~~v~~~~~   80 (90)
T PF13650_consen    1 VPVKVNGKPVRFLIDTGASISVISRSLAKKLGLKPRPKSVPISVSGAGGSVTVYRGRVDSITIGGITLKNVPFLVVDLGD   80 (90)
T ss_pred             CEEEECCEEEEEEEcCCCCcEEECHHHHHHcCCCCcCCceeEEEEeCCCCEEEEEEEEEEEEECCEEEEeEEEEEECCCC
Confidence            4688999999999999999999999998                  0111     1122688899888 68899999 56


Q ss_pred             Ccceeecccc
Q 039270          109 GYDVVLGTQW  118 (131)
Q Consensus       109 ~~DvILG~dW  118 (131)
                      .+|.|||+||
T Consensus        81 ~~~~iLG~df   90 (90)
T PF13650_consen   81 PIDGILGMDF   90 (90)
T ss_pred             CCEEEeCCcC
Confidence            8999999998

>cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases

Probab=99.21  E-value=5.3e-11  Score=74.34  Aligned_cols=66  Identities=38%  Similarity=0.639  Sum_probs=55.4

Q ss_pred             EEEECCeeeEEEEeCCCccccccceeE-------------------------eeeeeeeeEEEECcEEEEeeeEEecCCC
Q 039270           55 NGRIGNISPIVLVDSGSTRNFMSEQFY-------------------------STRKCTNVNLILQGVSVIVDFNLRDLEG  109 (131)
Q Consensus        55 ~~~I~~~~v~aLIDSGsThnFIs~~~a-------------------------~~g~~~~~~~~i~g~~f~~df~vl~l~~  109 (131)
                      .+.+++.++.+|+|+||++++++..++                         ..+.+..+.+.+++..+...|++.+...
T Consensus         2 ~~~~~~~~~~~liDtgs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   81 (92)
T cd00303           2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS   81 (92)
T ss_pred             EEEECCEEEEEEEcCCCcccccCHHHHHHcCCCcccCCCceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcCCC
Confidence            466888999999999999999988775                         0112246678888999999999999999


Q ss_pred             cceeecccccc
Q 039270          110 YDVVLGTQWLR  120 (131)
Q Consensus       110 ~DvILG~dWL~  120 (131)
                      +|+|||++||+
T Consensus        82 ~~~ilG~~~l~   92 (92)
T cd00303          82 YDVILGRPWLE   92 (92)
T ss_pred             cCEEecccccC
Confidence            99999999985

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

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

Probab=99.21  E-value=5.7e-11  Score=78.94  Aligned_cols=70  Identities=20%  Similarity=0.299  Sum_probs=58.2

Q ss_pred             eEEEEEEECCeeeEEEEeCCCccccccceeE-----------------eee-----eeeeeEEEECcEEEE-eeeEEecC
Q 039270           51 TMRINGRIGNISPIVLVDSGSTRNFMSEQFY-----------------STR-----KCTNVNLILQGVSVI-VDFNLRDL  107 (131)
Q Consensus        51 t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a-----------------~~g-----~~~~~~~~i~g~~f~-~df~vl~l  107 (131)
                      .+.+.+.|+++++.+|||+||++++|+.+++                 ..|     ...-..+++++..+. ..+.++++
T Consensus         2 ~~~v~v~i~~~~~~~llDTGa~~s~i~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~ig~~~~~~~~~~v~d~   81 (96)
T cd05483           2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAARVRLDSLQIGGITLRNVPAVVLPG   81 (96)
T ss_pred             cEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCccCCCcEEEEecCCCccceEEEcceEEECCcEEeccEEEEeCC
Confidence            5788999999999999999999999999876                 011     112346788999887 68999999


Q ss_pred             CC--cceeecccccc
Q 039270          108 EG--YDVVLGTQWLR  120 (131)
Q Consensus       108 ~~--~DvILG~dWL~  120 (131)
                      ..  .|.|||+|||+
T Consensus        82 ~~~~~~gIlG~d~l~   96 (96)
T cd05483          82 DALGVDGLLGMDFLR   96 (96)
T ss_pred             cccCCceEeChHHhC
Confidence            87  99999999985

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.

>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family

Probab=99.19  E-value=1.5e-10  Score=82.91  Aligned_cols=83  Identities=19%  Similarity=0.233  Sum_probs=67.3

Q ss_pred             ccCCeEEEEEEECCeeeEEEEeCCCccccccceeE------------------eeeeeee-----eEEEECcEEEE-eee
Q 039270           47 RASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------STRKCTN-----VNLILQGVSVI-VDF  102 (131)
Q Consensus        47 ~~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------~~g~~~~-----~~~~i~g~~f~-~df  102 (131)
                      .....+.+.++|||+++.+|||+|||+++|+++++                  ..|....     -.+++++..+. ..+
T Consensus         7 ~~~g~~~v~~~InG~~~~flVDTGAs~t~is~~~A~~Lgl~~~~~~~~~~~~ta~G~~~~~~~~l~~l~iG~~~~~nv~~   86 (121)
T TIGR02281         7 DGDGHFYATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIKAARVTLDRVAIGGIVVNDVDA   86 (121)
T ss_pred             cCCCeEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCcccCCceEEEEeCCCcEEEEEEEeCEEEECCEEEeCcEE
Confidence            34578999999999999999999999999999998                  1222211     24778888877 889


Q ss_pred             EEecCCC-cceeecccccccCCCeeeee
Q 039270          103 NLRDLEG-YDVVLGTQWLRTLEPILWDF  129 (131)
Q Consensus       103 ~vl~l~~-~DvILG~dWL~~~~pi~idw  129 (131)
                      .|+|.+. .|.+|||++|+++.++.+|-
T Consensus        87 ~v~~~~~~~~~LLGm~fL~~~~~~~~~~  114 (121)
T TIGR02281        87 MVAEGGALSESLLGMSFLNRLSRFTVRG  114 (121)
T ss_pred             EEeCCCcCCceEcCHHHHhccccEEEEC
Confidence            9999873 58999999999999877763

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).

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

Probab=99.03  E-value=3.4e-10  Score=94.03  Aligned_cols=84  Identities=21%  Similarity=0.303  Sum_probs=76.8

Q ss_pred             ccCCeEEEEEEECCeeeEEEEeCCCccccccceeE------------------------eeeeeeeeEEEECcEEEEeee
Q 039270           47 RASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLILQGVSVIVDF  102 (131)
Q Consensus        47 ~~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------------~~g~~~~~~~~i~g~~f~~df  102 (131)
                      ..-..++|.|+|+|++|+|+|||||..|.||..||                        ..|+++.+.+++++..+.+.|
T Consensus       231 ~~v~ML~iN~~ing~~VKAfVDsGaq~timS~~Caer~gL~rlid~r~~g~a~gvg~~ki~g~Ih~~~lki~~~~l~c~f  310 (380)
T KOG0012|consen  231 TQVTMLYINCEINGVPVKAFVDSGAQTTIMSAACAERCGLNRLIDKRFQGEARGVGTEKILGRIHQAQLKIEDLYLPCSF  310 (380)
T ss_pred             ccceEEEEEEEECCEEEEEEEcccchhhhhhHHHHHHhChHHHhhhhhhccccCCCcccccceeEEEEEEeccEeeccce
Confidence            34467889999999999999999999999999999                        357788999999999999999


Q ss_pred             EEecCCCcceeecccccccCCCeeeeecC
Q 039270          103 NLRDLEGYDVVLGTQWLRTLEPILWDFAS  131 (131)
Q Consensus       103 ~vl~l~~~DvILG~dWL~~~~pi~idw~~  131 (131)
                      -|++-...|+.||.|-|++|+. .||.++
T Consensus       311 tV~d~~~~d~llGLd~Lrr~~c-cIdL~~  338 (380)
T KOG0012|consen  311 TVLDRRDMDLLLGLDMLRRHQC-CIDLKT  338 (380)
T ss_pred             EEecCCCcchhhhHHHHHhccc-eeeccc
Confidence            9999999999999999999999 598763

>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=98.92  E-value=6.4e-09  Score=80.79  Aligned_cols=81  Identities=21%  Similarity=0.317  Sum_probs=65.6

Q ss_pred             CCeEEEEEEE--CC---eeeEEEEeCCCccccccceeE-----------------------eeeeeeeeEEEECcEEEEe
Q 039270           49 SETMRINGRI--GN---ISPIVLVDSGSTRNFMSEQFY-----------------------STRKCTNVNLILQGVSVIV  100 (131)
Q Consensus        49 ~~t~rv~~~I--~~---~~v~aLIDSGsThnFIs~~~a-----------------------~~g~~~~~~~~i~g~~f~~  100 (131)
                      |+.+++++++  .|   ..+.++||+|||.+.++..+.                       ...+|.++.+.+.|+.|..
T Consensus         2 pNsiyI~~~i~~~gy~~~~~~~~vDTGAt~C~~~~~iiP~e~we~~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~I   81 (201)
T PF02160_consen    2 PNSIYIKVKISFPGYKKFNYHCYVDTGATICCASKKIIPEEYWEKSKKPIKVKGANGSIIQINKKAKNGKIQIADKIFRI   81 (201)
T ss_pred             CccEEEEEEEEEcCceeEEEEEEEeCCCceEEecCCcCCHHHHHhCCCcEEEEEecCCceEEEEEecCceEEEccEEEec
Confidence            5666666664  44   457889999999999999988                       3456788999999999997


Q ss_pred             eeEEecCCCcceeecccccccCCCeeeeec
Q 039270          101 DFNLRDLEGYDVVLGTQWLRTLEPILWDFA  130 (131)
Q Consensus       101 df~vl~l~~~DvILG~dWL~~~~pi~idw~  130 (131)
                      .+.-.--.|.|+|||++||+.++|. +.|.
T Consensus        82 P~iYq~~~g~d~IlG~NF~r~y~Pf-iq~~  110 (201)
T PF02160_consen   82 PTIYQQESGIDIILGNNFLRLYEPF-IQTE  110 (201)
T ss_pred             cEEEEecCCCCEEecchHHHhcCCc-EEEc
Confidence            7654433799999999999999994 8875

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

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

Probab=98.89  E-value=6.2e-09  Score=69.95  Aligned_cols=65  Identities=22%  Similarity=0.250  Sum_probs=52.3

Q ss_pred             EEEECCeeeEEEEeCCCccccccceeE--------------eeee----ee-ee-EEEECcEEEEeeeEEecCCCcceee
Q 039270           55 NGRIGNISPIVLVDSGSTRNFMSEQFY--------------STRK----CT-NV-NLILQGVSVIVDFNLRDLEGYDVVL  114 (131)
Q Consensus        55 ~~~I~~~~v~aLIDSGsThnFIs~~~a--------------~~g~----~~-~~-~~~i~g~~f~~df~vl~l~~~DvIL  114 (131)
                      .+.|||+++.+|||+||+++.|+.+.+              ..|.    .. -. .++++++....++.+.+- ..|.||
T Consensus         2 ~v~InG~~~~fLvDTGA~~tii~~~~a~~~~~~~~~~~v~gagG~~~~~v~~~~~~v~vg~~~~~~~~~v~~~-~~~~lL   80 (86)
T cd06095           2 TITVEGVPIVFLVDTGATHSVLKSDLGPKQELSTTSVLIRGVSGQSQQPVTTYRTLVDLGGHTVSHSFLVVPN-CPDPLL   80 (86)
T ss_pred             EEEECCEEEEEEEECCCCeEEECHHHhhhccCCCCcEEEEeCCCcccccEEEeeeEEEECCEEEEEEEEEEcC-CCCcEe
Confidence            578999999999999999999999877              1121    11 12 488999999999988874 469999


Q ss_pred             cccccc
Q 039270          115 GTQWLR  120 (131)
Q Consensus       115 G~dWL~  120 (131)
                      |||||+
T Consensus        81 G~dfL~   86 (86)
T cd06095          81 GRDLLS   86 (86)
T ss_pred             chhhcC
Confidence            999985

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

>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family

Probab=98.86  E-value=9.1e-09  Score=72.22  Aligned_cols=69  Identities=17%  Similarity=0.289  Sum_probs=54.1

Q ss_pred             eeeEEEEeCCCcccc-ccceeE---------------eeeee-----eeeEEEECcEEEEeeeEEecCCCcceeeccccc
Q 039270           61 ISPIVLVDSGSTRNF-MSEQFY---------------STRKC-----TNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWL  119 (131)
Q Consensus        61 ~~v~aLIDSGsThnF-Is~~~a---------------~~g~~-----~~~~~~i~g~~f~~df~vl~l~~~DvILG~dWL  119 (131)
                      .++.+|||||||+.. ++.+.+               .+|..     ....+.++|....+.+.+.+... +.+|||.||
T Consensus        15 ~~v~~LVDTGat~~~~l~~~~a~~lgl~~~~~~~~~tA~G~~~~~~v~~~~v~igg~~~~~~v~~~~~~~-~~LLG~~~L   93 (107)
T TIGR03698        15 MEVRALVDTGFSGFLLVPPDIVNKLGLPELDQRRVYLADGREVLTDVAKASIIINGLEIDAFVESLGYVD-EPLLGTELL   93 (107)
T ss_pred             eEEEEEEECCCCeEEecCHHHHHHcCCCcccCcEEEecCCcEEEEEEEEEEEEECCEEEEEEEEecCCCC-ccEecHHHH
Confidence            378999999999998 998888               23422     34567788888766655556556 899999999


Q ss_pred             ccCCCeeeeecC
Q 039270          120 RTLEPILWDFAS  131 (131)
Q Consensus       120 ~~~~pi~idw~~  131 (131)
                      ++++. .+||++
T Consensus        94 ~~l~l-~id~~~  104 (107)
T TIGR03698        94 EGLGI-VIDYRN  104 (107)
T ss_pred             hhCCE-EEehhh
Confidence            99997 799974

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.

