Citrus Sinensis ID: 039663

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100--
Protein Sequence
MSFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQPIKLVGAQNILPKPTQSIHLQSRIFTSP
Secondary Structure (PSIPRED)
cEEEEEEccccEEEEcEEEccEEEEEccEEEEEEEEEEEcccEEEEEEHHHHHHHccEEEEcccEEEEEEEccEEEEEEEcccccccccEEEEEEccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEcccEEEcccEcccEEEEEEcEEEEEEEEEEEccccHEHHHHHHHHHcccEEEEcHEEEEEEEEcccEEEEEccccccccccEEEEEEccccccc
Coil and Loop (DISEMBL)
msflvdvgngerirseghcskvkfemqgveFEVDFHildfsganAGLAVQWLEKLGKIVTDHKAltmeftyrrqpiklvgaqnilpkptqsihlqsriftsp
Flexible Loop (DISEMBL)
msflvdvgngerirseghcskVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQPIKlvgaqnilpkptqsihlqsriftsp
Low Complexity Region (SEG)
MSFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQPIKLVGAQNILPKPTQSIHLQSRIFTSP
Disordered region (IsUnstruct)
****************GHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQPIKLVGAQNILP****************
Disordered Region (DISOPRED)
*SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQPIKLVGAQN************S******
Disordered Region (DISEMBL)
MSFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQPIKLVGAQNILPKPTQSIHLQSRIFTSP
Disordered Region (DISPRO)
*SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQPIKLVGAQNILPKPTQSIHLQSRI****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQPIKLVGAQNILPKPTQSIHLQSRIFTSP
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	102
225016150	1261	retrotransposon protein [Glycine max] gi	0.774	0.062	0.443	7e-12
147843077	1366	hypothetical protein VITISV_044100 [Viti	0.745	0.055	0.460	9e-12
147774273	1469	hypothetical protein VITISV_026680 [Viti	0.745	0.051	0.460	1e-11
147772855	1308	hypothetical protein VITISV_003711 [Viti	0.911	0.071	0.416	1e-11
359479937	787	PREDICTED: uncharacterized protein LOC10	0.774	0.100	0.443	1e-10
147789424	2822	hypothetical protein VITISV_017554 [Viti	0.745	0.026	0.447	1e-10
89887334	1359	polyprotein [Primula vulgaris]	0.774	0.058	0.443	2e-10
147773289	1575	hypothetical protein VITISV_003835 [Viti	0.774	0.050	0.417	2e-10
147841216	1852	hypothetical protein VITISV_020633 [Viti	0.892	0.049	0.357	1e-09
147842329	522	hypothetical protein VITISV_041623 [Viti	0.803	0.157	0.392	1e-09

>gi|225016150|gb|ACN78974.1| retrotransposon protein [Glycine max] gi|225016158|gb|ACN78981.1| retrotransposon protein [Glycine max]

 Score = 74.7 bits (182), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 49/79 (62%)

Query: 5   VDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKA 64
           V VGNGE ++    C +V   +Q   F VDFHIL   GA+  L VQWL+ LG ++TD+  
Sbjct: 458 VTVGNGEELQCNQVCPEVAVHIQAHTFLVDFHILPICGADVVLGVQWLKSLGPVLTDYAT 517

Query: 65  LTMEFTYRRQPIKLVGAQN 83
           LTM+F Y  + I+L G ++
Sbjct: 518 LTMKFIYNDKLIELKGDRD 536

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 74.3 bits (181), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 35/76 (46%), Positives = 46/76 (60%)

Query: 5   VDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKA 64
           V V NG+ +RSEG C+ V   MQG  + +DF+IL   G +  L VQWL+ LG I+ D   
Sbjct: 373 VKVANGQAVRSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIVLGVQWLQTLGPILWDFSR 432

Query: 65  LTMEFTYRRQPIKLVG 80
           L MEF+   +P KL G
Sbjct: 433 LQMEFSVWDKPRKLQG 448

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 73.9 bits (180), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 35/76 (46%), Positives = 46/76 (60%)

Query: 5   VDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKA 64
           V V NG+ +RSEG C+ V   MQG  + +DF+IL   G +  L VQWL+ LG I+ D   
Sbjct: 406 VKVANGQAVRSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIVLGVQWLQTLGPILWDFSR 465

Query: 65  LTMEFTYRRQPIKLVG 80
           L MEF+   +P KL G
Sbjct: 466 LQMEFSVWDKPRKLQG 481

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 73.6 bits (179), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 40/96 (41%), Positives = 55/96 (57%), Gaps = 3/96 (3%)

Query: 3   FLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDH 62
           F V V NGER+  +G   K+   +QG EF +DF  +  +G +  L +QWLE LG +V D 
Sbjct: 268 FTVRVANGERLSCKGKYEKLTVNLQGNEFHLDFFSVPLNGLDMVLGIQWLETLGSVVCDW 327

Query: 63  KALTMEFTYRRQPIKLVGAQNILPKPTQSIHLQSRI 98
           K  TM+F + +QP KL G +  +P P Q   LQ  I
Sbjct: 328 KKRTMDFIWEQQPKKLQGIE--IP-PIQDTTLQGFI 360

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359479937|ref|XP_002269588.2| PREDICTED: uncharacterized protein LOC100257206 [Vitis vinifera]

 Score = 70.9 bits (172), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 48/79 (60%)

Query: 2   SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTD 61
           +F V V NGER++ +G   KV+ E+QG EF +    L  SG +  L VQWLE LG +V +
Sbjct: 373 TFPVWVANGERLKCQGRYDKVRVELQGTEFYLTLFSLPLSGLDLVLGVQWLEMLGSVVCN 432

