Citrus Sinensis ID: 041134

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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-------230-------240-------250-------260-------
Protein Sequence
CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKVEDKQPQNQNNFLKKDQIENSTSEPEQIVNTIMAPLPLEVHMTKERNVYCKKREIEAPEEFSKKCVKLDVQSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSLLTDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTIYGIEEIGGDQATTRTCASNGMGKQNRELGSTRNQPWKK
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHHHHHHHHcccccEEEEcccccccccccccccccccccccccEEEEEEcccccHHHHHHHHHHHcccccEEcccccccccccccccccEEEcccccccccccccccEEEEEEEEccEEEEEEEEccccccccccHHHHHHHcccccccccccccEEEEcccEEEEEcEEEEEEEEEcccccEEEEEcHHHHHHcEEccccccEEEEEEccccEEEEcccHHHHHHHHHcccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHccccccccccEEEEEcccccccccHHHHHHHHHHHHHHHHHccccccHcccHHHEEEEccccccccEEccccccEEEccEEEEEEEEEEEEcccHHHHHHcHHHHHHccccccEEccccccEccccccccccccEEEEEEEEEcccccHHHHHcHHHHHHHHHHHHHHHHHHcccccccEEEEEcccHHEEEccHccHHHccccccccccccccc
Coil and Loop (DISEMBL)
cafhndcrhytRDCRTLKKYIEELISKGqlkefvkvedkqpqnqnnflkkdqienstsepeQIVNTimaplplevhmtkernvyckkreieapeefsKKCVKLDvqsevsflpqdlkliqsphddALVISIKIGNCLVRRILidngssvnilddATVEKMRLEqdkikpfeqpligfsgivtysdgsllTDFLVVKatspynailgrqWIHKmrvvpstyhQVLCYQTIYGieeiggdqattrtcasngmgkqnrelgstrnqpwkk
Flexible Loop (DISEMBL)
cafhndcrhytrdcrTLKKYIEELISKGQLKEFVkvedkqpqnqnnflkkdqienstsepEQIVNTimaplplevhmTKERNVYCKKReieapeefskkcVKLDVQSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVRRilidngssvnilDDATVEKMRLEQDkikpfeqpliGFSGIVTYSDGSLLTDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTIYGIEEIGGDQATTRTCasngmgkqnrelgstrnqpwkk
Low Complexity Region (SEG)
CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKVEDKQPQNQNNFLKKDQIENSTSEPEQIVNTIMAPLPLEVHMTKERNVYCKKREIEAPEEFSKKCVKLDVQSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSLLTDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTIYGIEEIGGDQATTRTCASNGMGKQNRELGSTRNQPWKK
Disordered region (IsUnstruct)
****NDCRHYTRDCRTLKKYIEELISKGQLKEFV****************************IVNTIMAPLPLEVHMTKERNVYCKKREIEAPEEFSKKCVKLDVQSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSLLTDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTIYGIEEIGGD*****************************
Disordered Region (DISOPRED)
CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKV*********************SEPEQIVNTIMAPLPLEVHMTKERNVYCKKREIEAP*E*******LDVQSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSLLTDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTIYGIEEIGGDQATTRTCAS********************
Disordered Region (DISEMBL)
CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKVEDKQPQNQNNFLKKDQIENSTSEPEQIVNTIMAPLPLEVHMTKERNVYCKKREIEAPEEFSKKCVKLDVQSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSLLTDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTIYGIEEIGGDQATTRTCASNGMGKQ**************
Disordered Region (DISPRO)
C*F*NDCRHYTRDCRTLKKYIEELISKGQ***************************TSEPEQIVNTIMAPLPLEVHMTKERNVYCKKREIEAPEEFSKKCVKLDVQSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSLLTDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTIYGIEEIGGDQATTRTCASNGM*****************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKVEDKQPQNQNNFLKKDQIENSTSEPEQIVNTIMAPLPLEVHMTKERNVYCKKREIEAPEEFSKKCVKLDVQSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSLLTDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTIYGIEEIGGDQATTRTCASNGMGKQNRELGSTRNQPWKK
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	267
147815945	539	hypothetical protein VITISV_038340 [Viti	0.917	0.454	0.305	2e-29
158828139	672	gag-pol polymerase [Arabidopsis lyrata s	0.880	0.349	0.329	2e-28
147788587	534	hypothetical protein VITISV_042456 [Viti	0.872	0.436	0.316	8e-27
147780457	455	hypothetical protein VITISV_007594 [Viti	0.943	0.553	0.303	1e-26
147769210	512	hypothetical protein VITISV_008148 [Viti	0.891	0.464	0.308	2e-26
147854055	467	hypothetical protein VITISV_021698 [Viti	0.891	0.509	0.296	2e-26
147775423	500	hypothetical protein VITISV_005211 [Viti	0.891	0.476	0.300	3e-26
147785767	537	hypothetical protein VITISV_016419 [Viti	0.902	0.448	0.304	4e-26
147835120	549	hypothetical protein VITISV_035289 [Viti	0.902	0.438	0.307	4e-26
147781482	502	hypothetical protein VITISV_006740 [Viti	0.868	0.462	0.319	4e-26

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

 Score =  135 bits (340), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 88/288 (30%), Positives = 145/288 (50%), Gaps = 43/288 (14%)

Query: 1   CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKVEDK---QPQNQNNFLKKDQIENST 57
           CA+H +  H T  CR+L   +E +I  G LK++++ + +    P+N N+   K  I    
Sbjct: 256 CAYHKEHGHTTERCRSLHYLVERVIKVGHLKQYLRSKARVRDTPRNHNSGTSKTPIV--- 312

Query: 58  SEPEQIVNTIM-APLPLEVHMTKERNVYCKKREIEAPEEFSKKCVK-----------LDV 105
             P+ ++N I   PL  E +  +++    + + +       ++C+              +
Sbjct: 313 --PKAVINYIHRGPLDEEYNSKRKKQRLLRAKSV-------RECINSIWPGITGGSARPI 363

Query: 106 QSEVSFLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQD 165
              + F P D   I  PH DAL++ + IG+  VRRILID G+SV++L  + + +M LE  
Sbjct: 364 DGTIVFPPIDPTRILQPHRDALILFLGIGDFDVRRILIDPGNSVDLLQASVINQMGLELS 423

Query: 166 KIKPFEQPLIGFSGIVTYSDGSLL-----------TDFLVVKATSPYNAILGRQWIHKMR 214
            ++     L GF+G  T S G ++             FLVV   SP+NAILGR W+H M+
Sbjct: 424 DLENPGLILSGFNGAATTSLGDIMLSVQVGPVTLNVQFLVVGDLSPFNAILGRTWLHYMK 483

Query: 215 VVPSTYHQVLCYQTIYGIEEIGGDQATTRTCASNGMGKQNRELGSTRN 262
            +PSTYHQ++ + T  G  ++ G Q   R C      +  RE+GS+++
Sbjct: 484 TIPSTYHQMVSFLTEDGQIDLYGSQLAARQCY-----QIAREVGSSKD 526

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  132 bits (331), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 89/270 (32%), Positives = 137/270 (50%), Gaps = 35/270 (12%)

Query: 1   CAFHNDCRHYTRDCRTLKKYIEELISKGQL-----KEFVKVEDKQPQNQNNFLKKDQIEN 55
           C  H    H T+DC  LKK++ EL + G L     K+FVK   +  +N  +   K    +
Sbjct: 403 CDIHKVTGHLTKDCSILKKHLAELWASGDLSKFDIKDFVKEYHEAKENSKDQDSKRPRLS 462

Query: 56  STSEPEQI---VNTIMAPLPL---EVHMTKE--RNVYCKKREIEAPEEFSKKCVKLDVQ- 106
           +  EP      +N I+         +   K+  RNV  K    E          ++D Q 
Sbjct: 463 NEEEPRSSKGRINVILGGSRFCGDSISSIKKHRRNVLLKASLSE----------EIDFQG 512

Query: 107 SEVSFLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDK 166
           + +SF  ++ + ++ PHDDALVI++ + N  V RILID GSSV+++  +T+EKM + +  
Sbjct: 513 ASISFNEEETRHLERPHDDALVITLDVANFEVSRILIDTGSSVDLIFLSTLEKMGISRGD 572

Query: 167 IKPFEQPLIGFSGIVTYSDGSL-----------LTDFLVVKATSPYNAILGRQWIHKMRV 215
           I     PL+ F+     S G++           + DF+V    + YN ILG  WI++M+ 
Sbjct: 573 IVGPPSPLVAFTSESAMSLGTIKLPVLAKKVSKIVDFVVFDKPAAYNIILGTPWIYRMKA 632

