Citrus Sinensis ID: 038652

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170----
Protein Sequence
MIRALGTSVAESSNFIRKSGNFRRLTKDEIRAKIAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGVCRNYKWLETLGVTHINWKTRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVEMQG
Secondary Structure (PSIPRED)
cHHccccccccccHHHHHcccccccccccccHHHHHHHHHHHHccccccEEEEEEEEccEEEEEEEEcccccccccHHHHHHHccccccccEEEEEEEcccEEEEcEEEEcEEEEccccEEEEEcccEEEEEEEccEEEEEEccccccEEEEEHHHHHHHHcccccEEEEEEcc
Secondary Structure Prediction (SSPRO)
cccEccccccccccHHccccccccccHHHHcccccEEEEEHHcccccccEEEEEEEEccEEEEEEEEcccccccccHHHHHHcccccccccccEEEEEcccEEccccEEcccHHHHHcccEEEEccEEEEEEEEccEEEEEEccccccccEEcHHHHHHHHcccccEEEEEEcc
Coil and Loop (DISEMBL)
MIRALGtsvaessnfirksgnfrrLTKDEIRAKIAKVLLNAVmgltlpktfnvlgfvgEHKVTIVIdsgaspnfisaeqvdelklpiseaEAYGVIlgtgkskktqgvcrnyKWLETLGVTHINWKTRVMKftfgksqivlqgdPSIQKMLISLNAIVRAIRHEGHGYWVEMQG
Flexible Loop (DISEMBL)
miralgtsvaessnfirksgnfrrltKDEIRAKIAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVIlgtgkskktqgvcRNYKWLETLGVTHINWKTRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVEMQG
Low Complexity Region (SEG)
MIRALGTSVAESSNFIRKSGNFRRLTKDEIRAKIAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGVCRNYKWLETLGVTHINWKTRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVEMQG
Disordered region (IsUnstruct)
********************NFRRLTKDEIRAKIAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGVCRNYKWLETLGVTHINWKTRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWV****
Disordered Region (DISOPRED)
*************************************LLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGVCRNYKWLETLGVTHINWKTRVMKFTFGKSQIVLQGDPSIQK***************GHGYWVEMQG
Disordered Region (DISEMBL)
***********SSNFIRKSGNFRRLTKDEIRAKIAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGVCRNYKWLETLGVTHINWKTRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVEMQG
Disordered Region (DISPRO)
********VAESSNFIRKSGNFRRLTKDEIRAKIAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGVCRNYKWLETLGVTHINWKTRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVEMQG
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MIRALGTSVAESSNFIRKSGNFRRLTKDEIRAKIAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGVCRNYKWLETLGVTHINWKTRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVEMQG
Positional Conservation
no confident homologs detected

---

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	174
387965727	1631	Ty3/gypsy retrotransposon protein [Beta	0.787	0.083	0.357	9e-25
147807720	1448	hypothetical protein VITISV_018166 [Viti	0.672	0.080	0.381	3e-21
449443978	431	PREDICTED: uncharacterized protein LOC10	0.781	0.315	0.402	5e-21
261865347	1583	hypothetical protein [Beta vulgaris]	0.873	0.096	0.320	8e-21
449465222	2712	PREDICTED: uncharacterized protein LOC10	0.810	0.051	0.327	2e-20
449472371	764	PREDICTED: uncharacterized protein LOC10	0.810	0.184	0.327	1e-19
449457325	718	PREDICTED: uncharacterized protein LOC10	0.810	0.196	0.321	3e-19
449531517	392	PREDICTED: uncharacterized protein LOC10	0.781	0.346	0.331	4e-18
449511951	707	PREDICTED: uncharacterized protein LOC10	0.810	0.199	0.291	2e-16
449526327	426	PREDICTED: uncharacterized protein LOC10	0.810	0.330	0.303	2e-16

>gi|387965727|gb|AFK13856.1| Ty3/gypsy retrotransposon protein [Beta vulgaris subsp. vulgaris]

 Score =  118 bits (296), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 59/165 (35%), Positives = 92/165 (55%), Gaps = 28/165 (16%)

Query: 35  AKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYG 94
            +V LN+V+GL+ PKT  + G +  H+V ++ID GA+ NF+S + +D+L +P++E+E +G
Sbjct: 467 PEVSLNSVIGLSNPKTMKLSGLIDNHEVVVMIDPGATHNFLSLKAIDKLGIPVTESEEFG 526

Query: 95  VILGTGKSKKTQGVCR----------------------------NYKWLETLGVTHINWK 126
           V LG G++ +  G+CR                              +WLETLG    NWK
Sbjct: 527 VSLGDGQAVRGTGICRAVALYLDGGLVVVEDFLPLGLGNSDVILGVQWLETLGTVVSNWK 586

Query: 127 TRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVE 171
           T+ M F  G     L GDP++ +  +SL A++R +R EG G W+E
Sbjct: 587 TQKMSFQLGGVPYTLTGDPTLARSKVSLKAMLRTLRKEGGGLWLE 631

Source: Beta vulgaris subsp. vulgaris

Species: Beta vulgaris

Genus: Beta

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147807720|emb|CAN66553.1| hypothetical protein VITISV_018166 [Vitis vinifera]

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 55/144 (38%), Positives = 79/144 (54%), Gaps = 27/144 (18%)

Query: 55  GFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGVCRN--- 111
           G +G  +V I++DSGA+ NF+S E V +L LP++   +Y V++GTG S K +G+CR    
Sbjct: 5   GMIGSKEVIILVDSGATHNFLSLELVQQLALPLTTTTSYEVMMGTGISVKGKGICRGVCI 64

Query: 112 ------------------------YKWLETLGVTHINWKTRVMKFTFGKSQIVLQGDPSI 147
                                     WL TLG   +NWK   MK   GK+ IVL+GDPS+
Sbjct: 65  SMQGLTVVEDFLPLELGNTDVILGMPWLGTLGDVKVNWKMLTMKIKMGKAVIVLKGDPSL 124

Query: 148 QKMLISLNAIVRAIRHEGHGYWVE 171
            ++ +SL A+ RA++H   G WVE
Sbjct: 125 SRIEVSLKAMTRALQHHSQGVWVE 148

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449443978|ref|XP_004139752.1| PREDICTED: uncharacterized protein LOC101213746 [Cucumis sativus]

 Score =  105 bits (263), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 56/139 (40%), Positives = 86/139 (61%), Gaps = 3/139 (2%)

Query: 39  LNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILG 98
           +N+++GL+ P T  + G + E KV I+IDSGA+ +FI+   V  L LP++E   YGVILG
Sbjct: 36  INSIVGLSNPGTMKLKGKIKERKVVIIIDSGATHSFIAKNFVTTLSLPMTETSNYGVILG 95

Query: 99  TGKSKKTQGVCRNYK---WLETLGVTHINWKTRVMKFTFGKSQIVLQGDPSIQKMLISLN 155
           +G + K +G+  N +   WL  LG+T  + K  VM F  G  +I ++GDPS+ K  +SL 
Sbjct: 96  SGVAVKGKGIRSNVEVTGWLHKLGMTEFDMKNLVMTFRHGGRKIEIKGDPSVTKTQVSLK 155

Query: 156 AIVRAIRHEGHGYWVEMQG 174
           +I++    + HGY VE + 
Sbjct: 156 SIIKTWGADNHGYLVECRA 174

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|261865347|gb|ACY01928.1| hypothetical protein [Beta vulgaris]

 Score =  105 bits (261), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 58/181 (32%), Positives = 97/181 (53%), Gaps = 29/181 (16%)

Query: 21  NFRRLTKDEIRAKI--AKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAE 78
           N +    D+ + +I   ++ LN+VMG++ PKT  + G +   KV +++D GA+ NFIS +
Sbjct: 388 NIQPAHPDDSQLEIHSPEISLNSVMGISSPKTLKMEGTIYGQKVIVMVDPGATHNFISLD 447

Query: 79  QVDELKLPISEAEAYGVILGTGKSKKTQGVCR-------------NY------------- 112
            V  L++PIS +  +GV LGTG     QG C+             +Y             
Sbjct: 448 TVRRLQIPISSSRPFGVSLGTGAEAHGQGECKAVPLHLQGVCVMEDYLPLTLGNSDLILG 507

Query: 113 -KWLETLGVTHINWKTRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVE 171
            +WLE LG    NWKT+ +++  G   + L+G+P++ +  +SL A+ R +R EG G+ V+
Sbjct: 508 VQWLEKLGTMVTNWKTQTLQYKEGNETVTLRGNPALSRTEVSLKAMYRTLRKEGGGFLVD 567

Query: 172 M 172
           +
Sbjct: 568 L 568

Source: Beta vulgaris

Species: Beta vulgaris

Genus: Beta

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449465222|ref|XP_004150327.1| PREDICTED: uncharacterized protein LOC101216833 [Cucumis sativus]

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 55/168 (32%), Positives = 88/168 (52%), Gaps = 27/168 (16%)

Query: 34   IAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAY 93
            I ++ +N+V+GLT PKT  V G + + +V I+ID GA+ NFIS + V EL LP      Y
Sbjct: 1313 IVELSINSVVGLTNPKTMKVRGKIKDREVIILIDCGATHNFISDKVVQELSLPTKTTSHY 1372

Query: 94   GVILGTGKSKKTQGVCR---------------------------NYKWLETLGVTHINWK 126
            GVILG+G + K +G+C                              +WL +LGVT ++WK
Sbjct: 1373 GVILGSGAAVKGKGICEGIELELEGWKVEANFLPLELGGVDGVLEMQWLYSLGVTEVDWK 1432

Query: 127  TRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVEMQG 174
               M F     ++ ++GDPS+ K ++ L  ++++ R    G+ +E + 
Sbjct: 1433 NLTMTFLHNGKKVKIKGDPSLTKAMVGLKNMIKSWRDSDQGFLIECRA 1480

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449472371|ref|XP_004153573.1| PREDICTED: uncharacterized protein LOC101213561, partial [Cucumis sativus]

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 55/168 (32%), Positives = 89/168 (52%), Gaps = 27/168 (16%)

Query: 34  IAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAY 93
           I ++ +N+V+GLT P T  V G + + +V I+ID GA+ NFIS + V EL LP      Y
Sbjct: 400 IVELSINSVVGLTNPGTMKVRGKIKDREVIILIDCGATHNFISDKVVQELSLPTKTTSHY 459

Query: 94  GVILGTGKSKKTQGVCR-------------NY--------------KWLETLGVTHINWK 126
           GVILG+G + K +G+C              N+              +WL +LGVT ++WK
Sbjct: 460 GVILGSGAAVKGKGICEGIELELEGWKVEANFLPLELGGVDGVLGMQWLYSLGVTEVDWK 519

Query: 127 TRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVEMQG 174
              M F     ++ ++GDPS+ K ++ L  ++++ R    G+ +E + 
Sbjct: 520 NLTMTFLHNGKKVKIKGDPSLTKAMVGLKNMIKSWRDSDQGFLIECRA 567

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449457325|ref|XP_004146399.1| PREDICTED: uncharacterized protein LOC101219499 [Cucumis sativus]

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 54/168 (32%), Positives = 89/168 (52%), Gaps = 27/168 (16%)

Query: 34  IAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAY 93
           I ++ +N+V+GLT P T  V G + + +V I+ID GA+ NFIS + V EL LP      Y
Sbjct: 373 IVELSINSVVGLTNPGTMKVRGKIKDREVIILIDCGATHNFISDKVVQELSLPTKTTSHY 432

Query: 94  GVILGTGKSKKTQGVCR-------------NY--------------KWLETLGVTHINWK 126
           GVILG+G + K +G+C              N+              +WL +LGVT ++WK
Sbjct: 433 GVILGSGAAVKGKGICEGIELELEGWKVEANFLPLELGGVDGVLGMQWLYSLGVTEVDWK 492

Query: 127 TRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVEMQG 174
              M F     ++ ++GDPS+ K ++ L  ++++ +    G+ +E + 
Sbjct: 493 NLTMTFLHNGKKVKIKGDPSLTKAMVGLKNMIKSWKDSDQGFLIECRA 540

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449531517|ref|XP_004172732.1| PREDICTED: uncharacterized protein LOC101232451 [Cucumis sativus]

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 54/163 (33%), Positives = 87/163 (53%), Gaps = 27/163 (16%)

Query: 39  LNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILG 98
           +N+V+GL+   T  V G +   +V ++ID GA+ +FI    V  LKLP++E    GVILG
Sbjct: 42  INSVVGLSNSGTMKVKGKIQGTEVVVLIDCGATHSFIVDNLVTSLKLPLTETSNCGVILG 101

Query: 99  TGKSKKTQGVC---------------------------RNYKWLETLGVTHINWKTRVMK 131
           +G + K +G+C                            + +WL +LGVT  NW+  VM 
Sbjct: 102 SGAAVKGKGICGQVEVMVGEWKIVDSFLPLELEGVDVILDMQWLHSLGVTEFNWRKLVMT 161

Query: 132 FTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVEMQG 174
           F     ++V++GDPS+ KM++SL +++++   E  GY VE + 
Sbjct: 162 FQHEGKKVVIRGDPSLTKMMVSLKSMMKSWNVEDQGYRVECRA 204

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449511951|ref|XP_004164098.1| PREDICTED: uncharacterized protein LOC101232566 [Cucumis sativus]

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 49/168 (29%), Positives = 89/168 (52%), Gaps = 27/168 (16%)

Query: 34  IAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAY 93
           + ++ +N+V+GL+ P+T  V G +   ++ ++ID  A+ NFI    V+EL++       Y
Sbjct: 394 VVELSINSVVGLSNPRTMKVKGKLLGRQIIVLIDCEATHNFIREGLVEELQISTKSTTNY 453

Query: 94  GVILGTGKSKKTQGVCR---------------------------NYKWLETLGVTHINWK 126
           GVILG+G + K +GVC                              +WL +LG+T ++WK
Sbjct: 454 GVILGSGTAIKGKGVCEAIEMMIGEWRVIDDFLPLELGGVDAILGMQWLYSLGITEVDWK 513

Query: 127 TRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVEMQG 174
             ++ FT    ++V++GDPS+ K  +SL A++++   +  G+ VE + 
Sbjct: 514 NLILTFTHHGEKVVIRGDPSLTKARVSLKALMKSWGDKDQGFLVECRA 561

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449526327|ref|XP_004170165.1| PREDICTED: uncharacterized protein LOC101232744 [Cucumis sativus]

 Score = 90.5 bits (223), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/168 (30%), Positives = 83/168 (49%), Gaps = 27/168 (16%)

Query: 34  IAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAY 93
           + ++ +N+++GLT   T  + G +   +V +++D GA+ NFIS + V  L +P  +   Y
Sbjct: 137 VVELCINSMVGLTNLGTMKIRGVIEGKEVIVLVDCGATHNFISDKLVMTLHIPTKDTSNY 196

Query: 94  GVILGTGKSKKTQGVCRNYK---------------------------WLETLGVTHINWK 126
           G ILG+G + K +GVC   K                           WL +LGVT ++WK
Sbjct: 197 GEILGSGTTIKGKGVCEQVKLSLNGWTVTADFLPLELGGVDMILGMQWLYSLGVTEVDWK 256

Query: 127 TRVMKFTFGKSQIVLQGDPSIQKMLISLNAIVRAIRHEGHGYWVEMQG 174
             VM F     ++V+ GDPS+ K  +SL  + ++      GY VE + 
Sbjct: 257 NLVMSFVHNNKKVVIIGDPSLTKTQVSLKCLTKSWTESDLGYLVECRA 304

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

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	174
TAIR|locus:2091793	421	AT3G29750 [Arabidopsis thalian	0.459	0.190	0.370	4.3e-08
TAIR|locus:2089696	603	AT3G30770 [Arabidopsis thalian	0.689	0.199	0.328	1.3e-06

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

 Score = 133 (51.9 bits), Expect = 4.3e-08, P = 4.3e-08
 Identities = 30/81 (37%), Positives = 44/81 (54%)

Query:    42 VMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGK 101
             V+ LT  K     GF+ +HKV + IDSGA+ NFI  E    LKLP S      V+LG  +
Sbjct:   115 VIDLTRNKGMRFYGFILDHKVVVAIDSGATDNFILVELAFSLKLPTSITNQASVLLGQRQ 174

Query:   102 SKKTQGVCRNYK-WLETLGVT 121
               ++ G C   + W++ + +T
Sbjct:   175 CIQSVGTCLGIRLWVQEVEIT 195

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

TAIR|locus:2089696 AT3G30770 [Arabidopsis thaliana (taxid:3702)]