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

Probab=98.74  E-value=5.2e-08  Score=73.78  Aligned_cols=75  Identities=16%  Similarity=0.227  Sum_probs=66.8

Q ss_pred             CeEEEEEEECCeeeEEEEeCCCccccccceeE--------------ee----------eeeeeeEEEECcEEEEeeeEEe
Q 039270           50 ETMRINGRIGNISPIVLVDSGSTRNFMSEQFY--------------ST----------RKCTNVNLILQGVSVIVDFNLR  105 (131)
Q Consensus        50 ~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a--------------~~----------g~~~~~~~~i~g~~f~~df~vl  105 (131)
                      ++..+...++|.++.+|+||||--|||+.+.+              ..          .+...+++.+++..+...++|+
T Consensus        33 ~T~~v~l~~~~t~i~vLfDSGSPTSfIr~di~~kL~L~~~~app~~fRG~vs~~~~~tsEAv~ld~~i~n~~i~i~aYV~  112 (177)
T PF12384_consen   33 KTAIVQLNCKGTPIKVLFDSGSPTSFIRSDIVEKLELPTHDAPPFRFRGFVSGESATTSEAVTLDFYIDNKLIDIAAYVT  112 (177)
T ss_pred             cEEEEEEeecCcEEEEEEeCCCccceeehhhHHhhCCccccCCCEEEeeeccCCceEEEEeEEEEEEECCeEEEEEEEEe
Confidence            67888999999999999999999999999998              11          1335778999999999999999


Q ss_pred             cCCCcceeecccccccCCC
Q 039270          106 DLEGYDVVLGTQWLRTLEP  124 (131)
Q Consensus       106 ~l~~~DvILG~dWL~~~~p  124 (131)
                      +.-++|+|+|.+.|++|..
T Consensus       113 d~m~~dlIIGnPiL~ryp~  131 (177)
T PF12384_consen  113 DNMDHDLIIGNPILDRYPT  131 (177)
T ss_pred             ccCCcceEeccHHHhhhHH
Confidence            9999999999999998864

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 [].

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

Probab=98.70  E-value=1.5e-08  Score=66.30  Aligned_cols=36  Identities=33%  Similarity=0.491  Sum_probs=33.7

Q ss_pred             cccCCeEEEEEEECCeeeEEEEeCCCccccccceeE
Q 039270           46 ARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY   81 (131)
Q Consensus        46 ~~~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a   81 (131)
                      ...+.++++.+.|+++.+.+|||||||||||+.+++
T Consensus         3 ~~~~g~~~v~~~I~g~~~~alvDtGat~~fis~~~a   38 (72)
T PF13975_consen    3 TPDPGLMYVPVSIGGVQVKALVDTGATHNFISESLA   38 (72)
T ss_pred             cccCCEEEEEEEECCEEEEEEEeCCCcceecCHHHH
Confidence            456789999999999999999999999999999999

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

Probab=97.78  E-value=8e-05  Score=50.96  Aligned_cols=60  Identities=18%  Similarity=0.244  Sum_probs=47.7

Q ss_pred             EEECC-eeeEEEEeCCCccccccceeE---------------------------eeeeeeeeEEEECcEEEEeeeEEecC
Q 039270           56 GRIGN-ISPIVLVDSGSTRNFMSEQFY---------------------------STRKCTNVNLILQGVSVIVDFNLRDL  107 (131)
Q Consensus        56 ~~I~~-~~v~aLIDSGsThnFIs~~~a---------------------------~~g~~~~~~~~i~g~~f~~df~vl~l  107 (131)
                      ..+++ +++.+++|+||+.|.|+.+..                           ..|. ..+.+++++..+..+|+|++.
T Consensus         3 ~~i~g~~~v~~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~~~G~-~~~~v~~~~~~~~~~f~Vvd~   81 (93)
T cd05481           3 MKINGKQSVKFQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIPVEGG-VKLKCRYRNPKYNLTFQVVKE   81 (93)
T ss_pred             eEeCCceeEEEEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEeeeeEE-EEEEEEECCcEEEEEEEEECC
Confidence            45778 999999999999999998875                           2344 478889999999999999996


Q ss_pred             CCcceeeccc
Q 039270          108 EGYDVVLGTQ  117 (131)
Q Consensus       108 ~~~DvILG~d  117 (131)
                      ... -|||.+
T Consensus        82 ~~~-~lLG~~   90 (93)
T cd05481          82 EGP-PLLGAK   90 (93)
T ss_pred             CCC-ceEccc
Confidence            643 345643

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

>cd06094 RP_Saci_like RP_Saci_like, retropepsin family

Probab=97.73  E-value=7.7e-05  Score=51.24  Aligned_cols=61  Identities=18%  Similarity=0.250  Sum_probs=46.6

Q ss_pred             eeeEEEEeCCCccccccceeE-------------eee------eeeeeEEEECc-EEEEeeeEEecCCCcceeecccccc
Q 039270           61 ISPIVLVDSGSTRNFMSEQFY-------------STR------KCTNVNLILQG-VSVIVDFNLRDLEGYDVVLGTQWLR  120 (131)
Q Consensus        61 ~~v~aLIDSGsThnFIs~~~a-------------~~g------~~~~~~~~i~g-~~f~~df~vl~l~~~DvILG~dWL~  120 (131)
                      -.+..|||+||.+|.|.....             .+|      -...+.+.++. +.|.-.|.|-+..  .-|||.|+|+
T Consensus         8 s~~~fLVDTGA~vSviP~~~~~~~~~~~~~~l~AANgt~I~tyG~~~l~ldlGlrr~~~w~FvvAdv~--~pIlGaDfL~   85 (89)
T cd06094           8 SGLRFLVDTGAAVSVLPASSTKKSLKPSPLTLQAANGTPIATYGTRSLTLDLGLRRPFAWNFVVADVP--HPILGADFLQ   85 (89)
T ss_pred             CCcEEEEeCCCceEeeccccccccccCCceEEEeCCCCeEeeeeeEEEEEEcCCCcEEeEEEEEcCCC--cceecHHHHH
Confidence            357899999999999987766             111      12455667775 4899999997775  4799999999


Q ss_pred             cCC
Q 039270          121 TLE  123 (131)
Q Consensus       121 ~~~  123 (131)
                      +|+
T Consensus        86 ~~~   88 (89)
T cd06094          86 HYG   88 (89)
T ss_pred             HcC
Confidence            986

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

>cd05482 HIV_retropepsin_like Retropepsins, pepsin-like aspartate proteases

Probab=97.40  E-value=0.0011  Score=45.22  Aligned_cols=66  Identities=15%  Similarity=0.093  Sum_probs=51.1

Q ss_pred             EEEECCeeeEEEEeCCCccccccceeE--------------------eeeeeeeeEEEECcEEEEeeeEEecCCCcceee
Q 039270           55 NGRIGNISPIVLVDSGSTRNFMSEQFY--------------------STRKCTNVNLILQGVSVIVDFNLRDLEGYDVVL  114 (131)
Q Consensus        55 ~~~I~~~~v~aLIDSGsThnFIs~~~a--------------------~~g~~~~~~~~i~g~~f~~df~vl~l~~~DvIL  114 (131)
                      ..+++|+.+.+|+|+||-++.|...-.                    -..++..+.+++.++.....+.+.+..-..-|+
T Consensus         2 ~~~i~g~~~~~llDTGAd~Tvi~~~~~p~~w~~~~~~~~i~GIGG~~~~~~~~~v~i~i~~~~~~g~vlv~~~~~P~nll   81 (87)
T cd05482           2 TLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVLSLPVNLW   81 (87)
T ss_pred             EEEECCEEEEEEEccCCCCeEEcccccCCCCccCCCCeEEEeccceEEEEEEeeEEEEEcCCeEEEEEEEccCCCcccEE
Confidence            467899999999999999999986553                    111345788999999888889998873445678


Q ss_pred             cccccc
Q 039270          115 GTQWLR  120 (131)
Q Consensus       115 G~dWL~  120 (131)
                      |.|-|+
T Consensus        82 GRd~L~   87 (87)
T cd05482          82 GRDILS   87 (87)
T ss_pred             ccccCC
Confidence            988763

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

>COG3577 Predicted aspartyl protease [General function prediction only]

Probab=97.33  E-value=0.00035  Score=54.75  Aligned_cols=88  Identities=23%  Similarity=0.288  Sum_probs=64.7

Q ss_pred             eeeehhhhcccccCCeEEEEEEECCeeeEEEEeCCCccccccceeE------------------eeeeeeee-----EEE
Q 039270           36 LEISLRVISGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------STRKCTNV-----NLI   92 (131)
Q Consensus        36 ~~iSl~Al~g~~~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------~~g~~~~~-----~~~   92 (131)
                      .+++|+    ......+...+.|||+++..|||+|||.--++++-|                  .+|+...-     +++
T Consensus        94 ~~v~La----k~~~GHF~a~~~VNGk~v~fLVDTGATsVal~~~dA~RlGid~~~l~y~~~v~TANG~~~AA~V~Ld~v~  169 (215)
T COG3577          94 QEVSLA----KSRDGHFEANGRVNGKKVDFLVDTGATSVALNEEDARRLGIDLNSLDYTITVSTANGRARAAPVTLDRVQ  169 (215)
T ss_pred             eEEEEE----ecCCCcEEEEEEECCEEEEEEEecCcceeecCHHHHHHhCCCccccCCceEEEccCCccccceEEeeeEE
Confidence            355553    234578999999999999999999999988877777                  34444332     456


Q ss_pred             ECcEEEE-eeeEEecCC-CcceeecccccccCCCeee
Q 039270           93 LQGVSVI-VDFNLRDLE-GYDVVLGTQWLRTLEPILW  127 (131)
Q Consensus        93 i~g~~f~-~df~vl~l~-~~DvILG~dWL~~~~pi~i  127 (131)
                      |++..+. .+.+|++-+ .-...|||.+|.+++-...
T Consensus       170 IG~I~~~nV~A~V~~~g~L~~sLLGMSfL~rL~~fq~  206 (215)
T COG3577         170 IGGIRVKNVDAMVAEDGALDESLLGMSFLNRLSGFQV  206 (215)
T ss_pred             EccEEEcCchhheecCCccchhhhhHHHHhhccceEe
Confidence            6777665 777888776 4567899999998876433

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

Probab=96.48  E-value=0.003  Score=46.69  Aligned_cols=21  Identities=38%  Similarity=0.683  Sum_probs=19.4

Q ss_pred             eeeEEEEeCCCccccccceeE
Q 039270           61 ISPIVLVDSGSTRNFMSEQFY   81 (131)
Q Consensus        61 ~~v~aLIDSGsThnFIs~~~a   81 (131)
                      +.+.+|+||||..|||+++++
T Consensus        11 ~~~~~LlDsGSq~SfIt~~la   31 (164)
T PF05585_consen   11 VEARALLDSGSQRSFITESLA   31 (164)
T ss_pred             EEEEEEEecCCchhHHhHHHH
Confidence            467899999999999999999

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

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

Probab=96.30  E-value=0.027  Score=40.94  Aligned_cols=79  Identities=18%  Similarity=0.182  Sum_probs=53.7

Q ss_pred             eEEEEEEE---CCeeeEEEEeCCCcc-ccccceeE---------------eeee-----eeeeEEEECcEEEEeeeEEec
Q 039270           51 TMRINGRI---GNISPIVLVDSGSTR-NFMSEQFY---------------STRK-----CTNVNLILQGVSVIVDFNLRD  106 (131)
Q Consensus        51 t~rv~~~I---~~~~v~aLIDSGsTh-nFIs~~~a---------------~~g~-----~~~~~~~i~g~~f~~df~vl~  106 (131)
                      ++.+....   +..-...|||+|.|. --++++++               ..|.     .....++++|.+..+-..+.+
T Consensus        12 ~v~~~f~~~~~Gd~~~~~LiDTGFtg~lvlp~~vaek~~~~~~~~~~~~~a~~~~v~t~V~~~~iki~g~e~~~~Vl~s~   91 (125)
T COG5550          12 TVPVTFRLPGQGDFVYDELIDTGFTGYLVLPPQVAEKLGLPLFSTIRIVLADGGVVKTSVALATIKIDGVEKVAFVLASD   91 (125)
T ss_pred             eEEEEEEecCCCcEEeeeEEecCCceeEEeCHHHHHhcCCCccCChhhhhhcCCEEEEEEEEEEEEECCEEEEEEEEccC
Confidence            34444444   333344599999983 44555555               2222     345578889998888888888


Q ss_pred             CCCcceeecccccccCCCeeeeecC
Q 039270          107 LEGYDVVLGTQWLRTLEPILWDFAS  131 (131)
Q Consensus       107 l~~~DvILG~dWL~~~~pi~idw~~  131 (131)
                      ....+ ++|++||+..+- .+|.++
T Consensus        92 ~~~~~-liG~~~lk~l~~-~vn~~~  114 (125)
T COG5550          92 NLPEP-LIGVNLLKLLGL-VVNPKT  114 (125)
T ss_pred             CCccc-chhhhhhhhccE-EEcCCc
Confidence            88788 899999999887 677653

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

Probab=92.02  E-value=0.29  Score=34.81  Aligned_cols=56  Identities=25%  Similarity=0.445  Sum_probs=40.2

Q ss_pred             EEEEEEECCe--eeEEEEeCCCccccccceeE-----------------------eeeeeeeeEEEECcEEEEeeeEEec
Q 039270           52 MRINGRIGNI--SPIVLVDSGSTRNFMSEQFY-----------------------STRKCTNVNLILQGVSVIVDFNLRD  106 (131)
Q Consensus        52 ~rv~~~I~~~--~v~aLIDSGsThnFIs~~~a-----------------------~~g~~~~~~~~i~g~~f~~df~vl~  106 (131)
                      |.+.+.+...  .+..|||+||..|.|.++.+                       .+.+...+.+.++|......|+|+.
T Consensus        35 mvlqa~lp~fkcsipclidtgaq~niiteetvrahklptrpw~~sviyggvyp~kinrkt~kl~i~lngisikteflvvk  114 (137)
T PF12382_consen   35 MVLQAKLPDFKCSIPCLIDTGAQVNIITEETVRAHKLPTRPWSQSVIYGGVYPNKINRKTIKLNINLNGISIKTEFLVVK  114 (137)
T ss_pred             hhhhhhCCCccccceeEEccCceeeeeehhhhhhccCCCCcchhheEeccccccccccceEEEEEEecceEEEEEEEEEE
Confidence            4444444332  35689999999999999887                       1223345678889999999999876


Q ss_pred             C
Q 039270          107 L  107 (131)
Q Consensus       107 l  107 (131)
                      -
T Consensus       115 k  115 (137)
T PF12382_consen  115 K  115 (137)
T ss_pred             e
Confidence            3

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.