Query: 62  HKALTMEFTYRRQPIKLVG 80
            K LTM+F +  Q  +L G
Sbjct: 433 WKQLTMDFIWENQDRRLQG 451

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 = 70.5 bits (171), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 34/76 (44%), Positives = 45/76 (59%)

Query: 5   VDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKA 64
           V V NG+ + SEG C+ V   MQG  + +DF+IL   G +  L VQWL+ LG I+ D   
Sbjct: 371 VKVANGQAVCSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIVLGVQWLQTLGPILWDFSR 430

Query: 65  LTMEFTYRRQPIKLVG 80
           L MEF+   +P KL G
Sbjct: 431 LQMEFSVWDKPQKLQG 446

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|89887334|gb|ABD78322.1| polyprotein [Primula vulgaris]

 Score = 70.1 bits (170), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 47/79 (59%)

Query: 5   VDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKA 64
           V + NG++I+S G C KVK  +Q  +FEVDF +L   G +  L V WL +LG I  D K 
Sbjct: 335 VKIANGDKIKSSGTCEKVKLLIQENQFEVDFLLLPLVGYDLVLGVHWLSQLGVINCDFKN 394

Query: 65  LTMEFTYRRQPIKLVGAQN 83
           LTM FT+  + + L G  N
Sbjct: 395 LTMTFTHGNKKVCLKGLNN 413

Source: Primula vulgaris

Species: Primula vulgaris

Genus: Primula

Family: Primulaceae

Order: Ericales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147773289|emb|CAN64782.1| hypothetical protein VITISV_003835 [Vitis vinifera]

 Score = 70.1 bits (170), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 33/79 (41%), Positives = 47/79 (59%)

Query: 2   SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTD 61
           SF+V V NGE +R +G   +V+  +QG  F +  + L  +G +  L +QWLE LG +  D
Sbjct: 674 SFMVRVANGENLRCQGRFEEVQINLQGTIFSLTLYSLPLTGLDIVLGIQWLELLGSVGCD 733

Query: 62  HKALTMEFTYRRQPIKLVG 80
            + LTMEF +  Q  KLVG
Sbjct: 734 WRELTMEFMWENQTKKLVG 752

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147841216|emb|CAN64356.1| hypothetical protein VITISV_020633 [Vitis vinifera]

 Score = 67.4 bits (163), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 53/95 (55%), Gaps = 4/95 (4%)

Query: 2   SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTD 61
           SF V V NGER+  +G   KV  ++QG+ F +  + L  +G +  L +QWL  LG +V +
Sbjct: 309 SFTVHVANGERLLCQGRFEKVPIDLQGIPFSLTCYSLPLAGLDMVLGIQWLXMLGSVVCN 368

Query: 62  HKALTMEFTYRRQPIKLVGAQNILPKPTQSIHLQS 96
            + LTM+F +  Q  +L G Q     P Q+  L++
Sbjct: 369 WQYLTMDFNWENQARRLQGIQG----PIQATSLET 399

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 67.4 bits (163), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/84 (39%), Positives = 50/84 (59%), Gaps = 2/84 (2%)

Query: 3   FLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDH 62
           F V V NG+ ++ +G    +   +QG+ F + F+ L  +G +  L VQWLE+LG +V D 
Sbjct: 362 FHVRVANGQPLKCQGRFDNIHILLQGIPFSITFYSLPLNGLDLVLGVQWLEQLGSVVCDW 421

Query: 63  KALTMEFTYRRQPIKLVG--AQNI 84
           K +TMEF +  +P  L G  AQN+
Sbjct: 422 KQMTMEFQWANKPRLLQGSRAQNL 445

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)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	102
TAIR|locus:2091793	421	AT3G29750 [Arabidopsis thalian	0.882	0.213	0.260	0.00055

TAIR|locus:2091793 AT3G29750 [Arabidopsis thaliana (taxid:3702)]

 Score = 95 (38.5 bits), Expect = 0.00055, P = 0.00055
 Identities = 24/92 (26%), Positives = 46/92 (50%)

Query:     7 VGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAG--LAVQWLEKLGKIVTDHKA 64
             +G  + I+S G C  ++  +Q VE   +F +LD +  +    L  +WL KLG+ + + + 
Sbjct:   170 LGQRQCIQSVGTCLGIRLWVQEVEITENFLLLDLAKTDVDVILGYEWLSKLGETMVNWQN 229

Query:    65 LTMEFTYRRQPIKLVGAQNILPKPTQSIHLQS 96
                 F++ +Q I L      L + T  + ++S
Sbjct:   230 QDFSFSHNQQWITLCAEHEELEQVTTKVKMKS 261


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.322   0.137   0.405    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      102       102   0.00091  102 3  11 22  0.38    30
                                                     29  0.48    31


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  581 (62 KB)
  Total size of DFA:  116 KB (2076 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  9.65u 0.11s 9.76t   Elapsed:  00:00:01
  Total cpu time:  9.65u 0.11s 9.76t   Elapsed:  00:00:01
  Start:  Sat May 11 11:08:08 2013   End:  Sat May 11 11:08:09 2013

GO:0000166 "nucleotide binding" evidence=IEA

GO:0004812 "aminoacyl-tRNA ligase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006418 "tRNA aminoacylation for protein translation" evidence=IEA

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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: GSVIVG00029562001 SubName- Full=Chromosome chr9 scaffold_49, whole genome shotgun sequence; (219 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	102
cd00303	92	cd00303, retropepsin_like, Retropepsins; pepsin-li	5e-06

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

 Score = 40.8 bits (96), Expect = 5e-06
 Identities = 15/47 (31%), Positives = 22/47 (46%)