 Score = 126 (49.4 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 41/125 (32%), Positives = 58/125 (46%)

Query:    34 IAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAY 93
             I +V   +    T  K     GF+  HKV +VIDSGA+ NFIS E    LKLP S     
Sbjct:   267 IRQVKRQSTTEFTKGKDMRFYGFISCHKVVVVIDSGATNNFISDELALVLKLPTSTTNQA 326

Query:    94 GVILGTGKSKKTQGVCRNYKWLETLGVTHINWKTRVMKFTFGKSQIVLQ--GDPSIQKM- 150
              V+LG  +  +T G C     L  +    IN    ++  T     ++L   G  ++++  
Sbjct:   327 SVLLGQRQCIQTIGTCFGINLL--VQEVEINENFLLLDLTKTDVDVILGYGGSQNLERQW 384

Query:   151 LISLN 155
             LI LN
Sbjct:   385 LIWLN 389


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        0.320   0.135   0.391    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      174       174   0.00075  109 3  11 22  0.40    32
                                                     31  0.49    34


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:  2
  No. of states in DFA:  593 (63 KB)
  Total size of DFA:  148 KB (2090 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:  15.29u 0.09s 15.38t   Elapsed:  00:00:00
  Total cpu time:  15.29u 0.09s 15.38t   Elapsed:  00:00:00
  Start:  Mon May 20 19:38:28 2013   End:  Mon May 20 19:38:28 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

---

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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	174
cd00303	92	cd00303, retropepsin_like, Retropepsins; pepsin-li	1e-06

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

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 21/58 (36%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 53  VLGFVGEHKVTIVIDSGASPNFISAEQVDELKLP-ISEAEAYGVILGTGKSKKTQGVC 109
           + G +    V  ++DSGAS NFIS     +L LP         V    G S KT GV 
Sbjct: 1   LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVI 58

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	174
PF08284	135	RVP_2: Retroviral aspartyl protease; InterPro: IPR	99.89
cd05479	124	RP_DDI RP_DDI; retropepsin-like domain of DNA dama	99.71
PF13975	72	gag-asp_proteas: gag-polyprotein putative aspartyl	99.58
cd05484	91	retropepsin_like_LTR_2 Retropepsins_like_LTR, peps	99.31
TIGR02281	121	clan_AA_DTGA clan AA aspartic protease, TIGR02281	99.05
PF13650	90	Asp_protease_2: Aspartyl protease	98.81
TIGR03698	107	clan_AA_DTGF clan AA aspartic protease, AF_0612 fa	98.75
cd05483	96	retropepsin_like_bacteria Bacterial aspartate prot	98.7
PF09668	124	Asp_protease: Aspartyl protease; InterPro: IPR0191	98.45
PF00077	100	RVP: Retroviral aspartyl protease The Prosite entr	98.29
cd00303	92	retropepsin_like Retropepsins; pepsin-like asparta	98.22
PF12384	177	Peptidase_A2B: Ty3 transposon peptidase; InterPro:	98.12
COG3577	215	Predicted aspartyl protease [General function pred	97.95
cd06095	86	RP_RTVL_H_like Retropepsin of the RTVL_H family of	97.87
cd05480	103	NRIP_C NRIP_C; putative nuclear receptor interacti	97.74
cd05481	93	retropepsin_like_LTR_1 Retropepsins_like_LTR; peps	97.7
PF02160	201	Peptidase_A3: Cauliflower mosaic virus peptidase (	97.56
PF05585	164	DUF1758: Putative peptidase (DUF1758); InterPro: I	97.46
KOG0012	380	consensus DNA damage inducible protein [Replicatio	97.19
cd06094	89	RP_Saci_like RP_Saci_like, retropepsin family. Ret	96.3
COG5550	125	Predicted aspartyl protease [Posttranslational mod	94.13
cd05482	87	HIV_retropepsin_like Retropepsins, pepsin-like asp	89.29
cd05476	265	pepsin_A_like_plant Chroloplast Nucleoids DNA-bind	85.3

>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=2e-23  Score=161.36  Aligned_cols=92  Identities=27%  Similarity=0.466  Sum_probs=81.8

Q ss_pred             eccCCCCCCeEEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccc-eeEEEecCCCeeeeeeeEeC--------
Q 038652           41 AVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAE-AYGVILGTGKSKKTQGVCRN--------  111 (174)
Q Consensus        41 A~~G~~~~~tmrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~-p~~V~vanG~~l~~~~~c~~--------  111 (174)
                      +-.+.+.+.+|...+.|+++++.+||||||||||||+++|.++++++.+++ |+.|. ++|+.+.|.+.|++        
T Consensus        12 ~~~~~~~~~vi~g~~~I~~~~~~vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~~V~-~~g~~~~~~~~~~~~~~~i~g~   90 (135)
T PF08284_consen   12 AEEAEESPDVITGTFLINSIPASVLIDSGATHSFISSSFAKKLGLPLEPLPRPIVVS-APGGSINCEGVCPDVPLSIQGH   90 (135)
T ss_pred             hhcccCCCCeEEEEEEeccEEEEEEEecCCCcEEccHHHHHhcCCEEEEccCeeEEe-cccccccccceeeeEEEEECCe
Confidence            444557899999999999999999999999999999999999999999874 66665 56777888888866        


Q ss_pred             -------------------eeeecccCceEEEeeeeEEEEEe
Q 038652          112 -------------------YKWLETLGVTHINWKTRVMKFTF  134 (174)
Q Consensus       112 -------------------mdWL~~~gp~~iDw~~~t~~f~~  134 (174)
                                         ||||++|+| .|||.+|+|+|..
T Consensus        91 ~~~~dl~vl~l~~~DvILGm~WL~~~~~-~IDw~~k~v~f~~  131 (135)
T PF08284_consen   91 EFVVDLLVLDLGGYDVILGMDWLKKHNP-VIDWATKTVTFNS  131 (135)
T ss_pred             EEEeeeEEecccceeeEeccchHHhCCC-EEEccCCEEEEeC
Confidence                               999999999 8999999999976

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=99.71  E-value=2.2e-17  Score=125.22  Aligned_cols=85  Identities=16%  Similarity=0.112  Sum_probs=72.6

Q ss_pred             CCCeEEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecCCCeeeeeeeEeC---------------
Q 038652           47 LPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGVCRN---------------  111 (174)
Q Consensus        47 ~~~tmrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~vanG~~l~~~~~c~~---------------  111 (174)
                      ....|++.+.|+|+++.+|||||||||||++++|+|++++.....++.+.+++++...+.+.|..               
T Consensus        13 ~~~~~~v~~~Ing~~~~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~~~~~   92 (124)
T cd05479          13 KVPMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRIHLAQVKIGNLFLPCSFT   92 (124)
T ss_pred             eeeEEEEEEEECCEEEEEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCCCcEEEeEEEEEEEEECCEEeeeEEE
Confidence            45679999999999999999999999999999999999998766677777776555566665533               


Q ss_pred             ------------eeeecccCceEEEeeeeEEEE
Q 038652          112 ------------YKWLETLGVTHINWKTRVMKF  132 (174)
Q Consensus       112 ------------mdWL~~~gp~~iDw~~~t~~f  132 (174)
                                  ||||++++. .|||++++|+|
T Consensus        93 Vl~~~~~d~ILG~d~L~~~~~-~ID~~~~~i~~  124 (124)
T cd05479          93 VLEDDDVDFLIGLDMLKRHQC-VIDLKENVLRI  124 (124)
T ss_pred             EECCCCcCEEecHHHHHhCCe-EEECCCCEEEC
Confidence                        999999995 99999999874

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.