Query: 216 VPSTYHQVLCYQTIYGIEEIGGDQATTRTC 245
           VPSTY+Q + + T  G+E I GDQ  +RTC
Sbjct: 633 VPSTYYQCIKFPTSNGVETIRGDQEASRTC 662

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147788587|emb|CAN63201.1| hypothetical protein VITISV_042456 [Vitis vinifera]

 Score =  126 bits (317), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 81/256 (31%), Positives = 129/256 (50%), Gaps = 23/256 (8%)

Query: 1   CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKVEDKQPQNQNNFLKKDQIENSTSEP 60
           C +H +  H T  CR+L  ++E+LI  G LK++++ + +      N         + + P
Sbjct: 266 CVYHKEHGHTTETCRSLHYFVEKLIKAGHLKQYLRSKARGRDASRN--HNSGTPRAPAAP 323

Query: 61  EQIVNTIMAPLPLEVHMTKERNVYCKKREIEAPEEFSKKCVKLDVQSEVSFLPQDLKLIQ 120
           + I+N I   L  E + +K      +KR+    +      V+  V S + F P D   I 
Sbjct: 324 KVIINYINGGLFDEEYDSK------RKRQ----KLLRVALVRERVNSTIIFPPVDPTRIL 373

Query: 121 SPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGI 180
            P+ DAL++S+KIG+  VRRIL+D  SS +++  + +  M      +K   Q L GF+G 
Sbjct: 374 RPYRDALILSLKIGDFDVRRILVDPDSSTDLVQASIISHMGRSLTGLKNPRQILPGFNGA 433

Query: 181 VTYSDGSLLTD-----------FLVVKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTI 229
            T S G ++             F VV+  SP+N ILGR W+H M+V+P TYHQ++ + T 
Sbjct: 434 STTSLGDIVLSVQADPVTLNIQFSVVQDLSPFNVILGRTWLHYMKVIPYTYHQMVSFLTK 493

Query: 230 YGIEEIGGDQATTRTC 245
            G  ++ G Q   R C
Sbjct: 494 DGQVDLYGSQLVARQC 509

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147780457|emb|CAN72634.1| hypothetical protein VITISV_007594 [Vitis vinifera]

 Score =  126 bits (316), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 85/280 (30%), Positives = 136/280 (48%), Gaps = 28/280 (10%)

Query: 1   CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKVEDK---QPQNQNNFLKKDQIENST 57
           C +HN   H T  CR+L   +E LI  G LK++++ + +     +N N+   K  +    
Sbjct: 169 CVYHNKHGHTTEMCRSLHYLVERLIKAGHLKQYLRFDARVRDTSRNHNSGTSKIPVA--- 225

Query: 58  SEPEQIVNTIM-APLPLEVHMTKERNVYCKKREIEAPEEFSKKCVK----LDVQSEVSFL 112
             P  ++N I   PL  E     +R    +   I       +  +       +   + F 
Sbjct: 226 --PRAVINYIHKGPLDEEYDSKGKRQRLLRAASIWERVNSIRPGIAGRGPRPIDGTIVFP 283

Query: 113 PQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQ 172
           P D   I  PH DAL++S+++ +  VRRILID GSS ++L  + +  M  +   ++   +
Sbjct: 284 PVDPTWILQPHHDALILSLEMRDFDVRRILIDLGSSADLLQTSVIGHMGRDLSGLENPGR 343

Query: 173 PLIGFSGIVTYSDGSLL-----------TDFLVVKATSPYNAILGRQWIHKMRVVPSTYH 221
            L GF+G  T S G ++             FLVV+  SP+NAILGR W+H M+V+PSTYH
Sbjct: 344 ILSGFNGATTTSLGDIVLPVQAGPVTLNVQFLVVQDLSPFNAILGRTWLHYMKVIPSTYH 403

Query: 222 QVLCYQTIYGIEEIGGDQATTRTCA----SNGMGKQNREL 257
           Q++ + T  G  ++  +Q  TR C       G  +++R L
Sbjct: 404 QMVSFLTEDGQIDLHDNQLATRQCYQIAREAGTNQEDRSL 443

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147769210|emb|CAN65075.1| hypothetical protein VITISV_008148 [Vitis vinifera]

 Score =  125 bits (314), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 82/266 (30%), Positives = 132/266 (49%), Gaps = 28/266 (10%)

Query: 1   CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKVEDKQ---PQNQNNFLKKDQIENST 57
           CAFH D  H T  CR+ +  +E LI  G LK++++ ++ +   PQ+ N    +     + 
Sbjct: 229 CAFHKDHGHTTETCRSFQYLVERLIKAGHLKQYLRSDNGRRDTPQHHNPGNLR-----AP 283

Query: 58  SEPEQIVNTIMA-PLPLEVHMTKERNVYCKKREIEA------PEEFSKKCVKLDVQSEVS 110
           + P+ ++N I+  P   E    ++R    +   I        P    +    +D    + 
Sbjct: 284 AAPKAVINYIIGGPSDEEYDSRRKRQKLLRAASIRERINSIRPGLTGEGPCPID--GTII 341

Query: 111 FLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPF 170
           F P D      PH DAL++S++IG+  VRRILID GSS +++  + +  M      ++  
Sbjct: 342 FPPVDPTRTLQPHRDALILSLEIGDFDVRRILIDPGSSADLVQASVMGHMGHTLTGLENP 401

Query: 171 EQPLIGFSGIVTYSDGSLL-----------TDFLVVKATSPYNAILGRQWIHKMRVVPST 219
           E+ L GF+G  T S G ++             F VV+  SP+N ILGR W+H M+ +PST
Sbjct: 402 ERILSGFNGSSTTSLGDIVLPVQAGPVTLNVQFSVVQELSPFNVILGRTWLHYMKAIPST 461

Query: 220 YHQVLCYQTIYGIEEIGGDQATTRTC 245
           YHQ++ + T  G  ++ G Q   R C
Sbjct: 462 YHQMVSFLTNDGQIDLYGSQLAARQC 487

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147854055|emb|CAN83396.1| hypothetical protein VITISV_021698 [Vitis vinifera]

 Score =  125 bits (314), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 79/266 (29%), Positives = 130/266 (48%), Gaps = 28/266 (10%)

Query: 1   CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKVED-----KQPQNQNNFLKKDQIEN 55
           CAFH D  H T  CR+ +  +E+LI  G LK++++ ++      Q  N  N         
Sbjct: 184 CAFHKDHGHTTETCRSFQFLVEKLIKAGHLKQYLRSDNGGRDASQRHNPGNL-------R 236

Query: 56  STSEPEQIVNTIMA-PLPLEVHMTKERNVYCKKREIEAPEEFSKKCVKLD----VQSEVS 110
           + + P+ ++N I   P   E    ++R    +   I       +  +  +    +   + 
Sbjct: 237 APAAPKAVINYITGGPSDEEYDSRRKRQKLLRAASIRERINSIRPGLTGEGPRPIDGTII 296

Query: 111 FLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPF 170
           F P D      PH DAL++S++IG+  VRRIL+D GSS +++  + V +M    + ++  
Sbjct: 297 FPPVDPTRTLQPHRDALILSLEIGDFDVRRILVDPGSSADLVQASVVGRMGRSLEGLENP 356

Query: 171 EQPLIGFSGIVTYSDGSLL-----------TDFLVVKATSPYNAILGRQWIHKMRVVPST 219
            + L GF+G  T S G ++             F VV+  SP+N ILGR W+H M+ +PST
Sbjct: 357 GRILSGFNGSSTTSLGDIILPVQAGPVTLNVQFSVVQELSPFNVILGRTWLHYMKAIPST 416

Query: 220 YHQVLCYQTIYGIEEIGGDQATTRTC 245
           YHQ++ + T  G  ++ G Q   R C
Sbjct: 417 YHQMVSFLTNDGQIDLYGSQLAARQC 442

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147775423|emb|CAN76097.1| hypothetical protein VITISV_005211 [Vitis vinifera]

 Score =  124 bits (312), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 77/256 (30%), Positives = 123/256 (48%), Gaps = 18/256 (7%)

Query: 1   CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKVEDKQPQNQNNFLKKDQIENSTSEP 60
           CAFH D  H T  CR L+  +E LI  G LK++++ +      ++ +   +         
Sbjct: 227 CAFHKDHDHTTETCRALQYLVERLIKAGHLKQYLRSDTG---GRDAYQHHNPGXPRAPAA 283

Query: 61  EQIVNTIMAPLPLEVHMTKERNVYCKKREIEAPEEFSKKCVKLDVQSEVSFLPQDLKLIQ 120
            + V   +   P +    KE +   K R    P +++       +   + F P D     
Sbjct: 284 PKAVINYINGRPAD----KEYDSXRKXRNCCRPRQYANALGPRPIDGTIIFPPVDPTRTL 339

