Citrus Sinensis ID: 045020

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-
Protein Sequence
MGRVETLKYYIRRFRLASAKVENCDDQLAIVTFKRGLPSNHPFFESLSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGIEEIRGDQATAWACAVLALKETKRKDSNFENQAKQDVK
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHHcccHHHHHHHHHcccccccccccccccEEEEcccccccccccccccEEEEEEEccEEEEEEEEccccccccccHHHHHHccccccccccccccEEEcccccccccEEEEEEEEEcccEEEEEEEEEEcccccEEEEcHHHHHHcccccccccEEEEEEccccEEEEEccHHHHHHHHHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHcccccHHcHHHHHHHHHHHHHcccccHccEEEEEcHcccccccccccccEEEEcEEccEEEEEEEEcccHHHHHHcHHHHHHccccHHHccccccccccccccccccccEEEEEEEEcccEEEEEEEEEcccccHHHHccHHHHHHHHHHHHHHHHHEcccccccEEEEEccHHHHHHHHHHHHHHHHcccccEcHcHHHccc
Coil and Loop (DISEMBL)
MGRVETLKYYIRRFRLasakvencdDQLAIVTfkrglpsnhpffeslsevsflpqdlkliqsphddALVISIKIGNCLVKRILidngssvnilddATVEKMRLEQDKIKlfeqpliglsgivtnsDGVITLLVIAKSYSLLTDFLVVKatspynvilGRQWIHkmravpstchqvLCYQTIYGIEEIRGDQATAWACAVLALKETkrkdsnfenqakqdvk
Flexible Loop (DISEMBL)
mgrvetlkYYIRRfrlasakvencdDQLAIVTFKRGLPSNHPFFESLSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVKRilidngssvnilDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGIEEIRGDQATAWACAVLALKetkrkdsnfenqakqdvk
Low Complexity Region (SEG)
MGRVETLKYYIRRFRLASAKVENCDDQLAIVTFKRGLPSNHPFFESLSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGIEEIRGDQATAWACAVLALKETKRKDSNFENQAKQDVK
Disordered region (IsUnstruct)
****ETLKYYIRRFRLASAKVENCDDQLAIVTFKRGLPSNHPFFESLSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGIEEIRGDQATAWACAVLALK******************
Disordered Region (DISOPRED)
*****************S**VENCD******************FESLSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGIEEIRGDQATAWACAVLA********************
Disordered Region (DISEMBL)
MGRVETLKYYIRRFRLASAKVENCDDQLAIVTFKRGLPSNHPFFESLSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGIEEIRGDQATAWACAVLALKETKRKDS***********
Disordered Region (DISPRO)
**RVETLKYYIRRFRLASAKVENCDDQLAIVTFKRGLPSNHPFFESLSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGIEEIRGDQATAWACAVLALKETKRKDSNFE*Q******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGRVETLKYYIRRFRLASAKVENCDDQLAIVTFKRGLPSNHPFFESLSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNIxxxxxxxxxxxxxxxxxxxxxPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGIEEIRGDQATAWACAVLALKETKRKDSNFENQAKQDVK
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	221
158828139	672	gag-pol polymerase [Arabidopsis lyrata s	0.669	0.220	0.418	2e-26
4417309	889	putative retroelement pol polyprotein [A	0.723	0.179	0.375	3e-24
4406792	764	putative retroelement pol polyprotein [A	0.692	0.200	0.392	1e-23
3377834	681	T24H24.13 gene product [Arabidopsis thal	0.823	0.267	0.356	1e-23
4836930	1295	Hypothetical protein [Arabidopsis thalia	0.660	0.112	0.390	1e-22
147773339	483	hypothetical protein VITISV_014549 [Viti	0.660	0.302	0.397	2e-21
147807570	465	hypothetical protein VITISV_025184 [Viti	0.850	0.404	0.360	2e-21
147844137	533	hypothetical protein VITISV_004508 [Viti	0.678	0.281	0.4	3e-21
147835120	549	hypothetical protein VITISV_035289 [Viti	0.665	0.267	0.405	4e-21
147815945	539	hypothetical protein VITISV_038340 [Viti	0.714	0.293	0.390	4e-21

>gi|158828139|gb|ABW81018.1| gag-pol polymerase [Arabidopsis lyrata subsp. lyrata]

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 62/148 (41%), Positives = 93/148 (62%)

Query: 50  VSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIK 109
           +SF  ++ + ++ PHDDALVI++ + N  V RILID GSSV+++  +T+EKM + +  I 
Sbjct: 515 ISFNEEETRHLERPHDDALVITLDVANFEVSRILIDTGSSVDLIFLSTLEKMGISRGDIV 574

Query: 110 LFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVP 169
               PL+  +     S G I L V+AK  S + DF+V    + YN+ILG  WI++M+AVP
Sbjct: 575 GPPSPLVAFTSESAMSLGTIKLPVLAKKVSKIVDFVVFDKPAAYNIILGTPWIYRMKAVP 634

Query: 170 STCHQVLCYQTIYGIEEIRGDQATAWAC 197
           ST +Q + + T  G+E IRGDQ  +  C
Sbjct: 635 STYYQCIKFPTSNGVETIRGDQEASRTC 662

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|4417309|gb|AAD20433.1| putative retroelement pol polyprotein [Arabidopsis thaliana]

 Score =  117 bits (294), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 60/160 (37%), Positives = 94/160 (58%)

Query: 50  VSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIK 109
           ++F   ++  +  PHDDALVI I +GN  +  I++D GSSV++L     ++      K++
Sbjct: 47  ITFWESEITDLDKPHDDALVIRIDVGNYELSCIMVDTGSSVDVLFYDAFKRTGHLDSKLQ 106

Query: 110 LFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVP 169
             + PL G +G  T S G I L  IA+    LT+FLVV   +P+N ILGR W+H M+AVP
Sbjct: 107 GRKTPLTGFAGDTTFSIGTIQLPTIARGVRQLTNFLVVDKKAPFNAILGRPWLHVMKAVP 166

Query: 170 STCHQVLCYQTIYGIEEIRGDQATAWACAVLALKETKRKD 209
           ST HQ + + +  GI  + G Q ++  C + + ++ K+ D
Sbjct: 167 STYHQCIKFPSYKGIAVVYGSQRSSRKCYMGSYEDIKKAD 206

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|4406792|gb|AAD20101.1| putative retroelement pol polyprotein [Arabidopsis thaliana]

 Score =  115 bits (289), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 60/153 (39%), Positives = 88/153 (57%)

Query: 42  PFFESLSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKM 101
           P  + ++ ++F  +DL  +  PH+D LVI + IG   V RILID GSSVN++    ++KM
Sbjct: 322 PATKEMTPLTFTSEDLFGVDLPHNDPLVIELHIGESEVTRILIDTGSSVNVVFKDVLQKM 381

Query: 102 RLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQW 161
           ++    IK   +PL G  G    ++G I L +     +    F+VV   + YN+ILG  W
Sbjct: 382 KVHDRHIKPSVRPLTGFDGNTMMTNGTIKLPIYLGGAATWHKFVVVDKPTIYNIILGTPW 441

Query: 162 IHKMRAVPSTCHQVLCYQTIYGIEEIRGDQATA 194
           IH M+A+PS+ HQ +   T  GIE IRG+Q  A
Sbjct: 442 IHDMQAIPSSYHQCIKIPTSIGIETIRGNQNLA 474

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|3377834|gb|AAC28207.1| T24H24.13 gene product [Arabidopsis thaliana] gi|7267161|emb|CAB77873.1| putative transposon protein [Arabidopsis thaliana]

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 68/191 (35%), Positives = 101/191 (52%), Gaps = 9/191 (4%)

Query: 24  CDDQL-AIVTFKRGLPS----NHPFFESLSEVSFLPQDLKLIQSPHDDALVISIKIGNCL 78
           C+D + +I T +R   S      P      +++F   +   +  PHDDALVI I +GN  
Sbjct: 490 CNDSINSIKTHQRKADSYTKGKSPMMGPNHQITFWESETTDLNKPHDDALVIRIDVGNYE 549

Query: 79  VKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSY 138
           +  I+ID GSSV++L     ++M     +++  + PL G +G  T S G I L  IA+  
Sbjct: 550 LSHIMIDTGSSVDVLFYDAFKRMGHLDSELQGRKTPLTGFAGDTTFSLGTIQLPTIARGV 609

Query: 139 SLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGIEEIRGDQATA---- 194
             LT FLVV   +P+N ILGR W+H M+AVPST HQ + + +  GI  +    A      
Sbjct: 610 RRLTSFLVVNKKAPFNAILGRPWLHAMKAVPSTYHQCIKFPSDKGIAVVSAANAAPENAI 669

Query: 195 WACAVLALKET 205
           WA  +L+ + T
Sbjct: 670 WAVTILSKRLT 680

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|4836930|gb|AAD30632.1|AC006085_5 Hypothetical protein [Arabidopsis thaliana]

 Score =  112 bits (280), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 57/146 (39%), Positives = 90/146 (61%)

Query: 49  EVSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKI 108
           E+SF  ++   +  PHDDALVIS+ +GNC V+R+LID GSSV+++   T+ +M + +  I
Sbjct: 447 EISFSEEETSDLDKPHDDALVISLDVGNCEVQRVLIDTGSSVDLIFLDTLVRMGISKKDI 506

Query: 109 KLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAV 168
           K    PL+  +   +     ITL V A+    + +F V    + YN+ILG  W+++M+AV
Sbjct: 507 KGALSPLVSFTSETSMLLRTITLPVTAQGIVKMIEFTVFDRPAAYNIILGTPWLYEMKAV 566

Query: 169 PSTCHQVLCYQTIYGIEEIRGDQATA 194
           PST HQ + + T  G+++I G Q T+
Sbjct: 567 PSTYHQCVKFPTPTGVKQILGSQRTS 592

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147773339|emb|CAN60477.1| hypothetical protein VITISV_014549 [Vitis vinifera]

 Score =  108 bits (270), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 58/146 (39%), Positives = 84/146 (57%)

Query: 52  FLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLF 111
           F P D      PH DAL++S++IG+  V+RIL+D GSS +++  + V  M      ++  
Sbjct: 337 FPPADPARTLQPHHDALILSLEIGDFDVRRILVDPGSSADLVQASVVSHMGHSLTGLENP 396

Query: 112 EQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPST 171
            Q L G +G  T S G I L V A   +L   F VV+  SP+N+ILGR W+H M+A+PST
Sbjct: 397 GQILSGFNGSSTTSLGDIVLPVQAGPVTLNVQFSVVQELSPFNIILGRTWLHYMKAIPST 456

Query: 172 CHQVLCYQTIYGIEEIRGDQATAWAC 197
            HQ++ + T  G  ++ G Q  A  C
Sbjct: 457 YHQIVSFLTNNGQTDLYGSQLAARQC 482

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147807570|emb|CAN66184.1| hypothetical protein VITISV_025184 [Vitis vinifera]

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 71/197 (36%), Positives = 104/197 (52%), Gaps = 9/197 (4%)

Query: 8   KYYIRRFR---LASAKVENCDDQLAIVTFKRGLPSNHPFFESLSEVSFLPQDLKLIQSPH 64
           +Y  RR R   L +A V  C     I + + GL    P       + F P D      PH
Sbjct: 275 EYDSRRKRQKLLRAASVREC-----INSIRPGLTGGGPRPID-GTIIFPPVDPTRTLQPH 328

Query: 65  DDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTN 124
            DAL++S++IG+  V+RIL+D GSS +++  + V  M      ++   + L G +G  T 
Sbjct: 329 HDALILSLEIGDFDVRRILVDPGSSADLIQASVVSHMGHSLTGLENPGRVLSGFNGSSTT 388

Query: 125 SDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGI 184
           S G I L V A   +L   FLVV+  SP+N+ILGR W+H M+A+PST HQ++ + T  G 
Sbjct: 389 SLGDIVLPVQAGPVTLNVQFLVVQELSPFNIILGRTWLHYMKAIPSTYHQMVSFLTNEGQ 448

Query: 185 EEIRGDQATAWACAVLA 201
            ++ G Q  A  C  +A
Sbjct: 449 IDLYGSQLAARQCYQIA 465

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147844137|emb|CAN80571.1| hypothetical protein VITISV_004508 [Vitis vinifera]

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 60/150 (40%), Positives = 86/150 (57%)

Query: 52  FLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLF 111
           F P D      PH DAL++S++IG+  V+RIL+D GSS N++  + V  M      +K  
Sbjct: 378 FPPVDPTRTLQPHRDALILSLEIGDFDVRRILVDPGSSTNLVQASVVGHMGHSLTGLKNP 437

Query: 112 EQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPST 171
            + L G +G  T S G I L V A   +L   F VV+  SP+N+ILGR W+H M+A+PST
Sbjct: 438 GRILSGFNGSSTTSLGDIILPVQAGPVTLNVQFSVVQELSPFNIILGRTWLHYMKAIPST 497

Query: 172 CHQVLCYQTIYGIEEIRGDQATAWACAVLA 201
            HQ++ + T  G  ++ G Q  A  C  +A
Sbjct: 498 YHQMVSFLTNEGQIDLYGSQLAARQCYQIA 527

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147835120|emb|CAN63372.1| hypothetical protein VITISV_035289 [Vitis vinifera]

 Score =  107 bits (267), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 62/153 (40%), Positives = 89/153 (58%), Gaps = 6/153 (3%)