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

Probab=99.58  E-value=1e-14  Score=101.10  Aligned_cols=67  Identities=28%  Similarity=0.411  Sum_probs=61.9

Q ss_pred             CCCCCCeEEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccc-eeEEEecCCCeeeeeeeEe
Q 038652           44 GLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAE-AYGVILGTGKSKKTQGVCR  110 (174)
Q Consensus        44 G~~~~~tmrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~-p~~V~vanG~~l~~~~~c~  110 (174)
                      ....+++|++.+.|+|+++.+|||||||||||+.++|+||+++....+ +..|++|||....+.+...
T Consensus         2 ~~~~~g~~~v~~~I~g~~~~alvDtGat~~fis~~~a~rLgl~~~~~~~~~~v~~a~g~~~~~~g~~~   69 (72)
T PF13975_consen    2 KTPDPGLMYVPVSIGGVQVKALVDTGATHNFISESLAKRLGLPLEKPPSPIRVKLANGSVIEIRGVAE   69 (72)
T ss_pred             CcccCCEEEEEEEECCEEEEEEEeCCCcceecCHHHHHHhCCCcccCCCCEEEEECCCCccccceEEE
Confidence            356789999999999999999999999999999999999999999987 9999999999998887754

>cd05484 retropepsin_like_LTR_2 Retropepsins_like_LTR, pepsin-like aspartate proteases

Probab=99.31  E-value=5.9e-12  Score=90.04  Aligned_cols=58  Identities=19%  Similarity=0.209  Sum_probs=53.6

Q ss_pred             EEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecCCCeeeeeeeE
Q 038652           52 NVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGVC  109 (174)
Q Consensus        52 rl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~vanG~~l~~~~~c  109 (174)
                      .+++.|+|+++.+|||+||++|||+++.+.+++++........+..+||..+.+.+.|
T Consensus         2 ~~~~~Ing~~i~~lvDTGA~~svis~~~~~~lg~~~~~~~~~~v~~a~G~~~~~~G~~   59 (91)
T cd05484           2 TVTLLVNGKPLKFQLDTGSAITVISEKTWRKLGSPPLKPTKKRLRTATGTKLSVLGQI   59 (91)
T ss_pred             EEEEEECCEEEEEEEcCCcceEEeCHHHHHHhCCCccccccEEEEecCCCEeeEeEEE
Confidence            5789999999999999999999999999999999985556799999999999999887

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

>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family

Probab=99.05  E-value=1.6e-09  Score=82.08  Aligned_cols=60  Identities=22%  Similarity=0.295  Sum_probs=52.4

Q ss_pred             CCCCeEEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCccccc-ceeEEEecCCCeeee
Q 038652           46 TLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEA-EAYGVILGTGKSKKT  105 (174)
Q Consensus        46 ~~~~tmrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~-~p~~V~vanG~~l~~  105 (174)
                      ...+++.+.+.|+|+++.+|||+|||++.|++++|+++++..... .+..+..|||.....
T Consensus         7 ~~~g~~~v~~~InG~~~~flVDTGAs~t~is~~~A~~Lgl~~~~~~~~~~~~ta~G~~~~~   67 (121)
T TIGR02281         7 DGDGHFYATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIKAA   67 (121)
T ss_pred             cCCCeEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCcccCCceEEEEeCCCcEEEE
Confidence            356789999999999999999999999999999999999987663 478888999976533

This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Sequences in the seed alignment and those scoring above the trusted cutoff are Proteobacterial; homologs scroing between trusted and noise are found in Pyrobaculum aerophilum str. IM2 (archaeal), Pirellula sp. (Planctomycetes), and Nostoc sp. PCC 7120 (Cyanobacteria).

>PF13650 Asp_protease_2: Aspartyl protease

Probab=98.81  E-value=2.3e-08  Score=69.46  Aligned_cols=55  Identities=27%  Similarity=0.238  Sum_probs=47.4

Q ss_pred             EEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccc-eeEEEecCCCeeeeee
Q 038652           53 VLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAE-AYGVILGTGKSKKTQG  107 (174)
Q Consensus        53 l~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~-p~~V~vanG~~l~~~~  107 (174)
                      +.+.|+|+++.+||||||++++|+++++++++++..+.. +..+..++|.......
T Consensus         1 V~v~vng~~~~~liDTGa~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~   56 (90)
T PF13650_consen    1 VPVKVNGKPVRFLIDTGASISVISRSLAKKLGLKPRPKSVPISVSGAGGSVTVYRG   56 (90)
T ss_pred             CEEEECCEEEEEEEcCCCCcEEECHHHHHHcCCCCcCCceeEEEEeCCCCEEEEEE
Confidence            367899999999999999999999999999999988775 7888999998544333

>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family

Probab=98.75  E-value=1.9e-08  Score=74.73  Aligned_cols=69  Identities=25%  Similarity=0.365  Sum_probs=54.0

Q ss_pred             CEEEEEEeecCCCCcc-ccHHHHhhcCCcccccceeEEEecCCCeeeeeee------------------------EeCee
Q 038652           59 EHKVTIVIDSGASPNF-ISAEQVDELKLPISEAEAYGVILGTGKSKKTQGV------------------------CRNYK  113 (174)
Q Consensus        59 ~~~v~~LIDSGSThnF-Is~~~v~~l~l~~~~~~p~~V~vanG~~l~~~~~------------------------c~~md  113 (174)
                      ..++.+|||||||+.. |++++|++++++...  ...+..|||........                        ..+|.
T Consensus        14 ~~~v~~LVDTGat~~~~l~~~~a~~lgl~~~~--~~~~~tA~G~~~~~~v~~~~v~igg~~~~~~v~~~~~~~~~LLG~~   91 (107)
T TIGR03698        14 FMEVRALVDTGFSGFLLVPPDIVNKLGLPELD--QRRVYLADGREVLTDVAKASIIINGLEIDAFVESLGYVDEPLLGTE   91 (107)
T ss_pred             ceEEEEEEECCCCeEEecCHHHHHHcCCCccc--CcEEEecCCcEEEEEEEEEEEEECCEEEEEEEEecCCCCccEecHH
Confidence            3489999999999999 999999999998754  56889999964322211                        11299


Q ss_pred             eecccCceEEEeeeeEE
Q 038652          114 WLETLGVTHINWKTRVM  130 (174)
Q Consensus       114 WL~~~gp~~iDw~~~t~  130 (174)
                      ||++++. .+||+++++
T Consensus        92 ~L~~l~l-~id~~~~~~  107 (107)
T TIGR03698        92 LLEGLGI-VIDYRNQGL  107 (107)
T ss_pred             HHhhCCE-EEehhhCcC
Confidence            9999985 899998754

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.

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

Probab=98.70  E-value=7.5e-08  Score=67.49  Aligned_cols=60  Identities=25%  Similarity=0.347  Sum_probs=51.4

Q ss_pred             CeEEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecCCCeeeeeee
Q 038652           49 KTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGV  108 (174)
Q Consensus        49 ~tmrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~vanG~~l~~~~~  108 (174)
                      +.+.+.+.|+++++.+|||+||++++|+.+++++++++.....+..+..++|........
T Consensus         1 ~~~~v~v~i~~~~~~~llDTGa~~s~i~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~   60 (96)
T cd05483           1 GHFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAARVR   60 (96)
T ss_pred             CcEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCccCCCcEEEEecCCCccceEEE
Confidence            357899999999999999999999999999999999855555778899999987665443

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.

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

Probab=98.45  E-value=3.5e-07  Score=70.20  Aligned_cols=41  Identities=15%  Similarity=0.138  Sum_probs=32.7

Q ss_pred             CCCeEEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcc
Q 038652           47 LPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPI   87 (174)
Q Consensus        47 ~~~tmrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~   87 (174)
                      ....+.+...|||+++.++|||||-+|-||.++|+|+||.-
T Consensus        21 ~v~mLyI~~~ing~~vkA~VDtGAQ~tims~~~a~r~gL~~   61 (124)
T PF09668_consen   21 QVSMLYINCKINGVPVKAFVDTGAQSTIMSKSCAERCGLMR   61 (124)
T ss_dssp             -----EEEEEETTEEEEEEEETT-SS-EEEHHHHHHTTGGG
T ss_pred             CcceEEEEEEECCEEEEEEEeCCCCccccCHHHHHHcCChh
Confidence            45678999999999999999999999999999999999963

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=98.29  E-value=1.4e-06  Score=62.56  Aligned_cols=54  Identities=22%  Similarity=0.282  Sum_probs=44.5

Q ss_pred             EEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecCCCeeeeeee
Q 038652           52 NVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGV  108 (174)
Q Consensus        52 rl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~vanG~~l~~~~~  108 (174)
                      ++...|+|+++.+|||+||+.++|+.+.+.+...+  ...+..+..++|.. ...+.
T Consensus         7 ~i~v~i~g~~i~~LlDTGA~vsiI~~~~~~~~~~~--~~~~~~v~~~~g~~-~~~~~   60 (100)
T PF00077_consen    7 YITVKINGKKIKALLDTGADVSIISEKDWKKLGPP--PKTSITVRGAGGSS-SILGS   60 (100)
T ss_dssp             EEEEEETTEEEEEEEETTBSSEEESSGGSSSTSSE--EEEEEEEEETTEEE-EEEEE
T ss_pred             eEEEeECCEEEEEEEecCCCcceeccccccccccc--ccCCceeccCCCcc-eeeeE
Confidence            56788999999999999999999999999888755  55667788888876 55443

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 ....

>cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases

Probab=98.22  E-value=5.9e-06  Score=53.98  Aligned_cols=55  Identities=38%  Similarity=0.414  Sum_probs=45.3

Q ss_pred             EEEECCEEEEEEeecCCCCccccHHHHhhcCC-cccccceeEEEecCCCeeeeeee
Q 038652           54 LGFVGEHKVTIVIDSGASPNFISAEQVDELKL-PISEAEAYGVILGTGKSKKTQGV  108 (174)
Q Consensus        54 ~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l-~~~~~~p~~V~vanG~~l~~~~~  108 (174)
                      .+.++++++.+|+|+||++++++..++.++++ +.....+..+..++|......+.
T Consensus         2 ~~~~~~~~~~~liDtgs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   57 (92)
T cd00303           2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGV   57 (92)
T ss_pred             EEEECCEEEEEEEcCCCcccccCHHHHHHcCCCcccCCCceEEEecCCCEeccCcE
Confidence            45688999999999999999999999999998 55556788888888876555443

The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples

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

Probab=98.12  E-value=1.1e-05  Score=64.84  Aligned_cols=54  Identities=24%  Similarity=0.298  Sum_probs=49.8

Q ss_pred             CCCCCeEEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEec
Q 038652           45 LTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILG   98 (174)
Q Consensus        45 ~~~~~tmrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~va   98 (174)
                      -+-.+|....-.++|.++.+|+||||--|||+.+++++|+|+.-..+|++++-+
T Consensus        29 Pevg~T~~v~l~~~~t~i~vLfDSGSPTSfIr~di~~kL~L~~~~app~~fRG~   82 (177)
T PF12384_consen   29 PEVGKTAIVQLNCKGTPIKVLFDSGSPTSFIRSDIVEKLELPTHDAPPFRFRGF   82 (177)
T ss_pred             cccCcEEEEEEeecCcEEEEEEeCCCccceeehhhHHhhCCccccCCCEEEeee
Confidence            445678899999999999999999999999999999999999999999999854

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 [].

>COG3577 Predicted aspartyl protease [General function prediction only]

Probab=97.95  E-value=2.8e-05  Score=64.41  Aligned_cols=66  Identities=21%  Similarity=0.334  Sum_probs=57.7

Q ss_pred             ceeEeeeeccCCCCCCeEEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCccccc-ceeEEEecCCCee
Q 038652           34 IAKVLLNAVMGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEA-EAYGVILGTGKSK  103 (174)
Q Consensus        34 ~~~iSl~A~~G~~~~~tmrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~-~p~~V~vanG~~l  103 (174)
                      -.++++++    ...+++...|.|||+++..|||+|||--=++.+-|+|+++..-.+ -++.|..|||+..
T Consensus        93 ~~~v~Lak----~~~GHF~a~~~VNGk~v~fLVDTGATsVal~~~dA~RlGid~~~l~y~~~v~TANG~~~  159 (215)
T COG3577          93 YQEVSLAK----SRDGHFEANGRVNGKKVDFLVDTGATSVALNEEDARRLGIDLNSLDYTITVSTANGRAR  159 (215)
T ss_pred             ceEEEEEe----cCCCcEEEEEEECCEEEEEEEecCcceeecCHHHHHHhCCCccccCCceEEEccCCccc
Confidence            34566654    455899999999999999999999999999999999999999987 4899999999764

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

Probab=97.87  E-value=3.1e-05  Score=54.89  Aligned_cols=46  Identities=13%  Similarity=0.102  Sum_probs=40.2

Q ss_pred             EEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecCCCe
Q 038652           54 LGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKS  102 (174)
Q Consensus        54 ~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~vanG~~  102 (174)
                      ...|||+++.+|+|+||+++-|+++.++++   .....+..+..++|..
T Consensus         2 ~v~InG~~~~fLvDTGA~~tii~~~~a~~~---~~~~~~~~v~gagG~~   47 (86)
T cd06095           2 TITVEGVPIVFLVDTGATHSVLKSDLGPKQ---ELSTTSVLIRGVSGQS   47 (86)
T ss_pred             EEEECCEEEEEEEECCCCeEEECHHHhhhc---cCCCCcEEEEeCCCcc
Confidence            578999999999999999999999999997   2334788899999975

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=97.74  E-value=4e-05  Score=56.90  Aligned_cols=33  Identities=27%  Similarity=0.366  Sum_probs=31.5

Q ss_pred             EEEECCEEEEEEeecCCCCccccHHHHhhcCCc
Q 038652           54 LGFVGEHKVTIVIDSGASPNFISAEQVDELKLP   86 (174)
Q Consensus        54 ~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~   86 (174)
                      .+++||+|+.++|||||-+|.||+..|+|+||.
T Consensus         2 nCk~nG~~vkAfVDsGaQ~timS~~caercgL~   34 (103)
T cd05480           2 SCQCAGKELRALVDTGCQYNLISAACLDRLGLK   34 (103)
T ss_pred             ceeECCEEEEEEEecCCchhhcCHHHHHHcChH
Confidence            468999999999999999999999999999997

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.

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

Probab=97.70  E-value=0.0001  Score=53.47  Aligned_cols=53  Identities=17%  Similarity=0.213  Sum_probs=46.1

Q ss_pred             EECC-EEEEEEeecCCCCccccHHHHhhcC---CcccccceeEEEecCCCeeeeeee
Q 038652           56 FVGE-HKVTIVIDSGASPNFISAEQVDELK---LPISEAEAYGVILGTGKSKKTQGV  108 (174)
Q Consensus        56 ~I~~-~~v~~LIDSGSThnFIs~~~v~~l~---l~~~~~~p~~V~vanG~~l~~~~~  108 (174)
                      .|++ +++.+++|+||+.|.|+.+..++++   .+.....++.+..+||..+...|.
T Consensus         4 ~i~g~~~v~~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~~~G~   60 (93)
T cd05481           4 KINGKQSVKFQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIPVEGG   60 (93)
T ss_pred             EeCCceeEEEEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEeeeeEE
Confidence            5777 9999999999999999999999998   555555679999999999888775

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

>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=97.56  E-value=0.00022  Score=58.91  Aligned_cols=91  Identities=13%  Similarity=0.138  Sum_probs=66.4

Q ss_pred             CCeEEEEEEE--CC---EEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecCCCeeeeeeeEeC-----------
Q 038652           48 PKTFNVLGFV--GE---HKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGVCRN-----------  111 (174)
Q Consensus        48 ~~tmrl~g~I--~~---~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~vanG~~l~~~~~c~~-----------  111 (174)
                      |+.+.+++.+  .|   ..+.++||+|||-+.++...+-..-.. ....|+.|+.|||.......+|++           
T Consensus         2 pNsiyI~~~i~~~gy~~~~~~~~vDTGAt~C~~~~~iiP~e~we-~~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~   80 (201)
T PF02160_consen    2 PNSIYIKVKISFPGYKKFNYHCYVDTGATICCASKKIIPEEYWE-KSKKPIKVKGANGSIIQINKKAKNGKIQIADKIFR   80 (201)
T ss_pred             CccEEEEEEEEEcCceeEEEEEEEeCCCceEEecCCcCCHHHHH-hCCCcEEEEEecCCceEEEEEecCceEEEccEEEe
Confidence            5555555554  44   457889999999999987765332211 113578999999998888887776           


Q ss_pred             ----------------eeeecccCceEEEeeeeEEEEEeCC-eEEEE
Q 038652          112 ----------------YKWLETLGVTHINWKTRVMKFTFGK-SQIVL  141 (174)
Q Consensus       112 ----------------mdWL~~~gp~~iDw~~~t~~f~~~g-~~V~L  141 (174)
                                      ++.++.+.| -+.|. ..+.|+..+ +.+..
T Consensus        81 IP~iYq~~~g~d~IlG~NF~r~y~P-fiq~~-~~I~f~~~~~~~~~~  125 (201)
T PF02160_consen   81 IPTIYQQESGIDIILGNNFLRLYEP-FIQTE-DRIQFHKKGLQKVEI  125 (201)
T ss_pred             ccEEEEecCCCCEEecchHHHhcCC-cEEEc-cEEEEEeCCcceeeh
Confidence                            899999999 59997 579999877 55443