Query: 121 SPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGI 180
            PH DAL++S++IG+  VRRIL+D GSS +++  + V  M      ++   + L GF+G 
Sbjct: 340 QPHRDALILSLEIGDFDVRRILVDPGSSADLVQASVVSHMGHSLTGLENPRRILSGFNGS 399

Query: 181 VTYSDGSLL-----------TDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTI 229
            T S G ++             F VV+  SP+N ILGR W+H M+ +PSTYHQ++ + T 
Sbjct: 400 STTSLGDIILPVQAGPVTLNVQFSVVQELSPFNVILGRTWLHYMKDIPSTYHQMVSFLTN 459

Query: 230 YGIEEIGGDQATTRTC 245
            G  ++ G Q   R C
Sbjct: 460 EGQIDLYGSQLAARQC 475

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147785767|emb|CAN62122.1| hypothetical protein VITISV_016419 [Vitis vinifera]

 Score =  124 bits (312), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 80/263 (30%), Positives = 129/263 (49%), Gaps = 22/263 (8%)

Query: 1   CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKVE--DKQPQNQNNFLKKDQIENSTS 58
           CAFH D  H    CR+L+  +E+LI  G LK++V+ +   K     +N     +   + +
Sbjct: 254 CAFHKDHGHTIEACRSLQYLVEKLIKAGHLKQYVRSDAGGKVTSQHHN----PEAPRAPT 309

Query: 59  EPEQIVNTI-MAPLPLEVHMTKERNVYCK----KREIEAPEEFSKKCVKLDVQSEVSFLP 113
            P+ I+N I   P   E    ++R    +    +  I +      +     +   + F P
Sbjct: 310 VPKAIINYINGGPSNEEYDSRRKRQKLLRAASIRERINSTRPGLTRGGPRPIDGTIIFPP 369

Query: 114 QDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQP 173
            D      PH DAL++S++IG+  VRRIL+D GSS +++  + V  M      ++   + 
Sbjct: 370 VDPTRTLQPHRDALILSLEIGDFDVRRILVDPGSSADLVQASVVGHMGHSLTGLENLGRV 429

Query: 174 LIGFSGIVTYSDGSLL-----------TDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQ 222
           + GF+G  T S G ++             F VV+  SP+N ILGR W+H M+V+PSTYHQ
Sbjct: 430 MSGFNGSSTTSLGDIILPVQVGPVTLNVQFSVVQELSPFNVILGRTWLHYMKVIPSTYHQ 489

Query: 223 VLCYQTIYGIEEIGGDQATTRTC 245
           ++ + T  G  ++ G Q   R C
Sbjct: 490 MVSFLTDEGQIDLYGSQLAARQC 512

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 =  124 bits (311), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 81/263 (30%), Positives = 127/263 (48%), Gaps = 22/263 (8%)

Query: 1   CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFV--KVEDKQPQNQNNFLKKDQIENSTS 58
           CAFH D  H T  CR  +  +E LI  G LK+++    ED+     NN          + 
Sbjct: 266 CAFHKDHGHTTETCRVFQFLVERLIKAGHLKQYLCTDTEDRDISQHNN----PGAPRVSV 321

Query: 59  EPEQIVNTI-MAPLPLEVHMTKERNVYCKKREIEAPEEFSKKCVKLD----VQSEVSFLP 113
            P+ ++N I   P   E    ++R    +   I       +  +  +    +   + F P
Sbjct: 322 APKAVINYINGGPSDEEYDSRRKRQKLLRAASIRERINSIRPGLTGEGPRPIDGTIIFPP 381

Query: 114 QDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQP 173
            D      PH DAL++S++IG+  VRRIL+D GSSV+++  + V++M      ++   + 
Sbjct: 382 VDPARTLQPHRDALILSLEIGDFDVRRILVDPGSSVDLVQASVVDRMGHSLAGLENPGRI 441

Query: 174 LIGFSGIVTYSDGSLL-----------TDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQ 222
           L GF+G  T S G ++             F VV+  SP+N ILGR W+H M+ +PSTYHQ
Sbjct: 442 LSGFNGSSTTSLGDIILPVQAGPVTLNVQFSVVQELSPFNVILGRTWLHYMKAIPSTYHQ 501

Query: 223 VLCYQTIYGIEEIGGDQATTRTC 245
           ++ + T  G  ++ G Q   R C
Sbjct: 502 MVSFLTNDGQIDLYGSQLAARQC 524

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147781482|emb|CAN64960.1| hypothetical protein VITISV_006740 [Vitis vinifera]

 Score =  124 bits (311), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 83/260 (31%), Positives = 131/260 (50%), Gaps = 28/260 (10%)

Query: 1   CAFHNDCRHYTRDCRTLKKYIEELISKGQLKEFVKVEDKQ---PQNQNNFLKKDQIENST 57
           CAFH D  H T  CR+L+  +E LI  GQLK++++ +       Q+ N+   +  +    
Sbjct: 231 CAFHKDHGHTTETCRSLQYLVERLIKAGQLKQYIRSDTGGRDVSQHHNSGASRAPVA--- 287

Query: 58  SEPEQIVNTI-MAPLPLEVHMTKERNVYCKKREIEAPEEFSKKCVKL------DVQSEVS 110
             P+ ++N I   P   E +  ++R    +   I   E  +     L       +   + 
Sbjct: 288 --PKAVINYINGGPSDEEYNSRRKRQKLLRAASIR--ERINSIRPGLTGEGPRPIDGTII 343

Query: 111 FLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPF 170
           F P D      PH DAL++S++IG+  VRRIL+D GSS +++  + +  M   +  +   
Sbjct: 344 FPPVDPTRTLQPHRDALILSLEIGDFDVRRILVDPGSSADLVQASVIGHM---EHSLAGL 400

Query: 171 EQP---LIGFSGIVTYSDGSLLTDFLVVKAT--SPYNAILGRQWIHKMRVVPSTYHQVLC 225
           E P   L GF+G  T S G ++   L V+A   SP+N ILGR W+H M+ +PSTYHQ++ 
Sbjct: 401 ENPGRILSGFNGSSTTSLGDII---LPVQAGPLSPFNVILGRTWLHYMKAIPSTYHQLVS 457

Query: 226 YQTIYGIEEIGGDQATTRTC 245
           + T  G  ++ G Q   R C
Sbjct: 458 FLTNEGQTDLYGSQLAARQC 477

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	267
cd00303	92	cd00303, retropepsin_like, Retropepsins; pepsin-li	5e-11

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

 Score = 57.7 bits (140), Expect = 5e-11
 Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 15/95 (15%)

Query: 129 ISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL 188
           +  KI   +  R L+D+G+SVN + ++  +K+ L   ++ P    + G +G    + G +
Sbjct: 1   LKGKING-VPVRALVDSGASVNFISESLAKKLGLP-PRLLPTPLKVKGANGSSVKTLGVI 58

Query: 189 L------------TDFLVVKATSPYNAILGRQWIH 211
           L             DF V+     Y+ ILGR 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	267
cd05484	91	retropepsin_like_LTR_2 Retropepsins_like_LTR, peps	99.37
cd05479	124	RP_DDI RP_DDI; retropepsin-like domain of DNA dama	98.94
cd05481	93	retropepsin_like_LTR_1 Retropepsins_like_LTR; peps	98.93
PF09668	124	Asp_protease: Aspartyl protease; InterPro: IPR0191	98.68
PF00077	100	RVP: Retroviral aspartyl protease The Prosite entr	98.64
cd00303	92	retropepsin_like Retropepsins; pepsin-like asparta	98.61
PF08284	135	RVP_2: Retroviral aspartyl protease; InterPro: IPR	98.56
PF13650	90	Asp_protease_2: Aspartyl protease	98.54
cd05483	96	retropepsin_like_bacteria Bacterial aspartate prot	97.91
TIGR02281	121	clan_AA_DTGA clan AA aspartic protease, TIGR02281	97.9
cd06094	89	RP_Saci_like RP_Saci_like, retropepsin family. Ret	97.68
PF13975	72	gag-asp_proteas: gag-polyprotein putative aspartyl	97.38
cd06095	86	RP_RTVL_H_like Retropepsin of the RTVL_H family of	97.27
cd05480	103	NRIP_C NRIP_C; putative nuclear receptor interacti	96.7
KOG0012	380	consensus DNA damage inducible protein [Replicatio	96.34
TIGR03698	107	clan_AA_DTGF clan AA aspartic protease, AF_0612 fa	96.15
PF12384	177	Peptidase_A2B: Ty3 transposon peptidase; InterPro:	95.76
COG3577	215	Predicted aspartyl protease [General function pred	93.86
COG5550	125	Predicted aspartyl protease [Posttranslational mod	92.2
PF05585	164	DUF1758: Putative peptidase (DUF1758); InterPro: I	85.17
cd05482	87	HIV_retropepsin_like Retropepsins, pepsin-like asp	82.53