>PF05618 Zn_protease: Putative ATP-dependant zinc protease; InterPro: IPR008503 This family consists of several hypothetical proteins from different archaeal and bacterial species

Probab=90.34  E-value=1.9  Score=31.53  Aligned_cols=35  Identities=31%  Similarity=0.556  Sum_probs=26.3

Q ss_pred             eeEEEECcEEEEeeeEEecCC--Ccceeec-ccccccC
Q 039270           88 NVNLILQGVSVIVDFNLRDLE--GYDVVLG-TQWLRTL  122 (131)
Q Consensus        88 ~~~~~i~g~~f~~df~vl~l~--~~DvILG-~dWL~~~  122 (131)
                      ...+.++|..+.+.|-+.+=.  .|.++|| -.||+..
T Consensus        87 ~~~~~lg~~~~~~e~tL~dR~~m~yp~LlGrR~~l~~~  124 (138)
T PF05618_consen   87 ETTLCLGGKTWKIEFTLTDRSNMKYPMLLGRRNFLRGR  124 (138)
T ss_dssp             EEEEEETTEEEEEEEEEE-S--SS-SEEE-HHHHHHTT
T ss_pred             EEEEEECCEEEEEEEEEcCCCcCcCCEEEEehHHhcCC
Confidence            567889999999999988854  7999999 9998754

; PDB: 2PMA_B.

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

Probab=89.65  E-value=1.3  Score=34.57  Aligned_cols=62  Identities=18%  Similarity=0.343  Sum_probs=39.7

Q ss_pred             eEEEEeCCCccccccceeEeeeeeeeeEEEEC-cEEEEee--------------eEEecC-CCcceeecccccccCCCee
Q 039270           63 PIVLVDSGSTRNFMSEQFYSTRKCTNVNLILQ-GVSVIVD--------------FNLRDL-EGYDVVLGTQWLRTLEPIL  126 (131)
Q Consensus        63 v~aLIDSGsThnFIs~~~a~~g~~~~~~~~i~-g~~f~~d--------------f~vl~l-~~~DvILG~dWL~~~~pi~  126 (131)
                      ..++||||++-.++.++..     +.+.+.++ +..+...              +-++.. ..--.|||..||+.+-- .
T Consensus       177 ~~ai~DTGTs~~~lp~~~~-----P~i~~~f~~~~~~~i~~~~y~~~~~~~~~C~~~~~~~~~~~~ilG~~fl~~~~~-v  250 (265)
T cd05476         177 GGTIIDSGTTLTYLPDPAY-----PDLTLHFDGGADLELPPENYFVDVGEGVVCLAILSSSSGGVSILGNIQQQNFLV-E  250 (265)
T ss_pred             CcEEEeCCCcceEcCcccc-----CCEEEEECCCCEEEeCcccEEEECCCCCEEEEEecCCCCCcEEEChhhcccEEE-E
Confidence            3489999999998887765     55555555 4333211              111222 23458999999998876 3


Q ss_pred             eeec
Q 039270          127 WDFA  130 (131)
Q Consensus       127 idw~  130 (131)
                      .|++
T Consensus       251 FD~~  254 (265)
T cd05476         251 YDLE  254 (265)
T ss_pred             EECC
Confidence            6654

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

>cd06097 Aspergillopepsin_like Aspergillopepsin_like, aspartic proteases of fungal origin

Probab=85.67  E-value=0.63  Score=36.62  Aligned_cols=58  Identities=17%  Similarity=0.260  Sum_probs=35.2

Q ss_pred             eeEEEEeCCCccccccceeE------eeee---------eeeeEEEECcEEEEeeeEEecCCCcceeecccccccCCCee
Q 039270           62 SPIVLVDSGSTRNFMSEQFY------STRK---------CTNVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPIL  126 (131)
Q Consensus        62 ~v~aLIDSGsThnFIs~~~a------~~g~---------~~~~~~~i~g~~f~~df~vl~l~~~DvILG~dWL~~~~pi~  126 (131)
                      ...++||||++-.++..+.+      ..|.         ...|.-.+-...|..          ..|||-.+|+++-. .
T Consensus       198 ~~~~iiDSGTs~~~lP~~~~~~l~~~l~g~~~~~~~~~~~~~C~~~~P~i~f~~----------~~ilGd~fl~~~y~-v  266 (278)
T cd06097         198 GFSAIADTGTTLILLPDAIVEAYYSQVPGAYYDSEYGGWVFPCDTTLPDLSFAV----------FSILGDVFLKAQYV-V  266 (278)
T ss_pred             CceEEeecCCchhcCCHHHHHHHHHhCcCCcccCCCCEEEEECCCCCCCEEEEE----------EEEEcchhhCceeE-E
Confidence            45699999999999887665      1011         011111111111111          57999999999887 4


Q ss_pred             eeec
Q 039270          127 WDFA  130 (131)
Q Consensus       127 idw~  130 (131)
                      .||.
T Consensus       267 fD~~  270 (278)
T cd06097         267 FDVG  270 (278)
T ss_pred             EcCC
Confidence            7774

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-

>cd05477 gastricsin Gastricsins, asparate proteases produced in gastric mucosa

Probab=84.45  E-value=2.7  Score=33.62  Aligned_cols=66  Identities=18%  Similarity=0.290  Sum_probs=43.8

Q ss_pred             EEEEeCCCccccccceeE--------------------eee--eeeeeEEEECcEEEEeee-------------EEecC-
Q 039270           64 IVLVDSGSTRNFMSEQFY--------------------STR--KCTNVNLILQGVSVIVDF-------------NLRDL-  107 (131)
Q Consensus        64 ~aLIDSGsThnFIs~~~a--------------------~~g--~~~~~~~~i~g~~f~~df-------------~vl~l-  107 (131)
                      .++||||++..++.....                    |..  ..+.+.+.++|..+...-             -+.+. 
T Consensus       203 ~~iiDSGtt~~~lP~~~~~~l~~~~~~~~~~~~~~~~~C~~~~~~p~l~~~f~g~~~~v~~~~y~~~~~~~C~~~i~~~~  282 (318)
T cd05477         203 QAIVDTGTSLLTAPQQVMSTLMQSIGAQQDQYGQYVVNCNNIQNLPTLTFTINGVSFPLPPSAYILQNNGYCTVGIEPTY  282 (318)
T ss_pred             eeeECCCCccEECCHHHHHHHHHHhCCccccCCCEEEeCCccccCCcEEEEECCEEEEECHHHeEecCCCeEEEEEEecc
Confidence            589999999988887766                    221  124677778887765331             11111 


Q ss_pred             -----CCcceeecccccccCCCeeeeec
Q 039270          108 -----EGYDVVLGTQWLRTLEPILWDFA  130 (131)
Q Consensus       108 -----~~~DvILG~dWL~~~~pi~idw~  130 (131)
                           +....|||..+|+.+-. ..|+.
T Consensus       283 ~~~~~~~~~~ilG~~fl~~~y~-vfD~~  309 (318)
T cd05477         283 LPSQNGQPLWILGDVFLRQYYS-VYDLG  309 (318)
T ss_pred             cCCCCCCceEEEcHHHhhheEE-EEeCC
Confidence                 22458999999999877 46764

Gastricsin is also called pepsinogen C. Gastricsins are produced in gastric mucosa of mammals. It is synthesized by the chief cells in the stomach as an inactive zymogen. It is self-converted to a mature enzyme under acidic conditions. Human gastricsin is distributed throughout all parts of the stomach. Gastricsin is synthesized as an inactive progastricsin that has an approximately 40 residue prosequence. It is self-converting to a mature enzyme being triggered by a drop in pH from neutrality to acidic conditions. Like other aspartic proteases, gastricsin are characterized by two catalytic aspartic residues at the active site, and display optimal activity at acidic pH. Mature enzyme has a pseudo-2-fold symmetry that passes through the active site between the catalytic aspartate residues. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic aspartate residue, with an exten

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

Probab=84.21  E-value=8.3  Score=30.16  Aligned_cols=25  Identities=36%  Similarity=0.513  Sum_probs=20.9

Q ss_pred             EEEEEEC--CeeeEEEEeCCCcccccc
Q 039270           53 RINGRIG--NISPIVLVDSGSTRNFMS   77 (131)
Q Consensus        53 rv~~~I~--~~~v~aLIDSGsThnFIs   77 (131)
                      .+...|+  .+++.++||+||+..++.
T Consensus         3 ~~~v~iGtp~q~~~~~iDTGS~~~wv~   29 (317)
T PF00026_consen    3 YINVTIGTPPQTFRVLIDTGSSDTWVP   29 (317)
T ss_dssp             EEEEEETTTTEEEEEEEETTBSSEEEE
T ss_pred             EEEEEECCCCeEEEEEEecccceeeec
Confidence            3567787  799999999999988876

; 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 ....

>cd05485 Cathepsin_D_like Cathepsin_D_like, pepsin family of proteinases

Probab=82.49  E-value=4  Score=33.09  Aligned_cols=67  Identities=13%  Similarity=0.181  Sum_probs=43.5

Q ss_pred             eEEEEeCCCccccccceeE--------------------eee--eeeeeEEEECcEEEEee---eE----------E---
Q 039270           63 PIVLVDSGSTRNFMSEQFY--------------------STR--KCTNVNLILQGVSVIVD---FN----------L---  104 (131)
Q Consensus        63 v~aLIDSGsThnFIs~~~a--------------------~~g--~~~~~~~~i~g~~f~~d---f~----------v---  104 (131)
                      ..++||||++..++..+..                    |..  ..+.+.+.+++..|...   +.          +   
T Consensus       211 ~~~iiDSGtt~~~lP~~~~~~l~~~~~~~~~~~~~~~~~C~~~~~~p~i~f~fgg~~~~i~~~~yi~~~~~~~~~~C~~~  290 (329)
T cd05485         211 CQAIADTGTSLIAGPVDEIEKLNNAIGAKPIIGGEYMVNCSAIPSLPDITFVLGGKSFSLTGKDYVLKVTQMGQTICLSG  290 (329)
T ss_pred             cEEEEccCCcceeCCHHHHHHHHHHhCCccccCCcEEEeccccccCCcEEEEECCEEeEEChHHeEEEecCCCCCEEeee
Confidence            3699999999988877655                    221  23567777777766432   11          1   


Q ss_pred             -ec-----CCCcceeecccccccCCCeeeeec
Q 039270          105 -RD-----LEGYDVVLGTQWLRTLEPILWDFA  130 (131)
Q Consensus       105 -l~-----l~~~DvILG~dWL~~~~pi~idw~  130 (131)
                       ..     -.+...|||..+|+.+-. ..||+
T Consensus       291 ~~~~~~~~~~~~~~IlG~~fl~~~y~-vFD~~  321 (329)
T cd05485         291 FMGIDIPPPAGPLWILGDVFIGKYYT-EFDLG  321 (329)
T ss_pred             EEECcCCCCCCCeEEEchHHhccceE-EEeCC
Confidence             10     112348999999999887 47764

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=81.47  E-value=1.3  Score=34.74  Aligned_cols=67  Identities=15%  Similarity=0.454  Sum_probs=45.1

Q ss_pred             eEEEEeCCCccccccceeE-------------------eeee--eeeeEEEECcEEEEee-----------------eEE
Q 039270           63 PIVLVDSGSTRNFMSEQFY-------------------STRK--CTNVNLILQGVSVIVD-----------------FNL  104 (131)
Q Consensus        63 v~aLIDSGsThnFIs~~~a-------------------~~g~--~~~~~~~i~g~~f~~d-----------------f~v  104 (131)
                      ..++||||++..++..+..                   |...  .+.+.+.+++..+...                 +.+
T Consensus       200 ~~~~~Dtgt~~i~lp~~~~~~i~~~l~~~~~~~~~~~~c~~~~~~p~l~f~~~~~~~~i~~~~~~~~~~~~~~~~C~~~i  279 (317)
T PF00026_consen  200 QQAILDTGTSYIYLPRSIFDAIIKALGGSYSDGVYSVPCNSTDSLPDLTFTFGGVTFTIPPSDYIFKIEDGNGGYCYLGI  279 (317)
T ss_dssp             EEEEEETTBSSEEEEHHHHHHHHHHHTTEEECSEEEEETTGGGGSEEEEEEETTEEEEEEHHHHEEEESSTTSSEEEESE
T ss_pred             eeeecccccccccccchhhHHHHhhhcccccceeEEEecccccccceEEEeeCCEEEEecchHhcccccccccceeEeee
Confidence            5799999999988887766                   2211  3556677776655321                 222


Q ss_pred             ec----CCCcceeecccccccCCCeeeeec
Q 039270          105 RD----LEGYDVVLGTQWLRTLEPILWDFA  130 (131)
Q Consensus       105 l~----l~~~DvILG~dWL~~~~pi~idw~  130 (131)
                      .+    -.....|||+.||+++-. ..|++
T Consensus       280 ~~~~~~~~~~~~iLG~~fl~~~y~-vfD~~  308 (317)
T PF00026_consen  280 QPMDSSDDSDDWILGSPFLRNYYV-VFDYE  308 (317)
T ss_dssp             EEESSTTSSSEEEEEHHHHTTEEE-EEETT
T ss_pred             ecccccccCCceEecHHHhhceEE-EEeCC
Confidence            22    346789999999999877 46664

; 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 ....

>PF03539 Spuma_A9PTase: Spumavirus aspartic protease (A9); InterPro: IPR001641 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=81.41  E-value=7.3  Score=29.40  Aligned_cols=62  Identities=19%  Similarity=0.282  Sum_probs=39.8

Q ss_pred             ECCeeeEEEEeCCCccccccceeE-------------eee----eeeeeEEEECcEEEEeeeEEecCCCcceee----cc
Q 039270           58 IGNISPIVLVDSGSTRNFMSEQFY-------------STR----KCTNVNLILQGVSVIVDFNLRDLEGYDVVL----GT  116 (131)
Q Consensus        58 I~~~~v~aLIDSGsThnFIs~~~a-------------~~g----~~~~~~~~i~g~~f~~df~vl~l~~~DvIL----G~  116 (131)
                      |.|..+.+.-||||+..+|-..|.             ..|    ..-=+.++++|+...+.+..-+   ||.||    -+
T Consensus         1 ikg~~l~~~wDsga~ITCiP~~fl~~E~Pi~~~~i~Tihg~~~~~vYYl~fKi~grkv~aEVi~s~---~dy~li~p~di   77 (163)
T PF03539_consen    1 IKGTKLKGHWDSGAQITCIPESFLEEEQPIGKTLIKTIHGEKEQDVYYLTFKINGRKVEAEVIASP---YDYILISPSDI   77 (163)
T ss_dssp             ETTEEEEEEE-TT-SSEEEEGGGTTT---SEEEEEE-SS-EEEEEEEEEEEEESS-EEEEEEEEES---SSSEEE-TTT-
T ss_pred             CCCceeeEEecCCCeEEEccHHHhCccccccceEEEEecCceeccEEEEEEEEcCeEEEEEEecCc---cceEEEccccc
Confidence            457788899999999999988887             112    2223678889988887777666   44444    34


Q ss_pred             cccccC
Q 039270          117 QWLRTL  122 (131)
Q Consensus       117 dWL~~~  122 (131)
                      +|+.+.
T Consensus        78 Pw~~~~   83 (163)
T PF03539_consen   78 PWYKKK   83 (163)
T ss_dssp             HHHHS-
T ss_pred             ccccCC
Confidence            787654

Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to MEROPS peptidase family A9 (spumapepsin family, clan AA). Foamy viruses are single-stranded enveloped retroviruses that have been noted to infect monkeys, cats and humans. In the human virus, the aspartic protease is encoded by the retroviral gag gene [], and in monkeys by the pol gene []. At present, the virus has not been proven to cause any particular disease. However, studies have shown Human foamy virus causes neurological disorders in infected mice []. It is not clear whether the Foamy virus/spumavirus proteases share a common evolutionary origin with other aspartic proteases. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 2JYS_A.