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

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

Probab=97.46  E-value=0.00019  Score=56.38  Aligned_cols=39  Identities=21%  Similarity=0.352  Sum_probs=32.6

Q ss_pred             CEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEe
Q 038652           59 EHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVIL   97 (174)
Q Consensus        59 ~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~v   97 (174)
                      -.++.+|+||||.-|||++++|++|+|+......+.+.+
T Consensus        10 ~~~~~~LlDsGSq~SfIt~~la~~L~L~~~~~~~~~~~~   48 (164)
T PF05585_consen   10 QVEARALLDSGSQRSFITESLANKLNLPGTGEKILVIGT   48 (164)
T ss_pred             EEEEEEEEecCCchhHHhHHHHHHhCCCCCCceEEEEec
Confidence            356889999999999999999999999988776544443

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

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

Probab=97.19  E-value=0.00041  Score=61.66  Aligned_cols=90  Identities=16%  Similarity=0.090  Sum_probs=65.2

Q ss_pred             CCCCeEEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccc-------------------eeEEEecCCCeeeee
Q 038652           46 TLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAE-------------------AYGVILGTGKSKKTQ  106 (174)
Q Consensus        46 ~~~~tmrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~-------------------p~~V~vanG~~l~~~  106 (174)
                      +.-..+.+.+.|||+||.++|||||--|-||..+|+|+|+.---.+                   ...|++. ...+.|.
T Consensus       231 ~~v~ML~iN~~ing~~VKAfVDsGaq~timS~~Caer~gL~rlid~r~~g~a~gvg~~ki~g~Ih~~~lki~-~~~l~c~  309 (380)
T KOG0012|consen  231 TQVTMLYINCEINGVPVKAFVDSGAQTTIMSAACAERCGLNRLIDKRFQGEARGVGTEKILGRIHQAQLKIE-DLYLPCS  309 (380)
T ss_pred             ccceEEEEEEEECCEEEEEEEcccchhhhhhHHHHHHhChHHHhhhhhhccccCCCcccccceeEEEEEEec-cEeeccc
Confidence            4556688999999999999999999999999999999998733211                   1222222 1233444


Q ss_pred             eeEeC---------eeeecccCceEEEeeeeEEEEEeCCe
Q 038652          107 GVCRN---------YKWLETLGVTHINWKTRVMKFTFGKS  137 (174)
Q Consensus       107 ~~c~~---------mdWL~~~gp~~iDw~~~t~~f~~~g~  137 (174)
                      ..+-+         .|=|+.|.. .||.++..+.|...+.
T Consensus       310 ftV~d~~~~d~llGLd~Lrr~~c-cIdL~~~~L~ig~~~t  348 (380)
T KOG0012|consen  310 FTVLDRRDMDLLLGLDMLRRHQC-CIDLKTNVLRIGNTET  348 (380)
T ss_pred             eEEecCCCcchhhhHHHHHhccc-eeecccCeEEecCCCc
Confidence            33322         677889987 8999999998876555

>cd06094 RP_Saci_like RP_Saci_like, retropepsin family

Probab=96.30  E-value=0.0033  Score=45.71  Aligned_cols=44  Identities=16%  Similarity=0.289  Sum_probs=35.9

Q ss_pred             EEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecCCCeeeeeee
Q 038652           61 KVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGV  108 (174)
Q Consensus        61 ~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~vanG~~l~~~~~  108 (174)
                      .+..|||+||.+|-|.+...++.    ....++.+..|||.++..-|.
T Consensus         9 ~~~fLVDTGA~vSviP~~~~~~~----~~~~~~~l~AANgt~I~tyG~   52 (89)
T cd06094           9 GLRFLVDTGAAVSVLPASSTKKS----LKPSPLTLQAANGTPIATYGT   52 (89)
T ss_pred             CcEEEEeCCCceEeecccccccc----ccCCceEEEeCCCCeEeeeee
Confidence            36789999999999998877763    345678999999999887664

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

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

Probab=94.13  E-value=0.1  Score=40.20  Aligned_cols=79  Identities=24%  Similarity=0.294  Sum_probs=50.9

Q ss_pred             eEEEEEEE---CCEEEEEEeecCCC-CccccHHHHhhcCCcccccceeEEEecCCCeeeeeeeE-----e----------
Q 038652           50 TFNVLGFV---GEHKVTIVIDSGAS-PNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQGVC-----R----------  110 (174)
Q Consensus        50 tmrl~g~I---~~~~v~~LIDSGST-hnFIs~~~v~~l~l~~~~~~p~~V~vanG~~l~~~~~c-----~----------  110 (174)
                      |+.+....   +......|||+|.| ---++++++++++.+.....+  +..++|+++.+.-..     .          
T Consensus        12 ~v~~~f~~~~~Gd~~~~~LiDTGFtg~lvlp~~vaek~~~~~~~~~~--~~~a~~~~v~t~V~~~~iki~g~e~~~~Vl~   89 (125)
T COG5550          12 TVPVTFRLPGQGDFVYDELIDTGFTGYLVLPPQVAEKLGLPLFSTIR--IVLADGGVVKTSVALATIKIDGVEKVAFVLA   89 (125)
T ss_pred             eEEEEEEecCCCcEEeeeEEecCCceeEEeCHHHHHhcCCCccCChh--hhhhcCCEEEEEEEEEEEEECCEEEEEEEEc
Confidence            44444444   33334459999999 555799999999999876543  345666666543211     0          


Q ss_pred             ---------CeeeecccCceEEEeeeeEEE
Q 038652          111 ---------NYKWLETLGVTHINWKTRVMK  131 (174)
Q Consensus       111 ---------~mdWL~~~gp~~iDw~~~t~~  131 (174)
                               +++||+.++- .+|.+...++
T Consensus        90 s~~~~~~liG~~~lk~l~~-~vn~~~g~LE  118 (125)
T COG5550          90 SDNLPEPLIGVNLLKLLGL-VVNPKTGKLE  118 (125)
T ss_pred             cCCCcccchhhhhhhhccE-EEcCCcceEe
Confidence                     1888888875 7777655443

>cd05482 HIV_retropepsin_like Retropepsins, pepsin-like aspartate proteases

Probab=89.29  E-value=0.4  Score=34.53  Aligned_cols=24  Identities=17%  Similarity=0.302  Sum_probs=21.8

Q ss_pred             EEEECCEEEEEEeecCCCCccccH
Q 038652           54 LGFVGEHKVTIVIDSGASPNFISA   77 (174)
Q Consensus        54 ~g~I~~~~v~~LIDSGSThnFIs~   77 (174)
                      ...|+|+++.+|+|+||-++.|+.
T Consensus         2 ~~~i~g~~~~~llDTGAd~Tvi~~   25 (87)
T cd05482           2 TLYINGKLFEGLLDTGADVSIIAE   25 (87)
T ss_pred             EEEECCEEEEEEEccCCCCeEEcc
Confidence            457899999999999999999986

This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This gro

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

Probab=85.30  E-value=4  Score=33.87  Aligned_cols=18  Identities=22%  Similarity=0.471  Sum_probs=16.0

Q ss_pred             EEEeecCCCCccccHHHH
Q 038652           63 TIVIDSGASPNFISAEQV   80 (174)
Q Consensus        63 ~~LIDSGSThnFIs~~~v   80 (174)
                      .++||||+|-.++.+++.
T Consensus       178 ~ai~DTGTs~~~lp~~~~  195 (265)
T cd05476         178 GTIIDSGTTLTYLPDPAY  195 (265)
T ss_pred             cEEEeCCCcceEcCcccc
Confidence            389999999999988876

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

---

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	174
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 47.5 bits (112), Expect = 6e-07
 Identities = 22/139 (15%), Positives = 48/139 (34%), Gaps = 27/139 (19%)

Query: 56  FVGEHKVTIVIDSGASPNFISAEQVDE-LKLPISEAEAYGVILGTGKSKKTQGVCR---- 110
           FV       V D     + +S E++D  +    + +     +  T  SK+ + V +    
Sbjct: 29  FVDNFDCKDVQDM--PKSILSKEEIDHIIMSKDAVSGTL-RLFWTLLSKQEEMVQKFVEE 85