Query: 52  FLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLF 111
           F P D      PH DAL++S++IG+  V+RIL+D GSSV+++  + V++M      +   
Sbjct: 379 FPPVDPARTLQPHRDALILSLEIGDFDVRRILVDPGSSVDLVQASVVDRM---GHSLAGL 435

Query: 112 EQP---LIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAV 168
           E P   L G +G  T S G I L V A   +L   F VV+  SP+NVILGR W+H M+A+
Sbjct: 436 ENPGRILSGFNGSSTTSLGDIILPVQAGPVTLNVQFSVVQELSPFNVILGRTWLHYMKAI 495

Query: 169 PSTCHQVLCYQTIYGIEEIRGDQATAWACAVLA 201
           PST HQ++ + T  G  ++ G Q  A  C  +A
Sbjct: 496 PSTYHQMVSFLTNDGQIDLYGSQLAARQCYQIA 528

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147815945|emb|CAN77145.1| hypothetical protein VITISV_038340 [Vitis vinifera]

 Score =  107 bits (267), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 64/164 (39%), Positives = 90/164 (54%), Gaps = 6/164 (3%)

Query: 50  VSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIK 109
           + F P D   I  PH DAL++ + IG+  V+RILID G+SV++L  + + +M LE   + 
Sbjct: 367 IVFPPIDPTRILQPHRDALILFLGIGDFDVRRILIDPGNSVDLLQASVINQMGLE---LS 423

Query: 110 LFEQP---LIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMR 166
             E P   L G +G  T S G I L V     +L   FLVV   SP+N ILGR W+H M+
Sbjct: 424 DLENPGLILSGFNGAATTSLGDIMLSVQVGPVTLNVQFLVVGDLSPFNAILGRTWLHYMK 483

Query: 167 AVPSTCHQVLCYQTIYGIEEIRGDQATAWACAVLALKETKRKDS 210
            +PST HQ++ + T  G  ++ G Q  A  C  +A +    KD 
Sbjct: 484 TIPSTYHQMVSFLTEDGQIDLYGSQLAARQCYQIAREVGSSKDG 527

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: AT2G14380 transposable element gene; gypsy-like retrotransposon family, has a 1.6e-123 P-value blast match to GB-AAD19359 polyprotein (gypsy_Ty3-element) (Sorghum bicolor) (1117 aa) (Arabidopsis thaliana)

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	221
cd00303	92	cd00303, retropepsin_like, Retropepsins; pepsin-li	3e-11

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

 Score = 57.7 bits (140), Expect = 3e-11
 Identities = 27/95 (28%), Positives = 47/95 (49%), Gaps = 4/95 (4%)

Query: 70  ISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVI 129
           +  KI   +  R L+D+G+SVN + ++  +K+ L   ++      + G +G    + GVI
Sbjct: 1   LKGKING-VPVRALVDSGASVNFISESLAKKLGLP-PRLLPTPLKVKGANGSSVKTLGVI 58

Query: 130 TLLVIA-KSYSLLTDFLVVKATSPYNVILGRQWIH 163
             + I     +   DF V+     Y+VILGR W+ 
Sbjct: 59  LPVTIGIGGKTFTVDFYVLD-LLSYDVILGRPWLE 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	221
cd05484	91	retropepsin_like_LTR_2 Retropepsins_like_LTR, peps	99.73
cd05481	93	retropepsin_like_LTR_1 Retropepsins_like_LTR; peps	99.59
cd05479	124	RP_DDI RP_DDI; retropepsin-like domain of DNA dama	99.5
PF08284	135	RVP_2: Retroviral aspartyl protease; InterPro: IPR	99.47
PF00077	100	RVP: Retroviral aspartyl protease The Prosite entr	99.41
PF09668	124	Asp_protease: Aspartyl protease; InterPro: IPR0191	99.3
PF13650	90	Asp_protease_2: Aspartyl protease	99.18
cd00303	92	retropepsin_like Retropepsins; pepsin-like asparta	99.16
cd06095	86	RP_RTVL_H_like Retropepsin of the RTVL_H family of	98.79
cd05483	96	retropepsin_like_bacteria Bacterial aspartate prot	98.74
cd06094	89	RP_Saci_like RP_Saci_like, retropepsin family. Ret	98.73
TIGR02281	121	clan_AA_DTGA clan AA aspartic protease, TIGR02281	98.61
cd05480	103	NRIP_C NRIP_C; putative nuclear receptor interacti	98.59
KOG0012	380	consensus DNA damage inducible protein [Replicatio	98.46
TIGR03698	107	clan_AA_DTGF clan AA aspartic protease, AF_0612 fa	98.18
PF13975	72	gag-asp_proteas: gag-polyprotein putative aspartyl	98.13
PF12384	177	Peptidase_A2B: Ty3 transposon peptidase; InterPro:	98.13
COG3577	215	Predicted aspartyl protease [General function pred	96.78
PF02160	201	Peptidase_A3: Cauliflower mosaic virus peptidase (	96.75
cd05482	87	HIV_retropepsin_like Retropepsins, pepsin-like asp	96.1
PF05585	164	DUF1758: Putative peptidase (DUF1758); InterPro: I	95.72
COG5550	125	Predicted aspartyl protease [Posttranslational mod	95.6
PF03732	96	Retrotrans_gag: Retrotransposon gag protein ; Inte	95.5
PF05618	138	Zn_protease: Putative ATP-dependant zinc protease;	90.85
PF12382	137	Peptidase_A2E: Retrotransposon peptidase; InterPro	90.54
COG4067	162	Uncharacterized protein conserved in archaea [Post	87.39

>cd05484 retropepsin_like_LTR_2 Retropepsins_like_LTR, pepsin-like aspartate proteases

Probab=99.73  E-value=2.3e-17  Score=120.32  Aligned_cols=90  Identities=21%  Similarity=0.326  Sum_probs=85.2

Q ss_pred             EEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEe
Q 045020           69 VISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVK  148 (221)
Q Consensus        69 ~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd  148 (221)
                      ++++.|+|.++. +|||+||++|+|+.+.++++|.++  ++++...+.+|+|.....+|.+.+.+++|+.+..++|+|++
T Consensus         2 ~~~~~Ing~~i~-~lvDTGA~~svis~~~~~~lg~~~--~~~~~~~v~~a~G~~~~~~G~~~~~v~~~~~~~~~~~~v~~   78 (91)
T cd05484           2 TVTLLVNGKPLK-FQLDTGSAITVISEKTWRKLGSPP--LKPTKKRLRTATGTKLSVLGQILVTVKYGGKTKVLTLYVVK   78 (91)
T ss_pred             EEEEEECCEEEE-EEEcCCcceEEeCHHHHHHhCCCc--cccccEEEEecCCCEeeEeEEEEEEEEECCEEEEEEEEEEE
Confidence            678999999985 999999999999999999999987  99999999999999999999999999999999999999998


Q ss_pred             eCCceeeEEcchhhh
Q 045020          149 ATSPYNVILGRQWIH  163 (221)
Q Consensus       149 ~~~~yn~ILGr~wL~  163 (221)
                      ..  |+.||||+||.
T Consensus        79 ~~--~~~lLG~~wl~   91 (91)
T cd05484          79 NE--GLNLLGRDWLD   91 (91)
T ss_pred             CC--CCCccChhhcC
Confidence            76  99999999984

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

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

Probab=99.59  E-value=6.2e-15  Score=108.26  Aligned_cols=88  Identities=22%  Similarity=0.293  Sum_probs=77.8

Q ss_pred             EEEEcC-eeeeEEEecCCCccccccHHHHHhhcc-ccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEe
Q 045020           71 SIKIGN-CLVKRILIDNGSSVNILDDATVEKMRL-EQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVK  148 (221)
Q Consensus        71 ~~~I~~-~~v~riLVD~GSsvnil~~~~~~~mg~-~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd  148 (221)
                      .+.|++ ..++ ++||+||++|+||.+++++||. ...+|+++...|++|+|+...+.|.+++++++|+.+.++.|+|+|
T Consensus         2 ~~~i~g~~~v~-~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~~~G~~~~~v~~~~~~~~~~f~Vvd   80 (93)
T cd05481           2 DMKINGKQSVK-FQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIPVEGGVKLKCRYRNPKYNLTFQVVK   80 (93)
T ss_pred             ceEeCCceeEE-EEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEeeeeEEEEEEEEECCcEEEEEEEEEC
Confidence            356777 5555 9999999999999999999983 245799999999999999999999999999999999999999999


Q ss_pred             eCCceeeEEcchh
Q 045020          149 ATSPYNVILGRQW  161 (221)
Q Consensus       149 ~~~~yn~ILGr~w  161 (221)
                      ...+  .|||+..
T Consensus        81 ~~~~--~lLG~~~   91 (93)
T cd05481          81 EEGP--PLLGAKA   91 (93)
T ss_pred             CCCC--ceEcccc
Confidence            8665  7999864

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

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

Probab=99.50  E-value=1.9e-13  Score=105.32  Aligned_cols=109  Identities=22%  Similarity=0.280  Sum_probs=86.8

Q ss_pred             CCCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceee-EEEEEcCeeEEE
Q 045020           64 HDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVIT-LLVIAKSYSLLT  142 (221)
Q Consensus        64 h~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~-L~v~~g~~t~~~  142 (221)
                      ....+++.+.|++..+ ++|||+||+.|+++.+..+++|++...-.+......|-+  .....|.+. .++++|+.++.+
T Consensus        13 ~~~~~~v~~~Ing~~~-~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g--~~~~~g~~~~~~l~i~~~~~~~   89 (124)
T cd05479          13 KVPMLYINVEINGVPV-KAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVG--TQKILGRIHLAQVKIGNLFLPC   89 (124)
T ss_pred             eeeEEEEEEEECCEEE-EEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCC--CcEEEeEEEEEEEEECCEEeee
Confidence            3456899999999997 599999999999999999999997542222223344433  356788874 799999999999


Q ss_pred             EEEEEeeCCceeeEEcchhhhhccccccCcccee
Q 045020          143 DFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVL  176 (221)
Q Consensus       143 ~F~Vvd~~~~yn~ILGr~wL~~~~~i~st~~q~v  176 (221)
                      +|.|++.. .++.|||.+||.+++++...-.+.|
T Consensus        90 ~~~Vl~~~-~~d~ILG~d~L~~~~~~ID~~~~~i  122 (124)
T cd05479          90 SFTVLEDD-DVDFLIGLDMLKRHQCVIDLKENVL  122 (124)
T ss_pred             EEEEECCC-CcCEEecHHHHHhCCeEEECCCCEE
Confidence            99999855 8899999999999999877665554

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.

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

Probab=99.47  E-value=7.2e-13  Score=103.70  Aligned_cols=119  Identities=20%  Similarity=0.329  Sum_probs=99.0

Q ss_pred             CCCCCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCccccccee-eEEEEEcCeeE
Q 045020           62 SPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVI-TLLVIAKSYSL  140 (221)
Q Consensus        62 ~~h~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i-~L~v~~g~~t~  140 (221)
                      +.+++.+...+.|+++.+. +|+|+||+-|+|..+..++++++...+..+-.. .+. |......+.+ .+++.+++.++
T Consensus        16 ~~~~~vi~g~~~I~~~~~~-vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~~V-~~~-g~~~~~~~~~~~~~~~i~g~~~   92 (135)
T PF08284_consen   16 EESPDVITGTFLINSIPAS-VLIDSGATHSFISSSFAKKLGLPLEPLPRPIVV-SAP-GGSINCEGVCPDVPLSIQGHEF   92 (135)
T ss_pred             cCCCCeEEEEEEeccEEEE-EEEecCCCcEEccHHHHHhcCCEEEEccCeeEE-ecc-cccccccceeeeEEEEECCeEE
Confidence            4556677778889999988 999999999999999999999998888664433 343 4444455554 59999999999


Q ss_pred             EEEEEEEeeCCceeeEEcchhhhhccccccCccceeeeecCCcE
Q 045020          141 LTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGI  184 (221)
Q Consensus       141 ~~~F~Vvd~~~~yn~ILGr~wL~~~~~i~st~~q~vk~~~~~g~  184 (221)
                      ..+|.|.+ ...|++|||.+||.+..+......-+|.|..|.|.
T Consensus        93 ~~dl~vl~-l~~~DvILGm~WL~~~~~~IDw~~k~v~f~~p~~~  135 (135)
T PF08284_consen   93 VVDLLVLD-LGGYDVILGMDWLKKHNPVIDWATKTVTFNSPSGE  135 (135)
T ss_pred             EeeeEEec-ccceeeEeccchHHhCCCEEEccCCEEEEeCCCCC
Confidence            99999998 57799999999999999998888999999888873

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.