Query: 7  VGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLE 53
            NG  +++ G    V   + G  F VDF++LD    +  L   WLE
Sbjct: 46 GANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDVILGRPWLE 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	102
PF08284	135	RVP_2: Retroviral aspartyl protease; InterPro: IPR	99.89
cd05479	124	RP_DDI RP_DDI; retropepsin-like domain of DNA dama	99.67
cd05484	91	retropepsin_like_LTR_2 Retropepsins_like_LTR, peps	99.16
PF02160	201	Peptidase_A3: Cauliflower mosaic virus peptidase (	98.59
cd00303	92	retropepsin_like Retropepsins; pepsin-like asparta	98.51
TIGR03698	107	clan_AA_DTGF clan AA aspartic protease, AF_0612 fa	98.35
PF09668	124	Asp_protease: Aspartyl protease; InterPro: IPR0191	97.98
PF00077	100	RVP: Retroviral aspartyl protease The Prosite entr	97.94
cd05483	96	retropepsin_like_bacteria Bacterial aspartate prot	97.82
PF13650	90	Asp_protease_2: Aspartyl protease	97.8
TIGR02281	121	clan_AA_DTGA clan AA aspartic protease, TIGR02281	97.62
cd06094	89	RP_Saci_like RP_Saci_like, retropepsin family. Ret	96.97
cd06095	86	RP_RTVL_H_like Retropepsin of the RTVL_H family of	96.94
cd05480	103	NRIP_C NRIP_C; putative nuclear receptor interacti	96.93
COG5550	125	Predicted aspartyl protease [Posttranslational mod	95.98
cd05481	93	retropepsin_like_LTR_1 Retropepsins_like_LTR; peps	95.11
KOG0012	380	consensus DNA damage inducible protein [Replicatio	93.14
PF12384	177	Peptidase_A2B: Ty3 transposon peptidase; InterPro:	91.72
COG2383	109	Uncharacterized conserved protein [Function unknow	86.2
COG3577	215	Predicted aspartyl protease [General function pred	81.69

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

Probab=99.89  E-value=4.2e-23  Score=144.41  Aligned_cols=69  Identities=35%  Similarity=0.611  Sum_probs=64.2

Q ss_pred             ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEEEEeC
Q 039663            2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYR   72 (102)
Q Consensus         2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f~~~   72 (102)
                      |+.|. ++|+.+.|.+.|++|+|++||++|.+||++|||++||||||||||++|+| .+||++++++|+..
T Consensus        64 ~~~V~-~~g~~~~~~~~~~~~~~~i~g~~~~~dl~vl~l~~~DvILGm~WL~~~~~-~IDw~~k~v~f~~p  132 (135)
T PF08284_consen   64 PIVVS-APGGSINCEGVCPDVPLSIQGHEFVVDLLVLDLGGYDVILGMDWLKKHNP-VIDWATKTVTFNSP  132 (135)
T ss_pred             eeEEe-cccccccccceeeeEEEEECCeEEEeeeEEecccceeeEeccchHHhCCC-EEEccCCEEEEeCC
Confidence            56666 56888999999999999999999999999999999999999999999998 79999999999864

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=99.67  E-value=2.7e-16  Score=107.76  Aligned_cols=67  Identities=12%  Similarity=0.127  Sum_probs=61.6

Q ss_pred             ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEEE
Q 039663            2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEF   69 (102)
Q Consensus         2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f   69 (102)
                      ++.+++++++...+.+.|+.++++++|.+|..+|.|+|+.++|+|||||||++++ +.+||++++|+|
T Consensus        58 ~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~~~~~Vl~~~~~d~ILG~d~L~~~~-~~ID~~~~~i~~  124 (124)
T cd05479          58 RFQGIAKGVGTQKILGRIHLAQVKIGNLFLPCSFTVLEDDDVDFLIGLDMLKRHQ-CVIDLKENVLRI  124 (124)
T ss_pred             ceEEEEecCCCcEEEeEEEEEEEEECCEEeeeEEEEECCCCcCEEecHHHHHhCC-eEEECCCCEEEC
Confidence            3567788767789999999999999999999999999999999999999999999 689999999975

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=99.16  E-value=8.7e-11  Score=75.92  Aligned_cols=50  Identities=14%  Similarity=0.229  Sum_probs=47.7

Q ss_pred             ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHh
Q 039663            2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLE   53 (102)
Q Consensus         2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~   53 (102)
                      ..+|+.|||+.+.+.+.| .+++++||.+|..+++|++.+ +|.+||+|||+
T Consensus        42 ~~~v~~a~G~~~~~~G~~-~~~v~~~~~~~~~~~~v~~~~-~~~lLG~~wl~   91 (91)
T cd05484          42 KKRLRTATGTKLSVLGQI-LVTVKYGGKTKVLTLYVVKNE-GLNLLGRDWLD   91 (91)
T ss_pred             cEEEEecCCCEeeEeEEE-EEEEEECCEEEEEEEEEEECC-CCCccChhhcC
Confidence            468999999999999999 899999999999999999999 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

>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=98.59  E-value=4.2e-07  Score=67.95  Aligned_cols=73  Identities=16%  Similarity=0.215  Sum_probs=64.5