>cd05478 pepsin_A Pepsin A, aspartic protease produced in gastric mucosa of mammals

Probab=81.06  E-value=4.3  Score=32.54  Aligned_cols=74  Identities=18%  Similarity=0.230  Sum_probs=48.6

Q ss_pred             EEECCeee------EEEEeCCCccccccceeE--------------------eee--eeeeeEEEECcEEEEeee-----
Q 039270           56 GRIGNISP------IVLVDSGSTRNFMSEQFY--------------------STR--KCTNVNLILQGVSVIVDF-----  102 (131)
Q Consensus        56 ~~I~~~~v------~aLIDSGsThnFIs~~~a--------------------~~g--~~~~~~~~i~g~~f~~df-----  102 (131)
                      ..|+++.+      .++||||++..++.....                    |..  ..+.+.+.++|..|....     
T Consensus       194 v~v~g~~~~~~~~~~~iiDTGts~~~lp~~~~~~l~~~~~~~~~~~~~~~~~C~~~~~~P~~~f~f~g~~~~i~~~~y~~  273 (317)
T cd05478         194 VTINGQVVACSGGCQAIVDTGTSLLVGPSSDIANIQSDIGASQNQNGEMVVNCSSISSMPDVVFTINGVQYPLPPSAYIL  273 (317)
T ss_pred             EEECCEEEccCCCCEEEECCCchhhhCCHHHHHHHHHHhCCccccCCcEEeCCcCcccCCcEEEEECCEEEEECHHHhee
Confidence            45676654      589999999988886655                    322  235667778887765331     


Q ss_pred             --------EEecCC-CcceeecccccccCCCeeeeec
Q 039270          103 --------NLRDLE-GYDVVLGTQWLRTLEPILWDFA  130 (131)
Q Consensus       103 --------~vl~l~-~~DvILG~dWL~~~~pi~idw~  130 (131)
                              .+.+.+ .-..|||-.+|+.+-. ..|+.
T Consensus       274 ~~~~~C~~~~~~~~~~~~~IlG~~fl~~~y~-vfD~~  309 (317)
T cd05478         274 QDQGSCTSGFQSMGLGELWILGDVFIRQYYS-VFDRA  309 (317)
T ss_pred             cCCCEEeEEEEeCCCCCeEEechHHhcceEE-EEeCC
Confidence                    122222 2458999999998877 36664

Pepsin, a well-known aspartic protease, is produced by the human gastric mucosa in seven different zymogen isoforms, subdivided into two types: pepsinogen A and pepsinogen C. The prosequence of the zymogens are self cleaved under acidic pH. The mature enzymes are called pepsin A and pepsin C, correspondingly. The well researched porcine pepsin is also in this pepsin A family. Pepsins play an integral role in the digestion process of vertebrates. Pepsins are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. More recently evolved enzymes have similar three-dimensional structures, however their amino acid sequences are more divergent except for the conserved catalytic site motif. Pepsins specifically cleave bonds in peptides which

>PTZ00147 plasmepsin-1; Provisional

Probab=80.82  E-value=11  Score=32.69  Aligned_cols=25  Identities=16%  Similarity=0.278  Sum_probs=21.1

Q ss_pred             EEEEEEC--CeeeEEEEeCCCcccccc
Q 039270           53 RINGRIG--NISPIVLVDSGSTRNFMS   77 (131)
Q Consensus        53 rv~~~I~--~~~v~aLIDSGsThnFIs   77 (131)
                      .....|+  .+++.+++|+||+..++.
T Consensus       141 ~~~I~IGTP~Q~f~Vi~DTGSsdlWVp  167 (453)
T PTZ00147        141 YGEAKLGDNGQKFNFIFDTGSANLWVP  167 (453)
T ss_pred             EEEEEECCCCeEEEEEEeCCCCcEEEe
Confidence            3567787  688999999999999885

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

Probab=80.40  E-value=1.4  Score=33.77  Aligned_cols=61  Identities=18%  Similarity=0.268  Sum_probs=36.5

Q ss_pred             eeeEEEEeCCCccccccceeE------eeeeee--------eeEEEECcEEEEeeeEEecCCCcceeecccccccCCCee
Q 039270           61 ISPIVLVDSGSTRNFMSEQFY------STRKCT--------NVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPIL  126 (131)
Q Consensus        61 ~~v~aLIDSGsThnFIs~~~a------~~g~~~--------~~~~~i~g~~f~~df~vl~l~~~DvILG~dWL~~~~pi~  126 (131)
                      ....++||||++-.++...+.      ....+.        .+.-...--.+...|        ..|||..+|+.+-. .
T Consensus       201 ~~~~~iiDsGt~~~~lp~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~p~i~f~f--------~~ilG~~fl~~~y~-v  271 (283)
T cd05471         201 GGGGAIVDSGTSLIYLPSSVYDAILKALGAAVSSSDGGYGVDCSPCDTLPDITFTF--------LWILGDVFLRNYYT-V  271 (283)
T ss_pred             CCcEEEEecCCCCEeCCHHHHHHHHHHhCCcccccCCcEEEeCcccCcCCCEEEEE--------EEEccHhhhhheEE-E
Confidence            457899999999999988877      111110        000000011122222        89999999999877 4


Q ss_pred             eeec
Q 039270          127 WDFA  130 (131)
Q Consensus       127 idw~  130 (131)
                      .|+.
T Consensus       272 fD~~  275 (283)
T cd05471         272 FDLD  275 (283)
T ss_pred             EeCC
Confidence            6653

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

---

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

ID	Length	Definition	E-value
Query	131
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	5e-06

>3s8i_A Protein DDI1 homolog 1; protease, structural genomics, structural genomics consortiu retropepsin-like domain, protein turnover, hydrolase; 1.70A {Homo sapiens} Length = 148

 Score = 42.4 bits (99), Expect = 5e-06
 Identities = 15/99 (15%), Positives = 33/99 (33%), Gaps = 24/99 (24%)

Query: 52  MRINGRIGNISPIVLVDSGSTRNFMSEQF------------------------YSTRKCT 87
           + IN ++        VDSG+    MS+                              +  
Sbjct: 25  LYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIIGRVH 84

Query: 88  NVNLILQGVSVIVDFNLRDLEGYDVVLGTQWLRTLEPIL 126
              + ++G  +   F++ + +  D++LG   LR  +  +
Sbjct: 85  LAQIQIEGDFLQCSFSILEDQPMDMLLGLDMLRRHQCSI 123

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	131
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	99.79
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	99.69
3slz_A	132	GAG-Pro-POL polyprotein; beta sheet and dimer, pro	98.52
3ec0_A	99	Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1	98.13
2hs1_A	99	HIV-1 protease; ultra-high resolution active site	98.09
1fmb_A	104	EIAV protease; hydrolase (acid proteinase), RNA-di	97.92
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	97.57
2hah_A	116	Protease, retropepsin; retroviral, aspartyl, hydro	97.36
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	96.84
2pma_A	146	Uncharacterized protein; APC86035.2, protein LPG00	95.05
3sqf_A	114	Protease; folded monomer, retropepsin, D-type retr	94.83
2rsp_A	124	RSV protease; hydrolase(aspartyl proteinase); 2.00	94.17
2jys_A	107	Protease/reverse transcriptase; retroviral proteas	93.9

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

Probab=99.79  E-value=1.8e-19  Score=132.25  Aligned_cols=83  Identities=19%  Similarity=0.266  Sum_probs=75.4

Q ss_pred             cCCeEEEEEEECCeeeEEEEeCCCccccccceeE------------------------eeeeeeeeEEEECcEEEEeeeE
Q 039270           48 ASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLILQGVSVIVDFN  103 (131)
Q Consensus        48 ~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------------~~g~~~~~~~~i~g~~f~~df~  103 (131)
                      ....+++.++|||+++.+||||||+++||+.++|                        +.|++..+++++++..+..+|.
T Consensus        21 ~~~~l~v~~~Ing~~v~~LVDTGAs~s~Is~~~A~rlGL~~~~~~~~~~~a~g~G~~~~~g~v~~~~I~Ig~~~~~~~~~  100 (148)
T 3s8i_A           21 QVTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIIGRVHLAQIQIEGDFLQCSFS  100 (148)
T ss_dssp             -CCCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHTTCGGGEEGGGCEECCC---CEEEEEEEEEEEEETTEEEEEEEE
T ss_pred             ccCEEEEEEEECCEEEEEEEeCCCCcEeeCHHHHHHcCCccccCcceeEEEEcCCccEEEEEEEEEEEEECCEEEEEEEE
Confidence            3468999999999999999999999999999998                        2456677899999999999999


Q ss_pred             EecCCCcceeecccccccCCCeeeeecC
Q 039270          104 LRDLEGYDVVLGTQWLRTLEPILWDFAS  131 (131)
Q Consensus       104 vl~l~~~DvILG~dWL~~~~pi~idw~~  131 (131)
                      |++...+|+|||||||++++. .|||++
T Consensus       101 Vle~~~~d~LLGmD~L~~~~~-~ID~~~  127 (148)
T 3s8i_A          101 ILEDQPMDMLLGLDMLRRHQC-SIDLKK  127 (148)
T ss_dssp             EETTCSSSEEECHHHHHHTTC-EEETTT
T ss_pred             EeCCCCcCeeccHHHHHhCCE-EEEcCC
Confidence            999999999999999999997 799974

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

Probab=99.69  E-value=4.4e-17  Score=117.59  Aligned_cols=82  Identities=20%  Similarity=0.280  Sum_probs=71.3

Q ss_pred             cCCeEEEEEEECCeeeEEEEeCCCccccccceeE------------------------eeeeeeeeEEEECcEEEEeeeE
Q 039270           48 ASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY------------------------STRKCTNVNLILQGVSVIVDFN  103 (131)
Q Consensus        48 ~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------------------~~g~~~~~~~~i~g~~f~~df~  103 (131)
                      ..+.+.+.+.|+|+++.+||||||++++|+.+++                        +.+.+...++++++..+..+|.
T Consensus        23 ~~~~~~v~v~InG~~~~~LvDTGAs~s~is~~~a~~lgl~~~~~~~~~~~a~g~g~~~~~~~~~~~~i~ig~~~~~~~~~  102 (148)
T 2i1a_A           23 QVPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGKIIGRIHQAQVKIETQYIPCSFT  102 (148)
T ss_dssp             CCCCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHHTGGGGCBCCCC-----------CEEEEEEEEEETTEEEEEEEE
T ss_pred             ccceEEEEEEECCEEEEEEEECCCCccccCHHHHHHcCCCccCCcceEEEEecCCCcccccEEEEEEEEECCEEeceeEE
Confidence            4578999999999999999999999999998887                        0223445688999999999999


Q ss_pred             EecCCCcceeecccccccCCCeeeeecC
Q 039270          104 LRDLEGYDVVLGTQWLRTLEPILWDFAS  131 (131)
Q Consensus       104 vl~l~~~DvILG~dWL~~~~pi~idw~~  131 (131)
                      |++ .++|.|||||||++++. .|||+.
T Consensus       103 vl~-~~~d~iLG~d~L~~~~~-~ID~~~  128 (148)
T 2i1a_A          103 VLD-TDIDVLIGLDMLKRHLA-CVDLKE  128 (148)
T ss_dssp             EEC-SSCSEEECHHHHHHTTC-EEETTT
T ss_pred             Eec-CCCCeEecHHHHhhCCE-EEECCC
Confidence            999 78999999999999988 799863

>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=98.52  E-value=3.6e-07  Score=65.83  Aligned_cols=85  Identities=21%  Similarity=0.211  Sum_probs=63.0

Q ss_pred             cccccCCeEEEEEEECCeeeEEEEeCCCccccccceeE-----------eee-----eeeeeEEEECcEEEEeeeEEecC
Q 039270           44 SGARASETMRINGRIGNISPIVLVDSGSTRNFMSEQFY-----------STR-----KCTNVNLILQGVSVIVDFNLRDL  107 (131)
Q Consensus        44 ~g~~~~~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a-----------~~g-----~~~~~~~~i~g~~f~~df~vl~l  107 (131)
                      +|..+.+.-.+.++|+|+++.+|+|+||+...++..-+           ..|     .+..+++++.++.....+.|++-
T Consensus        15 ~~~d~~~RP~v~i~I~G~~~~~LlDTGAd~tVl~~~~~p~~~~p~~I~GiGG~i~vr~~~~i~IeI~g~~~~~~~lV~~~   94 (132)
T 3slz_A           15 QGQEPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLSDKSAWVQGATGGKRYRWTTDRKVHLATGKVTHSFLHVPD   94 (132)
T ss_dssp             ---CCCCSSEEEEEETTEEEEEEECTTCSSCEECSCCCSEEEEEEEEECSSCEEEEEEECCEEEEETTEEEEECCEECTT
T ss_pred             cCCCccCCCEEEEEECCEEEEEEEeCCCCeEEEccccCCCCCCceEEEccCCEEEEEEEeeeEEEECCeeecceEEEECC
Confidence            44556667788899999999999999999999987544           111     22346788999988888877432


Q ss_pred             CCcceeecccccccCCCeeeeec
Q 039270          108 EGYDVVLGTQWLRTLEPILWDFA  130 (131)
Q Consensus       108 ~~~DvILG~dWL~~~~pi~idw~  130 (131)
                      . ..-|||+|||.+++. .+|+.
T Consensus        95 t-PvnLLGrd~Ltqlg~-tL~fp  115 (132)
T 3slz_A           95 C-PYPLLGRDLLTKLKA-QIHFE  115 (132)
T ss_dssp             S-SSCEECHHHHHHHTC-EEEEE
T ss_pred             C-CccEECHhhHhhCCc-EEECC
Confidence            2 357899999999998 67764