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

Probab=99.41  E-value=4.1e-13  Score=99.02  Aligned_cols=97  Identities=29%  Similarity=0.396  Sum_probs=85.1

Q ss_pred             CCCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEE
Q 045020           64 HDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTD  143 (221)
Q Consensus        64 h~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~  143 (221)
                      +++..++++.|++..+. +|+|+||++++++.+.++..+.+    ......+.|.+|.. ...|...+.++++.......
T Consensus         2 ~~~rp~i~v~i~g~~i~-~LlDTGA~vsiI~~~~~~~~~~~----~~~~~~v~~~~g~~-~~~~~~~~~v~~~~~~~~~~   75 (100)
T PF00077_consen    2 LSNRPYITVKINGKKIK-ALLDTGADVSIISEKDWKKLGPP----PKTSITVRGAGGSS-SILGSTTVEVKIGGKEFNHT   75 (100)
T ss_dssp             SSSSSEEEEEETTEEEE-EEEETTBSSEEESSGGSSSTSSE----EEEEEEEEETTEEE-EEEEEEEEEEEETTEEEEEE
T ss_pred             CCCCceEEEeECCEEEE-EEEecCCCcceeccccccccccc----ccCCceeccCCCcc-eeeeEEEEEEEEECccceEE
Confidence            34455889999999988 99999999999999988776543    56667889999988 99999999999999999999


Q ss_pred             EEEEeeCCceeeEEcchhhhhcccc
Q 045020          144 FLVVKATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       144 F~Vvd~~~~yn~ILGr~wL~~~~~i  168 (221)
                      |+|++. .++| ||||+||.++++.
T Consensus        76 ~~v~~~-~~~~-ILG~D~L~~~~~~   98 (100)
T PF00077_consen   76 FLVVPD-LPMN-ILGRDFLKKLNAV   98 (100)
T ss_dssp             EEESST-CSSE-EEEHHHHTTTTCE
T ss_pred             EEecCC-CCCC-EeChhHHHHcCCE
Confidence            999987 8888 9999999999875

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 ....

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

Probab=99.30  E-value=1.7e-11  Score=94.33  Aligned_cols=101  Identities=17%  Similarity=0.212  Sum_probs=73.7

Q ss_pred             CCCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceee-EEEEEcCeeEEE
Q 045020           64 HDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVIT-LLVIAKSYSLLT  142 (221)
Q Consensus        64 h~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~-L~v~~g~~t~~~  142 (221)
                      ....|+|.+.|+|.++. ++||+|+..|+|+.+.++++|+..  +-.....-...+-.+..++|.|. +++++|+..+++
T Consensus        21 ~v~mLyI~~~ing~~vk-A~VDtGAQ~tims~~~a~r~gL~~--lid~r~~g~a~GvG~~~i~G~Ih~~~l~ig~~~~~~   97 (124)
T PF09668_consen   21 QVSMLYINCKINGVPVK-AFVDTGAQSTIMSKSCAERCGLMR--LIDKRFAGVAKGVGTQKILGRIHSVQLKIGGLFFPC   97 (124)
T ss_dssp             -----EEEEEETTEEEE-EEEETT-SS-EEEHHHHHHTTGGG--GEEGGG-EE-------EEEEEEEEEEEEETTEEEEE
T ss_pred             CcceEEEEEEECCEEEE-EEEeCCCCccccCHHHHHHcCChh--hccccccccccCCCcCceeEEEEEEEEEECCEEEEE
Confidence            34579999999999994 999999999999999999999853  44443322222224567999997 999999999999


Q ss_pred             EEEEEeeCCceeeEEcchhhhhcccc
Q 045020          143 DFLVVKATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       143 ~F~Vvd~~~~yn~ILGr~wL~~~~~i  168 (221)
                      .|.|++ ..+-+.|||.+||.+.+++
T Consensus        98 s~~Vle-~~~~d~llGld~L~~~~c~  122 (124)
T PF09668_consen   98 SFTVLE-DQDVDLLLGLDMLKRHKCC  122 (124)
T ss_dssp             EEEEET-TSSSSEEEEHHHHHHTT-E
T ss_pred             EEEEeC-CCCcceeeeHHHHHHhCcc
Confidence            999999 4455899999999998875

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.

>PF13650 Asp_protease_2: Aspartyl protease

Probab=99.18  E-value=2.1e-10  Score=82.01  Aligned_cols=89  Identities=27%  Similarity=0.444  Sum_probs=74.2

Q ss_pred             EEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeE-EEEEEEEe
Q 045020           70 ISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSL-LTDFLVVK  148 (221)
Q Consensus        70 i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~-~~~F~Vvd  148 (221)
                      |++.|+|..+ ++++|+||+.++++.+.++++|+....... ...+.+++|......+.+. .+++|+.++ ++.|.+++
T Consensus         1 V~v~vng~~~-~~liDTGa~~~~i~~~~~~~l~~~~~~~~~-~~~~~~~~g~~~~~~~~~~-~i~ig~~~~~~~~~~v~~   77 (90)
T PF13650_consen    1 VPVKVNGKPV-RFLIDTGASISVISRSLAKKLGLKPRPKSV-PISVSGAGGSVTVYRGRVD-SITIGGITLKNVPFLVVD   77 (90)
T ss_pred             CEEEECCEEE-EEEEcCCCCcEEECHHHHHHcCCCCcCCce-eEEEEeCCCCEEEEEEEEE-EEEECCEEEEeEEEEEEC
Confidence            4678999977 599999999999999999999987654432 3566888998666666666 899999887 89999999


Q ss_pred             eCCceeeEEcchh
Q 045020          149 ATSPYNVILGRQW  161 (221)
Q Consensus       149 ~~~~yn~ILGr~w  161 (221)
                      ...+++.|||.+|
T Consensus        78 ~~~~~~~iLG~df   90 (90)
T PF13650_consen   78 LGDPIDGILGMDF   90 (90)
T ss_pred             CCCCCEEEeCCcC
Confidence            7788999999998

>cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases

Probab=99.16  E-value=4.1e-10  Score=77.41  Aligned_cols=90  Identities=28%  Similarity=0.483  Sum_probs=73.9

Q ss_pred             EEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccce-eeEEEEEcCeeEEEEEEEEee
Q 045020           71 SIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGV-ITLLVIAKSYSLLTDFLVVKA  149 (221)
Q Consensus        71 ~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~-i~L~v~~g~~t~~~~F~Vvd~  149 (221)
                      ++.+++. ..++|+|+||++|++..+.+.+++. ..........+.+++|......+. ..+.+.++.......|++++.
T Consensus         2 ~~~~~~~-~~~~liDtgs~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~   79 (92)
T cd00303           2 KGKINGV-PVRALVDSGASVNFISESLAKKLGL-PPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDL   79 (92)
T ss_pred             EEEECCE-EEEEEEcCCCcccccCHHHHHHcCC-CcccCCCceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcC
Confidence            4567774 4469999999999999999999987 223445567788888887777777 578889999999999999986


Q ss_pred             CCceeeEEcchhhh
Q 045020          150 TSPYNVILGRQWIH  163 (221)
Q Consensus       150 ~~~yn~ILGr~wL~  163 (221)
                      . .|+.|||++||+
T Consensus        80 ~-~~~~ilG~~~l~   92 (92)
T cd00303          80 L-SYDVILGRPWLE   92 (92)
T ss_pred             C-CcCEEecccccC
Confidence            6 899999999984

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

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

Probab=98.79  E-value=4.4e-08  Score=70.56  Aligned_cols=85  Identities=22%  Similarity=0.353  Sum_probs=68.2

Q ss_pred             EEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEee
Q 045020           70 ISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKA  149 (221)
Q Consensus        70 i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd~  149 (221)
                      +++.|+|.++. +||||||+..+++...++++     .+......+.|.+|....+.....-.+++|+.+....|.|++.
T Consensus         1 ~~v~InG~~~~-fLvDTGA~~tii~~~~a~~~-----~~~~~~~~v~gagG~~~~~v~~~~~~v~vg~~~~~~~~~v~~~   74 (86)
T cd06095           1 VTITVEGVPIV-FLVDTGATHSVLKSDLGPKQ-----ELSTTSVLIRGVSGQSQQPVTTYRTLVDLGGHTVSHSFLVVPN   74 (86)
T ss_pred             CEEEECCEEEE-EEEECCCCeEEECHHHhhhc-----cCCCCcEEEEeCCCcccccEEEeeeEEEECCEEEEEEEEEEcC
Confidence            36789999887 99999999999999999987     3456778899999987444443322689999999889988864


Q ss_pred             CCceeeEEcchhh
Q 045020          150 TSPYNVILGRQWI  162 (221)
Q Consensus       150 ~~~yn~ILGr~wL  162 (221)
                      . + +.|||+.||
T Consensus        75 ~-~-~~lLG~dfL   85 (86)
T cd06095          75 C-P-DPLLGRDLL   85 (86)
T ss_pred             C-C-CcEechhhc
Confidence            3 3 789999987

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

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

Probab=98.74  E-value=9.5e-08  Score=68.81  Aligned_cols=92  Identities=16%  Similarity=0.224  Sum_probs=71.2

Q ss_pred             eEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeE-EEEEEE
Q 045020           68 LVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSL-LTDFLV  146 (221)
Q Consensus        68 L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~-~~~F~V  146 (221)
                      +++++.|++..+. +++|+||+.++++.+..++++..  ..........+.+|........ .-.+++|+.++ ++.+.|
T Consensus         3 ~~v~v~i~~~~~~-~llDTGa~~s~i~~~~~~~l~~~--~~~~~~~~~~~~~G~~~~~~~~-~~~i~ig~~~~~~~~~~v   78 (96)
T cd05483           3 FVVPVTINGQPVR-FLLDTGASTTVISEELAERLGLP--LTLGGKVTVQTANGRVRAARVR-LDSLQIGGITLRNVPAVV   78 (96)
T ss_pred             EEEEEEECCEEEE-EEEECCCCcEEcCHHHHHHcCCC--ccCCCcEEEEecCCCccceEEE-cceEEECCcEEeccEEEE
Confidence            6789999988875 99999999999999999999872  2333445566677765544444 45788999875 588999


Q ss_pred             EeeCC-ceeeEEcchhhh
Q 045020          147 VKATS-PYNVILGRQWIH  163 (221)
Q Consensus       147 vd~~~-~yn~ILGr~wL~  163 (221)
                      +|... +.+.|||.+||.
T Consensus        79 ~d~~~~~~~gIlG~d~l~   96 (96)
T cd05483          79 LPGDALGVDGLLGMDFLR   96 (96)
T ss_pred             eCCcccCCceEeChHHhC
Confidence            98765 578999999974

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.

>cd06094 RP_Saci_like RP_Saci_like, retropepsin family

Probab=98.73  E-value=2.3e-08  Score=72.29  Aligned_cols=78  Identities=22%  Similarity=0.330  Sum_probs=67.5

Q ss_pred             eEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCe-eEEEEEEEEeeCCceeeEEc
Q 045020           80 KRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSY-SLLTDFLVVKATSPYNVILG  158 (221)
Q Consensus        80 ~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~-t~~~~F~Vvd~~~~yn~ILG  158 (221)
                      .+.|||+||.++++|.+..++.      ++++...|.+.||+.....|...+.+..|.. .+...|.|.|.+.   +|||
T Consensus        10 ~~fLVDTGA~vSviP~~~~~~~------~~~~~~~l~AANgt~I~tyG~~~l~ldlGlrr~~~w~FvvAdv~~---pIlG   80 (89)
T cd06094          10 LRFLVDTGAAVSVLPASSTKKS------LKPSPLTLQAANGTPIATYGTRSLTLDLGLRRPFAWNFVVADVPH---PILG   80 (89)
T ss_pred             cEEEEeCCCceEeecccccccc------ccCCceEEEeCCCCeEeeeeeEEEEEEcCCCcEEeEEEEEcCCCc---ceec
Confidence            3599999999999998866542      6777789999999999999999999999986 8888999988766   5999


Q ss_pred             chhhhhcc
Q 045020          159 RQWIHKMR  166 (221)
Q Consensus       159 r~wL~~~~  166 (221)
                      ..+|++++
T Consensus        81 aDfL~~~~   88 (89)
T cd06094          81 ADFLQHYG   88 (89)
T ss_pred             HHHHHHcC
Confidence            99999875

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

>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family

Probab=98.61  E-value=3.4e-07  Score=70.28  Aligned_cols=101  Identities=14%  Similarity=0.284  Sum_probs=78.3

Q ss_pred             CCCCCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceee-EEEEEcCeeE
Q 045020           62 SPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVIT-LLVIAKSYSL  140 (221)
Q Consensus        62 ~~h~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~-L~v~~g~~t~  140 (221)
                      +.+...+++.+.|+|.++. ++|||||+..+++....+++|+....+ .....+.+.+|....  ..+. -.+++|+.++
T Consensus         6 ~~~~g~~~v~~~InG~~~~-flVDTGAs~t~is~~~A~~Lgl~~~~~-~~~~~~~ta~G~~~~--~~~~l~~l~iG~~~~   81 (121)
T TIGR02281         6 KDGDGHFYATGRVNGRNVR-FLVDTGATSVALNEEDAQRLGLDLNRL-GYTVTVSTANGQIKA--ARVTLDRVAIGGIVV   81 (121)
T ss_pred             EcCCCeEEEEEEECCEEEE-EEEECCCCcEEcCHHHHHHcCCCcccC-CceEEEEeCCCcEEE--EEEEeCEEEECCEEE
Confidence            4456678999999999775 999999999999999999999976543 234556667776432  3334 4588999876


Q ss_pred             E-EEEEEEeeCCceeeEEcchhhhhcc
Q 045020          141 L-TDFLVVKATSPYNVILGRQWIHKMR  166 (221)
Q Consensus       141 ~-~~F~Vvd~~~~yn~ILGr~wL~~~~  166 (221)
                      . +.+.|++.....+.+||-.+|.+++
T Consensus        82 ~nv~~~v~~~~~~~~~LLGm~fL~~~~  108 (121)
T TIGR02281        82 NDVDAMVAEGGALSESLLGMSFLNRLS  108 (121)
T ss_pred             eCcEEEEeCCCcCCceEcCHHHHhccc
Confidence            4 8999987654447999999999986

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).

>cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein

Probab=98.59  E-value=3.3e-07  Score=67.44  Aligned_cols=96  Identities=20%  Similarity=0.253  Sum_probs=73.8

Q ss_pred             EEEEcCeeeeEEEecCCCccccccHHHHHhhcccccccc-ccccceecccCCcccccceee-EEEEEcCeeEEEEEEEEe
Q 045020           71 SIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIK-LFEQPLIGLSGIVTNSDGVIT-LLVIAKSYSLLTDFLVVK  148 (221)
Q Consensus        71 ~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~-~~~~~l~gf~g~~~~~lG~i~-L~v~~g~~t~~~~F~Vvd  148 (221)
                      ...++|++|. ++||+|+-.|||+....+++|+...-.+ ...-.-.| -|++...+|.|. +++++|...++..|.|+|
T Consensus         2 nCk~nG~~vk-AfVDsGaQ~timS~~caercgL~r~v~~~r~~g~A~g-vgt~~kiiGrih~~~ikig~~~~~CSftVld   79 (103)
T cd05480           2 SCQCAGKELR-ALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPS-LPTSVKVIGQIERLVLQLGQLTVECSAQVVD   79 (103)
T ss_pred             ceeECCEEEE-EEEecCCchhhcCHHHHHHcChHhhhhhccccccccC-CCcceeEeeEEEEEEEEeCCEEeeEEEEEEc
Confidence            4578999998 9999999999999999999998532111 11111111 123357889996 999999999999999999


Q ss_pred             eCCceeeEEcchhhhhccccc
Q 045020          149 ATSPYNVILGRQWIHKMRAVP  169 (221)
Q Consensus       149 ~~~~yn~ILGr~wL~~~~~i~  169 (221)
                       ..+.+.+||-..|.+.++..
T Consensus        80 -~~~~d~llGLdmLkrhqc~I   99 (103)
T cd05480          80 -DNEKNFSLGLQTLKSLKCVI   99 (103)
T ss_pred             -CCCcceEeeHHHHhhcceee
Confidence             45678999999999887753

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.

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

Probab=98.46  E-value=4.8e-07  Score=80.09  Aligned_cols=124  Identities=20%  Similarity=0.279  Sum_probs=93.4

Q ss_pred             ccccCCCCCCCcCCCCCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCccccccee
Q 045020           50 VSFLPQDLKLIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVI  129 (221)
Q Consensus        50 I~F~~~d~~~~~~~h~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i  129 (221)
                      |..+|++...     -.-|+|.+.|+|++|+ +.||+|+-.|||+....+++|+..--.+...-...|.+  +.+.+|.|
T Consensus       223 i~~~pe~f~~-----v~ML~iN~~ing~~VK-AfVDsGaq~timS~~Caer~gL~rlid~r~~g~a~gvg--~~ki~g~I  294 (380)
T KOG0012|consen  223 IEYHPEDFTQ-----VTMLYINCEINGVPVK-AFVDSGAQTTIMSAACAERCGLNRLIDKRFQGEARGVG--TEKILGRI  294 (380)
T ss_pred             hhcCcccccc-----ceEEEEEEEECCEEEE-EEEcccchhhhhhHHHHHHhChHHHhhhhhhccccCCC--ccccccee
Confidence            5555554332     3568999999999998 99999999999999999999986532222222222221  55678999


Q ss_pred             e-EEEEEcCeeEEEEEEEEeeCCceeeEEcchhhhhccccccCccceeeeecCC
Q 045020          130 T-LLVIAKSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIY  182 (221)
Q Consensus       130 ~-L~v~~g~~t~~~~F~Vvd~~~~yn~ILGr~wL~~~~~i~st~~q~vk~~~~~  182 (221)
                      . +++++|..++...|.|+|. .+-+++||-.-|.+.++...--+-.+.+-...
T Consensus       295 h~~~lki~~~~l~c~ftV~d~-~~~d~llGLd~Lrr~~ccIdL~~~~L~ig~~~  347 (380)
T KOG0012|consen  295 HQAQLKIEDLYLPCSFTVLDR-RDMDLLLGLDMLRRHQCCIDLKTNVLRIGNTE  347 (380)
T ss_pred             EEEEEEeccEeeccceEEecC-CCcchhhhHHHHHhccceeecccCeEEecCCC
Confidence            6 9999999999999999995 44589999999999999876655555554333

>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family

Probab=98.18  E-value=1.2e-05  Score=60.33  Aligned_cols=86  Identities=17%  Similarity=0.168  Sum_probs=59.7

Q ss_pred             eeeEEEecCCCcccc-ccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEeeCCceeeE
Q 045020           78 LVKRILIDNGSSVNI-LDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKATSPYNVI  156 (221)
Q Consensus        78 ~v~riLVD~GSsvni-l~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd~~~~yn~I  156 (221)
                      .|. +|||+|++..+ +|.+.++++|+++..    .......+|...... .....|.+|+........+.+ ..+ ..+
T Consensus        16 ~v~-~LVDTGat~~~~l~~~~a~~lgl~~~~----~~~~~tA~G~~~~~~-v~~~~v~igg~~~~~~v~~~~-~~~-~~L   87 (107)
T TIGR03698        16 EVR-ALVDTGFSGFLLVPPDIVNKLGLPELD----QRRVYLADGREVLTD-VAKASIIINGLEIDAFVESLG-YVD-EPL   87 (107)
T ss_pred             EEE-EEEECCCCeEEecCHHHHHHcCCCccc----CcEEEecCCcEEEEE-EEEEEEEECCEEEEEEEEecC-CCC-ccE
Confidence            444 99999999997 999999999997642    345555677432221 224667788887744433323 224 679


Q ss_pred             EcchhhhhccccccC
Q 045020          157 LGRQWIHKMRAVPST  171 (221)
Q Consensus       157 LGr~wL~~~~~i~st  171 (221)
                      ||..||.+++.+...
T Consensus        88 LG~~~L~~l~l~id~  102 (107)
T TIGR03698        88 LGTELLEGLGIVIDY  102 (107)
T ss_pred             ecHHHHhhCCEEEeh
Confidence            999999999887644

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.

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

Probab=98.13  E-value=9.2e-06  Score=56.57  Aligned_cols=65  Identities=23%  Similarity=0.385  Sum_probs=51.5

Q ss_pred             CCCCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCccccccee
Q 045020           63 PHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVI  129 (221)
Q Consensus        63 ~h~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i  129 (221)
                      .+...+++.+.|++..+. .|||+||+.|+|+.+..+++|++..... ....+.-.+|......|.+
T Consensus         4 ~~~g~~~v~~~I~g~~~~-alvDtGat~~fis~~~a~rLgl~~~~~~-~~~~v~~a~g~~~~~~g~~   68 (72)
T PF13975_consen    4 PDPGLMYVPVSIGGVQVK-ALVDTGATHNFISESLAKRLGLPLEKPP-SPIRVKLANGSVIEIRGVA   68 (72)
T ss_pred             ccCCEEEEEEEECCEEEE-EEEeCCCcceecCHHHHHHhCCCcccCC-CCEEEEECCCCccccceEE
Confidence            455668999999999888 9999999999999999999998764332 2355566688877776655

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

Probab=98.13  E-value=2.1e-05  Score=62.93  Aligned_cols=103  Identities=15%  Similarity=0.220  Sum_probs=81.8

Q ss_pred             CCCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccC-CcccccceeeEEEEEcCeeEEE
Q 045020           64 HDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSG-IVTNSDGVITLLVIAKSYSLLT  142 (221)
Q Consensus        64 h~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g-~~~~~lG~i~L~v~~g~~t~~~  142 (221)
                      =++.+...+.|.+-.+. +|.|+||-..++......+|+++..  ..+...+.|+.+ +....--.+++++..+...+.+
T Consensus        31 vg~T~~v~l~~~~t~i~-vLfDSGSPTSfIr~di~~kL~L~~~--~app~~fRG~vs~~~~~tsEAv~ld~~i~n~~i~i  107 (177)
T PF12384_consen   31 VGKTAIVQLNCKGTPIK-VLFDSGSPTSFIRSDIVEKLELPTH--DAPPFRFRGFVSGESATTSEAVTLDFYIDNKLIDI  107 (177)
T ss_pred             cCcEEEEEEeecCcEEE-EEEeCCCccceeehhhHHhhCCccc--cCCCEEEeeeccCCceEEEEeEEEEEEECCeEEEE
Confidence            35667888899999988 9999999999999999999987653  334455666654 3444555677999999999999


Q ss_pred             EEEEEeeCCceeeEEcchhhhhcccccc
Q 045020          143 DFLVVKATSPYNVILGRQWIHKMRAVPS  170 (221)
Q Consensus       143 ~F~Vvd~~~~yn~ILGr~wL~~~~~i~s  170 (221)
                      .++|.| .-++++|+|-|.|.++.-+-.
T Consensus       108 ~aYV~d-~m~~dlIIGnPiL~ryp~l~~  134 (177)
T PF12384_consen  108 AAYVTD-NMDHDLIIGNPILDRYPTLLY  134 (177)
T ss_pred             EEEEec-cCCcceEeccHHHhhhHHHHH
Confidence            999998 556899999999988766533

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=96.78  E-value=0.0066  Score=50.46  Aligned_cols=133  Identities=14%  Similarity=0.197  Sum_probs=91.9

Q ss_pred             cHHHHHHHHhcCCCCCCCcccccccccccCCCC--C-CCcCCCCCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhh
Q 045020           25 DDQLAIVTFKRGLPSNHPFFESLSEVSFLPQDL--K-LIQSPHDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKM  101 (221)
Q Consensus        25 ~~~~~~~~fk~~~~~~~~~~es~~~I~F~~~d~--~-~~~~~h~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~m  101 (221)
                      +...+-...+++.-|+.||---       ..|-  . ......+-.+.+...|||..|. .|||||+|.=.+......++
T Consensus        67 ~l~~~~~~v~~gl~P~~~~a~~-------~~~g~~~v~Lak~~~GHF~a~~~VNGk~v~-fLVDTGATsVal~~~dA~Rl  138 (215)
T COG3577          67 ELQDATHRVLRGLNPGRAWATL-------VGDGYQEVSLAKSRDGHFEANGRVNGKKVD-FLVDTGATSVALNEEDARRL  138 (215)
T ss_pred             ccccchhHHHhhcCCCCCcccc-------CCCCceEEEEEecCCCcEEEEEEECCEEEE-EEEecCcceeecCHHHHHHh
Confidence            3333444556666667777321       1111  0 1224455568889999999998 99999999999999999999


Q ss_pred             ccccccccccccceecccCCcccccceee-EEEEEcCe-eEEEEEEEEeeCCceeeEEcchhhhhcccc
Q 045020          102 RLEQDKIKLFEQPLIGLSGIVTNSDGVIT-LLVIAKSY-SLLTDFLVVKATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       102 g~~~~~L~~~~~~l~gf~g~~~~~lG~i~-L~v~~g~~-t~~~~F~Vvd~~~~yn~ILGr~wL~~~~~i  168 (221)
                      |+....|.-+ .++..-||...-.  .++ =.|++|++ ..+++=+|++....-+.+||-.+|.+++-.
T Consensus       139 Gid~~~l~y~-~~v~TANG~~~AA--~V~Ld~v~IG~I~~~nV~A~V~~~g~L~~sLLGMSfL~rL~~f  204 (215)
T COG3577         139 GIDLNSLDYT-ITVSTANGRARAA--PVTLDRVQIGGIRVKNVDAMVAEDGALDESLLGMSFLNRLSGF  204 (215)
T ss_pred             CCCccccCCc-eEEEccCCccccc--eEEeeeEEEccEEEcCchhheecCCccchhhhhHHHHhhccce
Confidence            9988766544 5556567754221  122 35778877 458888899877677899999999887643

>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=96.75  E-value=0.0049  Score=51.25  Aligned_cols=104  Identities=10%  Similarity=0.117  Sum_probs=69.9

Q ss_pred             EEEEcCe---eeeEEEecCCCccccccHHHHHhhccccccccccc--cceecccCCccccccee-eEEEEEcCeeEEEEE
Q 045020           71 SIKIGNC---LVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFE--QPLIGLSGIVTNSDGVI-TLLVIAKSYSLLTDF  144 (221)
Q Consensus        71 ~~~I~~~---~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~--~~l~gf~g~~~~~lG~i-~L~v~~g~~t~~~~F  144 (221)
                      .+.+.|.   .+. .+|||||+++++.....     |...++.+.  ..++|+|++..+..=.+ .+.+.+++..+.+.|
T Consensus        10 ~i~~~gy~~~~~~-~~vDTGAt~C~~~~~ii-----P~e~we~~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~IP~   83 (201)
T PF02160_consen   10 KISFPGYKKFNYH-CYVDTGATICCASKKII-----PEEYWEKSKKPIKVKGANGSIIQINKKAKNGKIQIADKIFRIPT   83 (201)
T ss_pred             EEEEcCceeEEEE-EEEeCCCceEEecCCcC-----CHHHHHhCCCcEEEEEecCCceEEEEEecCceEEEccEEEeccE
Confidence            4445553   334 79999999988776654     333344444  47888998865444444 388888988877777


Q ss_pred             EEEeeCCceeeEEcchhhhhccccccCccceeeeecCC
Q 045020          145 LVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIY  182 (221)
Q Consensus       145 ~Vvd~~~~yn~ILGr~wL~~~~~i~st~~q~vk~~~~~  182 (221)
                      .-.. .+..++|||.+||..+....-+. ..+.|-.++
T Consensus        84 iYq~-~~g~d~IlG~NF~r~y~Pfiq~~-~~I~f~~~~  119 (201)
T PF02160_consen   84 IYQQ-ESGIDIILGNNFLRLYEPFIQTE-DRIQFHKKG  119 (201)
T ss_pred             EEEe-cCCCCEEecchHHHhcCCcEEEc-cEEEEEeCC
Confidence            6644 46789999999999888764443 345555544