>cd05484 retropepsin_like_LTR_2 Retropepsins_like_LTR, pepsin-like aspartate proteases

Probab=99.37  E-value=2.1e-12  Score=98.07  Aligned_cols=79  Identities=22%  Similarity=0.425  Sum_probs=72.7

Q ss_pred             EEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee-----------eEEEEEee
Q 041134          128 VISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL-----------LTDFLVVK  196 (267)
Q Consensus       128 vi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i-----------~v~F~Vvd  196 (267)
                      ++++.|+|..+ ++|||+||++|+|+.+.+.++|.++  ++++...+.+|+|.....+|.+           .++|.|++
T Consensus         2 ~~~~~Ing~~i-~~lvDTGA~~svis~~~~~~lg~~~--~~~~~~~v~~a~G~~~~~~G~~~~~v~~~~~~~~~~~~v~~   78 (91)
T cd05484           2 TVTLLVNGKPL-KFQLDTGSAITVISEKTWRKLGSPP--LKPTKKRLRTATGTKLSVLGQILVTVKYGGKTKVLTLYVVK   78 (91)
T ss_pred             EEEEEECCEEE-EEEEcCCcceEEeCHHHHHHhCCCc--cccccEEEEecCCCEeeEeEEEEEEEEECCEEEEEEEEEEE
Confidence            57889999988 8999999999999999999999987  9999999999999999899886           77899998


Q ss_pred             eCCccceeecchhhh
Q 041134          197 ATSPYNAILGRQWIH  211 (267)
Q Consensus       197 ~~~~yn~iLGrpwLh  211 (267)
                      ..  |+.||||.||.
T Consensus        79 ~~--~~~lLG~~wl~   91 (91)
T cd05484          79 NE--GLNLLGRDWLD   91 (91)
T ss_pred             CC--CCCccChhhcC
Confidence            87  99999999983

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

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

Probab=98.94  E-value=3.5e-09  Score=85.09  Aligned_cols=95  Identities=20%  Similarity=0.278  Sum_probs=70.6

Q ss_pred             CCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee------------eEE
Q 041134          124 DDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL------------LTD  191 (267)
Q Consensus       124 ~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i------------~v~  191 (267)
                      ...+++.+.|++..+ +.|||+||+.|++..+..+++|+....-.+......|.++  ....|.+            .++
T Consensus        14 ~~~~~v~~~Ing~~~-~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g~--~~~~g~~~~~~l~i~~~~~~~~   90 (124)
T cd05479          14 VPMLYINVEINGVPV-KAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGT--QKILGRIHLAQVKIGNLFLPCS   90 (124)
T ss_pred             eeEEEEEEEECCEEE-EEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCCC--cEEEeEEEEEEEEECCEEeeeE
Confidence            346899999999986 8999999999999999999999975431122223333332  3344544            678


Q ss_pred             EEEeeeCCccceeecchhhhhccccccccee
Q 041134          192 FLVVKATSPYNAILGRQWIHKMRVVPSTYHQ  222 (267)
Q Consensus       192 F~Vvd~~~~yn~iLGrpwLh~~~aipst~hq  222 (267)
                      |.|++.. .++.|||.+||..++++...-.+
T Consensus        91 ~~Vl~~~-~~d~ILG~d~L~~~~~~ID~~~~  120 (124)
T cd05479          91 FTVLEDD-DVDFLIGLDMLKRHQCVIDLKEN  120 (124)
T ss_pred             EEEECCC-CcCEEecHHHHHhCCeEEECCCC
Confidence            8888776 88999999999999987654443

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.

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

Probab=98.93  E-value=2.7e-09  Score=81.76  Aligned_cols=76  Identities=21%  Similarity=0.370  Sum_probs=63.3

Q ss_pred             eeeCCeeeeEEeecCCCccccchHHHHHhhcc-CcCCCCCCCccEEeeeCCeeeeccee-----------eEEEEEeeeC
Q 041134          131 IKIGNCLVRRILIDNGSSVNILDDATVEKMRL-EQDKIKPFEQPLIGFSGIVTYSDGSL-----------LTDFLVVKAT  198 (267)
Q Consensus       131 ~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~-~~~~L~~~~~~l~gf~g~~~~~lG~i-----------~v~F~Vvd~~  198 (267)
                      +.|++..--|.+||+||++|+||.+++++||- ....|+++...|++|+|+...+.|.+           ++.|.|+|..
T Consensus         3 ~~i~g~~~v~~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~~~G~~~~~v~~~~~~~~~~f~Vvd~~   82 (93)
T cd05481           3 MKINGKQSVKFQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIPVEGGVKLKCRYRNPKYNLTFQVVKEE   82 (93)
T ss_pred             eEeCCceeEEEEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEeeeeEEEEEEEEECCcEEEEEEEEECCC
Confidence            45666345578999999999999999999983 34679999999999999999999976           8889999875


Q ss_pred             Cccceeecch
Q 041134          199 SPYNAILGRQ  208 (267)
Q Consensus       199 ~~yn~iLGrp  208 (267)
                      .  ..|||+.
T Consensus        83 ~--~~lLG~~   90 (93)
T cd05481          83 G--PPLLGAK   90 (93)
T ss_pred             C--CceEccc
Confidence            3  3588875

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

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

Probab=98.68  E-value=4.3e-08  Score=78.85  Aligned_cols=89  Identities=17%  Similarity=0.229  Sum_probs=61.3

Q ss_pred             CCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee------------eEE
Q 041134          124 DDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL------------LTD  191 (267)
Q Consensus       124 ~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i------------~v~  191 (267)
                      ...|+|.+.|+|..| +.+||+|+..|||+.+.++++|+..  +-.....-...+-.+..++|.|            .+.
T Consensus        22 v~mLyI~~~ing~~v-kA~VDtGAQ~tims~~~a~r~gL~~--lid~r~~g~a~GvG~~~i~G~Ih~~~l~ig~~~~~~s   98 (124)
T PF09668_consen   22 VSMLYINCKINGVPV-KAFVDTGAQSTIMSKSCAERCGLMR--LIDKRFAGVAKGVGTQKILGRIHSVQLKIGGLFFPCS   98 (124)
T ss_dssp             ----EEEEEETTEEE-EEEEETT-SS-EEEHHHHHHTTGGG--GEEGGG-EE-------EEEEEEEEEEEEETTEEEEEE
T ss_pred             cceEEEEEEECCEEE-EEEEeCCCCccccCHHHHHHcCChh--hccccccccccCCCcCceeEEEEEEEEEECCEEEEEE
Confidence            347999999999999 9999999999999999999999843  4433322222222455688888            788


Q ss_pred             EEEeeeCCccceeecchhhhhcccc
Q 041134          192 FLVVKATSPYNAILGRQWIHKMRVV  216 (267)
Q Consensus       192 F~Vvd~~~~yn~iLGrpwLh~~~ai  216 (267)
                      |.|+++ .+...|||..||.+.+++
T Consensus        99 ~~Vle~-~~~d~llGld~L~~~~c~  122 (124)
T PF09668_consen   99 FTVLED-QDVDLLLGLDMLKRHKCC  122 (124)
T ss_dssp             EEEETT-SSSSEEEEHHHHHHTT-E
T ss_pred             EEEeCC-CCcceeeeHHHHHHhCcc
Confidence            999984 455899999999987765

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

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

Probab=98.64  E-value=1.7e-08  Score=77.34  Aligned_cols=84  Identities=30%  Similarity=0.446  Sum_probs=67.0

Q ss_pred             CceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee-----------eEEEE
Q 041134          125 DALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL-----------LTDFL  193 (267)
Q Consensus       125 ~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i-----------~v~F~  193 (267)
                      ..-++++.|++..+ +.|||+||++++++.+.++..+..    ......+.|++|.. ...|..           ...|.
T Consensus         4 ~rp~i~v~i~g~~i-~~LlDTGA~vsiI~~~~~~~~~~~----~~~~~~v~~~~g~~-~~~~~~~~~v~~~~~~~~~~~~   77 (100)
T PF00077_consen    4 NRPYITVKINGKKI-KALLDTGADVSIISEKDWKKLGPP----PKTSITVRGAGGSS-SILGSTTVEVKIGGKEFNHTFL   77 (100)
T ss_dssp             SSSEEEEEETTEEE-EEEEETTBSSEEESSGGSSSTSSE----EEEEEEEEETTEEE-EEEEEEEEEEEETTEEEEEEEE
T ss_pred             CCceEEEeECCEEE-EEEEecCCCcceeccccccccccc----ccCCceeccCCCcc-eeeeEEEEEEEEECccceEEEE
Confidence            34468899999866 689999999999999887666543    45566788888877 666666           55788


Q ss_pred             EeeeCCccceeecchhhhhcccc
Q 041134          194 VVKATSPYNAILGRQWIHKMRVV  216 (267)
Q Consensus       194 Vvd~~~~yn~iLGrpwLh~~~ai  216 (267)
                      |+++ .++| ||||.||.++++.
T Consensus        78 v~~~-~~~~-ILG~D~L~~~~~~   98 (100)
T PF00077_consen   78 VVPD-LPMN-ILGRDFLKKLNAV   98 (100)
T ss_dssp             ESST-CSSE-EEEHHHHTTTTCE
T ss_pred             ecCC-CCCC-EeChhHHHHcCCE
Confidence            8887 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 ....

>cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases

Probab=98.61  E-value=2.5e-07  Score=65.74  Aligned_cols=79  Identities=30%  Similarity=0.552  Sum_probs=61.3

Q ss_pred             EeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee------------eEEEEEeee
Q 041134          130 SIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL------------LTDFLVVKA  197 (267)
Q Consensus       130 ~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i------------~v~F~Vvd~  197 (267)
                      ++.+++ ...+.|+|+||+++++..+.+.+++. ..........+.++++......+..            ...|.|++.
T Consensus         2 ~~~~~~-~~~~~liDtgs~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~   79 (92)
T cd00303           2 KGKING-VPVRALVDSGASVNFISESLAKKLGL-PPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDL   79 (92)
T ss_pred             EEEECC-EEEEEEEcCCCcccccCHHHHHHcCC-CcccCCCceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcC
Confidence            456677 66689999999999999999999987 2334456677888888765555541            556777776


Q ss_pred             CCccceeecchhhh
Q 041134          198 TSPYNAILGRQWIH  211 (267)
Q Consensus       198 ~~~yn~iLGrpwLh  211 (267)
                      . .|+.|||++||+
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

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

Probab=98.56  E-value=3.3e-07  Score=74.89  Aligned_cols=104  Identities=20%  Similarity=0.349  Sum_probs=79.2

Q ss_pred             CCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee------------eEE
Q 041134          124 DDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL------------LTD  191 (267)
Q Consensus       124 ~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i------------~v~  191 (267)
                      .+.+...+.|++..+ .+|||.||+-|.+..+...+++++...+..+- .+.+.++. ....+..            .++
T Consensus        19 ~~vi~g~~~I~~~~~-~vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~-~V~~~g~~-~~~~~~~~~~~~~i~g~~~~~d   95 (135)
T PF08284_consen   19 PDVITGTFLINSIPA-SVLIDSGATHSFISSSFAKKLGLPLEPLPRPI-VVSAPGGS-INCEGVCPDVPLSIQGHEFVVD   95 (135)
T ss_pred             CCeEEEEEEeccEEE-EEEEecCCCcEEccHHHHHhcCCEEEEccCee-EEeccccc-ccccceeeeEEEEECCeEEEee
Confidence            455666677777665 68999999999999999999999988886543 33343332 2222221            667


Q ss_pred             EEEeeeCCccceeecchhhhhcccccccceeeeeeecCCc
Q 041134          192 FLVVKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTIYG  231 (267)
Q Consensus       192 F~Vvd~~~~yn~iLGrpwLh~~~aipst~hq~vk~~~~~G  231 (267)
                      |.|++. ..|.+|||.+||.+..+......-.|.|-.|+|
T Consensus        96 l~vl~l-~~~DvILGm~WL~~~~~~IDw~~k~v~f~~p~~  134 (135)
T PF08284_consen   96 LLVLDL-GGYDVILGMDWLKKHNPVIDWATKTVTFNSPSG  134 (135)
T ss_pred             eEEecc-cceeeEeccchHHhCCCEEEccCCEEEEeCCCC
Confidence            888776 569999999999999998888888888888887

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.

>PF13650 Asp_protease_2: Aspartyl protease

Probab=98.54  E-value=3.8e-07  Score=67.64  Aligned_cols=79  Identities=29%  Similarity=0.488  Sum_probs=63.0

Q ss_pred             EEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee-----------eEEEEEeee
Q 041134          129 ISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL-----------LTDFLVVKA  197 (267)
Q Consensus       129 i~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i-----------~v~F~Vvd~  197 (267)
                      |.+.|++..+ +.|+|+||+.+++..+.++++|+....... ...+.|++|......+.+           ++.|.|++.
T Consensus         1 V~v~vng~~~-~~liDTGa~~~~i~~~~~~~l~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~i~ig~~~~~~~~~~v~~~   78 (90)
T PF13650_consen    1 VPVKVNGKPV-RFLIDTGASISVISRSLAKKLGLKPRPKSV-PISVSGAGGSVTVYRGRVDSITIGGITLKNVPFLVVDL   78 (90)
T ss_pred             CEEEECCEEE-EEEEcCCCCcEEECHHHHHHcCCCCcCCce-eEEEEeCCCCEEEEEEEEEEEEECCEEEEeEEEEEECC
Confidence            4567888855 899999999999999999999997654432 356688888755554444           678888887


Q ss_pred             CCccceeecchh
Q 041134          198 TSPYNAILGRQW  209 (267)
Q Consensus       198 ~~~yn~iLGrpw  209 (267)
                      ...+..|||.+|
T Consensus        79 ~~~~~~iLG~df   90 (90)
T PF13650_consen   79 GDPIDGILGMDF   90 (90)
T ss_pred             CCCCEEEeCCcC
Confidence            889999999987

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

Probab=97.91  E-value=5.6e-05  Score=56.42  Aligned_cols=82  Identities=20%  Similarity=0.334  Sum_probs=59.2

Q ss_pred             eEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeee--------eccee---eEEEEEe
Q 041134          127 LVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTY--------SDGSL---LTDFLVV  195 (267)
Q Consensus       127 Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~--------~lG~i---~v~F~Vv  195 (267)
                      +++.+.|++..+ +.|+|+||+..+++.+..++++..  ..........+.+|....        .+|..   ++.+.|+
T Consensus         3 ~~v~v~i~~~~~-~~llDTGa~~s~i~~~~~~~l~~~--~~~~~~~~~~~~~G~~~~~~~~~~~i~ig~~~~~~~~~~v~   79 (96)
T cd05483           3 FVVPVTINGQPV-RFLLDTGASTTVISEELAERLGLP--LTLGGKVTVQTANGRVRAARVRLDSLQIGGITLRNVPAVVL   79 (96)
T ss_pred             EEEEEEECCEEE-EEEEECCCCcEEcCHHHHHHcCCC--ccCCCcEEEEecCCCccceEEEcceEEECCcEEeccEEEEe
Confidence            578889998665 899999999999999999999872  233344456666665332        23332   5678888


Q ss_pred             eeCC-ccceeecchhhh
Q 041134          196 KATS-PYNAILGRQWIH  211 (267)
Q Consensus       196 d~~~-~yn~iLGrpwLh  211 (267)
                      |... +...|||..||.
T Consensus        80 d~~~~~~~gIlG~d~l~   96 (96)
T cd05483          80 PGDALGVDGLLGMDFLR   96 (96)
T ss_pred             CCcccCCceEeChHHhC
Confidence            7765 578899999873

This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.