>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=98.13  E-value=1.7e-05  Score=54.49  Aligned_cols=74  Identities=18%  Similarity=0.210  Sum_probs=58.0

Q ss_pred             EEEEEECCeeeEEEEeCCCccccccceeE----------------eeeeeeeeEEEECcEEEEeeeEEecCCCcceeecc
Q 039270           53 RINGRIGNISPIVLVDSGSTRNFMSEQFY----------------STRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGT  116 (131)
Q Consensus        53 rv~~~I~~~~v~aLIDSGsThnFIs~~~a----------------~~g~~~~~~~~i~g~~f~~df~vl~l~~~DvILG~  116 (131)
                      .+..+|+|+.+.+|+|+||-++.++..-.                ....+..+++++.|+.....++|-+. .. =|+|.
T Consensus        10 ~vti~I~Gq~~e~LLDTGAD~TVl~~~~~Pg~w~pk~igGiGG~i~v~qy~~i~iei~g~~~~gtvlV~~t-Pv-niiGR   87 (99)
T 3ec0_A           10 VVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTGDT-PI-NIFGR   87 (99)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEESSCCCCSCCEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEECC-SS-CEECH
T ss_pred             eEEEEECCEEEEEEEecCCCceEEcCcccCCCCCceEEEecCCcEeeeEEeeEEEEECCeEEEEEEEeCCC-Cc-Ceeeh
Confidence            57789999999999999999999974322                12245678999999998888888442 23 56899


Q ss_pred             cccccCCCeeeee
Q 039270          117 QWLRTLEPILWDF  129 (131)
Q Consensus       117 dWL~~~~pi~idw  129 (131)
                      |+|.+.+. .++|
T Consensus        88 nlLtqlG~-tLnf   99 (99)
T 3ec0_A           88 NILTALGM-SLNL   99 (99)
T ss_dssp             HHHHHHTC-EEEC
T ss_pred             hhHhhcCc-EEeC
Confidence            99999998 5664

>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=98.09  E-value=2.6e-05  Score=53.50  Aligned_cols=75  Identities=16%  Similarity=0.255  Sum_probs=59.3

Q ss_pred             EEEEEEECCeeeEEEEeCCCccccccceeE----------------eeeeeeeeEEEECcEEEEeeeEEecCCCcceeec
Q 039270           52 MRINGRIGNISPIVLVDSGSTRNFMSEQFY----------------STRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLG  115 (131)
Q Consensus        52 ~rv~~~I~~~~v~aLIDSGsThnFIs~~~a----------------~~g~~~~~~~~i~g~~f~~df~vl~l~~~DvILG  115 (131)
                      -.+..+|+|+...+|+|+||-++.++..-.                ....+..+++++.|+.....++|-|.- . =|+|
T Consensus         9 P~vtvkI~Gq~~eaLLDTGAD~TVl~~~~~p~~wkpk~igGiGG~i~v~qy~qi~iei~g~~~~gtvlV~~tP-v-niiG   86 (99)
T 2hs1_A            9 PLVTIKIGGQLKEALLDTGADDTIIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTP-V-NIIG   86 (99)
T ss_dssp             CEEEEEETTEEEEEEECTTCSSEEESCCSSCCCCEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEESCCS-S-CEEC
T ss_pred             CEEEEEECCEEEEEEeccCCCcEEEecccCCCCCCCcEEEeCCCcEeeeEeccEEEEEeCCEEEEEEEeCCCc-c-Cchh
Confidence            357789999999999999999999985433                123567889999999999988885532 3 3789


Q ss_pred             ccccccCCCeeeee
Q 039270          116 TQWLRTLEPILWDF  129 (131)
Q Consensus       116 ~dWL~~~~pi~idw  129 (131)
                      .|||.+.+- .+||
T Consensus        87 Rd~Ltqlg~-tLnf   99 (99)
T 2hs1_A           87 RNLLTQIGA-TLNF   99 (99)
T ss_dssp             HHHHTTTTC-EEEC
T ss_pred             HhHHHHcCC-EEeC
Confidence            999999988 5664

>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=97.92  E-value=2.7e-05  Score=53.73  Aligned_cols=76  Identities=17%  Similarity=0.212  Sum_probs=59.0

Q ss_pred             eEEEEEEECCeeeEEEEeCCCccccccc----e-------eE----------eeeeeeeeEEEECcEEEEeeeEEecCCC
Q 039270           51 TMRINGRIGNISPIVLVDSGSTRNFMSE----Q-------FY----------STRKCTNVNLILQGVSVIVDFNLRDLEG  109 (131)
Q Consensus        51 t~rv~~~I~~~~v~aLIDSGsThnFIs~----~-------~a----------~~g~~~~~~~~i~g~~f~~df~vl~l~~  109 (131)
                      ...+..+|+|+...+|+|+||-.+.++.    +       ..          ...++..+++++.|+.....++|-+.  
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~~t--   85 (104)
T 1fmb_A            8 RPTTIVLINDTPLNVLLDTGADTSVLTTAHYNRLKYRGRKYQGTGIGGVGGNVETFSTPVTIKKKGRHIKTRMLVADI--   85 (104)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHCSSCCCCEECCCEEETTEEECCEEEEEEEEETTEEEEEEEEEESC--
T ss_pred             CCEEEEEECCEEEEEEeccCCCcEEEccccCcccCCCCccCCccEEEeCCCeEEeeEeeeEEEECCeEEEEEEEECCC--
Confidence            3457899999999999999999999992    1       11          11126788999999999888888663  


Q ss_pred             cceeecccccccCCCeeeee
Q 039270          110 YDVVLGTQWLRTLEPILWDF  129 (131)
Q Consensus       110 ~DvILG~dWL~~~~pi~idw  129 (131)
                      ..=|+|.|||.+.+- .+||
T Consensus        86 p~niiGRd~L~qlg~-tLnf  104 (104)
T 1fmb_A           86 PVTILGRDILQDLGA-KLVL  104 (104)
T ss_dssp             SSCEECHHHHHHTTC-CCCC
T ss_pred             CCCEecHhHHhhcCc-EEeC
Confidence            346889999999987 4553

>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=97.57  E-value=0.00047  Score=52.74  Aligned_cols=76  Identities=17%  Similarity=0.236  Sum_probs=59.8

Q ss_pred             EEEEEEECCeeeEEEEeCCCcccccccee---------E-------eeeeeeeeEEEECcEEEEeeeEEecCCCcceeec
Q 039270           52 MRINGRIGNISPIVLVDSGSTRNFMSEQF---------Y-------STRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLG  115 (131)
Q Consensus        52 ~rv~~~I~~~~v~aLIDSGsThnFIs~~~---------a-------~~g~~~~~~~~i~g~~f~~df~vl~l~~~DvILG  115 (131)
                      ..+..+|+|+++.+|+|+||.++.+...-         .       ....+..+++++.|+.....++|-+.  ..=|+|
T Consensus         9 P~vtv~I~Gq~~e~LLDTGAD~TVl~~~~lpg~w~pk~igGIGG~i~vrqy~~i~iei~g~~~~gtvlVg~t--PvnIiG   86 (203)
T 3ka2_A            9 PLVTIRIGGQLKEALLDTGADDTVIEELNLPGXWKPKLIGGIAGFIKVRQYDQIPVEIXGHKAIGTVLVGPT--PVNIIG   86 (203)
T ss_dssp             CEEEEEETTEEEEEEECTTCSSCEECSCCCSSCEEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEESCC--SSCEEC
T ss_pred             CeEEEEECCEEEEEEEecCCCceEEecccCCCCCCceEEEEccCcEEEEEEcceeEEEcCeEEEEEEeeCCC--CcCccc
Confidence            46789999999999999999999986321         1       12345678999999998888888553  344899


Q ss_pred             ccccccCCCeeeeec
Q 039270          116 TQWLRTLEPILWDFA  130 (131)
Q Consensus       116 ~dWL~~~~pi~idw~  130 (131)
                      .|.|.+.+- .+|+.
T Consensus        87 Rd~LtqlG~-tLnf~  100 (203)
T 3ka2_A           87 RNLLTQIGX-TLNFX  100 (203)
T ss_dssp             HHHHTTTTC-EEEGG
T ss_pred             hhhhhhcCc-eEEec
Confidence            999999998 67764

>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=97.36  E-value=0.00073  Score=47.43  Aligned_cols=69  Identities=13%  Similarity=0.173  Sum_probs=53.0

Q ss_pred             EEECCeeeEEEEeCCCccccccce-e------------E-------eeeeeeeeEEEECcEE-----EEeeeEEec-CCC
Q 039270           56 GRIGNISPIVLVDSGSTRNFMSEQ-F------------Y-------STRKCTNVNLILQGVS-----VIVDFNLRD-LEG  109 (131)
Q Consensus        56 ~~I~~~~v~aLIDSGsThnFIs~~-~------------a-------~~g~~~~~~~~i~g~~-----f~~df~vl~-l~~  109 (131)
                      .+|+|+.+.+|+|+||-++.++.. +            .       ....+..+.+++.++.     ....++|.| .-.
T Consensus        18 ikI~Gq~~eaLLDTGAD~TVi~~~~~~~~p~~wkpk~~igGiGG~i~v~qy~qv~iei~g~~~~~~~~~gtvlV~p~tP~   97 (116)
T 2hah_A           18 IFVNGYPIKFLLDTGADITVLNRRDFQVKNSIENGRQMIGGIGGFIRGTNYINVHLEIRDENYKTQCIFGNVCVLEDNST   97 (116)
T ss_dssp             EEETTEEEEEEECTTCSSCEEEGGGCCCTTCEEEEEEEEEETTEEEEEEEEEEEEEEECCTTSCCEEEEEEEEEETTCCC
T ss_pred             EEECCEEEEEEecCCCCcEEEcccccccCCCCCCCceEEecCCCceeeeEEccEEEEEeCCCCCcceeEEEEEECCCCCc
Confidence            999999999999999999988763 2            1       1124567888888877     777888887 431


Q ss_pred             cceeecccccccCCC
Q 039270          110 YDVVLGTQWLRTLEP  124 (131)
Q Consensus       110 ~DvILG~dWL~~~~p  124 (131)
                      -==|+|.|||.+.+-
T Consensus        98 ~vniiGRd~Ltqlg~  112 (116)
T 2hah_A           98 PVNILGRDNMIKFNI  112 (116)
T ss_dssp             SSEEECHHHHTTTTC
T ss_pred             cccEecHHHHhHcCC
Confidence            124789999999886

>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=96.84  E-value=0.0083  Score=45.79  Aligned_cols=75  Identities=17%  Similarity=0.279  Sum_probs=58.5

Q ss_pred             EEEEEEECCeeeEEEEeCCCccccccceeE----------------eeeeeeeeEEEECcEEEEeeeEEecCCCcceeec
Q 039270           52 MRINGRIGNISPIVLVDSGSTRNFMSEQFY----------------STRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLG  115 (131)
Q Consensus        52 ~rv~~~I~~~~v~aLIDSGsThnFIs~~~a----------------~~g~~~~~~~~i~g~~f~~df~vl~l~~~DvILG  115 (131)
                      -.+..+++|+.+.+|+|+||-++.+...-.                ...++..+++++.|+.....++|-|. .+. |+|
T Consensus       113 P~~~iki~Gq~~e~LlDTGAD~TVl~~~~lpg~w~pk~igGiGg~i~v~qy~~i~iei~g~~~~~tvlVgpt-Pvn-iiG  190 (203)
T 3ka2_A          113 PLVTIRIGGQLKEALLDTGADDTVIEELNLPGXWKPKLIGGIGGFIKVRQYDQIPVEIXGHKAIGTVLVGPT-PVN-IIG  190 (203)
T ss_dssp             CEEEEEETTEEEEEEECTTCSSCEECSCCCCSCCEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEESCC-SSC-EEC
T ss_pred             CcEEEEECCEEEeeeecccCCceeeecccCCCCCCceEEeeccceEEEEEeccEEEEECCeEEEEEEEECCC-CcC-eec
Confidence            457899999999999999999999974322                12245678899999998888888774 344 569


Q ss_pred             ccccccCCCeeeee
Q 039270          116 TQWLRTLEPILWDF  129 (131)
Q Consensus       116 ~dWL~~~~pi~idw  129 (131)
                      .|-|.+.+- .++|
T Consensus       191 Rn~LtqlG~-tl~f  203 (203)
T 3ka2_A          191 RNLLTQIGX-TLNF  203 (203)
T ss_dssp             HHHHGGGTC-EEEC
T ss_pred             hhhHHHhCC-eeeC
Confidence            999999998 5654

>2pma_A Uncharacterized protein; APC86035.2, protein LPG0085, DUF785, legionella pneumophila pneumophila STR. philadelphia 1; 1.89A {Legionella pneumophila subsp} SCOP: b.50.1.3

Probab=95.05  E-value=0.1  Score=37.69  Aligned_cols=40  Identities=20%  Similarity=0.253  Sum_probs=32.4

Q ss_pred             eeEEEECcEEEEeeeEEecCC--CcceeecccccccCCCeeee
Q 039270           88 NVNLILQGVSVIVDFNLRDLE--GYDVVLGTQWLRTLEPILWD  128 (131)
Q Consensus        88 ~~~~~i~g~~f~~df~vl~l~--~~DvILG~dWL~~~~pi~id  128 (131)
                      ...+.+++..+.+.|-+.+=.  .|.++||-.||+..+- .+|
T Consensus        95 ~~~i~lG~~~~~ie~tLtdRs~m~ypmLLGR~~L~~~~~-lVD  136 (146)
T 2pma_A           95 LLNIKLGDKVRTIKVNLTNRKRFLYPLLLGRDAIIDFNG-AVD  136 (146)
T ss_dssp             EEEEEETTEEEEEEEEEECCCCCSCSEEECHHHHHHTTE-EEE
T ss_pred             EEEEEECCEEEEEEEEEcCCCcCCCCEEechhHHhhCCE-EEC
Confidence            457788999999999998854  7999999999987654 344

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

Probab=94.83  E-value=0.08  Score=36.88  Aligned_cols=75  Identities=7%  Similarity=0.050  Sum_probs=47.7