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

>cd05482 HIV_retropepsin_like Retropepsins, pepsin-like aspartate proteases

Probab=96.10  E-value=0.042  Score=39.72  Aligned_cols=85  Identities=25%  Similarity=0.336  Sum_probs=57.2

Q ss_pred             EEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEeeC
Q 045020           71 SIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVKAT  150 (221)
Q Consensus        71 ~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd~~  150 (221)
                      ++.|++..+. .|+|+||-..++....+..-    -.+......+.|.+|.. .+.-.-.+++++.+....-.|.|....
T Consensus         2 ~~~i~g~~~~-~llDTGAd~Tvi~~~~~p~~----w~~~~~~~~i~GIGG~~-~~~~~~~v~i~i~~~~~~g~vlv~~~~   75 (87)
T cd05482           2 TLYINGKLFE-GLLDTGADVSIIAENDWPKN----WPIQPAPSNLTGIGGAI-TPSQSSVLLLEIDGEGHLGTILVYVLS   75 (87)
T ss_pred             EEEECCEEEE-EEEccCCCCeEEcccccCCC----CccCCCCeEEEeccceE-EEEEEeeEEEEEcCCeEEEEEEEccCC
Confidence            5678888877 99999999999876443211    12445667788888753 333333688888877666677776533


Q ss_pred             CceeeEEcchhh
Q 045020          151 SPYNVILGRQWI  162 (221)
Q Consensus       151 ~~yn~ILGr~wL  162 (221)
                      .|.| |+||..|
T Consensus        76 ~P~n-llGRd~L   86 (87)
T cd05482          76 LPVN-LWGRDIL   86 (87)
T ss_pred             Cccc-EEccccC
Confidence            4443 7899876

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

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

Probab=95.72  E-value=0.033  Score=44.47  Aligned_cols=71  Identities=23%  Similarity=0.245  Sum_probs=49.2

Q ss_pred             eeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCc-ccccc--eeeEEEEEcCeeEEEEEEEEeeC
Q 045020           77 CLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIV-TNSDG--VITLLVIAKSYSLLTDFLVVKAT  150 (221)
Q Consensus        77 ~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~-~~~lG--~i~L~v~~g~~t~~~~F~Vvd~~  150 (221)
                      ...-|+|+|+||..+++..+..++|+++..   +......|..|.. .....  .+.+.+..+.....+..++++..
T Consensus        10 ~~~~~~LlDsGSq~SfIt~~la~~L~L~~~---~~~~~~~~~~g~~~~~~~~~~~~~i~~~~~~~~~~i~alvv~~I   83 (164)
T PF05585_consen   10 QVEARALLDSGSQRSFITESLANKLNLPGT---GEKILVIGTFGSSSPKSKKCVRVKISSRTSNNSLEIEALVVPKI   83 (164)
T ss_pred             EEEEEEEEecCCchhHHhHHHHHHhCCCCC---CceEEEEeccCccCccceeEEEEEEEEecCCCceEEEEEecCcc
Confidence            444679999999999999999999998653   3444445544443 22333  34466666777788888888654

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

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

Probab=95.60  E-value=0.084  Score=40.49  Aligned_cols=86  Identities=20%  Similarity=0.261  Sum_probs=56.7

Q ss_pred             EcCeeeeEEEecCCCc-cccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCe----eEEEEEEEEe
Q 045020           74 IGNCLVKRILIDNGSS-VNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSY----SLLTDFLVVK  148 (221)
Q Consensus        74 I~~~~v~riLVD~GSs-vnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~----t~~~~F~Vvd  148 (221)
                      .+++.-.+ |||||.+ --++|.+.+.++|.++.  ......+.        .-|.+...|....+    ...+.|..+.
T Consensus        22 ~Gd~~~~~-LiDTGFtg~lvlp~~vaek~~~~~~--~~~~~~~a--------~~~~v~t~V~~~~iki~g~e~~~~Vl~s   90 (125)
T COG5550          22 QGDFVYDE-LIDTGFTGYLVLPPQVAEKLGLPLF--STIRIVLA--------DGGVVKTSVALATIKIDGVEKVAFVLAS   90 (125)
T ss_pred             CCcEEeee-EEecCCceeEEeCHHHHHhcCCCcc--CChhhhhh--------cCCEEEEEEEEEEEEECCEEEEEEEEcc
Confidence            34554444 9999998 78899999999998752  22222222        22333344443332    4566777777


Q ss_pred             eCCceeeEEcchhhhhccccccC
Q 045020          149 ATSPYNVILGRQWIHKMRAVPST  171 (221)
Q Consensus       149 ~~~~yn~ILGr~wL~~~~~i~st  171 (221)
                      +..+-+ ++|+.||+........
T Consensus        91 ~~~~~~-liG~~~lk~l~~~vn~  112 (125)
T COG5550          91 DNLPEP-LIGVNLLKLLGLVVNP  112 (125)
T ss_pred             CCCccc-chhhhhhhhccEEEcC
Confidence            777877 9999999988876543

>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes

Probab=95.50  E-value=0.018  Score=40.85  Aligned_cols=37  Identities=27%  Similarity=0.526  Sum_probs=34.1

Q ss_pred             CCcchHHHHHHHHHHhcccccc-ccHHHHHHHHhcCCC
Q 045020            2 GRVETLKYYIRRFRLASAKVEN-CDDQLAIVTFKRGLP   38 (221)
Q Consensus         2 ~~~eslr~~~k~f~~~~l~ve~-~~~~~~~~~fk~~~~   38 (221)
                      |.+||+++|+.||+..+.+++. .+++..+..|.+|+.
T Consensus        58 Q~~esv~~y~~rf~~l~~~~~~~~~e~~~v~~f~~GL~   95 (96)
T PF03732_consen   58 QGNESVREYVNRFRELARRAPPPMDEEMLVERFIRGLR   95 (96)
T ss_pred             ccCCcHHHHHHHHHHHHHHCCCCcCHHHHHHHHHHCCC
Confidence            4699999999999999999996 999999999999975

Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.

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

Probab=90.85  E-value=0.48  Score=37.15  Aligned_cols=47  Identities=17%  Similarity=0.282  Sum_probs=32.4

Q ss_pred             eeeEEEEEcCeeEEEEEEEEeeCC-ceeeEEc-chhhhhcccc-ccCccc
Q 045020          128 VITLLVIAKSYSLLTDFLVVKATS-PYNVILG-RQWIHKMRAV-PSTCHQ  174 (221)
Q Consensus       128 ~i~L~v~~g~~t~~~~F~Vvd~~~-~yn~ILG-r~wL~~~~~i-~st~~q  174 (221)
                      -|.+.+++|+.+..+.|.+.|-.. .|.++|| |.||...-+| |+-.|.
T Consensus        85 VV~~~~~lg~~~~~~e~tL~dR~~m~yp~LlGrR~~l~~~~lVD~s~~~~  134 (138)
T PF05618_consen   85 VVETTLCLGGKTWKIEFTLTDRSNMKYPMLLGRRNFLRGRFLVDVSRSFL  134 (138)
T ss_dssp             EEEEEEEETTEEEEEEEEEE-S--SS-SEEE-HHHHHHTTEEEETT---T
T ss_pred             EEEEEEEECCEEEEEEEEEcCCCcCcCCEEEEehHHhcCCEEECCChhhc
Confidence            357999999999999999998655 7999999 9999876555 554443

; PDB: 2PMA_B.

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

Probab=90.54  E-value=1.8  Score=32.10  Aligned_cols=84  Identities=27%  Similarity=0.290  Sum_probs=55.7

Q ss_pred             CceEEEEEEcCeeee-EEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEE
Q 045020           66 DALVISIKIGNCLVK-RILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDF  144 (221)
Q Consensus        66 ~~L~i~~~I~~~~v~-riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F  144 (221)
                      .-+++...+-+|+.+ -.|+|+|+.+|++-..+.+.-.++......+ ++..|.-.. ..-.-.+.|.+...++...+.|
T Consensus        33 yemvlqa~lp~fkcsipclidtgaq~niiteetvrahklptrpw~~s-viyggvyp~-kinrkt~kl~i~lngisiktef  110 (137)
T PF12382_consen   33 YEMVLQAKLPDFKCSIPCLIDTGAQVNIITEETVRAHKLPTRPWSQS-VIYGGVYPN-KINRKTIKLNINLNGISIKTEF  110 (137)
T ss_pred             hHhhhhhhCCCccccceeEEccCceeeeeehhhhhhccCCCCcchhh-eEecccccc-ccccceEEEEEEecceEEEEEE
Confidence            346667777666542 2799999999999999998876655433222 222221111 1123356788999999999999


Q ss_pred             EEEeeCC
Q 045020          145 LVVKATS  151 (221)
Q Consensus       145 ~Vvd~~~  151 (221)
                      .||..-+
T Consensus       111 lvvkkfs  117 (137)
T PF12382_consen  111 LVVKKFS  117 (137)
T ss_pred             EEEEecc
Confidence            9997533

Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. This entry represents a small family of fungal retroviral aspartyl peptidases.

>COG4067 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]

Probab=87.39  E-value=1  Score=35.91  Aligned_cols=42  Identities=26%  Similarity=0.414  Sum_probs=36.0

Q ss_pred             ceeeEEEEEcCeeEEEEEEEEeeCC-ceeeEEcchhhhhcccc
Q 045020          127 GVITLLVIAKSYSLLTDFLVVKATS-PYNVILGRQWIHKMRAV  168 (221)
Q Consensus       127 G~i~L~v~~g~~t~~~~F~Vvd~~~-~yn~ILGr~wL~~~~~i  168 (221)
                      =-|.+.+.+|+...++.|...|-.. .|.++|||..|+++.++
T Consensus       108 pVV~~~l~lG~~~~~~E~tLtDR~~m~Yp~LlGrk~l~~~~~~  150 (162)
T COG4067         108 PVVRLTLCLGGRILPIEFTLTDRSNMRYPVLLGRKALRHFGAV  150 (162)
T ss_pred             cEEEEEEeeCCeeeeEEEEeecccccccceEecHHHHhhCCeE
Confidence            3467899999999999999998655 79999999999996665

---

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	221
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	2e-07
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	3e-06

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

 Score = 47.8 bits (113), Expect = 2e-07
 Identities = 20/114 (17%), Positives = 44/114 (38%), Gaps = 5/114 (4%)

Query: 64  HDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVT 123
               L I+ K+    +K   +D+G+ + I+  A  E+  + +   + +     G+     
Sbjct: 21  QVTMLYINCKVNGHPLK-AFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVG--TQ 77

Query: 124 NSDGVITLLVIA-KSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVL 176
              G + L  I  +   L   F ++    P +++LG   + + +        VL
Sbjct: 78  RIIGRVHLAQIQIEGDFLQCSFSIL-EDQPMDMLLGLDMLRRHQCSIDLKKNVL 130

>2i1a_A DNA damage-inducible protein DDI1; acid protease fold, dimer, retroviral protease domain, protein turnover; HET: DNA; 2.30A {Saccharomyces cerevisiae} Length = 148

 Score = 44.7 bits (105), Expect = 3e-06
 Identities = 24/111 (21%), Positives = 43/111 (38%), Gaps = 6/111 (5%)

Query: 67  ALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSD 126
            L I+I+I N  VK   +D G+   I+     +K  L +   K F     G+        
Sbjct: 26  MLYINIEINNYPVK-AFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVG--TGKII 82

Query: 127 GVITLLVIA-KSYSLLTDFLVVKATSPYNVILGRQWIHKMRAVPSTCHQVL 176
           G I    +  ++  +   F V+   +  +V++G   + +  A       VL
Sbjct: 83  GRIHQAQVKIETQYIPCSFTVLD--TDIDVLIGLDMLKRHLACVDLKENVL 131

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	221
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	99.41
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	99.29
1fmb_A	104	EIAV protease; hydrolase (acid proteinase), RNA-di	98.13
3slz_A	132	GAG-Pro-POL polyprotein; beta sheet and dimer, pro	98.05
2hs1_A	99	HIV-1 protease; ultra-high resolution active site	97.61
3ec0_A	99	Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1	97.3
2hah_A	116	Protease, retropepsin; retroviral, aspartyl, hydro	97.29
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	96.0
2pma_A	146	Uncharacterized protein; APC86035.2, protein LPG00	93.92
3sqf_A	114	Protease; folded monomer, retropepsin, D-type retr	93.14
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	92.47
2rsp_A	124	RSV protease; hydrolase(aspartyl proteinase); 2.00	91.4

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

Probab=99.41  E-value=1.8e-12  Score=101.80  Aligned_cols=119  Identities=16%  Similarity=0.221  Sum_probs=92.9