Q ss_pred             ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeE-eecCCCcceeechhHHhhhCceEEeccceEEEEEeCC-eEEE
Q 039663            2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFH-ILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRR-QPIK   77 (102)
Q Consensus         2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~-vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f~~~g-~~v~   77 (102)
                      |+.|+.|||+....+.+|+++.+.|.|+.|...++ ..+ .|.|+|||+.+++.+.|. +.|. .++.|+..+ ..+.
T Consensus        50 ~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~IP~iYq~~-~g~d~IlG~NF~r~y~Pf-iq~~-~~I~f~~~~~~~~~  124 (201)
T PF02160_consen   50 PIKVKGANGSIIQINKKAKNGKIQIADKIFRIPTIYQQE-SGIDIILGNNFLRLYEPF-IQTE-DRIQFHKKGLQKVE  124 (201)
T ss_pred             cEEEEEecCCceEEEEEecCceEEEccEEEeccEEEEec-CCCCEEecchHHHhcCCc-EEEc-cEEEEEeCCcceee
Confidence            68999999999999999999999999999999655 666 689999999999999996 8886 479999887 4443

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

>cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases

Probab=98.51  E-value=4.9e-07  Score=53.23  Aligned_cols=52  Identities=31%  Similarity=0.505  Sum_probs=47.0

Q ss_pred             ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHh
Q 039663            2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLE   53 (102)
Q Consensus         2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~   53 (102)
                      +..+..++|......+.+..+.+.+++..+...+++.+..++|+|||++||.
T Consensus        41 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~ilG~~~l~   92 (92)
T cd00303          41 PLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDVILGRPWLE   92 (92)
T ss_pred             ceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcCCCcCEEecccccC
Confidence            4567788888888888888999999999999999999999999999999984

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

>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family

Probab=98.35  E-value=2.2e-06  Score=57.57  Aligned_cols=62  Identities=23%  Similarity=0.349  Sum_probs=50.0

Q ss_pred             ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEE
Q 039663            2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTM   67 (102)
Q Consensus         2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm   67 (102)
                      +..|..|||......-  .-..+.++|++..+...+.+... ++.|||.||++++ +.+||+++++
T Consensus        46 ~~~~~tA~G~~~~~~v--~~~~v~igg~~~~~~v~~~~~~~-~~LLG~~~L~~l~-l~id~~~~~~  107 (107)
T TIGR03698        46 QRRVYLADGREVLTDV--AKASIIINGLEIDAFVESLGYVD-EPLLGTELLEGLG-IVIDYRNQGL  107 (107)
T ss_pred             CcEEEecCCcEEEEEE--EEEEEEECCEEEEEEEEecCCCC-ccEecHHHHhhCC-EEEehhhCcC
Confidence            3578999998777664  47889999999866666666666 9999999999998 5799998764

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.

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

Probab=97.98  E-value=3.1e-05  Score=53.92  Aligned_cols=50  Identities=18%  Similarity=0.293  Sum_probs=42.8

Q ss_pred             CeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEe
Q 039663           11 ERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTD   61 (102)
Q Consensus        11 ~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D   61 (102)
                      +.-+.-|+...+++++++..|+..|.|+|=...|++||.|||.+|.- .+|
T Consensus        75 G~~~i~G~Ih~~~l~ig~~~~~~s~~Vle~~~~d~llGld~L~~~~c-~ID  124 (124)
T PF09668_consen   75 GTQKILGRIHSVQLKIGGLFFPCSFTVLEDQDVDLLLGLDMLKRHKC-CID  124 (124)
T ss_dssp             ---EEEEEEEEEEEEETTEEEEEEEEEETTSSSSEEEEHHHHHHTT--EEE
T ss_pred             CcCceeEEEEEEEEEECCEEEEEEEEEeCCCCcceeeeHHHHHHhCc-ccC
Confidence            56678889999999999999999999999889999999999999974 455

Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This family of eukaryotic aspartyl proteases have a fold similar to retroviral proteases which implies they function proteolytically during regulated protein turnover []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 3S8I_A 2I1A_B.

>PF00077 RVP: Retroviral aspartyl protease The Prosite entry also includes Pfam:PF00026; InterPro: IPR018061 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=97.94  E-value=4.4e-05  Score=49.33  Aligned_cols=52  Identities=25%  Similarity=0.316  Sum_probs=45.0

Q ss_pred             eEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCc
Q 039663            3 FLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGK   57 (102)
Q Consensus         3 ~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~   57 (102)
                      ..|.-++|.. ...+.+ .+++++.+..|...+++.|-..+| |||+|||++++.
T Consensus        46 ~~v~~~~g~~-~~~~~~-~~~v~~~~~~~~~~~~v~~~~~~~-ILG~D~L~~~~~   97 (100)
T PF00077_consen   46 ITVRGAGGSS-SILGST-TVEVKIGGKEFNHTFLVVPDLPMN-ILGRDFLKKLNA   97 (100)
T ss_dssp             EEEEETTEEE-EEEEEE-EEEEEETTEEEEEEEEESSTCSSE-EEEHHHHTTTTC
T ss_pred             ceeccCCCcc-eeeeEE-EEEEEEECccceEEEEecCCCCCC-EeChhHHHHcCC
Confidence            4677787877 776665 799999999999999999987788 999999999985

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 ....

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

Probab=97.82  E-value=5.9e-05  Score=47.37  Aligned_cols=50  Identities=16%  Similarity=0.232  Sum_probs=42.6

Q ss_pred             ceEEEecCCCeEEecceeeceEEEEcCEEEE-eeeEeecCCC--cceeechhHHh
Q 039663            2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFE-VDFHILDFSG--ANAGLAVQWLE   53 (102)
Q Consensus         2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~-~dl~vL~L~~--~DvILGmdWL~   53 (102)
                      +.+++.++|........  --++++++..|. ..+.++|...  .|.|||+|||+
T Consensus        44 ~~~~~~~~G~~~~~~~~--~~~i~ig~~~~~~~~~~v~d~~~~~~~gIlG~d~l~   96 (96)
T cd05483          44 KVTVQTANGRVRAARVR--LDSLQIGGITLRNVPAVVLPGDALGVDGLLGMDFLR   96 (96)
T ss_pred             cEEEEecCCCccceEEE--cceEEECCcEEeccEEEEeCCcccCCceEeChHHhC
Confidence            45788899998887776  457799999998 5899999998  99999999984

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.