Q ss_pred             EEEEEECCeeeEEEEeCCCccccccceeE--------------------eeeeeeeeE-EE-ECcEEEEeeeEEecCCCc
Q 039270           53 RINGRIGNISPIVLVDSGSTRNFMSEQFY--------------------STRKCTNVN-LI-LQGVSVIVDFNLRDLEGY  110 (131)
Q Consensus        53 rv~~~I~~~~v~aLIDSGsThnFIs~~~a--------------------~~g~~~~~~-~~-i~g~~f~~df~vl~l~~~  110 (131)
                      .+..+|+|+.+.+|+|+||-.+.+...-.                    ...++..+. ++ +.|+.-....+|++--..
T Consensus        11 ~vti~I~Gq~~eaLLDTGADdTVi~~~~lpg~W~p~~~~k~igGIGG~i~v~qy~~~~~~~~i~g~k~i~tvlV~~ptPv   90 (114)
T 3sqf_A           11 SLTLWLDDKMFTGLINTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPNLPV   90 (114)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEEEGGGSCTTSCEEECCCCCTTCCGGGCCEEESSCEEEECTTCCEEEECCEEETTCSS
T ss_pred             eEEEEECCEEEEEEEccCCCceEEecccCCCCcccCcCceEEEeccceEEEEEeccceEEEecCCCEEEEEEEECCCCcc
Confidence            46789999999999999998888853222                    011222232 23 577776666677643344


Q ss_pred             ceeecccccccCCCeeeee
Q 039270          111 DVVLGTQWLRTLEPILWDF  129 (131)
Q Consensus       111 DvILG~dWL~~~~pi~idw  129 (131)
                      . |+|.+-|.+.+- ..++
T Consensus        91 N-IiGRn~LtqlG~-tLnf  107 (114)
T 3sqf_A           91 N-LWGRDLLSQMKI-MMAS  107 (114)
T ss_dssp             C-EECHHHHTTSCC-----
T ss_pred             c-EEchhhHhhcCc-EEEC
Confidence            4 469999999987 4554

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

Probab=94.17  E-value=0.057  Score=38.15  Aligned_cols=71  Identities=23%  Similarity=0.190  Sum_probs=46.1

Q ss_pred             ECCeeeEEEEeCCCccccccceeE---------------------eeeeee-eeEEEECcE--EEEeeeEEecCC--Ccc
Q 039270           58 IGNISPIVLVDSGSTRNFMSEQFY---------------------STRKCT-NVNLILQGV--SVIVDFNLRDLE--GYD  111 (131)
Q Consensus        58 I~~~~v~aLIDSGsThnFIs~~~a---------------------~~g~~~-~~~~~i~g~--~f~~df~vl~l~--~~D  111 (131)
                      |+|+...+|+|+||-++++...-.                     ...++. .+++++-|+  .....+.|.|.-  -.-
T Consensus        27 i~gq~~eaLLDTGAD~TVl~~~~lP~~W~k~~~~~~~igGIGG~i~v~qy~~~i~iei~g~~g~~~~tvlV~P~~~~tPv  106 (124)
T 2rsp_A           27 QRSVYITALLDSGADITIISEEDWPTDWPVMEAANPQIHGIGGGIPMRKSRDMIELGVINRDGSLERPLLLFPAVAMVRG  106 (124)
T ss_dssp             CSEEEEEEEECTTCSSCEEETTTSCTTSCEEECC---------CCCEEEESSCEEEEEECTTSCBCCCEEECCEEESCSS
T ss_pred             CCCEEEEEEecCCCCcEEEecccCCCcceeeccccceeeecCceEeeEEeCCceEEEEeCCCCcEEEEEEECcCCCCCce
Confidence            888999999999999988864322                     011233 555666555  444456665620  123


Q ss_pred             eeecccccccCCCeeee
Q 039270          112 VVLGTQWLRTLEPILWD  128 (131)
Q Consensus       112 vILG~dWL~~~~pi~id  128 (131)
                      =|+|.|.|.+.+-...|
T Consensus       107 nIiGRdlLtqlG~tL~N  123 (124)
T 2rsp_A          107 SILGRDCLQGLGLRLTN  123 (124)
T ss_dssp             EEECHHHHHHTTCEEEC
T ss_pred             eEECHhHHhhCCcEEec
Confidence            47899999999886544

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

Probab=93.90  E-value=0.32  Score=33.07  Aligned_cols=67  Identities=22%  Similarity=0.312  Sum_probs=49.2

Q ss_pred             EEEEECCeeeEEEEeCCCccccccceeE-------------eeee----eeeeEEEECcEEEEeeeEEecCCCcceee--
Q 039270           54 INGRIGNISPIVLVDSGSTRNFMSEQFY-------------STRK----CTNVNLILQGVSVIVDFNLRDLEGYDVVL--  114 (131)
Q Consensus        54 v~~~I~~~~v~aLIDSGsThnFIs~~~a-------------~~g~----~~~~~~~i~g~~f~~df~vl~l~~~DvIL--  114 (131)
                      +.+.|.|..+.+--||||+...|-..|.             ..|.    .-=+.++++|+...+.....+   ||.||  
T Consensus        10 L~vEiKg~kLkg~WDsGA~ITCiP~~fL~~E~PI~~~~I~TIHG~k~q~vYYl~fKv~GRKveaEVi~sp---~dYvli~   86 (107)
T 2jys_A           10 LEAEIKGTKLKAHWDSGATITCVPEAFLEDERPIQTMLIKTIHGEKQQDVYYLTFKVQGRKVEAEVLASP---YDYILLN   86 (107)
T ss_dssp             EEEEETTEEEEEEECTTCSSEEEEGGGTTTCCCSEEEEEECSSCEEEEEEEEEEEEESSCEEEEEEEEES---SSSEEEC
T ss_pred             eeEEEeCcEEEEEecCCCeEEEcchHHhcccccccceEEEEecCceeceEEEEEEEEcCeEEEEEEecCc---ccEEEEc
Confidence            6788999999999999999999988887             1122    123578889988877776666   44444  


Q ss_pred             --cccccccCC
Q 039270          115 --GTQWLRTLE  123 (131)
Q Consensus       115 --G~dWL~~~~  123 (131)
                        -++|+.+..
T Consensus        87 P~DiPW~~~~p   97 (107)
T 2jys_A           87 PSDVPWLMKKP   97 (107)
T ss_dssp             TTTCHHHHSCC
T ss_pred             CcCccccccCc
Confidence              357887543

---

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	131
d2fmba_	104	EIAV protease {Equine infectious anemia virus [Tax	98.3
d4fiva_	113	Feline immunodeficiency virus (FIV) protease {Feli	97.63
d2nmza1	99	Human immunodeficiency virus type 1 protease {Huma	97.23
d1hvca_	203	Human immunodeficiency virus type 1 protease {Huma	97.01
d1nsoa_	107	Mason-Pfizer monkey virus protease {Simian retrovi	96.72
d3ecga1	99	Human immunodeficiency virus type 2 (HIV-2) protea	96.05
d2pmaa1	141	Uncharacterized protein LPG0085 {Legionella pneumo	95.09
d1hvca_	203	Human immunodeficiency virus type 1 protease {Huma	93.84
d1izea_	323	Acid protease {Fungus (Aspergillus oryzae) [TaxId:	92.9
d1bxoa_	323	Acid protease {Fungus (Penicillium janthinellum),	92.44
d1oewa_	330	Endothiapepsin {Chestnut blight fungus (Endothia p	90.72
d1wkra_	340	Acid protease {Irpex lacteus (Polyporus tulipifera	89.12
d1am5a_	324	Pepsin(ogen) {Atlantic cod (Gadus morhua) [TaxId:	89.08
d3cmsa_	323	Chymosin (synonym: renin) {Cow (Bos taurus) [TaxId	87.9
d1bxoa_	323	Acid protease {Fungus (Penicillium janthinellum),	82.95
d1miqa_	373	Plasmepsin (a hemoglobin-degrading enzyme) {Plasmo	82.08
d2bjua1	329	Plasmepsin (a hemoglobin-degrading enzyme) {Plasmo	81.09

>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=98.30  E-value=7.7e-07  Score=59.86  Aligned_cols=73  Identities=19%  Similarity=0.270  Sum_probs=56.5

Q ss_pred             CeEEEEEEECCeeeEEEEeCCCccccccceeE---------------------eeeeeeeeEEEECcEEEEeeeEEecCC
Q 039270           50 ETMRINGRIGNISPIVLVDSGSTRNFMSEQFY---------------------STRKCTNVNLILQGVSVIVDFNLRDLE  108 (131)
Q Consensus        50 ~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a---------------------~~g~~~~~~~~i~g~~f~~df~vl~l~  108 (131)
                      +.-.++.+|+|+++.+|+|+||.++.|+.+-.                     .......+.+++.|+.....++|.|. 
T Consensus         7 ~RP~~~i~I~Gq~v~~LLDTGAD~TVI~~~~~p~~~~~~~~~~~~~igg~g~~~~~~~~~v~i~~~g~~~~~~~lV~p~-   85 (104)
T d2fmba_           7 KRPTTIVLINDTPLNVLLDTGADTSVLTTAHYNRLKYRGRKYQGTGIGGVGGNVETFSTPVTIKKKGRHIKTRMLVADI-   85 (104)
T ss_dssp             SCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHCSSCCCCEECCCEEETTEEECCEEEEEEEEETTEEEEEEEEEESC-
T ss_pred             cCeEEEEEECCEEEEEEEeCCCCeEEEcccccCccCCCCCCcceeEEEEecceEEEEEEEEEEEECCeEEEEEEEECCC-
Confidence            44568899999999999999999999965311                     11122457888899999999999884 


Q ss_pred             CcceeecccccccCCC
Q 039270          109 GYDVVLGTQWLRTLEP  124 (131)
Q Consensus       109 ~~DvILG~dWL~~~~p  124 (131)
                      .+. |||.|.|++.|-
T Consensus        86 Pvn-LlGRdlL~qlG~  100 (104)
T d2fmba_          86 PVT-ILGRDILQDLGA  100 (104)
T ss_dssp             SSC-EECHHHHHHHTC
T ss_pred             Ccc-eecHHHHHHhCC
Confidence            233 899999999876

>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=97.63  E-value=2e-05  Score=53.59  Aligned_cols=75  Identities=12%  Similarity=0.117  Sum_probs=53.2

Q ss_pred             CeEEEEEEECCeeeEEEEeCCCccccccceeE--------------------eeeeeeeeEEEECcEEEE-----eeeEE
Q 039270           50 ETMRINGRIGNISPIVLVDSGSTRNFMSEQFY--------------------STRKCTNVNLILQGVSVI-----VDFNL  104 (131)
Q Consensus        50 ~t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a--------------------~~g~~~~~~~~i~g~~f~-----~df~v  104 (131)
                      +.-+++.+|+|+++.+|+|+||-++.|+..-.                    ...++.++.+++.++...     ..+-|
T Consensus         9 ~RP~v~v~I~Gq~v~~LLDTGAD~TVi~~~d~p~~~~~~~~~~~~~GIGG~~~v~~~~~v~i~~~~~~~~gtvl~g~~pv   88 (113)
T d4fiva_           9 KRPEILIFVNGYPIKFLLDTGADITILNRRDFQVKNSIENGRQNMIGVGGGKRGTNYINVHLEIRDENYKTQCIFGNVCV   88 (113)
T ss_dssp             SCCEEEEEETTEEEEEEECTTCSSCEEEGGGCCCTTCEEEEEEEEECSSCEEEEEEEEEEEEEECCTTSCCCEEEEEEEE
T ss_pred             cCCeEEEEECCEEEEEEEcCCCCcEEEeccccCCCCCCCCCCCeEEecCeEEeeeEEceEEEEEcCCeEeEEEEEccccc
Confidence            34567889999999999999999999975321                    122456777887765544     34445


Q ss_pred             ecCCCcc-eeecccccccCCC
Q 039270          105 RDLEGYD-VVLGTQWLRTLEP  124 (131)
Q Consensus       105 l~l~~~D-vILG~dWL~~~~p  124 (131)
                      +|...+. =|||.|+|++.|-
T Consensus        89 lp~~~~p~nllGRd~LtqlG~  109 (113)
T d4fiva_          89 LEDNSLIQPLLGRDNMIKFNI  109 (113)
T ss_dssp             ETTCCCSSCEECHHHHHHTTC
T ss_pred             cCCCCCcCCEEChhhhHHhCC
Confidence            5544432 3889999999886

>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=97.23  E-value=0.0018  Score=42.60  Aligned_cols=74  Identities=16%  Similarity=0.281  Sum_probs=58.6

Q ss_pred             EEEEEECCeeeEEEEeCCCccccccceeE----------------eeeeeeeeEEEECcEEEEeeeEEecCCCcceeecc
Q 039270           53 RINGRIGNISPIVLVDSGSTRNFMSEQFY----------------STRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLGT  116 (131)
Q Consensus        53 rv~~~I~~~~v~aLIDSGsThnFIs~~~a----------------~~g~~~~~~~~i~g~~f~~df~vl~l~~~DvILG~  116 (131)
                      .+.++|+|+..-||+|+||-...+..--.                .-..+.++++++-|+.-...++|-| ...++ +|.
T Consensus        10 ~vtvkIgGq~~eaLLDTGADdTVleei~lpg~WkPk~IgGIGGfikVrqYd~i~iei~g~k~~gtVLVgp-TPvNI-iGR   87 (99)
T d2nmza1          10 LVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGP-TPANI-IGR   87 (99)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEEESCCCCSCCEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEES-CSSCE-ECH
T ss_pred             eEEEEECCEEEEEeeccCCCceEEecccCCCCCCceEEEeccceEEEEEeCceEEEECCcEEEEEEEECC-CCccE-Ecc
Confidence            57889999999999999998877743111                1235678999999999999999988 45554 599


Q ss_pred             cccccCCCeeeee
Q 039270          117 QWLRTLEPILWDF  129 (131)
Q Consensus       117 dWL~~~~pi~idw  129 (131)
                      +-|.+.+- ..||
T Consensus        88 N~Ltq~Gc-tLnf   99 (99)
T d2nmza1          88 NLLTQIGA-TLNF   99 (99)
T ss_dssp             HHHTTTTC-EEEC
T ss_pred             cchhhcCc-eecC
Confidence            99999997 5664

>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=97.01  E-value=0.0017  Score=47.49  Aligned_cols=74  Identities=18%  Similarity=0.277  Sum_probs=59.7