Query: 111 ----NYKWLETLGVTHINWKTRVMKF-------TFGKSQIVLQGDPSIQKMLISLNAIVR 159
               NYK+L +   T     + + +         +  +Q+  + + S  +  + L   + 
Sbjct: 86  VLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALL 145

Query: 160 AIRHEG----HGYWVEMQG 174
            +R        G    + G
Sbjct: 146 ELRPAKNVLIDG----VLG 160

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 42.9 bits (100), Expect = 2e-05
 Identities = 17/90 (18%), Positives = 32/90 (35%), Gaps = 17/90 (18%)

Query: 71  SPNFIS-AEQVDELKLPISEAE-AYGVIL----GTGKSKKTQGVCRNYKWLETLGVTHIN 124
           +   +S  +   +L+  + E   A  V++    G+GK+     VC +YK    +    I 
Sbjct: 127 AKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMD-FKIF 185

Query: 125 WKTRVMKFTFGKSQIVLQGDPSIQKMLISL 154
           W                    ++ +ML  L
Sbjct: 186 W------LNLKNCNS----PETVLEMLQKL 205

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	174
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	99.6
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	99.28
3slz_A	132	GAG-Pro-POL polyprotein; beta sheet and dimer, pro	96.78
1fmb_A	104	EIAV protease; hydrolase (acid proteinase), RNA-di	96.66
3ec0_A	99	Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1	94.54
2hs1_A	99	HIV-1 protease; ultra-high resolution active site	94.1
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	90.73
2hah_A	116	Protease, retropepsin; retroviral, aspartyl, hydro	85.95
3sqf_A	114	Protease; folded monomer, retropepsin, D-type retr	80.99

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

Probab=99.60  E-value=5.4e-16  Score=120.39  Aligned_cols=99  Identities=13%  Similarity=0.088  Sum_probs=72.0

Q ss_pred             CCCCCeEEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecC------------------CCeeeee
Q 038652           45 LTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGT------------------GKSKKTQ  106 (174)
Q Consensus        45 ~~~~~tmrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~van------------------G~~l~~~  106 (174)
                      ......+.+.+.|||+++.+||||||++||||+++|+|+||+.....++...+..                  +..+.|+
T Consensus        19 ~~~~~~l~v~~~Ing~~v~~LVDTGAs~s~Is~~~A~rlGL~~~~~~~~~~~a~g~G~~~~~g~v~~~~I~Ig~~~~~~~   98 (148)
T 3s8i_A           19 SGQVTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIIGRVHLAQIQIEGDFLQCS   98 (148)
T ss_dssp             ---CCCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHTTCGGGEEGGGCEECCC---CEEEEEEEEEEEEETTEEEEEE
T ss_pred             ccccCEEEEEEEECCEEEEEEEeCCCCcEeeCHHHHHHcCCccccCcceeEEEEcCCccEEEEEEEEEEEEECCEEEEEE
Confidence            4467789999999999999999999999999999999999975422112222111                  1122222


Q ss_pred             e---------eEeCeeeecccCceEEEeeeeEEEEEeCCeEEEEecC
Q 038652          107 G---------VCRNYKWLETLGVTHINWKTRVMKFTFGKSQIVLQGD  144 (174)
Q Consensus       107 ~---------~c~~mdWL~~~gp~~iDw~~~t~~f~~~g~~V~L~G~  144 (174)
                      .         .+.+||||.+++. .|||++++|.|...++.|.+-..
T Consensus        99 ~~Vle~~~~d~LLGmD~L~~~~~-~ID~~~~~L~l~~~~~~~pfl~~  144 (148)
T 3s8i_A           99 FSILEDQPMDMLLGLDMLRRHQC-SIDLKKNVLVIGTTGTQTYFLPE  144 (148)
T ss_dssp             EEEETTCSSSEEECHHHHHHTTC-EEETTTTEEECTTTCCEEECCCG
T ss_pred             EEEeCCCCcCeeccHHHHHhCCE-EEEcCCCEEEEccCCeEEeecCc
Confidence            2         1333999999996 89999999999877777776554

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

Probab=99.28  E-value=3.2e-12  Score=97.40  Aligned_cols=96  Identities=13%  Similarity=0.100  Sum_probs=68.4

Q ss_pred             CCCCeEEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeE-EEecC-----------------CCeeeeee
Q 038652           46 TLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYG-VILGT-----------------GKSKKTQG  107 (174)
Q Consensus        46 ~~~~tmrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~-V~van-----------------G~~l~~~~  107 (174)
                      ...+.+.+.+.|+|+++.+|||||||++||++++|++++++......+. ...+.                 |....+..
T Consensus        22 ~~~~~~~v~v~InG~~~~~LvDTGAs~s~is~~~a~~lgl~~~~~~~~~~~a~g~g~~~~~~~~~~~~i~ig~~~~~~~~  101 (148)
T 2i1a_A           22 TQVPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGKIIGRIHQAQVKIETQYIPCSF  101 (148)
T ss_dssp             -CCCCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHHTGGGGCBCCCC-----------CEEEEEEEEEETTEEEEEEE
T ss_pred             cccceEEEEEEECCEEEEEEEECCCCccccCHHHHHHcCCCccCCcceEEEEecCCCcccccEEEEEEEEECCEEeceeE
Confidence            3578899999999999999999999999999999999999754332222 11111                 11111111


Q ss_pred             --------eEeCeeeecccCceEEEeeeeEEEEEeCCeEEEEecC
Q 038652          108 --------VCRNYKWLETLGVTHINWKTRVMKFTFGKSQIVLQGD  144 (174)
Q Consensus       108 --------~c~~mdWL~~~gp~~iDw~~~t~~f~~~g~~V~L~G~  144 (174)
                              ...+||||++++. .|||.+++|.|.  ++.+.+...
T Consensus       102 ~vl~~~~d~iLG~d~L~~~~~-~ID~~~~~l~l~--~~~~~f~~~  143 (148)
T 2i1a_A          102 TVLDTDIDVLIGLDMLKRHLA-CVDLKENVLRIA--EVETSFLSE  143 (148)
T ss_dssp             EEECSSCSEEECHHHHHHTTC-EEETTTTEEEET--TEEEECCCT
T ss_pred             EEecCCCCeEecHHHHhhCCE-EEECCCCEEEEc--cEEEecCCh
Confidence                    2333999999987 999999999986  466666544

>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=96.78  E-value=0.00088  Score=50.82  Aligned_cols=54  Identities=24%  Similarity=0.308  Sum_probs=37.9

Q ss_pred             cCCCCCCeEEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecCCCe
Q 038652           43 MGLTLPKTFNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKS  102 (174)
Q Consensus        43 ~G~~~~~tmrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~vanG~~  102 (174)
                      .|..+.+--.+..+|+|+++.+|+|+||+.+-++..-+     +. .-+|..|.-++|..
T Consensus        15 ~~~d~~~RP~v~i~I~G~~~~~LlDTGAd~tVl~~~~~-----p~-~~~p~~I~GiGG~i   68 (132)
T 3slz_A           15 QGQEPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPG-----PL-SDKSAWVQGATGGK   68 (132)
T ss_dssp             ---CCCCSSEEEEEETTEEEEEEECTTCSSCEECSCCC-----SE-EEEEEEEECSSCEE
T ss_pred             cCCCccCCCEEEEEECCEEEEEEEeCCCCeEEEccccC-----CC-CCCceEEEccCCEE
Confidence            55666667778899999999999999999999986533     32 12455666666643

>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=96.66  E-value=0.0012  Score=48.06  Aligned_cols=54  Identities=17%  Similarity=0.316  Sum_probs=41.7

Q ss_pred             EEEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecCCCeeee
Q 038652           51 FNVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKT  105 (174)
Q Consensus        51 mrl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~vanG~~l~~  105 (174)
                      ..+..+|+|++..+|+|+||-.+.++.+...++++|..+-+| ....+.|+.+..
T Consensus         9 P~v~v~I~Gq~~e~LLDTGAD~TVl~~~~w~~i~lp~~~w~p-~~i~GiGG~i~v   62 (104)
T 1fmb_A            9 PTTIVLINDTPLNVLLDTGADTSVLTTAHYNRLKYRGRKYQG-TGIGGVGGNVET   62 (104)
T ss_dssp             CEEEEEETTEEEEEEECTTCSSCEEEHHHHHHCSSCCCCEEC-CCEEETTEEECC
T ss_pred             CEEEEEECCEEEEEEeccCCCcEEEccccCcccCCCCccCCc-cEEEeCCCeEEe
Confidence            356789999999999999999999999999999998772233 334555655443