>PF13650 Asp_protease_2: Aspartyl protease

Probab=97.80  E-value=0.00013  Score=45.42  Aligned_cols=48  Identities=17%  Similarity=0.302  Sum_probs=38.9

Q ss_pred             ceEEEecCCCeEEecceeeceEEEEcCEEE-EeeeEeec-CCCcceeechhH
Q 039663            2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEF-EVDFHILD-FSGANAGLAVQW   51 (102)
Q Consensus         2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F-~~dl~vL~-L~~~DvILGmdW   51 (102)
                      +..++.++|.........+  ++++++..+ ..++.+.+ -..+|.||||||
T Consensus        41 ~~~~~~~~g~~~~~~~~~~--~i~ig~~~~~~~~~~v~~~~~~~~~iLG~df   90 (90)
T PF13650_consen   41 PISVSGAGGSVTVYRGRVD--SITIGGITLKNVPFLVVDLGDPIDGILGMDF   90 (90)
T ss_pred             eEEEEeCCCCEEEEEEEEE--EEEECCEEEEeEEEEEECCCCCCEEEeCCcC
Confidence            3677889999555445544  899999999 67899999 668999999998

>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family

Probab=97.62  E-value=0.00057  Score=46.71  Aligned_cols=64  Identities=16%  Similarity=0.285  Sum_probs=49.5

Q ss_pred             ceEEEecCCCeEEecceeeceEEEEcCEEEE-eeeEeecCCC-cceeechhHHhhhCceEEeccceEE
Q 039663            2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFE-VDFHILDFSG-ANAGLAVQWLEKLGKIVTDHKALTM   67 (102)
Q Consensus         2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~-~dl~vL~L~~-~DvILGmdWL~~~g~i~~D~~~~tm   67 (102)
                      +..+..|||....  ....--++++++.++. .++.|+|.+. -|.+||||.|+++.++.+|-.+.++
T Consensus        54 ~~~~~ta~G~~~~--~~~~l~~l~iG~~~~~nv~~~v~~~~~~~~~LLGm~fL~~~~~~~~~~~~l~l  119 (121)
T TIGR02281        54 TVTVSTANGQIKA--ARVTLDRVAIGGIVVNDVDAMVAEGGALSESLLGMSFLNRLSRFTVRGGKLIL  119 (121)
T ss_pred             eEEEEeCCCcEEE--EEEEeCEEEECCEEEeCcEEEEeCCCcCCceEcCHHHHhccccEEEECCEEEE
Confidence            3578899997543  3345667999999998 7899999874 5899999999999877666655443

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).

>cd06094 RP_Saci_like RP_Saci_like, retropepsin family

Probab=96.97  E-value=0.004  Score=41.27  Aligned_cols=53  Identities=19%  Similarity=0.379  Sum_probs=46.9

Q ss_pred             CceEEEecCCCeEEecceeeceEEEEcCE-EEEeeeEeecCCCcceeechhHHhhhC
Q 039663            1 MSFLVDVGNGERIRSEGHCSKVKFEMQGV-EFEVDFHILDFSGANAGLAVQWLEKLG   56 (102)
Q Consensus         1 ~~~~V~va~G~~l~~~~~~~~v~~~iqg~-~F~~dl~vL~L~~~DvILGmdWL~~~g   56 (102)
                      +++.+..|||..|..-|. ..+.+.++.. .|.-+|.|=|..  .-|||+|.|++||
T Consensus        35 ~~~~l~AANgt~I~tyG~-~~l~ldlGlrr~~~w~FvvAdv~--~pIlGaDfL~~~~   88 (89)
T cd06094          35 SPLTLQAANGTPIATYGT-RSLTLDLGLRRPFAWNFVVADVP--HPILGADFLQHYG   88 (89)
T ss_pred             CceEEEeCCCCeEeeeee-EEEEEEcCCCcEEeEEEEEcCCC--cceecHHHHHHcC
Confidence            467899999999999995 6899999885 999999998886  4799999999986

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

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

Probab=96.94  E-value=0.0028  Score=40.50  Aligned_cols=50  Identities=14%  Similarity=0.155  Sum_probs=36.8

Q ss_pred             ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHh
Q 039663            2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLE   53 (102)
Q Consensus         2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~   53 (102)
                      +..+.-++|..-..-....+ .+.++++++..++.+.|- ..|.|||||+|.
T Consensus        37 ~~~v~gagG~~~~~v~~~~~-~v~vg~~~~~~~~~v~~~-~~~~lLG~dfL~   86 (86)
T cd06095          37 SVLIRGVSGQSQQPVTTYRT-LVDLGGHTVSHSFLVVPN-CPDPLLGRDLLS   86 (86)
T ss_pred             cEEEEeCCCcccccEEEeee-EEEECCEEEEEEEEEEcC-CCCcEechhhcC
Confidence            46788888886212222222 699999999999988873 479999999984

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

>cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein

Probab=96.93  E-value=0.0048  Score=41.87  Aligned_cols=54  Identities=17%  Similarity=0.237  Sum_probs=47.4

Q ss_pred             CCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEecc
Q 039663            9 NGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHK   63 (102)
Q Consensus         9 ~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~   63 (102)
                      -|...+-.|....++++|++..++-.|-|||-...|++||.|=|.+|.. .+|.+
T Consensus        49 vgt~~kiiGrih~~~ikig~~~~~CSftVld~~~~d~llGLdmLkrhqc-~IdL~  102 (103)
T cd05480          49 LPTSVKVIGQIERLVLQLGQLTVECSAQVVDDNEKNFSLGLQTLKSLKC-VINLE  102 (103)
T ss_pred             CCcceeEeeEEEEEEEEeCCEEeeEEEEEEcCCCcceEeeHHHHhhcce-eeecc
Confidence            3445677889999999999999999999999889999999999999975 57765

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.