>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family

Probab=97.90  E-value=5.6e-05  Score=60.51  Aligned_cols=90  Identities=16%  Similarity=0.362  Sum_probs=68.3

Q ss_pred             CCCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeee--------ccee---eEE
Q 041134          123 HDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYS--------DGSL---LTD  191 (267)
Q Consensus       123 h~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~--------lG~i---~v~  191 (267)
                      ....+++.+.|+|..+ +.|||+|++..+++....+++|+.+..+. ....+.+.+|...-.        +|.+   ++.
T Consensus         8 ~~g~~~v~~~InG~~~-~flVDTGAs~t~is~~~A~~Lgl~~~~~~-~~~~~~ta~G~~~~~~~~l~~l~iG~~~~~nv~   85 (121)
T TIGR02281         8 GDGHFYATGRVNGRNV-RFLVDTGATSVALNEEDAQRLGLDLNRLG-YTVTVSTANGQIKAARVTLDRVAIGGIVVNDVD   85 (121)
T ss_pred             CCCeEEEEEEECCEEE-EEEEECCCCcEEcCHHHHHHcCCCcccCC-ceEEEEeCCCcEEEEEEEeCEEEECCEEEeCcE
Confidence            4456899999999855 89999999999999999999999876543 345566777753322        2332   678


Q ss_pred             EEEeeeCCccceeecchhhhhcc
Q 041134          192 FLVVKATSPYNAILGRQWIHKMR  214 (267)
Q Consensus       192 F~Vvd~~~~yn~iLGrpwLh~~~  214 (267)
                      +.|++.......|||-.+|.+++
T Consensus        86 ~~v~~~~~~~~~LLGm~fL~~~~  108 (121)
T TIGR02281        86 AMVAEGGALSESLLGMSFLNRLS  108 (121)
T ss_pred             EEEeCCCcCCceEcCHHHHhccc
Confidence            88887654457899999998875

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

>cd06094 RP_Saci_like RP_Saci_like, retropepsin family

Probab=97.68  E-value=5.1e-05  Score=57.45  Aligned_cols=67  Identities=25%  Similarity=0.444  Sum_probs=54.1

Q ss_pred             eEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee------------eEEEEEeeeCCccceeec
Q 041134          139 RRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL------------LTDFLVVKATSPYNAILG  206 (267)
Q Consensus       139 ~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i------------~v~F~Vvd~~~~yn~iLG  206 (267)
                      .+.|||+||.++++|.+..+..      ++++...|.+.||+...+.|..            ...|.|.|...   +|||
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            3679999999999998876542      5677778999999988888876            56788888765   5999


Q ss_pred             chhhhhcc
Q 041134          207 RQWIHKMR  214 (267)
Q Consensus       207 rpwLh~~~  214 (267)
                      ..+|.+++
T Consensus        81 aDfL~~~~   88 (89)
T cd06094          81 ADFLQHYG   88 (89)
T ss_pred             HHHHHHcC
Confidence            99998754

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

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

Probab=97.38  E-value=0.00075  Score=48.95  Aligned_cols=63  Identities=19%  Similarity=0.311  Sum_probs=49.5

Q ss_pred             CCCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeecce
Q 041134          123 HDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGS  187 (267)
Q Consensus       123 h~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~  187 (267)
                      ....+++.+.|++..+. .|||+||+.|+|+.++.++||++..... ....+.-.||+.....|.
T Consensus         5 ~~g~~~v~~~I~g~~~~-alvDtGat~~fis~~~a~rLgl~~~~~~-~~~~v~~a~g~~~~~~g~   67 (72)
T PF13975_consen    5 DPGLMYVPVSIGGVQVK-ALVDTGATHNFISESLAKRLGLPLEKPP-SPIRVKLANGSVIEIRGV   67 (72)
T ss_pred             cCCEEEEEEEECCEEEE-EEEeCCCcceecCHHHHHHhCCCcccCC-CCEEEEECCCCccccceE
Confidence            34568899999998888 9999999999999999999998754332 246667777776665554

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

Probab=97.27  E-value=0.00098  Score=49.88  Aligned_cols=73  Identities=23%  Similarity=0.389  Sum_probs=53.1

Q ss_pred             EeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeecc----ee-------eEEEEEeeeC
Q 041134          130 SIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDG----SL-------LTDFLVVKAT  198 (267)
Q Consensus       130 ~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG----~i-------~v~F~Vvd~~  198 (267)
                      ++.|+|..+ +.|||+|++..+++...++++     .+......+.|.+|....+..    .+       ...|.|++..
T Consensus         2 ~v~InG~~~-~fLvDTGA~~tii~~~~a~~~-----~~~~~~~~v~gagG~~~~~v~~~~~~v~vg~~~~~~~~~v~~~~   75 (86)
T cd06095           2 TITVEGVPI-VFLVDTGATHSVLKSDLGPKQ-----ELSTTSVLIRGVSGQSQQPVTTYRTLVDLGGHTVSHSFLVVPNC   75 (86)
T ss_pred             EEEECCEEE-EEEEECCCCeEEECHHHhhhc-----cCCCCcEEEEeCCCcccccEEEeeeEEEECCEEEEEEEEEEcCC
Confidence            567888864 679999999999999999887     345577889999997522221    12       4456666532


Q ss_pred             Cccceeecchhh
Q 041134          199 SPYNAILGRQWI  210 (267)
Q Consensus       199 ~~yn~iLGrpwL  210 (267)
                       + ..|||+.||
T Consensus        76 -~-~~lLG~dfL   85 (86)
T cd06095          76 -P-DPLLGRDLL   85 (86)
T ss_pred             -C-CcEechhhc
Confidence             3 779999987

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

>cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein

Probab=96.70  E-value=0.0053  Score=47.46  Aligned_cols=84  Identities=21%  Similarity=0.281  Sum_probs=57.9

Q ss_pred             EeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCC-CCCccEEeeeCCeeeeccee------------eEEEEEee
Q 041134          130 SIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIK-PFEQPLIGFSGIVTYSDGSL------------LTDFLVVK  196 (267)
Q Consensus       130 ~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~-~~~~~l~gf~g~~~~~lG~i------------~v~F~Vvd  196 (267)
                      ...|+|+.| +.+||.|+..|||++...+++|+..--.. ...-.-.|. |++...+|.|            ...|.|+|
T Consensus         2 nCk~nG~~v-kAfVDsGaQ~timS~~caercgL~r~v~~~r~~g~A~gv-gt~~kiiGrih~~~ikig~~~~~CSftVld   79 (103)
T cd05480           2 SCQCAGKEL-RALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSL-PTSVKVIGQIERLVLQLGQLTVECSAQVVD   79 (103)
T ss_pred             ceeECCEEE-EEEEecCCchhhcCHHHHHHcChHhhhhhccccccccCC-CcceeEeeEEEEEEEEeCCEEeeEEEEEEc
Confidence            456888887 68999999999999999999998532111 111111111 1223556666            77899998


Q ss_pred             eCCccceeecchhhhhcccc
Q 041134          197 ATSPYNAILGRQWIHKMRVV  216 (267)
Q Consensus       197 ~~~~yn~iLGrpwLh~~~ai  216 (267)
                      . .+.+.+||-.-|.+.++.
T Consensus        80 ~-~~~d~llGLdmLkrhqc~   98 (103)
T cd05480          80 D-NEKNFSLGLQTLKSLKCV   98 (103)
T ss_pred             C-CCcceEeeHHHHhhccee
Confidence            4 567899999888776654

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=96.34  E-value=0.0038  Score=58.20  Aligned_cols=97  Identities=20%  Similarity=0.330  Sum_probs=71.2

Q ss_pred             eeEeCCCCCccccCCCCCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCC-----ee
Q 041134          108 EVSFLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGI-----VT  182 (267)
Q Consensus       108 ~I~F~~~d~~~v~~ph~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~-----~~  182 (267)
                      .|+..|++...     -..|+|.+.|+|+.| +++||.|+..|||++...+++|++.-       +-..|.|.     +.
T Consensus       222 ai~~~pe~f~~-----v~ML~iN~~ing~~V-KAfVDsGaq~timS~~Caer~gL~rl-------id~r~~g~a~gvg~~  288 (380)
T KOG0012|consen  222 AIEYHPEDFTQ-----VTMLYINCEINGVPV-KAFVDSGAQTTIMSAACAERCGLNRL-------IDKRFQGEARGVGTE  288 (380)
T ss_pred             hhhcCcccccc-----ceEEEEEEEECCEEE-EEEEcccchhhhhhHHHHHHhChHHH-------hhhhhhccccCCCcc
Confidence            45555555432     357999999999999 58999999999999999999998653       33344442     33


Q ss_pred             eeccee------------eEEEEEeeeCCccceeecchhhhhcccccc
Q 041134          183 YSDGSL------------LTDFLVVKATSPYNAILGRQWIHKMRVVPS  218 (267)
Q Consensus       183 ~~lG~i------------~v~F~Vvd~~~~yn~iLGrpwLh~~~aips  218 (267)
                      ..+|.|            ...|.|+|... -+.+||-.-|.+.+|...
T Consensus       289 ki~g~Ih~~~lki~~~~l~c~ftV~d~~~-~d~llGLd~Lrr~~ccId  335 (380)
T KOG0012|consen  289 KILGRIHQAQLKIEDLYLPCSFTVLDRRD-MDLLLGLDMLRRHQCCID  335 (380)
T ss_pred             cccceeEEEEEEeccEeeccceEEecCCC-cchhhhHHHHHhccceee
Confidence            446666            55788887653 478899999988776653

>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family

Probab=96.15  E-value=0.016  Score=45.34  Aligned_cols=73  Identities=21%  Similarity=0.225  Sum_probs=48.4