Q ss_pred             CCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceee-EEEEEcCeeEEEE
Q 045020           65 DDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVIT-LLVIAKSYSLLTD  143 (221)
Q Consensus        65 ~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~-L~v~~g~~t~~~~  143 (221)
                      ...+++.+.|++.+++ +|||+||+.++|+.+..+++|+....-........|.+  .....|.+. +++++|+.++.+.
T Consensus        22 ~~~l~v~~~Ing~~v~-~LVDTGAs~s~Is~~~A~rlGL~~~~~~~~~~~a~g~G--~~~~~g~v~~~~I~Ig~~~~~~~   98 (148)
T 3s8i_A           22 VTMLYINCKVNGHPLK-AFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVG--TQRIIGRVHLAQIQIEGDFLQCS   98 (148)
T ss_dssp             CCCCEEEEEETTEEEE-EEECTTCSSCEEEHHHHHHTTCGGGEEGGGCEECCC-----CEEEEEEEEEEEEETTEEEEEE
T ss_pred             cCEEEEEEEECCEEEE-EEEeCCCCcEeeCHHHHHHcCCccccCcceeEEEEcCC--ccEEEEEEEEEEEEECCEEEEEE
Confidence            4568999999999986 99999999999999999999986531111222334432  345678775 8999999999999


Q ss_pred             EEEEeeCCceeeEEcchhhhhccccccCccceeeeecCCcEEEE
Q 045020          144 FLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGIEEI  187 (221)
Q Consensus       144 F~Vvd~~~~yn~ILGr~wL~~~~~i~st~~q~vk~~~~~g~i~l  187 (221)
                      |.|++ ...++.|||.+||.+++++......+|.+...+..+.-
T Consensus        99 ~~Vle-~~~~d~LLGmD~L~~~~~~ID~~~~~L~l~~~~~~~pf  141 (148)
T 3s8i_A           99 FSILE-DQPMDMLLGLDMLRRHQCSIDLKKNVLVIGTTGTQTYF  141 (148)
T ss_dssp             EEEET-TCSSSEEECHHHHHHTTCEEETTTTEEECTTTCCEEEC
T ss_pred             EEEeC-CCCcCeeccHHHHHhCCEEEEcCCCEEEEccCCeEEee
Confidence            99998 44579999999999999998888888877665555553

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

Probab=99.29  E-value=3.5e-11  Score=93.76  Aligned_cols=110  Identities=23%  Similarity=0.244  Sum_probs=80.4

Q ss_pred             CCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceee-EEEEEcCeeEEEE
Q 045020           65 DDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVIT-LLVIAKSYSLLTD  143 (221)
Q Consensus        65 ~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~-L~v~~g~~t~~~~  143 (221)
                      ...+++.+.|+|..+. +|||+||+.++++.+..+++|+....-........|.++.  ...|.+. ..+++|+.+..+.
T Consensus        24 ~~~~~v~v~InG~~~~-~LvDTGAs~s~is~~~a~~lgl~~~~~~~~~~~a~g~g~~--~~~~~~~~~~i~ig~~~~~~~  100 (148)
T 2i1a_A           24 VPMLYINIEINNYPVK-AFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTG--KIIGRIHQAQVKIETQYIPCS  100 (148)
T ss_dssp             CCCCEEEEEETTEEEE-EEECTTCSSCEEEHHHHHHHTGGGGCBCCCC-------------CEEEEEEEEEETTEEEEEE
T ss_pred             cceEEEEEEECCEEEE-EEEECCCCccccCHHHHHHcCCCccCCcceEEEEecCCCc--ccccEEEEEEEEECCEEecee
Confidence            3457999999999776 9999999999999999999998653211111123455443  2356665 5889999999999


Q ss_pred             EEEEeeCCceeeEEcchhhhhccccccCccceeeee
Q 045020          144 FLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQ  179 (221)
Q Consensus       144 F~Vvd~~~~yn~ILGr~wL~~~~~i~st~~q~vk~~  179 (221)
                      |.|++  .+++.|||.+||.++++.......+|.+.
T Consensus       101 ~~vl~--~~~d~iLG~d~L~~~~~~ID~~~~~l~l~  134 (148)
T 2i1a_A          101 FTVLD--TDIDVLIGLDMLKRHLACVDLKENVLRIA  134 (148)
T ss_dssp             EEEEC--SSCSEEECHHHHHHTTCEEETTTTEEEET
T ss_pred             EEEec--CCCCeEecHHHHhhCCEEEECCCCEEEEc
Confidence            99998  46899999999999999877777777664

>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=98.13  E-value=2.4e-05  Score=57.49  Aligned_cols=92  Identities=21%  Similarity=0.350  Sum_probs=71.0

Q ss_pred             EEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEe
Q 045020           69 VISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVK  148 (221)
Q Consensus        69 ~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd  148 (221)
                      ++++.|++..+. .|+|+||-..++.......|+.+..+.++  ..+.|.+|. ..+. .-.+++.+++......++|- 
T Consensus        10 ~v~v~I~Gq~~e-~LLDTGAD~TVl~~~~w~~i~lp~~~w~p--~~i~GiGG~-i~v~-~~~i~i~i~g~~~~gtvlv~-   83 (104)
T 1fmb_A           10 TTIVLINDTPLN-VLLDTGADTSVLTTAHYNRLKYRGRKYQG--TGIGGVGGN-VETF-STPVTIKKKGRHIKTRMLVA-   83 (104)
T ss_dssp             EEEEEETTEEEE-EEECTTCSSCEEEHHHHHHCSSCCCCEEC--CCEEETTEE-ECCE-EEEEEEEETTEEEEEEEEEE-
T ss_pred             EEEEEECCEEEE-EEeccCCCcEEEccccCcccCCCCccCCc--cEEEeCCCe-EEee-EeeeEEEECCeEEEEEEEEC-
Confidence            578999999765 99999999999999999888876532333  567776554 3455 77799999887777776664 


Q ss_pred             eCCceeeEEcchhhhhcccc
Q 045020          149 ATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       149 ~~~~yn~ILGr~wL~~~~~i  168 (221)
                       +.|.| |+||.||.++++.
T Consensus        84 -~tp~n-iiGRd~L~qlg~t  101 (104)
T 1fmb_A           84 -DIPVT-ILGRDILQDLGAK  101 (104)
T ss_dssp             -SCSSC-EECHHHHHHTTCC
T ss_pred             -CCCCC-EecHhHHhhcCcE
Confidence             45655 8999999999875

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

Probab=98.05  E-value=7e-06  Score=62.84  Aligned_cols=101  Identities=21%  Similarity=0.282  Sum_probs=70.4

Q ss_pred             CCCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEE
Q 045020           64 HDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTD  143 (221)
Q Consensus        64 h~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~  143 (221)
                      ..+| ++++.|++..+. +|+|+||+.-++...-+.        +......+.|.+|... ..-.-.+++++++......
T Consensus        20 ~~RP-~v~i~I~G~~~~-~LlDTGAd~tVl~~~~~p--------~~~~p~~I~GiGG~i~-vr~~~~i~IeI~g~~~~~~   88 (132)
T 3slz_A           20 PPEP-RITLKVGGQPVT-FLVDTGAQHSVLTQNPGP--------LSDKSAWVQGATGGKR-YRWTTDRKVHLATGKVTHS   88 (132)
T ss_dssp             CCSS-EEEEEETTEEEE-EEECTTCSSCEECSCCCS--------EEEEEEEEECSSCEEE-EEEECCEEEEETTEEEEEC
T ss_pred             cCCC-EEEEEECCEEEE-EEEeCCCCeEEEccccCC--------CCCCceEEEccCCEEE-EEEEeeeEEEECCeeecce
Confidence            3344 678999999877 999999999888754221        2333467788888754 2222237899998887777


Q ss_pred             EEEEeeCCceeeEEcchhhhhccccccCccceeeeecCCcE
Q 045020          144 FLVVKATSPYNVILGRQWIHKMRAVPSTCHQVLCYQTIYGI  184 (221)
Q Consensus       144 F~Vvd~~~~yn~ILGr~wL~~~~~i~st~~q~vk~~~~~g~  184 (221)
                      |.|. ...|. .||||.||.++++.       +.|+.+++.
T Consensus        89 ~lV~-~~tPv-nLLGrd~Ltqlg~t-------L~fp~~g~~  120 (132)
T 3slz_A           89 FLHV-PDCPY-PLLGRDLLTKLKAQ-------IHFEGSGAQ  120 (132)
T ss_dssp             CEEC-TTSSS-CEECHHHHHHHTCE-------EEEETTEEE
T ss_pred             EEEE-CCCCc-cEECHhhHhhCCcE-------EECCCCCce
Confidence            7553 45665 46999999999987       446554444

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

Probab=97.61  E-value=0.00011  Score=53.38  Aligned_cols=87  Identities=25%  Similarity=0.460  Sum_probs=62.7

Q ss_pred             EEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEe
Q 045020           69 VISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVK  148 (221)
Q Consensus        69 ~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd  148 (221)
                      ++++.|++..+. .|+|+||-..++..     +..+. ..+|  ..+.|.+| ...+...-.+++.+.+....-.++|  
T Consensus        10 ~vtvkI~Gq~~e-aLLDTGAD~TVl~~-----~~~p~-~wkp--k~igGiGG-~i~v~qy~qi~iei~g~~~~gtvlV--   77 (99)
T 2hs1_A           10 LVTIKIGGQLKE-ALLDTGADDTIIEE-----MSLPG-RWKP--KMIGGIGG-FIKVRQYDQIIIEIAGHKAIGTVLV--   77 (99)
T ss_dssp             EEEEEETTEEEE-EEECTTCSSEEESC-----CSSCC-CCEE--EEEEETTE-EEEEEEEEEEEEEETTEEEEEEEEE--
T ss_pred             EEEEEECCEEEE-EEeccCCCcEEEec-----ccCCC-CCCC--cEEEeCCC-cEeeeEeccEEEEEeCCEEEEEEEe--
Confidence            578999998876 99999999888863     22221 1222  35666544 3566677788999988777777777  


Q ss_pred             eCCceeeEEcchhhhhcccc
Q 045020          149 ATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       149 ~~~~yn~ILGr~wL~~~~~i  168 (221)
                      .+.|.| |+||.||.++++-
T Consensus        78 ~~tPvn-iiGRd~Ltqlg~t   96 (99)
T 2hs1_A           78 GPTPVN-IIGRNLLTQIGAT   96 (99)
T ss_dssp             SCCSSC-EECHHHHTTTTCE
T ss_pred             CCCccC-chhHhHHHHcCCE
Confidence            456665 8999999998874

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

Probab=97.30  E-value=0.00078  Score=48.83  Aligned_cols=87  Identities=18%  Similarity=0.299  Sum_probs=61.3

Q ss_pred             EEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEe
Q 045020           69 VISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVK  148 (221)
Q Consensus        69 ~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd  148 (221)
                      ++++.|+|..+. .|+|+||-..++.     .+..+ ...+|.  .+.|.+| ...+...-.+++.+.+....-.++|- 
T Consensus        10 ~vti~I~Gq~~e-~LLDTGAD~TVl~-----~~~~P-g~w~pk--~igGiGG-~i~v~qy~~i~iei~g~~~~gtvlV~-   78 (99)
T 3ec0_A           10 VVTAYIEGQPVE-VLLDTGADDSIVA-----GIELG-NNYSPK--IVGGIGG-FINTKEYKNVEIEVLNKKVRATIMTG-   78 (99)
T ss_dssp             EEEEEETTEEEE-EEECTTCSSCEES-----SCCCC-SCCEEE--EEEETTE-EEEEEEEEEEEEEETTEEEEEEEEEE-
T ss_pred             eEEEEECCEEEE-EEEecCCCceEEc-----CcccC-CCCCce--EEEecCC-cEeeeEEeeEEEEECCeEEEEEEEeC-
Confidence            678999998877 9999999888883     22222 222222  4666544 44555666788999888877777774 


Q ss_pred             eCCceeeEEcchhhhhcccc
Q 045020          149 ATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       149 ~~~~yn~ILGr~wL~~~~~i  168 (221)
                       +.|.| |+||.+|.++++-
T Consensus        79 -~tPvn-iiGRnlLtqlG~t   96 (99)
T 3ec0_A           79 -DTPIN-IFGRNILTALGMS   96 (99)
T ss_dssp             -CCSSC-EECHHHHHHHTCE
T ss_pred             -CCCcC-eeehhhHhhcCcE
Confidence             56664 6999999998874

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

Probab=97.29  E-value=0.0014  Score=48.94  Aligned_cols=96  Identities=19%  Similarity=0.358  Sum_probs=61.2

Q ss_pred             CCCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCee----
Q 045020           64 HDDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYS----  139 (221)
Q Consensus        64 h~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t----  139 (221)
                      ..+|++  +.|++..+. .|+|+||-..++...-+..   .+...++ ...+.|.+|. ..+.....+++++.+..    
T Consensus        12 ~~rP~v--ikI~Gq~~e-aLLDTGAD~TVi~~~~~~~---~p~~wkp-k~~igGiGG~-i~v~qy~qv~iei~g~~~~~~   83 (116)
T 2hah_A           12 KRPEIL--IFVNGYPIK-FLLDTGADITVLNRRDFQV---KNSIENG-RQMIGGIGGF-IRGTNYINVHLEIRDENYKTQ   83 (116)
T ss_dssp             SCCEEE--EEETTEEEE-EEECTTCSSCEEEGGGCCC---TTCEEEE-EEEEEETTEE-EEEEEEEEEEEEECCTTSCCE
T ss_pred             cCCCEE--EEECCEEEE-EEecCCCCcEEEccccccc---CCCCCCC-ceEEecCCCc-eeeeEEccEEEEEeCCCCCcc
Confidence            346666  999998876 9999999998887532200   1122222 1226665553 34445556788776544    