Q ss_pred             EEEEEEECCeeeEEEEeCCCccccccceeE-----------------eeeeeeeeEEEECcEEEEeeeEEecCCCcceee
Q 039270           52 MRINGRIGNISPIVLVDSGSTRNFMSEQFY-----------------STRKCTNVNLILQGVSVIVDFNLRDLEGYDVVL  114 (131)
Q Consensus        52 ~rv~~~I~~~~v~aLIDSGsThnFIs~~~a-----------------~~g~~~~~~~~i~g~~f~~df~vl~l~~~DvIL  114 (131)
                      -.+..+|+|+.+.||+|+||-++.+.. .-                 .-..+.++++++.|+....+++|-| ..++ ||
T Consensus         9 P~VtVkIgGQ~~eaLLDTGADDTVLe~-inLpG~WkPkiIGGIGGfIkVrqY~~V~IeI~gkk~~gTVLVgP-TPvN-II   85 (203)
T d1hvca_           9 PLVTIRIGGQLKEALLDTGADDTVLEE-MNLPGKWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGP-TPVN-II   85 (203)
T ss_dssp             CEEEEESSSCEEEEEECTTCSSEEEEC-CCCSSCEEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEES-CSSC-EE
T ss_pred             CeEEEEECCEEEEEEecCCCCceEEec-ccCCCCCcccEEEecCceEEEEEeCCEEEEECCcEEEEEEEECC-CCcc-cc
Confidence            367899999999999999999988843 22                 1224678999999999999999998 4444 56


Q ss_pred             cccccccCCCeeeee
Q 039270          115 GTQWLRTLEPILWDF  129 (131)
Q Consensus       115 G~dWL~~~~pi~idw  129 (131)
                      |.+-|.+.+- .+++
T Consensus        86 GRNlLtqlG~-tLnF   99 (203)
T d1hvca_          86 GRNLLTQIGC-TLNF   99 (203)
T ss_dssp             CHHHHGGGTC-EEEC
T ss_pred             chhhhhhhhh-eeec
Confidence            9999999988 6665

>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=96.72  E-value=0.0003  Score=46.93  Aligned_cols=73  Identities=7%  Similarity=0.025  Sum_probs=45.6

Q ss_pred             EEEEEEECCeeeEEEEeCCCccccccceeE------------ee--e------eeeeeEEEE--CcEEEEeeeEEecCCC
Q 039270           52 MRINGRIGNISPIVLVDSGSTRNFMSEQFY------------ST--R------KCTNVNLIL--QGVSVIVDFNLRDLEG  109 (131)
Q Consensus        52 ~rv~~~I~~~~v~aLIDSGsThnFIs~~~a------------~~--g------~~~~~~~~i--~g~~f~~df~vl~l~~  109 (131)
                      -.++++|+|+++.+|+|+||-++.|...-.            ..  |      ++..+....  .+..-....++++--.
T Consensus        10 P~~~v~I~G~~v~~LLDTGAD~TVI~~~~~p~~wp~~~~~~~~~GiGg~~~~~~~~~~l~~~~~~~~~~~~~p~vv~~~P   89 (107)
T d1nsoa_          10 PSLTLWLDDKMFTGLINTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPNLP   89 (107)
T ss_dssp             SCEEEEETTEEEEECCCSSCSSCBCCGGGSCTTSCCCCCEEEECSSSEEEECCCBCCCEEEEETTTEEEEECCBBCTTCC
T ss_pred             cEEEEEECCEEEEeeecCCCCcEEEeccccCCCCCcCcCccEEEEecCeeeEEEeeeeEEEEeCCCceEEEcceECCCCC
Confidence            346788999999999999999999987532            00  1      122222222  2233333334554334


Q ss_pred             cceeecccccccCCCe
Q 039270          110 YDVVLGTQWLRTLEPI  125 (131)
Q Consensus       110 ~DvILG~dWL~~~~pi  125 (131)
                      +. |||.|-|.+.+-.
T Consensus        90 vn-llGRd~L~qlg~~  104 (107)
T d1nsoa_          90 VN-LWGRDLLSQMKIM  104 (107)
T ss_dssp             CC-BCCHHHHHHHHTS
T ss_pred             cC-cccHHHHHHhCCE
Confidence            44 8899999987653

>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=96.05  E-value=0.033  Score=36.28  Aligned_cols=69  Identities=19%  Similarity=0.265  Sum_probs=53.8

Q ss_pred             EEEEEECCeeeEEEEeCCCccccccceeE-----------------eeeeeeeeEEEECcEEEEeeeEEecCCCcceeec
Q 039270           53 RINGRIGNISPIVLVDSGSTRNFMSEQFY-----------------STRKCTNVNLILQGVSVIVDFNLRDLEGYDVVLG  115 (131)
Q Consensus        53 rv~~~I~~~~v~aLIDSGsThnFIs~~~a-----------------~~g~~~~~~~~i~g~~f~~df~vl~l~~~DvILG  115 (131)
                      .+.++|+|+..-||+|+||-.+.+.. .-                 .-..+.++++++-|+.-....+|=| ...+ |+|
T Consensus        10 ~vtvkIgGq~~eaLLDTGADdTVle~-i~lpg~WkPk~iGGIGGfikVrqYd~i~Ieicg~k~~gtVLvgp-TPvN-IiG   86 (99)
T d3ecga1          10 VVTAYIEGQPVEVLLDTGADDSIVAG-IELGNNYSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTGD-TPIN-IFG   86 (99)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEECS-CCCCSCCEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEC-CSSC-EEC
T ss_pred             eEEEEECCEEeeeecccCCCceeeec-cCCCCCCcceEEEEeeeeEEEEEeCcEEEEECCcEEEEEEEeCC-CCce-EEc
Confidence            46889999999999999998777632 21                 2235678999999999999888855 3344 569


Q ss_pred             ccccccCCC
Q 039270          116 TQWLRTLEP  124 (131)
Q Consensus       116 ~dWL~~~~p  124 (131)
                      .+-|.+.+.
T Consensus        87 RNlLtqlGc   95 (99)
T d3ecga1          87 RNILTALGM   95 (99)
T ss_dssp             HHHHHHTTC
T ss_pred             cchhhhhCc
Confidence            999999887

>d2pmaa1 b.50.1.3 (A:26-166) Uncharacterized protein LPG0085 {Legionella pneumophila [TaxId: 446]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: LPG0085-like
domain: Uncharacterized protein LPG0085
species: Legionella pneumophila [TaxId: 446]

Probab=95.09  E-value=0.057  Score=36.86  Aligned_cols=41  Identities=20%  Similarity=0.247  Sum_probs=33.0

Q ss_pred             eeeEEEECcEEEEeeeEEecCC--CcceeecccccccCCCeeee
Q 039270           87 TNVNLILQGVSVIVDFNLRDLE--GYDVVLGTQWLRTLEPILWD  128 (131)
Q Consensus        87 ~~~~~~i~g~~f~~df~vl~l~--~~DvILG~dWL~~~~pi~id  128 (131)
                      ..+++.++|..+.+.|-+.+=+  .|.++||-.||+..+- .+|
T Consensus        91 V~~~i~ig~~~~~ie~tL~dR~~m~yp~LiGR~~L~~~~~-~VD  133 (141)
T d2pmaa1          91 VLLNIKLGDKVRTIKVNLTNRKRFLYPLLLGRDAIIDFNG-AVD  133 (141)
T ss_dssp             EEEEEEETTEEEEEEEEEECCCCCSCSEEECHHHHHHTTE-EEE
T ss_pred             EEEEEEECCEEEEEEEEECCCCCCCCCEEECHHHHhcCCE-EEC
Confidence            3556788999999999988854  6999999999988765 344

>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=93.84  E-value=0.24  Score=35.71  Aligned_cols=76  Identities=16%  Similarity=0.243  Sum_probs=58.0

Q ss_pred             eEEEEEEECCeeeEEEEeCCCccccccceeE----------------eeeeeeeeEEEECcEEEEeeeEEecCCCcceee
Q 039270           51 TMRINGRIGNISPIVLVDSGSTRNFMSEQFY----------------STRKCTNVNLILQGVSVIVDFNLRDLEGYDVVL  114 (131)
Q Consensus        51 t~rv~~~I~~~~v~aLIDSGsThnFIs~~~a----------------~~g~~~~~~~~i~g~~f~~df~vl~l~~~DvIL  114 (131)
                      .-.+..+++++..-||+|+||-...+..--.                .-..+..+++++-|+.-....+|-| ...+ |+
T Consensus       112 rp~vt~ki~gq~~ealldtgaddtv~e~~~lpgrwkpk~iggiggfikvrqy~~v~iei~g~k~~gtvlvgp-tp~n-ii  189 (203)
T d1hvca_         112 RPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGP-TPVN-II  189 (203)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEESCCCSSCCEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEC-CSSC-EE
T ss_pred             cceEEEecchhHHHHHhcccCCceEEecccCCCCCcceEEEEeccccceeeEccEEEEECCCEEEEEEEECC-CCce-EE
Confidence            4567899999999999999997776632111                2235678999999999999988877 3444 55


Q ss_pred             cccccccCCCeeeee
Q 039270          115 GTQWLRTLEPILWDF  129 (131)
Q Consensus       115 G~dWL~~~~pi~idw  129 (131)
                      |.+-|.+.+- ..||
T Consensus       190 grn~ltq~g~-tlnf  203 (203)
T d1hvca_         190 GRNLLTQIGC-TLNF  203 (203)
T ss_dssp             CHHHHTTTTC-EEEC
T ss_pred             cccchhhcCc-cccC
Confidence            9999999987 5654

>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=92.90  E-value=0.026  Score=41.48  Aligned_cols=68  Identities=15%  Similarity=0.276  Sum_probs=44.5

Q ss_pred             eeEEEEeCCCccccccceeE----------------------eeeeeeeeEEEECcEEEEeee---------------EE
Q 039270           62 SPIVLVDSGSTRNFMSEQFY----------------------STRKCTNVNLILQGVSVIVDF---------------NL  104 (131)
Q Consensus        62 ~v~aLIDSGsThnFIs~~~a----------------------~~g~~~~~~~~i~g~~f~~df---------------~v  104 (131)
                      ...++||||.+..++..++.                      |....+.+.+.++|..+....               .+
T Consensus       208 ~~~~ivDSGts~~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~i~f~f~g~~~~ip~~~~~~~~~~~~~C~~~i  287 (323)
T d1izea_         208 SITGIADTGTTLLLLDDSIVDAYYEQVNGASYDSSQGGYVFPSSASLPDFSVTIGDYTATVPGEYISFADVGNGQTFGGI  287 (323)
T ss_dssp             CEEEEECTTCCSEEECHHHHHHHHTTSTTCEEETTTTEEEEETTCCCCCEEEEETTEEEEECHHHHEEEECSTTEEEESE
T ss_pred             CceEEeccCCccccCCHHHHHHHHHHcCCccccCCCCcEEeecccCCceEEEEECCEEEEcChHHEEEEeCCCCEEEEEE
Confidence            45789999999999988766                      222345677777776542211               12


Q ss_pred             ecCCCcc-eeecccccccCCCeeeeec
Q 039270          105 RDLEGYD-VVLGTQWLRTLEPILWDFA  130 (131)
Q Consensus       105 l~l~~~D-vILG~dWL~~~~pi~idw~  130 (131)
                      .+..+.+ .|||..||+.+-- ..|++
T Consensus       288 ~~~~~~~~~iLG~~flr~~y~-vfD~~  313 (323)
T d1izea_         288 QSNSGIGFSIFGDVFLKSQYV-VFDAS  313 (323)
T ss_dssp             EECTTTSSEEECHHHHTTEEE-EEETT
T ss_pred             ECCCCCCCEEECHHHhCCEEE-EEECC
Confidence            2333333 5999999998876 46764

>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=92.44  E-value=0.031  Score=40.95  Aligned_cols=68  Identities=13%  Similarity=0.267  Sum_probs=47.6

Q ss_pred             eeEEEEeCCCccccccceeE----------------------eeeeeeeeEEEECcEEEEeee----------------E
Q 039270           62 SPIVLVDSGSTRNFMSEQFY----------------------STRKCTNVNLILQGVSVIVDF----------------N  103 (131)
Q Consensus        62 ~v~aLIDSGsThnFIs~~~a----------------------~~g~~~~~~~~i~g~~f~~df----------------~  103 (131)
                      ...++||||++..++....+                      |....+.+.+.++|..+....                .
T Consensus       207 ~~~aiiDSGTs~~~lp~~~~~~l~~~i~~~~~~~~~~~~~~~c~~~~p~itf~f~g~~~~i~~~~~~~~~~~~~~~C~~~  286 (323)
T d1bxoa_         207 GFSGIADTGTTLLLLDDSVVSQYYSQVSGAQQDSNAGGYVFDCSTNLPDFSVSISGYTATVPGSLINYGPSGDGSTCLGG  286 (323)
T ss_dssp             EEEEEECTTCSSEEECHHHHHHHHTTSTTCEEETTTTEEEECTTCCCCCEEEEETTEEEEECHHHHEEEECSSSSCEEES
T ss_pred             CcceEEecccccccCCHHHHHHHHHHhCCccccCCCCcEEEeccCCCCcEEEEECCEEEEEChHHeEEEEcCCCCEEEEE
Confidence            46799999999999888877                      333456788888887654311                1


Q ss_pred             EecCCCcc-eeecccccccCCCeeeeec
Q 039270          104 LRDLEGYD-VVLGTQWLRTLEPILWDFA  130 (131)
Q Consensus       104 vl~l~~~D-vILG~dWL~~~~pi~idw~  130 (131)
                      +.+..+.+ .|||..||+.+-- ..|++
T Consensus       287 i~~~~~~~~~ILG~~flr~~y~-vfD~~  313 (323)
T d1bxoa_         287 IQSNSGIGFSIFGDIFLKSQYV-VFDSD  313 (323)
T ss_dssp             EEECTTCSSEEECHHHHTTEEE-EEETT
T ss_pred             EECCCCCCcEEECHHHhCCEEE-EEECC
Confidence            22334444 5899999998877 47764

>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=90.72  E-value=0.083  Score=39.26  Aligned_cols=78  Identities=9%  Similarity=0.123  Sum_probs=50.6