Q ss_pred             EEeecCCCcccc-chHHHHHhhccCcCCCCCCCccEEeeeCCe-eeec-------ceeeEEEEEeee-CCccceeecchh
Q 041134          140 RILIDNGSSVNI-LDDATVEKMRLEQDKIKPFEQPLIGFSGIV-TYSD-------GSLLTDFLVVKA-TSPYNAILGRQW  209 (267)
Q Consensus       140 riLvD~GSs~ni-l~~~~~~~mg~~~~~L~~~~~~l~gf~g~~-~~~l-------G~i~v~F~Vvd~-~~~yn~iLGrpw  209 (267)
                      +.|||+|++-.+ ++.+.+++||+++..    .....-.+|.. ....       |.+.....|+.. ..+ ..+||..|
T Consensus        18 ~~LVDTGat~~~~l~~~~a~~lgl~~~~----~~~~~tA~G~~~~~~v~~~~v~igg~~~~~~v~~~~~~~-~~LLG~~~   92 (107)
T TIGR03698        18 RALVDTGFSGFLLVPPDIVNKLGLPELD----QRRVYLADGREVLTDVAKASIIINGLEIDAFVESLGYVD-EPLLGTEL   92 (107)
T ss_pred             EEEEECCCCeEEecCHHHHHHcCCCccc----CcEEEecCCcEEEEEEEEEEEEECCEEEEEEEEecCCCC-ccEecHHH
Confidence            689999999997 999999999998743    34666667742 1111       111223333322 223 67999999


Q ss_pred             hhhccccc
Q 041134          210 IHKMRVVP  217 (267)
Q Consensus       210 Lh~~~aip  217 (267)
                      |.++..+.
T Consensus        93 L~~l~l~i  100 (107)
T TIGR03698        93 LEGLGIVI  100 (107)
T ss_pred             HhhCCEEE
Confidence            99887654

Members of this protein family are clan AA aspartic proteases, related to family TIGR02281. These proteins resemble retropepsins, pepsin-like proteases of retroviruses such as HIV. Members of this family are found in archaea and bacteria.

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

Probab=95.76  E-value=0.038  Score=46.55  Aligned_cols=92  Identities=14%  Similarity=0.244  Sum_probs=63.4

Q ss_pred             CCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCC-eeeeccee-----------eEE
Q 041134          124 DDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGI-VTYSDGSL-----------LTD  191 (267)
Q Consensus       124 ~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~-~~~~lG~i-----------~v~  191 (267)
                      ++.+.+.+.|.+-.+ ++|+|.||-..++......+|+++..  .-+..-+.||.+. ....--.+           .+.
T Consensus        32 g~T~~v~l~~~~t~i-~vLfDSGSPTSfIr~di~~kL~L~~~--~app~~fRG~vs~~~~~tsEAv~ld~~i~n~~i~i~  108 (177)
T PF12384_consen   32 GKTAIVQLNCKGTPI-KVLFDSGSPTSFIRSDIVEKLELPTH--DAPPFRFRGFVSGESATTSEAVTLDFYIDNKLIDIA  108 (177)
T ss_pred             CcEEEEEEeecCcEE-EEEEeCCCccceeehhhHHhhCCccc--cCCCEEEeeeccCCceEEEEeEEEEEEECCeEEEEE
Confidence            467888899998887 58999999999999999999987652  3334456666543 11111111           445


Q ss_pred             EEEeeeCCccceeecchhhhhccccccc
Q 041134          192 FLVVKATSPYNAILGRQWIHKMRVVPST  219 (267)
Q Consensus       192 F~Vvd~~~~yn~iLGrpwLh~~~aipst  219 (267)
                      ++|.|. -.+.+|+|-|.|.+..-+-++
T Consensus       109 aYV~d~-m~~dlIIGnPiL~ryp~l~~~  135 (177)
T PF12384_consen  109 AYVTDN-MDHDLIIGNPILDRYPTLLYS  135 (177)
T ss_pred             EEEecc-CCcceEeccHHHhhhHHHHHH
Confidence            555544 478999999999876655443

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=93.86  E-value=0.16  Score=44.24  Aligned_cols=89  Identities=13%  Similarity=0.318  Sum_probs=72.2

Q ss_pred             CCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCee--------eeccee---eEEE
Q 041134          124 DDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVT--------YSDGSL---LTDF  192 (267)
Q Consensus       124 ~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~--------~~lG~i---~v~F  192 (267)
                      +-.+.+...|++..|+ -|||+|++.=.+......++|+....|. .+.++..-||..+        ..+|.|   +|+-
T Consensus       103 ~GHF~a~~~VNGk~v~-fLVDTGATsVal~~~dA~RlGid~~~l~-y~~~v~TANG~~~AA~V~Ld~v~IG~I~~~nV~A  180 (215)
T COG3577         103 DGHFEANGRVNGKKVD-FLVDTGATSVALNEEDARRLGIDLNSLD-YTITVSTANGRARAAPVTLDRVQIGGIRVKNVDA  180 (215)
T ss_pred             CCcEEEEEEECCEEEE-EEEecCcceeecCHHHHHHhCCCccccC-CceEEEccCCccccceEEeeeEEEccEEEcCchh
Confidence            3457888999999985 7899999999999999999999988876 5567777787533        335655   7888


Q ss_pred             EEeeeCCccceeecchhhhhcc
Q 041134          193 LVVKATSPYNAILGRQWIHKMR  214 (267)
Q Consensus       193 ~Vvd~~~~yn~iLGrpwLh~~~  214 (267)
                      .|++....-+.+||..||.+..
T Consensus       181 ~V~~~g~L~~sLLGMSfL~rL~  202 (215)
T COG3577         181 MVAEDGALDESLLGMSFLNRLS  202 (215)
T ss_pred             heecCCccchhhhhHHHHhhcc
Confidence            8998888889999999997754

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

Probab=92.20  E-value=0.6  Score=37.52  Aligned_cols=82  Identities=17%  Similarity=0.171  Sum_probs=50.3

Q ss_pred             eeCCeeeeEEeecCCCc-cccchHHHHHhhccCcCCCC-----CCCccEEeeeCCeeeecceeeEEEEEeeeCCccceee
Q 041134          132 KIGNCLVRRILIDNGSS-VNILDDATVEKMRLEQDKIK-----PFEQPLIGFSGIVTYSDGSLLTDFLVVKATSPYNAIL  205 (267)
Q Consensus       132 ~I~~~~V~riLvD~GSs-~nil~~~~~~~mg~~~~~L~-----~~~~~l~gf~g~~~~~lG~i~v~F~Vvd~~~~yn~iL  205 (267)
                      +.+++.-.+ |||+|.+ -=++|..++++||.++.+--     .-+.......-....-.|.-.+.|..+-+..+-+ ++
T Consensus        21 ~~Gd~~~~~-LiDTGFtg~lvlp~~vaek~~~~~~~~~~~~~a~~~~v~t~V~~~~iki~g~e~~~~Vl~s~~~~~~-li   98 (125)
T COG5550          21 GQGDFVYDE-LIDTGFTGYLVLPPQVAEKLGLPLFSTIRIVLADGGVVKTSVALATIKIDGVEKVAFVLASDNLPEP-LI   98 (125)
T ss_pred             CCCcEEeee-EEecCCceeEEeCHHHHHhcCCCccCChhhhhhcCCEEEEEEEEEEEEECCEEEEEEEEccCCCccc-ch
Confidence            345555555 9999987 78899999999999874211     1111111111112222222255666666667777 99


Q ss_pred             cchhhhhccc
Q 041134          206 GRQWIHKMRV  215 (267)
Q Consensus       206 GrpwLh~~~a  215 (267)
                      |+-||+....
T Consensus        99 G~~~lk~l~~  108 (125)
T COG5550          99 GVNLLKLLGL  108 (125)
T ss_pred             hhhhhhhccE
Confidence            9999987544

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

Probab=85.17  E-value=2.2  Score=35.41  Aligned_cols=43  Identities=26%  Similarity=0.348  Sum_probs=33.2

Q ss_pred             CeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCC
Q 041134          135 NCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGI  180 (267)
Q Consensus       135 ~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~  180 (267)
                      +....|+|+|.||..+++..+.+++|+++..   +......|..|+
T Consensus         9 ~~~~~~~LlDsGSq~SfIt~~la~~L~L~~~---~~~~~~~~~~g~   51 (164)
T PF05585_consen    9 NQVEARALLDSGSQRSFITESLANKLNLPGT---GEKILVIGTFGS   51 (164)
T ss_pred             CEEEEEEEEecCCchhHHhHHHHHHhCCCCC---CceEEEEeccCc
Confidence            3566789999999999999999999998753   233455566554