Q ss_pred             -EEEEEEEEe-eCCceeeEEcchhhhhcccc
Q 045020          140 -LLTDFLVVK-ATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       140 -~~~~F~Vvd-~~~~yn~ILGr~wL~~~~~i  168 (221)
                       ..-.+.|.+ .+.+.| |+||.+|.++++.
T Consensus        84 ~~~gtvlV~p~tP~~vn-iiGRd~Ltqlg~t  113 (116)
T 2hah_A           84 CIFGNVCVLEDNSTPVN-ILGRDNMIKFNIR  113 (116)
T ss_dssp             EEEEEEEEETTCCCSSE-EECHHHHTTTTCC
T ss_pred             eeEEEEEECCCCCcccc-EecHHHHhHcCCE
Confidence             566666765 443365 8999999998874

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

Probab=96.00  E-value=0.031  Score=45.48  Aligned_cols=89  Identities=21%  Similarity=0.393  Sum_probs=60.7

Q ss_pred             EEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEe
Q 045020           69 VISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVK  148 (221)
Q Consensus        69 ~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd  148 (221)
                      .+++.|++..+. .|+|+||...++.     .+.++. ..+|  ..+.|.+|. ..+.=.-.+++.+.+......+.|  
T Consensus        10 ~vtv~I~Gq~~e-~LLDTGAD~TVl~-----~~~lpg-~w~p--k~igGIGG~-i~vrqy~~i~iei~g~~~~gtvlV--   77 (203)
T 3ka2_A           10 LVTIRIGGQLKE-ALLDTGADDTVIE-----ELNLPG-XWKP--KLIGGIAGF-IKVRQYDQIPVEIXGHKAIGTVLV--   77 (203)
T ss_dssp             EEEEEETTEEEE-EEECTTCSSCEEC-----SCCCSS-CEEE--EEEEETTEE-EEEEEEEEEEEEETTEEEEEEEEE--
T ss_pred             eEEEEECCEEEE-EEEecCCCceEEe-----cccCCC-CCCc--eEEEEccCc-EEEEEEcceeEEEcCeEEEEEEee--
Confidence            578999999766 9999999988875     233332 2222  246666543 222222357788888877777766  


Q ss_pred             eCCceeeEEcchhhhhcccccc
Q 045020          149 ATSPYNVILGRQWIHKMRAVPS  170 (221)
Q Consensus       149 ~~~~yn~ILGr~wL~~~~~i~s  170 (221)
                      .+.|.| |+||+.|.++++.-+
T Consensus        78 g~tPvn-IiGRd~LtqlG~tLn   98 (203)
T 3ka2_A           78 GPTPVN-IIGRNLLTQIGXTLN   98 (203)
T ss_dssp             SCCSSC-EECHHHHTTTTCEEE
T ss_pred             CCCCcC-ccchhhhhhcCceEE
Confidence            356877 799999999988643

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

Probab=93.92  E-value=0.098  Score=40.32  Aligned_cols=47  Identities=17%  Similarity=0.156  Sum_probs=37.3

Q ss_pred             eeeEEEEEcCeeEEEEEEEEeeCC-ceeeEEcchhhhh--ccccccCccc
Q 045020          128 VITLLVIAKSYSLLTDFLVVKATS-PYNVILGRQWIHK--MRAVPSTCHQ  174 (221)
Q Consensus       128 ~i~L~v~~g~~t~~~~F~Vvd~~~-~yn~ILGr~wL~~--~~~i~st~~q  174 (221)
                      .|.+.+++|+.+..+.|...|-.. .|.++|||.||..  +-+-|+.-|+
T Consensus        93 VV~~~i~lG~~~~~ie~tLtdRs~m~ypmLLGR~~L~~~~~lVD~s~~~l  142 (146)
T 2pma_A           93 VVLLNIKLGDKVRTIKVNLTNRKRFLYPLLLGRDAIIDFNGAVDPALTFT  142 (146)
T ss_dssp             EEEEEEEETTEEEEEEEEEECCCCCSCSEEECHHHHHHTTEEEETTCCCT
T ss_pred             EEEEEEEECCEEEEEEEEEcCCCcCCCCEEechhHHhhCCEEECCchhcc
Confidence            367999999999999999998555 7999999999954  4444655443

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

Probab=93.14  E-value=0.29  Score=36.08  Aligned_cols=91  Identities=18%  Similarity=0.229  Sum_probs=53.3

Q ss_pred             EEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccc--cccceecccCCcccccceeeEEEE-EcCeeEEEEEE
Q 045020           69 VISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKL--FEQPLIGLSGIVTNSDGVITLLVI-AKSYSLLTDFL  145 (221)
Q Consensus        69 ~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~--~~~~l~gf~g~~~~~lG~i~L~v~-~g~~t~~~~F~  145 (221)
                      .+++.|++..+. .|+|+||-..++..     +.++ ...++  +...+.|.+|....-.-...+..+ +.+......-+
T Consensus        11 ~vti~I~Gq~~e-aLLDTGADdTVi~~-----~~lp-g~W~p~~~~k~igGIGG~i~v~qy~~~~~~~~i~g~k~i~tvl   83 (114)
T 3sqf_A           11 SLTLWLDDKMFT-GLINTGADVTIIKL-----EDWP-PNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPF   83 (114)
T ss_dssp             EEEEEETTEEEE-EEECTTCSSCEEEG-----GGSC-TTSCEEECCCCCTTCCGGGCCEEESSCEEEECTTCCEEEECCE
T ss_pred             eEEEEECCEEEE-EEEccCCCceEEec-----ccCC-CCcccCcCceEEEeccceEEEEEeccceEEEecCCCEEEEEEE
Confidence            577999998877 99999998887753     3333 23444  446677777653211111122232 32332222224


Q ss_pred             EEeeCCceeeEEcchhhhhcccc
Q 045020          146 VVKATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       146 Vvd~~~~yn~ILGr~wL~~~~~i  168 (221)
                      |. .+.|.| |+||.-|.++++-
T Consensus        84 V~-~ptPvN-IiGRn~LtqlG~t  104 (114)
T 3sqf_A           84 VI-PNLPVN-LWGRDLLSQMKIM  104 (114)
T ss_dssp             EE-TTCSSC-EECHHHHTTSCC-
T ss_pred             EC-CCCccc-EEchhhHhhcCcE
Confidence            43 245655 5899999998874

>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=92.47  E-value=0.88  Score=36.83  Aligned_cols=90  Identities=21%  Similarity=0.397  Sum_probs=57.8

Q ss_pred             CCceEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEE
Q 045020           65 DDALVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDF  144 (221)
Q Consensus        65 ~~~L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F  144 (221)
                      .+| .+++.|++..+. .|+|+||-..++.     .+..+ .+.+|  ..+.|.+|.. .+.=.-.+++.+.+....-.|
T Consensus       111 ~rP-~~~iki~Gq~~e-~LlDTGAD~TVl~-----~~~lp-g~w~p--k~igGiGg~i-~v~qy~~i~iei~g~~~~~tv  179 (203)
T 3ka2_A          111 KRP-LVTIRIGGQLKE-ALLDTGADDTVIE-----ELNLP-GXWKP--KLIGGIGGFI-KVRQYDQIPVEIXGHKAIGTV  179 (203)
T ss_dssp             SCC-EEEEEETTEEEE-EEECTTCSSCEEC-----SCCCC-SCCEE--EEEEETTEEE-EEEEEEEEEEEETTEEEEEEE
T ss_pred             CCC-cEEEEECCEEEe-eeecccCCceeee-----cccCC-CCCCc--eEEeeccceE-EEEEeccEEEEECCeEEEEEE
Confidence            344 477999998766 9999999888873     22222 12222  2566665532 222223477777777766677


Q ss_pred             EEEeeCCceeeEEcchhhhhcccc
Q 045020          145 LVVKATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       145 ~Vvd~~~~yn~ILGr~wL~~~~~i  168 (221)
                      .|-  +.|.| |+||..|.++++-
T Consensus       180 lVg--ptPvn-iiGRn~LtqlG~t  200 (203)
T 3ka2_A          180 LVG--PTPVN-IIGRNLLTQIGXT  200 (203)
T ss_dssp             EES--CCSSC-EECHHHHGGGTCE
T ss_pred             EEC--CCCcC-eechhhHHHhCCe
Confidence            774  45655 7899999998874

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

Probab=91.40  E-value=0.22  Score=37.34  Aligned_cols=89  Identities=17%  Similarity=0.234  Sum_probs=42.9

Q ss_pred             EcCeeeeEEEecCCCccccccHHHHHhhccccc--cccccccceecccCCcccccceeeEEEEEcCe--eEEEEEEEEee
Q 045020           74 IGNCLVKRILIDNGSSVNILDDATVEKMRLEQD--KIKLFEQPLIGLSGIVTNSDGVITLLVIAKSY--SLLTDFLVVKA  149 (221)
Q Consensus        74 I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~--~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~--t~~~~F~Vvd~  149 (221)
                      |++..+. .|+|+||-..++..     +..+..  .+......+.|.+|....-.-...+++.+-+.  ...-.+.|...
T Consensus        27 i~gq~~e-aLLDTGAD~TVl~~-----~~lP~~W~k~~~~~~~igGIGG~i~v~qy~~~i~iei~g~~g~~~~tvlV~P~  100 (124)
T 2rsp_A           27 QRSVYIT-ALLDSGADITIISE-----EDWPTDWPVMEAANPQIHGIGGGIPMRKSRDMIELGVINRDGSLERPLLLFPA  100 (124)
T ss_dssp             CSEEEEE-EEECTTCSSCEEET-----TTSCTTSCEEECC---------CCCEEEESSCEEEEEECTTSCBCCCEEECCE
T ss_pred             CCCEEEE-EEecCCCCcEEEec-----ccCCCcceeeccccceeeecCceEeeEEeCCceEEEEeCCCCcEEEEEEECcC
Confidence            7777666 99999999888863     222211  11111113777766432222222455555322  22222334321


Q ss_pred             --CCceeeEEcchhhhhccccc
Q 045020          150 --TSPYNVILGRQWIHKMRAVP  169 (221)
Q Consensus       150 --~~~yn~ILGr~wL~~~~~i~  169 (221)
                        ..|.| |+||..|.++++.-
T Consensus       101 ~~~tPvn-IiGRdlLtqlG~tL  121 (124)
T 2rsp_A          101 VAMVRGS-ILGRDCLQGLGLRL  121 (124)
T ss_dssp             EESCSSE-EECHHHHHHTTCEE
T ss_pred             CCCCcee-EECHhHHhhCCcEE
Confidence              14555 89999999998754

---

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	221
d2fmba_	104	EIAV protease {Equine infectious anemia virus [Tax	98.17
d1nsoa_	107	Mason-Pfizer monkey virus protease {Simian retrovi	96.92
d4fiva_	113	Feline immunodeficiency virus (FIV) protease {Feli	96.45
d2pmaa1	141	Uncharacterized protein LPG0085 {Legionella pneumo	94.16
d2nmza1	99	Human immunodeficiency virus type 1 protease {Huma	93.7
d1hvca_	203	Human immunodeficiency virus type 1 protease {Huma	92.78
d3ecga1	99	Human immunodeficiency virus type 2 (HIV-2) protea	92.5
d2rspa_	124	Rous sarcoma virus protease {Rous sarcoma virus, s	84.38

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

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

Probab=98.17  E-value=6.7e-06  Score=58.67  Aligned_cols=92  Identities=22%  Similarity=0.363  Sum_probs=63.4

Q ss_pred             EEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEe
Q 045020           69 VISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVK  148 (221)
Q Consensus        69 ~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd  148 (221)
                      .+++.|+|..+. .|+|+||-..++...-+........  ........|..+.....  ...+.+.+.+.+....++|.+
T Consensus        10 ~~~i~I~Gq~v~-~LLDTGAD~TVI~~~~~p~~~~~~~--~~~~~~igg~g~~~~~~--~~~v~i~~~g~~~~~~~lV~p   84 (104)
T d2fmba_          10 TTIVLINDTPLN-VLLDTGADTSVLTTAHYNRLKYRGR--KYQGTGIGGVGGNVETF--STPVTIKKKGRHIKTRMLVAD   84 (104)
T ss_dssp             EEEEEETTEEEE-EEECTTCSSCEEEHHHHHHCSSCCC--CEECCCEEETTEEECCE--EEEEEEEETTEEEEEEEEEES
T ss_pred             EEEEEECCEEEE-EEEeCCCCeEEEcccccCccCCCCC--CcceeEEEEecceEEEE--EEEEEEEECCeEEEEEEEECC
Confidence            679999999998 9999999999998887765432211  11223344444433222  334677777777777777765


Q ss_pred             eCCceeeEEcchhhhhcccc
Q 045020          149 ATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       149 ~~~~yn~ILGr~wL~~~~~i  168 (221)
                        .|.| |+||+.|.++++-
T Consensus        85 --~Pvn-LlGRdlL~qlG~~  101 (104)
T d2fmba_          85 --IPVT-ILGRDILQDLGAK  101 (104)
T ss_dssp             --CSSC-EECHHHHHHHTCC
T ss_pred             --CCcc-eecHHHHHHhCCE
Confidence              6666 9999999998873

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

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

Probab=96.92  E-value=0.00038  Score=49.48  Aligned_cols=92  Identities=18%  Similarity=0.228  Sum_probs=57.8