Q ss_pred             eEEEE-EEECCee-----eEEEEeCCCccccccceeE----------------------eeeeeeeeEEEECcEEEEeee
Q 039270           51 TMRIN-GRIGNIS-----PIVLVDSGSTRNFMSEQFY----------------------STRKCTNVNLILQGVSVIVDF  102 (131)
Q Consensus        51 t~rv~-~~I~~~~-----v~aLIDSGsThnFIs~~~a----------------------~~g~~~~~~~~i~g~~f~~df  102 (131)
                      ++.+. ..+++..     ..++||||++..++...+.                      |....+.+.+.++|..+....
T Consensus       196 ~v~l~~i~v~~~~~~~~~~~~iiDSGts~~~lp~~~~~~i~~~~~~~~~~~~~~~~~~~C~~~~P~i~f~f~g~~~~lp~  275 (330)
T d1oewa_         196 EWTSTGYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVSGAKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPG  275 (330)
T ss_dssp             EEEEEEEEETTSCCEEEEEEEEECTTCCSEEECHHHHHHHHTTSTTCEEETTTTEEEEETTCCCCCEEEEETTEEEEECH
T ss_pred             EEEEeEEEEEeeeeecCCcceeeccccccccCCHHHHHHHHHHccCcccCcccceEEecccCCCCcEEEEECCEEEecCH
Confidence            44444 4466643     4589999999988887666                      333446788888887664311


Q ss_pred             -------------EE----ecCCCcc-eeecccccccCCCeeeee
Q 039270          103 -------------NL----RDLEGYD-VVLGTQWLRTLEPILWDF  129 (131)
Q Consensus       103 -------------~v----l~l~~~D-vILG~dWL~~~~pi~idw  129 (131)
                                   .+    .+..+.+ .|||..||+.+-. ..|+
T Consensus       276 ~~~~~~~~~~~~~~C~~~i~~~~~~~~~ILG~~flr~~y~-vfD~  319 (330)
T d1oewa_         276 DYIDFGPISTGSSSCFGGIQSSAGIGINIFGDVALKAAFV-VFNG  319 (330)
T ss_dssp             HHHEEEESSTTCSEEEESEEESTTTSSEEECHHHHTTEEE-EEEC
T ss_pred             HHeeEEEecCCCCEEEEEEECCCCCCCEEECHHHhCCEEE-EEEC
Confidence                         11    1223333 5899999998877 4676

>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=89.12  E-value=0.12  Score=38.14  Aligned_cols=78  Identities=18%  Similarity=0.323  Sum_probs=48.2

Q ss_pred             eEEEEEEECCe-----eeEEEEeCCCccccccceeE---------------------ee--eeeeeeEEEECcEEEEeee
Q 039270           51 TMRINGRIGNI-----SPIVLVDSGSTRNFMSEQFY---------------------ST--RKCTNVNLILQGVSVIVDF  102 (131)
Q Consensus        51 t~rv~~~I~~~-----~v~aLIDSGsThnFIs~~~a---------------------~~--g~~~~~~~~i~g~~f~~df  102 (131)
                      .+.+.....+.     ...++||||++-.++..++.                     |.  ...+.+.+.++|..+....
T Consensus       190 ~i~~~~~~~~~~~~~~~~~aiiDSGtt~~~lP~~~~~~l~~~~~~~~~~~~~~~~~~c~~~~~~P~i~f~f~g~~~~i~~  269 (340)
T d1wkra_         190 GINQSIRYGSSTSILSSTAGIVDTGTTLTLIASDAFAKYKKATGAVADNNTGLLRLTTAQYANLQSLFFTIGGQTFELTA  269 (340)
T ss_dssp             EEEEEEEETTTEEEEEEEEEEECTTBCSEEECHHHHHHHHHHHTCEECTTTSSEEECHHHHHTCCCEEEEETTEEEEECT
T ss_pred             EEEEEEEECCceEeccCcceEEecCCccEeccHHHHHHHHHHhCccccCCceEEEEeccccCCCCceEEEECCEEEEECh
Confidence            34455554443     23589999999998877666                     11  1235678888887765431


Q ss_pred             --EE----------------------ec---CCCcceeecccccccCCCeeeee
Q 039270          103 --NL----------------------RD---LEGYDVVLGTQWLRTLEPILWDF  129 (131)
Q Consensus       103 --~v----------------------l~---l~~~DvILG~dWL~~~~pi~idw  129 (131)
                        ++                      +.   -.+...|||..||+.+-. ..|.
T Consensus       270 ~~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ILG~~fl~~~yv-vfD~  322 (340)
T d1wkra_         270 NAQIWPRNLNTAIGGSASSVYLIVGDLGSDSGEGLDFINGLTFLERFYS-VYDT  322 (340)
T ss_dssp             GGGBCCGGGGGGGTCCSSCEEBCEEECSSCTTSSCCEEECHHHHTSEEE-EEET
T ss_pred             HHeEeeccCceeecCccceEEEEEecccCCCCCCCCEEechHHhCCEEE-EEEC
Confidence              11                      11   113457999999998754 3554

>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=89.08  E-value=0.21  Score=36.27  Aligned_cols=69  Identities=14%  Similarity=0.256  Sum_probs=45.6

Q ss_pred             eeeEEEEeCCCccccccceeE---------------------eeeeeeeeEEEECcEEEEee---------------eEE
Q 039270           61 ISPIVLVDSGSTRNFMSEQFY---------------------STRKCTNVNLILQGVSVIVD---------------FNL  104 (131)
Q Consensus        61 ~~v~aLIDSGsThnFIs~~~a---------------------~~g~~~~~~~~i~g~~f~~d---------------f~v  104 (131)
                      ....++||||++..++..+..                     +....+.+.+.++|..+...               +..
T Consensus       207 ~~~~~iiDsGts~~~lp~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~P~i~f~f~g~~~~l~~~~y~~~~~~~c~~~i~~  286 (324)
T d1am5a_         207 EGCQAIVDTGTSKIVAPVSALANIMKDIGASENQGEMMGNCASVQSLPDITFTINGVKQPLPPSAYIEGDQAFCTSGLGS  286 (324)
T ss_dssp             CCEEEEECTTCSSEEECTTTHHHHHHHHTCEECCCCEECCTTSSSSSCCEEEEETTEEEEECHHHHEEESSSCEEECEEE
T ss_pred             CCcceeeccCcccccCCHHHHHHHHHHhCCcccCCcccccccccccCCceEEEECCEEEEECHHHhEecCCCeEEEEEEe
Confidence            455799999999999998876                     12234677888888765322               222


Q ss_pred             ecCC---CcceeecccccccCCCeeeeec
Q 039270          105 RDLE---GYDVVLGTQWLRTLEPILWDFA  130 (131)
Q Consensus       105 l~l~---~~DvILG~dWL~~~~pi~idw~  130 (131)
                      +.+.   +.-.|||..||+.+-- ..|.+
T Consensus       287 ~~~~~~~~~~~ILG~~fl~~~y~-vfD~~  314 (324)
T d1am5a_         287 SGVPSNTSELWIFGDVFLRNYYT-IYDRT  314 (324)
T ss_dssp             CCSCCSSSCEEEECHHHHHHEEE-EEETT
T ss_pred             cCcCCCCCCCEEECHHhhcCEEE-EEECC
Confidence            2221   2225899999998876 35643

>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=87.90  E-value=0.21  Score=35.88  Aligned_cols=68  Identities=13%  Similarity=0.174  Sum_probs=45.2

Q ss_pred             eeEEEEeCCCccccccceeE----------------------eeeeeeeeEEEECcEEEEee-------------eEEec
Q 039270           62 SPIVLVDSGSTRNFMSEQFY----------------------STRKCTNVNLILQGVSVIVD-------------FNLRD  106 (131)
Q Consensus        62 ~v~aLIDSGsThnFIs~~~a----------------------~~g~~~~~~~~i~g~~f~~d-------------f~vl~  106 (131)
                      ...++||||.+..++...+.                      +....+.+.+.++|..+...             +-+.+
T Consensus       210 ~~~~iiDSGtt~~~lp~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~i~f~f~g~~~~l~~~~y~~~~~~~c~~~i~~  289 (323)
T d3cmsa_         210 GCQAILDTGTSKLVGPSSDILNIQQAIGATQNQYGEFDIDCDNLSYMPTVVFEINGKMYPLTPSAYTSQDQGFCTSGFQS  289 (323)
T ss_dssp             CEEEEECTTCCSEEECHHHHHHHHHHHTCEEETTTEEEECTTCTTTSCCEEEEETTEEEEECHHHHEEEETTEEEESEEE
T ss_pred             CeeEEEecCcceEEecHHHHHHHHHHhCceeccCCceeEeccccCCCCeEEEEECCEEEEECHHHeEEcCCCEEEEEEEe
Confidence            45799999999999988877                      11234677788887765321             12223


Q ss_pred             CCC-cceeecccccccCCCeeeeec
Q 039270          107 LEG-YDVVLGTQWLRTLEPILWDFA  130 (131)
Q Consensus       107 l~~-~DvILG~dWL~~~~pi~idw~  130 (131)
                      ..+ ...|||..||+.+.- ..|++
T Consensus       290 ~~~~~~~iLG~~~l~~~yv-vfD~~  313 (323)
T d3cmsa_         290 ENHSQKWILGDVFIREYYS-VFDRA  313 (323)
T ss_dssp             C---CCEEECHHHHTTEEE-EEETT
T ss_pred             CCCCCCEEEcHHhhCcEEE-EEECC
Confidence            333 347999999998876 46664

>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=82.95  E-value=3.9  Score=28.97  Aligned_cols=27  Identities=19%  Similarity=0.162  Sum_probs=22.0

Q ss_pred             EEEEEEECCeeeEEEEeCCCccccccc
Q 039270           52 MRINGRIGNISPIVLVDSGSTRNFMSE   78 (131)
Q Consensus        52 ~rv~~~I~~~~v~aLIDSGsThnFIs~   78 (131)
                      -.+...|++++..++||+||+..++..
T Consensus        17 Y~~~i~vG~~~~~v~~DTGSs~~Wv~~   43 (323)
T d1bxoa_          17 YITPVTIGGTTLNLNFDTGSADLWVFS   43 (323)
T ss_dssp             EEEEEEETTEEEEEEEETTCCCEEECB
T ss_pred             EEEEEEECCccEEEEEECCCcceEEEC
Confidence            346788999999999999999876643

>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=82.08  E-value=0.75  Score=33.99  Aligned_cols=78  Identities=17%  Similarity=0.374  Sum_probs=49.0

Q ss_pred             eEEEEEEECCe---eeEEEEeCCCccccccceeE--------------------e--eeeeeeeEEEECcEEEEee----
Q 039270           51 TMRINGRIGNI---SPIVLVDSGSTRNFMSEQFY--------------------S--TRKCTNVNLILQGVSVIVD----  101 (131)
Q Consensus        51 t~rv~~~I~~~---~v~aLIDSGsThnFIs~~~a--------------------~--~g~~~~~~~~i~g~~f~~d----  101 (131)
                      .+.+.+.+++.   ...++||||++..++..+..                    |  ....+.+.+.++|..|...    
T Consensus       240 ~i~l~~~~~~~~~~~~~~iiDTGTs~~~lP~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~P~itf~f~g~~~~l~p~~y  319 (373)
T d1miqa_         240 QIDLDVHFGKQTMEKANVIVDSGTTTITAPSEFLNKFFANLNVIKVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYY  319 (373)
T ss_dssp             EEEEEEEETTEEEEEEEEEECTTBSSEEECHHHHHHHHHHHTCEECTTSSCEEEETTCTTCCCEEEECSSCEEEECGGGS
T ss_pred             EEEEEEEECcEecCCcceEeccCCceeccCHHHHHHHHHHhCCeeccCCCeeEeccccCCCceEEEEECCEEEEECHHHe
Confidence            44555556553   45699999999988888776                    1  1223667777777655321    


Q ss_pred             ---------------eEEecCCCcceeecccccccCCCeeeee
Q 039270          102 ---------------FNLRDLEGYDVVLGTQWLRTLEPILWDF  129 (131)
Q Consensus       102 ---------------f~vl~l~~~DvILG~dWL~~~~pi~idw  129 (131)
                                     |...+.++--.|||..||+.+-- ..|.
T Consensus       320 ~~~~~~~~~~~C~~~~~~~~~~~~~~ILG~~fl~~~y~-vfD~  361 (373)
T d1miqa_         320 MNPILEVDDTLCMITMLPVDIDSNTFILGDPFMRKYFT-VFDY  361 (373)
T ss_dssp             EEESSSSSCSEEEESEEECCSSSSEEEECHHHHHHEEE-EEET
T ss_pred             eEEEEeCCCCEEEEEEEECCCCCCCEEEcHHhhCcEEE-EEEC
Confidence                           11122223336999999998766 3554

>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=81.09  E-value=0.47  Score=34.12  Aligned_cols=68  Identities=16%  Similarity=0.265  Sum_probs=42.7

Q ss_pred             eeEEEEeCCCccccccceeE--------------------e--eeeeeeeEEEECcEEEEe-------------------
Q 039270           62 SPIVLVDSGSTRNFMSEQFY--------------------S--TRKCTNVNLILQGVSVIV-------------------  100 (131)
Q Consensus        62 ~v~aLIDSGsThnFIs~~~a--------------------~--~g~~~~~~~~i~g~~f~~-------------------  100 (131)
                      ...++||||++..++.....                    |  ....+.+.+.++|..+..                   
T Consensus       208 ~~~~~iDSGt~~~~lp~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~f~~~g~~~~i~p~~y~~~~~~~~~~~C~~  287 (329)
T d2bjua1         208 KANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCML  287 (329)
T ss_dssp             EEEEEECTTCCSEEECHHHHHHHTTTSSCEECTTSSCEEEETTCTTCCCEEEECSSCEEEECHHHHEEECTTTSTTEEEE
T ss_pred             CCcccccccccceeCCHHHHHHHHHHhCCeecCCCCeeEeecccCCCCceeEEeCCEEEEECHHHhEEEeecCCCCEEEE
Confidence            56799999999999888777                    0  112344555555544322                   


Q ss_pred             eeEEecCCCcceeecccccccCCCeeeeec
Q 039270          101 DFNLRDLEGYDVVLGTQWLRTLEPILWDFA  130 (131)
Q Consensus       101 df~vl~l~~~DvILG~dWL~~~~pi~idw~  130 (131)
                      .|...+.+..-.|||..||+.+-- ..|++
T Consensus       288 ~i~~~~~~~~~~IlG~~fl~~~y~-vfD~~  316 (329)
T d2bjua1         288 NIIGLDFPVPTFILGDPFMRKYFT-VFDYD  316 (329)
T ss_dssp             CEEECCCSSCEEEECHHHHHHEEE-EEETT
T ss_pred             EEEECCCCCCCEEEchHhhCcEEE-EEECC
Confidence            111123334456999999999876 46764