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

Probab=95.98  E-value=0.026  Score=39.52  Aligned_cols=62  Identities=19%  Similarity=0.200  Sum_probs=50.4

Q ss_pred             eEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEE
Q 039663            3 FLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTME   68 (102)
Q Consensus         3 ~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~   68 (102)
                      .++..|+|+.+.+.-  .-..+++.|.+..+-..+.|....+ ++|++||+.+|- .+|.+...++
T Consensus        57 ~~~~~a~~~~v~t~V--~~~~iki~g~e~~~~Vl~s~~~~~~-liG~~~lk~l~~-~vn~~~g~LE  118 (125)
T COG5550          57 IRIVLADGGVVKTSV--ALATIKIDGVEKVAFVLASDNLPEP-LIGVNLLKLLGL-VVNPKTGKLE  118 (125)
T ss_pred             hhhhhhcCCEEEEEE--EEEEEEECCEEEEEEEEccCCCccc-chhhhhhhhccE-EEcCCcceEe
Confidence            356678888877654  4689999999999988888888888 999999999984 7898665554

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

Probab=95.11  E-value=0.11  Score=33.82  Aligned_cols=47  Identities=19%  Similarity=0.317  Sum_probs=40.1

Q ss_pred             CceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeech
Q 039663            1 MSFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAV   49 (102)
Q Consensus         1 ~~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGm   49 (102)
                      ++++++.+||..+...|. ..+++.+++..+..+|+|++-.+-. |||.
T Consensus        43 t~~~L~~~~g~~~~~~G~-~~~~v~~~~~~~~~~f~Vvd~~~~~-lLG~   89 (93)
T cd05481          43 SPVRLTAYGGSTIPVEGG-VKLKCRYRNPKYNLTFQVVKEEGPP-LLGA   89 (93)
T ss_pred             CCeEEEeeCCCEeeeeEE-EEEEEEECCcEEEEEEEEECCCCCc-eEcc
Confidence            367899999999999999 5899999999999999999986443 4554

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

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

Probab=93.14  E-value=0.2  Score=40.76  Aligned_cols=62  Identities=13%  Similarity=0.198  Sum_probs=56.1

Q ss_pred             eEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEEEEeCCe
Q 039663           12 RIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQ   74 (102)
Q Consensus        12 ~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f~~~g~   74 (102)
                      ..+-.|....++++|+...++-.|-|++=...|+-||.|=|++|+. .||.++..+.|...+.
T Consensus       287 ~~ki~g~Ih~~~lki~~~~l~c~ftV~d~~~~d~llGLd~Lrr~~c-cIdL~~~~L~ig~~~t  348 (380)
T KOG0012|consen  287 TEKILGRIHQAQLKIEDLYLPCSFTVLDRRDMDLLLGLDMLRRHQC-CIDLKTNVLRIGNTET  348 (380)
T ss_pred             cccccceeEEEEEEeccEeeccceEEecCCCcchhhhHHHHHhccc-eeecccCeEEecCCCc
Confidence            5566788899999999999999999999999999999999999997 6999999999866555

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

Probab=91.72  E-value=0.83  Score=33.71  Aligned_cols=46  Identities=9%  Similarity=0.106  Sum_probs=39.2

Q ss_pred             CeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCc
Q 039663           11 ERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGK   57 (102)
Q Consensus        11 ~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~   57 (102)
                      +...|... ..+++.+.+..|...+||+|--.+|+|+|..-|.+|..
T Consensus        86 ~~~~tsEA-v~ld~~i~n~~i~i~aYV~d~m~~dlIIGnPiL~ryp~  131 (177)
T PF12384_consen   86 ESATTSEA-VTLDFYIDNKLIDIAAYVTDNMDHDLIIGNPILDRYPT  131 (177)
T ss_pred             CceEEEEe-EEEEEEECCeEEEEEEEEeccCCcceEeccHHHhhhHH
Confidence            33445444 47999999999999999999999999999999999853

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 [].

>COG2383 Uncharacterized conserved protein [Function unknown]

Probab=86.20  E-value=0.21  Score=34.04  Aligned_cols=20  Identities=35%  Similarity=0.614  Sum_probs=17.9

Q ss_pred             eechhHHhhhCceEEeccce
Q 039663           46 GLAVQWLEKLGKIVTDHKAL   65 (102)
Q Consensus        46 ILGmdWL~~~g~i~~D~~~~   65 (102)
                      ||+..||+++|.|++||.+.
T Consensus        51 ilsl~~La~~GVItin~~al   70 (109)
T COG2383          51 ILSLFWLAQYGVITINWEAL   70 (109)
T ss_pred             HHHHHHHHHcCeEEEcHHHH
Confidence            68899999999999999763

>COG3577 Predicted aspartyl protease [General function prediction only]

Probab=81.69  E-value=2.8  Score=31.84  Aligned_cols=54  Identities=15%  Similarity=0.269  Sum_probs=41.7