Q ss_pred             EEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccc-cccccccceecccCCcccccceeeEEEEEcCee-EEEEEEE
Q 045020           69 VISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQD-KIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYS-LLTDFLV  146 (221)
Q Consensus        69 ~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~-~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t-~~~~F~V  146 (221)
                      .+++.|+|..+. .|+|+||-..++...-+     +.. .+.++...+.|.+|....-.-.-.+....+... ..+..+|
T Consensus        11 ~~~v~I~G~~v~-~LLDTGAD~TVI~~~~~-----p~~wp~~~~~~~~~GiGg~~~~~~~~~~l~~~~~~~~~~~~~p~v   84 (107)
T d1nsoa_          11 SLTLWLDDKMFT-GLINTGADVTIIKLEDW-----PPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFV   84 (107)
T ss_dssp             CEEEEETTEEEE-ECCCSSCSSCBCCGGGS-----CTTSCCCCCEEEECSSSEEEECCCBCCCEEEEETTTEEEEECCBB
T ss_pred             EEEEEECCEEEE-eeecCCCCcEEEecccc-----CCCCCcCcCccEEEEecCeeeEEEeeeeEEEEeCCCceEEEcceE
Confidence            568899999987 99999999988866533     222 345556677777554322111112333334333 3333345


Q ss_pred             EeeCCceeeEEcchhhhhcccc
Q 045020          147 VKATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       147 vd~~~~yn~ILGr~wL~~~~~i  168 (221)
                      +. +.|.| |+||+-|.+|++.
T Consensus        85 v~-~~Pvn-llGRd~L~qlg~~  104 (107)
T d1nsoa_          85 IP-NLPVN-LWGRDLLSQMKIM  104 (107)
T ss_dssp             CT-TCCCC-BCCHHHHHHHHTS
T ss_pred             CC-CCCcC-cccHHHHHHhCCE
Confidence            43 56777 9999999999874

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

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

Probab=96.45  E-value=0.0014  Score=46.94  Aligned_cols=94  Identities=20%  Similarity=0.296  Sum_probs=56.7

Q ss_pred             eEEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCee-----EEE
Q 045020           68 LVISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYS-----LLT  142 (221)
Q Consensus        68 L~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t-----~~~  142 (221)
                      ..+++.|+|..+. .|+|+||-..++...-+..-    ..+......+.|.+|.. .+.-.-.+++++.+..     +.-
T Consensus        11 P~v~v~I~Gq~v~-~LLDTGAD~TVi~~~d~p~~----~~~~~~~~~~~GIGG~~-~v~~~~~v~i~~~~~~~~gtvl~g   84 (113)
T d4fiva_          11 PEILIFVNGYPIK-FLLDTGADITILNRRDFQVK----NSIENGRQNMIGVGGGK-RGTNYINVHLEIRDENYKTQCIFG   84 (113)
T ss_dssp             CEEEEEETTEEEE-EEECTTCSSCEEEGGGCCCT----TCEEEEEEEEECSSCEE-EEEEEEEEEEEECCTTSCCCEEEE
T ss_pred             CeEEEEECCEEEE-EEEcCCCCcEEEeccccCCC----CCCCCCCCeEEecCeEE-eeeEEceEEEEEcCCeEeEEEEEc
Confidence            3789999999888 99999999988865432211    12233344566765543 3444446677765432     222


Q ss_pred             EEEEEe-eCCceeeEEcchhhhhcccc
Q 045020          143 DFLVVK-ATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       143 ~F~Vvd-~~~~yn~ILGr~wL~~~~~i  168 (221)
                      .+-|+. .+-|+| |+||+.|.++++-
T Consensus        85 ~~pvlp~~~~p~n-llGRd~LtqlG~~  110 (113)
T d4fiva_          85 NVCVLEDNSLIQP-LLGRDNMIKFNIR  110 (113)
T ss_dssp             EEEEETTCCCSSC-EECHHHHHHTTCC
T ss_pred             cccccCCCCCcCC-EEChhhhHHhCCE
Confidence            233322 112233 8999999998863

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

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

Probab=94.16  E-value=0.032  Score=40.91  Aligned_cols=44  Identities=18%  Similarity=0.216  Sum_probs=36.7

Q ss_pred             eeeEEEEEcCeeEEEEEEEEeeCC-ceeeEEcchhhhhcc--ccccC
Q 045020          128 VITLLVIAKSYSLLTDFLVVKATS-PYNVILGRQWIHKMR--AVPST  171 (221)
Q Consensus       128 ~i~L~v~~g~~t~~~~F~Vvd~~~-~yn~ILGr~wL~~~~--~i~st  171 (221)
                      .|.+++++|+.+..+.|...|-.. .|.++|||.||.+++  +-|+-
T Consensus        90 vV~~~i~ig~~~~~ie~tL~dR~~m~yp~LiGR~~L~~~~~~VD~s~  136 (141)
T d2pmaa1          90 VVLLNIKLGDKVRTIKVNLTNRKRFLYPLLLGRDAIIDFNGAVDPAL  136 (141)
T ss_dssp             EEEEEEEETTEEEEEEEEEECCCCCSCSEEECHHHHHHTTEEEETTC
T ss_pred             EEEEEEEECCEEEEEEEEECCCCCCCCCEEECHHHHhcCCEEECCch
Confidence            456999999999999999999777 899999999998754  34554

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

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

Probab=93.70  E-value=0.39  Score=32.54  Aligned_cols=86  Identities=24%  Similarity=0.459  Sum_probs=57.6

Q ss_pred             EEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEe
Q 045020           69 VISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVK  148 (221)
Q Consensus        69 ~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd  148 (221)
                      ++++.|++..+. +|+|+|+--.++-     .|.++. ..+  ...+.|.+|-. .+.-.-.+++.+.+....-+..|..
T Consensus        10 ~vtvkIgGq~~e-aLLDTGADdTVle-----ei~lpg-~Wk--Pk~IgGIGGfi-kVrqYd~i~iei~g~k~~gtVLVgp   79 (99)
T d2nmza1          10 LVTIKIGGQLKE-ALLDTGADDTVIE-----EMSLPG-RWK--PKMIGGIGGFI-KVRQYDQIIIEIAGHKAIGTVLVGP   79 (99)
T ss_dssp             EEEEEETTEEEE-EEECTTCSSCEEE-----SCCCCS-CCE--EEEEEETTEEE-EEEEEEEEEEEETTEEEEEEEEEES
T ss_pred             eEEEEECCEEEE-EeeccCCCceEEe-----cccCCC-CCC--ceEEEeccceE-EEEEeCceEEEECCcEEEEEEEECC
Confidence            678999999887 9999999776652     233321 122  23456655432 3333346888888887777777765


Q ss_pred             eCCceeeEEcchhhhhccc
Q 045020          149 ATSPYNVILGRQWIHKMRA  167 (221)
Q Consensus       149 ~~~~yn~ILGr~wL~~~~~  167 (221)
                        +|.| |+||.-|.++++
T Consensus        80 --TPvN-IiGRN~Ltq~Gc   95 (99)
T d2nmza1          80 --TPAN-IIGRNLLTQIGA   95 (99)
T ss_dssp             --CSSC-EECHHHHTTTTC
T ss_pred             --CCcc-EEcccchhhcCc
Confidence              4544 789999998876

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

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

Probab=92.78  E-value=0.35  Score=36.84  Aligned_cols=87  Identities=24%  Similarity=0.404  Sum_probs=60.5

Q ss_pred             EEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEe
Q 045020           69 VISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVK  148 (221)
Q Consensus        69 ~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd  148 (221)
                      .+++.|++..+. +|+|+|+--.++-     .+.++   -+.....+.|.+|- ..+.-.-.+++++.+....-.+.|..
T Consensus        10 ~VtVkIgGQ~~e-aLLDTGADDTVLe-----~inLp---G~WkPkiIGGIGGf-IkVrqY~~V~IeI~gkk~~gTVLVgP   79 (203)
T d1hvca_          10 LVTIRIGGQLKE-ALLDTGADDTVLE-----EMNLP---GKWKPKMIGGIGGF-IKVRQYDQILIEICGHKAIGTVLVGP   79 (203)
T ss_dssp             EEEEESSSCEEE-EEECTTCSSEEEE-----CCCCS---SCEEEEEEEETTEE-EEEEEEEEEEEEETTEEEEEEEEEES
T ss_pred             eEEEEECCEEEE-EEecCCCCceEEe-----cccCC---CCCcccEEEecCce-EEEEEeCCEEEEECCcEEEEEEEECC
Confidence            578999999888 9999999776662     23332   12223445566553 22333346888998888888888875


Q ss_pred             eCCceeeEEcchhhhhcccc
Q 045020          149 ATSPYNVILGRQWIHKMRAV  168 (221)
Q Consensus       149 ~~~~yn~ILGr~wL~~~~~i  168 (221)
                        +|.| ||||..|.++++-
T Consensus        80 --TPvN-IIGRNlLtqlG~t   96 (203)
T d1hvca_          80 --TPVN-IIGRNLLTQIGCT   96 (203)
T ss_dssp             --CSSC-EECHHHHGGGTCE
T ss_pred             --CCcc-ccchhhhhhhhhe
Confidence              5554 7899999999984

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

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

Probab=92.50  E-value=0.82  Score=30.86  Aligned_cols=86  Identities=19%  Similarity=0.324  Sum_probs=56.6

Q ss_pred             EEEEEEcCeeeeEEEecCCCccccccHHHHHhhccccccccccccceecccCCcccccceeeEEEEEcCeeEEEEEEEEe
Q 045020           69 VISIKIGNCLVKRILIDNGSSVNILDDATVEKMRLEQDKIKLFEQPLIGLSGIVTNSDGVITLLVIAKSYSLLTDFLVVK  148 (221)
Q Consensus        69 ~i~~~I~~~~v~riLVD~GSsvnil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~L~v~~g~~t~~~~F~Vvd  148 (221)
                      ++++.|++..+. +|+|+|+--.++     +.|.++. ..+|  ..+.|.+|- ..+.-.-.+++.+.+....-+-.|- 
T Consensus        10 ~vtvkIgGq~~e-aLLDTGADdTVl-----e~i~lpg-~WkP--k~iGGIGGf-ikVrqYd~i~Ieicg~k~~gtVLvg-   78 (99)
T d3ecga1          10 VVTAYIEGQPVE-VLLDTGADDSIV-----AGIELGN-NYSP--KIVGGIGGF-INTKEYKNVEIEVLNKKVRATIMTG-   78 (99)
T ss_dssp             EEEEEETTEEEE-EEECTTCSSCEE-----CSCCCCS-CCEE--EEEEETTEE-EEEEEEEEEEEEETTEEEEEEEEEE-
T ss_pred             eEEEEECCEEee-eecccCCCceee-----eccCCCC-CCcc--eEEEEeeee-EEEEEeCcEEEEECCcEEEEEEEeC-
Confidence            678999999887 999999977666     2343332 2222  345555443 2333344588888777766666664 


Q ss_pred             eCCceeeEEcchhhhhccc
Q 045020          149 ATSPYNVILGRQWIHKMRA  167 (221)
Q Consensus       149 ~~~~yn~ILGr~wL~~~~~  167 (221)
                       ++|.| |+||..|..+++
T Consensus        79 -pTPvN-IiGRNlLtqlGc   95 (99)
T d3ecga1          79 -DTPIN-IFGRNILTALGM   95 (99)
T ss_dssp             -CCSSC-EECHHHHHHTTC
T ss_pred             -CCCce-EEccchhhhhCc
Confidence             45544 789999998876

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

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

Probab=84.38  E-value=0.81  Score=32.36  Aligned_cols=85  Identities=20%  Similarity=0.285  Sum_probs=40.4

Q ss_pred             eEEEecCCCccccccHHHHHhhccccc-ccccc-ccceecccCCc--ccccceeeEEEEEcC--eeEEEEEEEEeeCCce
Q 045020           80 KRILIDNGSSVNILDDATVEKMRLEQD-KIKLF-EQPLIGLSGIV--TNSDGVITLLVIAKS--YSLLTDFLVVKATSPY  153 (221)
Q Consensus        80 ~riLVD~GSsvnil~~~~~~~mg~~~~-~L~~~-~~~l~gf~g~~--~~~lG~i~L~v~~g~--~t~~~~F~Vvd~~~~y  153 (221)
                      ...|+|+||-..++...-     .+.+ .+.+. ...+.|.+|..  .......+.......  ....+.+.+.-...|.
T Consensus        32 i~~LLDTGAD~TVI~~~d-----wp~~Wp~~~~~~~~i~GIGg~~~v~~~~~~~~~~~~~~~~~~~~~~~~~p~V~~tPv  106 (124)
T d2rspa_          32 ITALLDSGADITIISEED-----WPTDWPVMEAANPQIHGIGGGIPMRKSRDMIELGVINRDGSLERPLLLFPAVAMVRG  106 (124)
T ss_dssp             EEEEECTTCSSCEEETTT-----SCTTSCEEECC---------CCCEEEESSCEEEEEECTTSCBCCCEEECCEEESCSS
T ss_pred             EEEEEcCCCCeEEEcCCc-----cCCCCccCCCCCCEEEEcCCceeeEEeeeeEEEeeEecCCceeeeEEEecCCCCCcc
Confidence            449999999998886542     2221 22222 23455666643  222223333333322  2222222112235566


Q ss_pred             eeEEcchhhhhcccccc
Q 045020          154 NVILGRQWIHKMRAVPS  170 (221)
Q Consensus       154 n~ILGr~wL~~~~~i~s  170 (221)
                      | |+||.-|.+|++--+
T Consensus       107 n-i~GRdiL~qlG~tLt  122 (124)
T d2rspa_         107 S-ILGRDCLQGLGLRLT  122 (124)
T ss_dssp             E-EECHHHHHHTTCEEE
T ss_pred             c-EECHhHHHHhCCEEe
Confidence            5 899999999998643