>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=94.54  E-value=0.077  Score=38.22  Aligned_cols=48  Identities=19%  Similarity=0.378  Sum_probs=34.3

Q ss_pred             EEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecCCCeeeee
Q 038652           52 NVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKTQ  106 (174)
Q Consensus        52 rl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~vanG~~l~~~  106 (174)
                      .+..+|+|+++.+|+|+||.++-++     ...+|-.-. | ++..+.|+.+...
T Consensus        10 ~vti~I~Gq~~e~LLDTGAD~TVl~-----~~~~Pg~w~-p-k~igGiGG~i~v~   57 (99)
T 3ec0_A           10 VVTAYIEGQPVEVLLDTGADDSIVA-----GIELGNNYS-P-KIVGGIGGFINTK   57 (99)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEES-----SCCCCSCCE-E-EEEEETTEEEEEE
T ss_pred             eEEEEECCEEEEEEEecCCCceEEc-----CcccCCCCC-c-eEEEecCCcEeee
Confidence            4668899999999999999999995     344443322 2 2566778766543

>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=94.10  E-value=0.19  Score=36.10  Aligned_cols=47  Identities=26%  Similarity=0.266  Sum_probs=33.5

Q ss_pred             EEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecCCCeeee
Q 038652           52 NVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSKKT  105 (174)
Q Consensus        52 rl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~vanG~~l~~  105 (174)
                      .+..+|+|+...+|+|+||-++.++.     ..+|-.-. | ....+.|+.+..
T Consensus        10 ~vtvkI~Gq~~eaLLDTGAD~TVl~~-----~~~p~~wk-p-k~igGiGG~i~v   56 (99)
T 2hs1_A           10 LVTIKIGGQLKEALLDTGADDTIIEE-----MSLPGRWK-P-KMIGGIGGFIKV   56 (99)
T ss_dssp             EEEEEETTEEEEEEECTTCSSEEESC-----CSSCCCCE-E-EEEEETTEEEEE
T ss_pred             EEEEEECCEEEEEEeccCCCcEEEec-----ccCCCCCC-C-cEEEeCCCcEee
Confidence            46688999999999999999999974     34443322 2 345666766544

>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=90.73  E-value=1.7  Score=34.98  Aligned_cols=45  Identities=27%  Similarity=0.256  Sum_probs=31.8

Q ss_pred             EEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccceeEEEecCCCee
Q 038652           52 NVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEAYGVILGTGKSK  103 (174)
Q Consensus        52 rl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p~~V~vanG~~l  103 (174)
                      .+..+|+|++..+|+|+||.++-+.     ++++|-.- .|. +..+-|+.+
T Consensus        10 ~vtv~I~Gq~~e~LLDTGAD~TVl~-----~~~lpg~w-~pk-~igGIGG~i   54 (203)
T 3ka2_A           10 LVTIRIGGQLKEALLDTGADDTVIE-----ELNLPGXW-KPK-LIGGIAGFI   54 (203)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEEC-----SCCCSSCE-EEE-EEEETTEEE
T ss_pred             eEEEEECCEEEEEEEecCCCceEEe-----cccCCCCC-Cce-EEEEccCcE
Confidence            5678999999999999999999997     45665432 222 334555443

>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=85.95  E-value=0.68  Score=34.02  Aligned_cols=27  Identities=19%  Similarity=0.317  Sum_probs=23.8

Q ss_pred             CeEEEEEEECCEEEEEEeecCCCCccccH
Q 038652           49 KTFNVLGFVGEHKVTIVIDSGASPNFISA   77 (174)
Q Consensus        49 ~tmrl~g~I~~~~v~~LIDSGSThnFIs~   77 (174)
                      +.+.  .+|+|+++.+|+|+||-++.|+.
T Consensus        14 rP~v--ikI~Gq~~eaLLDTGAD~TVi~~   40 (116)
T 2hah_A           14 PEIL--IFVNGYPIKFLLDTGADITVLNR   40 (116)
T ss_dssp             CEEE--EEETTEEEEEEECTTCSSCEEEG
T ss_pred             CCEE--EEECCEEEEEEecCCCCcEEEcc
Confidence            4444  89999999999999999999985

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

Probab=80.99  E-value=1.5  Score=32.24  Aligned_cols=26  Identities=19%  Similarity=0.310  Sum_probs=22.7

Q ss_pred             EEEEEECCEEEEEEeecCCCCccccH
Q 038652           52 NVLGFVGEHKVTIVIDSGASPNFISA   77 (174)
Q Consensus        52 rl~g~I~~~~v~~LIDSGSThnFIs~   77 (174)
                      .+..+|+|+++.+|+|+||-.+-|..
T Consensus        11 ~vti~I~Gq~~eaLLDTGADdTVi~~   36 (114)
T 3sqf_A           11 SLTLWLDDKMFTGLINTGADVTIIKL   36 (114)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEEEG
T ss_pred             eEEEEECCEEEEEEEccCCCceEEec
Confidence            35588999999999999999998863

---

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	174
d2fmba_	104	EIAV protease {Equine infectious anemia virus [Tax	95.91
d4fiva_	113	Feline immunodeficiency virus (FIV) protease {Feli	93.11
d1nsoa_	107	Mason-Pfizer monkey virus protease {Simian retrovi	92.77

>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=95.91  E-value=0.028  Score=38.89  Aligned_cols=41  Identities=12%  Similarity=0.363  Sum_probs=32.9

Q ss_pred             EEEEEECCEEEEEEeecCCCCccccHHHHhhcCCcccccce
Q 038652           52 NVLGFVGEHKVTIVIDSGASPNFISAEQVDELKLPISEAEA   92 (174)
Q Consensus        52 rl~g~I~~~~v~~LIDSGSThnFIs~~~v~~l~l~~~~~~p   92 (174)
                      .++..|+|+++.+|+|+||.++=|+..--.+...+.....+
T Consensus        10 ~~~i~I~Gq~v~~LLDTGAD~TVI~~~~~p~~~~~~~~~~~   50 (104)
T d2fmba_          10 TTIVLINDTPLNVLLDTGADTSVLTTAHYNRLKYRGRKYQG   50 (104)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEEEHHHHHHCSSCCCCEEC
T ss_pred             EEEEEECCEEEEEEEeCCCCeEEEcccccCccCCCCCCcce
Confidence            56788999999999999999999998877766544444334

>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=93.11  E-value=0.042  Score=38.66  Aligned_cols=27  Identities=22%  Similarity=0.465  Sum_probs=23.8

Q ss_pred             EEEEEECCEEEEEEeecCCCCccccHH
Q 038652           52 NVLGFVGEHKVTIVIDSGASPNFISAE   78 (174)
Q Consensus        52 rl~g~I~~~~v~~LIDSGSThnFIs~~   78 (174)
                      +++..|+|+++.+|+|+||-++-|+..
T Consensus        12 ~v~v~I~Gq~v~~LLDTGAD~TVi~~~   38 (113)
T d4fiva_          12 EILIFVNGYPIKFLLDTGADITILNRR   38 (113)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEEEGG
T ss_pred             eEEEEECCEEEEEEEcCCCCcEEEecc
Confidence            567788999999999999999998654

>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=92.77  E-value=0.036  Score=38.55  Aligned_cols=26  Identities=23%  Similarity=0.345  Sum_probs=23.2

Q ss_pred             EEEEECCEEEEEEeecCCCCccccHH
Q 038652           53 VLGFVGEHKVTIVIDSGASPNFISAE   78 (174)
Q Consensus        53 l~g~I~~~~v~~LIDSGSThnFIs~~   78 (174)
                      ++..|+|+++.+|+|+||.|+=|+..
T Consensus        12 ~~v~I~G~~v~~LLDTGAD~TVI~~~   37 (107)
T d1nsoa_          12 LTLWLDDKMFTGLINTGADVTIIKLE   37 (107)
T ss_dssp             EEEEETTEEEEECCCSSCSSCBCCGG
T ss_pred             EEEEECCEEEEeeecCCCCcEEEecc
Confidence            45689999999999999999999765