Q ss_pred             ceEEEecCCCeEEecceeeceEEEEcCEEEEe-eeEeecCCCc-ceeechhHHhhhCc
Q 039663            2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEV-DFHILDFSGA-NAGLAVQWLEKLGK   57 (102)
Q Consensus         2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~-dl~vL~L~~~-DvILGmdWL~~~g~   57 (102)
                      ++.|+.|||+.-...-...  ++.|++.++.. +-+|++-+.. ..-|||.+|.+++-
T Consensus       148 ~~~v~TANG~~~AA~V~Ld--~v~IG~I~~~nV~A~V~~~g~L~~sLLGMSfL~rL~~  203 (215)
T COG3577         148 TITVSTANGRARAAPVTLD--RVQIGGIRVKNVDAMVAEDGALDESLLGMSFLNRLSG  203 (215)
T ss_pred             ceEEEccCCccccceEEee--eEEEccEEEcCchhheecCCccchhhhhHHHHhhccc
Confidence            6789999999776665553  45677777764 8889988854 46789999999985

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	102
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	99.46
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	99.12
3slz_A	132	GAG-Pro-POL polyprotein; beta sheet and dimer, pro	96.74
1fmb_A	104	EIAV protease; hydrolase (acid proteinase), RNA-di	94.6
3ec0_A	99	Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1	94.09
2hs1_A	99	HIV-1 protease; ultra-high resolution active site	92.17
2hah_A	116	Protease, retropepsin; retroviral, aspartyl, hydro	80.71

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

Probab=99.46  E-value=1.1e-13  Score=96.97  Aligned_cols=76  Identities=13%  Similarity=0.092  Sum_probs=63.8

Q ss_pred             EecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEEEEeCCeEEEEEecC
Q 039663            6 DVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQPIKLVGAQ   82 (102)
Q Consensus         6 ~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f~~~g~~v~l~g~~   82 (102)
                      .++..+...+.+.++.++++|+++.|..++.|+|...+|+|||||||++++. .+||++++|+|...+++|.|-...
T Consensus        70 ~a~g~G~~~~~g~v~~~~I~Ig~~~~~~~~~Vle~~~~d~LLGmD~L~~~~~-~ID~~~~~L~l~~~~~~~pfl~~~  145 (148)
T 3s8i_A           70 VAKGVGTQRIIGRVHLAQIQIEGDFLQCSFSILEDQPMDMLLGLDMLRRHQC-SIDLKKNVLVIGTTGTQTYFLPEG  145 (148)
T ss_dssp             ECCC---CEEEEEEEEEEEEETTEEEEEEEEEETTCSSSEEECHHHHHHTTC-EEETTTTEEECTTTCCEEECCCGG
T ss_pred             EEEcCCccEEEEEEEEEEEEECCEEEEEEEEEeCCCCcCeeccHHHHHhCCE-EEEcCCCEEEEccCCeEEeecCcc
Confidence            3333345677888999999999999999999999999999999999999994 899999999998777888776543

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

Probab=99.12  E-value=2.2e-10  Score=78.41  Aligned_cols=63  Identities=11%  Similarity=0.208  Sum_probs=54.2

Q ss_pred             ecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEEEEeCCeEEEEEec
Q 039663           15 SEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQPIKLVGA   81 (102)
Q Consensus        15 ~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f~~~g~~v~l~g~   81 (102)
                      +.+.+...++++++..|..++.|+| .++|+|||||||++++. .+||++++|+|.  ++++.+...
T Consensus        81 ~~~~~~~~~i~ig~~~~~~~~~vl~-~~~d~iLG~d~L~~~~~-~ID~~~~~l~l~--~~~~~f~~~  143 (148)
T 2i1a_A           81 IIGRIHQAQVKIETQYIPCSFTVLD-TDIDVLIGLDMLKRHLA-CVDLKENVLRIA--EVETSFLSE  143 (148)
T ss_dssp             -CEEEEEEEEEETTEEEEEEEEEEC-SSCSEEECHHHHHHTTC-EEETTTTEEEET--TEEEECCCT
T ss_pred             cccEEEEEEEEECCEEeceeEEEec-CCCCeEecHHHHhhCCE-EEECCCCEEEEc--cEEEecCCh
Confidence            4667778899999999999999999 78999999999999975 899999999985  466666543

>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=96.74  E-value=0.0033  Score=43.17  Aligned_cols=57  Identities=18%  Similarity=0.055  Sum_probs=39.6

Q ss_pred             ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEec
Q 039663            2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDH   62 (102)
Q Consensus         2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~   62 (102)
                      |..|.-++|. +. -.....++++|.|..+...+.|++- ...-|||+|||.++|. .+|+
T Consensus        58 p~~I~GiGG~-i~-vr~~~~i~IeI~g~~~~~~~lV~~~-tPvnLLGrd~Ltqlg~-tL~f  114 (132)
T 3slz_A           58 SAWVQGATGG-KR-YRWTTDRKVHLATGKVTHSFLHVPD-CPYPLLGRDLLTKLKA-QIHF  114 (132)
T ss_dssp             EEEEECSSCE-EE-EEEECCEEEEETTEEEEECCEECTT-SSSCEECHHHHHHHTC-EEEE
T ss_pred             ceEEEccCCE-EE-EEEEeeeEEEECCeeecceEEEECC-CCccEECHhhHhhCCc-EEEC
Confidence            3456666665 44 3334467999999999888866432 2457899999999995 3444

>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=94.60  E-value=0.064  Score=35.14  Aligned_cols=52  Identities=17%  Similarity=0.194  Sum_probs=42.0

Q ss_pred             EecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEec
Q 039663            6 DVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDH   62 (102)
Q Consensus         6 ~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~   62 (102)
                      ..+.|+.++..  ..++++++.|+.....++|-|.  ..=|+|-|||+++|. .+||
T Consensus        53 i~GiGG~i~v~--~~~i~i~i~g~~~~gtvlv~~t--p~niiGRd~L~qlg~-tLnf  104 (104)
T 1fmb_A           53 IGGVGGNVETF--STPVTIKKKGRHIKTRMLVADI--PVTILGRDILQDLGA-KLVL  104 (104)
T ss_dssp             EEETTEEECCE--EEEEEEEETTEEEEEEEEEESC--SSCEECHHHHHHTTC-CCCC
T ss_pred             EEeCCCeEEee--EeeeEEEECCeEEEEEEEECCC--CCCEecHhHHhhcCc-EEeC
Confidence            45678888887  6899999999999999888664  356999999999985 4443

>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=94.09  E-value=0.34  Score=31.58  Aligned_cols=55  Identities=16%  Similarity=0.099  Sum_probs=43.8

Q ss_pred             EEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEec
Q 039663            4 LVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDH   62 (102)
Q Consensus         4 ~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~   62 (102)
                      +...+-|+.++..+. .++++++.|+.....++|=|..  .=|+|-|+|+++|. .+||
T Consensus        45 k~igGiGG~i~v~qy-~~i~iei~g~~~~gtvlV~~tP--vniiGRnlLtqlG~-tLnf   99 (99)
T 3ec0_A           45 KIVGGIGGFINTKEY-KNVEIEVLNKKVRATIMTGDTP--INIFGRNILTALGM-SLNL   99 (99)
T ss_dssp             EEEEETTEEEEEEEE-EEEEEEETTEEEEEEEEEECCS--SCEECHHHHHHHTC-EEEC
T ss_pred             eEEEecCCcEeeeEE-eeEEEEECCeEEEEEEEeCCCC--cCeeehhhHhhcCc-EEeC
Confidence            356788999988884 7899999999999998885543  25799999999995 5554

>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=92.17  E-value=0.75  Score=29.81  Aligned_cols=54  Identities=13%  Similarity=0.120  Sum_probs=42.4

Q ss_pred             EEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEec
Q 039663            5 VDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDH   62 (102)
Q Consensus         5 V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~   62 (102)
                      ...+.|+.++..+ ..++++++.|+.....++|-|.. . =|+|-|||+++|. .+||
T Consensus        46 ~igGiGG~i~v~q-y~qi~iei~g~~~~gtvlV~~tP-v-niiGRd~Ltqlg~-tLnf   99 (99)
T 2hs1_A           46 MIGGIGGFIKVRQ-YDQIIIEIAGHKAIGTVLVGPTP-V-NIIGRNLLTQIGA-TLNF   99 (99)
T ss_dssp             EEEETTEEEEEEE-EEEEEEEETTEEEEEEEEESCCS-S-CEECHHHHTTTTC-EEEC
T ss_pred             EEEeCCCcEeeeE-eccEEEEEeCCEEEEEEEeCCCc-c-CchhHhHHHHcCC-EEeC
Confidence            4566788877765 46899999999999999886654 2 4899999999995 4554

>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=80.71  E-value=3.6  Score=27.22  Aligned_cols=51  Identities=20%  Similarity=0.133  Sum_probs=40.2

Q ss_pred             EecCCCeEEecceeeceEEEEcCEE-----EEeeeEeec-CCCcceeechhHHhhhCc
Q 039663            6 DVGNGERIRSEGHCSKVKFEMQGVE-----FEVDFHILD-FSGANAGLAVQWLEKLGK   57 (102)
Q Consensus         6 ~va~G~~l~~~~~~~~v~~~iqg~~-----F~~dl~vL~-L~~~DvILGmdWL~~~g~   57 (102)
                      ..+-|+.++.. ...++++++.|+.     ....++|.| ...--=|+|=|||+++|.
T Consensus        56 igGiGG~i~v~-qy~qv~iei~g~~~~~~~~~gtvlV~p~tP~~vniiGRd~Ltqlg~  112 (116)
T 2hah_A           56 IGGIGGFIRGT-NYINVHLEIRDENYKTQCIFGNVCVLEDNSTPVNILGRDNMIKFNI  112 (116)
T ss_dssp             EEETTEEEEEE-EEEEEEEEECCTTSCCEEEEEEEEEETTCCCSSEEECHHHHTTTTC
T ss_pred             EecCCCceeee-EEccEEEEEeCCCCCcceeEEEEEECCCCCccccEecHHHHhHcCC
Confidence            56778888876 4568999999988     888888888 541124899999999985

---

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	102
d2fmba_	104	EIAV protease {Equine infectious anemia virus [Tax	82.45

>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=82.45  E-value=1.4  Score=26.92  Aligned_cols=38  Identities=18%  Similarity=0.293  Sum_probs=32.1

Q ss_pred             eeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCc
Q 039663           18 HCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGK   57 (102)
Q Consensus        18 ~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~   57 (102)
                      ....+.|++.|+.....++|.|+.  .=|||=|.|+++|.
T Consensus        63 ~~~~v~i~~~g~~~~~~~lV~p~P--vnLlGRdlL~qlG~  100 (104)
T d2fmba_          63 FSTPVTIKKKGRHIKTRMLVADIP--VTILGRDILQDLGA  100 (104)
T ss_dssp             EEEEEEEEETTEEEEEEEEEESCS--SCEECHHHHHHHTC
T ss_pred             EEEEEEEEECCeEEEEEEEECCCC--cceecHHHHHHhCC
Confidence            345699999999999999999953  23999999999984