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

>cd05482 HIV_retropepsin_like Retropepsins, pepsin-like aspartate proteases

Probab=82.53  E-value=6.3  Score=29.68  Aligned_cols=74  Identities=30%  Similarity=0.462  Sum_probs=42.2

Q ss_pred             EeeeCCeeeeEEeecCCCccccchHHHHHhhccCcC-CCCCCCccEEeeeCCeeeecc-ee---------eEEEEEeeeC
Q 041134          130 SIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQD-KIKPFEQPLIGFSGIVTYSDG-SL---------LTDFLVVKAT  198 (267)
Q Consensus       130 ~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~-~L~~~~~~l~gf~g~~~~~lG-~i---------~v~F~Vvd~~  198 (267)
                      ++.|++.. .+.|+|+||-.-++...-+     +.. .+......+.|..|......- .+         .-.|.|....
T Consensus         2 ~~~i~g~~-~~~llDTGAd~Tvi~~~~~-----p~~w~~~~~~~~i~GIGG~~~~~~~~~v~i~i~~~~~~g~vlv~~~~   75 (87)
T cd05482           2 TLYINGKL-FEGLLDTGADVSIIAENDW-----PKNWPIQPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVLS   75 (87)
T ss_pred             EEEECCEE-EEEEEccCCCCeEEccccc-----CCCCccCCCCeEEEeccceEEEEEEeeEEEEEcCCeEEEEEEEccCC
Confidence            45566554 4679999999998876433     211 144456678888775222111 12         2234444433


Q ss_pred             Cccceeecchhh
Q 041134          199 SPYNAILGRQWI  210 (267)
Q Consensus       199 ~~yn~iLGrpwL  210 (267)
                      .|.| |+||..|
T Consensus        76 ~P~n-llGRd~L   86 (87)
T cd05482          76 LPVN-LWGRDIL   86 (87)
T ss_pred             Cccc-EEccccC
Confidence            5555 7888765

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

---

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	267
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	6e-06
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	3e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>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 = 44.4 bits (104), Expect = 6e-06
 Identities = 16/112 (14%), Positives = 38/112 (33%), Gaps = 12/112 (10%)

Query: 123 HDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGI-- 180
               L I+ K+    ++   +D+G+ + I+  A  E+  + +   + +     G      
Sbjct: 21  QVTMLYINCKVNGHPLK-AFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRI 79

Query: 181 --------VTYSDGSLLTDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQVL 224
                   +      L   F ++    P + +LG   + + +        VL
Sbjct: 80  IGRVHLAQIQIEGDFLQCSFSIL-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 = 42.0 bits (98), Expect = 3e-05
 Identities = 20/109 (18%), Positives = 36/109 (33%), Gaps = 13/109 (11%)

Query: 126 ALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGI----- 180
            L I+I+I N  V+   +D G+   I+     +K  L +   K F     G         
Sbjct: 26  MLYINIEINNYPVK-AFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGKIIGR 84

Query: 181 -----VTYSDGSLLTDFLVVKATSPYNAILGRQWIHKMRVVPSTYHQVL 224
                V      +   F V+   +  + ++G   + +          VL
Sbjct: 85  IHQAQVKIETQYIPCSFTVLD--TDIDVLIGLDMLKRHLACVDLKENVL 131

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

 Score = 41.0 bits (95), Expect = 3e-04
 Identities = 41/265 (15%), Positives = 86/265 (32%), Gaps = 89/265 (33%)

Query: 13  DCRTLKKYIEELISKGQLKEFVKVEDKQPQNQNNFLKKDQIENSTSEPEQIV-------- 64
           DC+ ++   + ++SK ++   +  +D    +    L         S+ E++V        
Sbjct: 34  DCKDVQDMPKSILSKEEIDHIIMSKD--AVSGTLRL----FWTLLSKQEEMVQKFVEEVL 87

Query: 65  ----NTIMAPL---PLEVHMTKERNVYCKKREIEAPEEFSKKCV--------------KL 103
                 +M+P+     +  M     +  + R     + F+K  V              +L
Sbjct: 88  RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLEL 147

Query: 104 DVQSEV----------SFLP----QDLKLIQSPHDDALVISIKIGNC------------L 137
                V          +++        K +Q   D   +  + + NC            L
Sbjct: 148 RPAKNVLIDGVLGSGKTWVALDVCLSYK-VQCKMDFK-IFWLNLKNCNSPETVLEMLQKL 205

Query: 138 VRRI------LIDNGSSVNI-LDDATVEKMRLEQDKIKPFEQPLI------------GFS 178
           + +I        D+ S++ + +     E  RL +   KP+E  L+             F+
Sbjct: 206 LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS--KPYENCLLVLLNVQNAKAWNAFN 263

Query: 179 G----IVTYSDGSLLTDFLVVKATS 199
                ++T      +TDFL    T+
Sbjct: 264 LSCKILLTTRFKQ-VTDFLSAATTT 287

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	267
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	98.63
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	98.47
1fmb_A	104	EIAV protease; hydrolase (acid proteinase), RNA-di	95.88
3slz_A	132	GAG-Pro-POL polyprotein; beta sheet and dimer, pro	93.84
3ec0_A	99	Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1	90.25
2hs1_A	99	HIV-1 protease; ultra-high resolution active site	86.06

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

Probab=98.63  E-value=7.4e-08  Score=78.70  Aligned_cols=108  Identities=15%  Similarity=0.204  Sum_probs=73.6

Q ss_pred             CceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCC--------eeeeccee--eEEEEE
Q 041134          125 DALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGI--------VTYSDGSL--LTDFLV  194 (267)
Q Consensus       125 ~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~--------~~~~lG~i--~v~F~V  194 (267)
                      ..|++.+.|++..+ ++|||+||+.++|+.+..+++|+....-........|.++.        ....+|..  .+.|.|
T Consensus        23 ~~l~v~~~Ing~~v-~~LVDTGAs~s~Is~~~A~rlGL~~~~~~~~~~~a~g~G~~~~~g~v~~~~I~Ig~~~~~~~~~V  101 (148)
T 3s8i_A           23 TMLYINCKVNGHPL-KAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIIGRVHLAQIQIEGDFLQCSFSI  101 (148)
T ss_dssp             CCCEEEEEETTEEE-EEEECTTCSSCEEEHHHHHHTTCGGGEEGGGCEECCC---CEEEEEEEEEEEEETTEEEEEEEEE
T ss_pred             CEEEEEEEECCEEE-EEEEeCCCCcEeeCHHHHHHcCCccccCcceeEEEEcCCccEEEEEEEEEEEEECCEEEEEEEEE
Confidence            46899999999977 89999999999999999999999643111111122233211        11223332  678888


Q ss_pred             eeeCCccceeecchhhhhcccccccceeeeeeecCCceEE
Q 041134          195 VKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTIYGIEE  234 (267)
Q Consensus       195 vd~~~~yn~iLGrpwLh~~~aipst~hq~vk~~~~~G~i~  234 (267)
                      +|. ..++.|||..||.+.+++......+|.+...+-.|.
T Consensus       102 le~-~~~d~LLGmD~L~~~~~~ID~~~~~L~l~~~~~~~p  140 (148)
T 3s8i_A          102 LED-QPMDMLLGLDMLRRHQCSIDLKKNVLVIGTTGTQTY  140 (148)
T ss_dssp             ETT-CSSSEEECHHHHHHTTCEEETTTTEEECTTTCCEEE
T ss_pred             eCC-CCcCeeccHHHHHhCCEEEEcCCCEEEEccCCeEEe
Confidence            874 457999999999999988777766665544332343

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

Probab=98.47  E-value=5.3e-07  Score=72.84  Aligned_cols=99  Identities=18%  Similarity=0.208  Sum_probs=66.0

Q ss_pred             CceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCe--------eeeccee--eEEEEE
Q 041134          125 DALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIV--------TYSDGSL--LTDFLV  194 (267)
Q Consensus       125 ~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~--------~~~lG~i--~v~F~V  194 (267)
                      ..+++.+.|++.. -+.|||+||+.++++.+..+++|+....-........|.++..        ...+|.+  .+.|.|
T Consensus        25 ~~~~v~v~InG~~-~~~LvDTGAs~s~is~~~a~~lgl~~~~~~~~~~~a~g~g~~~~~~~~~~~~i~ig~~~~~~~~~v  103 (148)
T 2i1a_A           25 PMLYINIEINNYP-VKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGKIIGRIHQAQVKIETQYIPCSFTV  103 (148)
T ss_dssp             CCCEEEEEETTEE-EEEEECTTCSSCEEEHHHHHHHTGGGGCBCCCC-----------CEEEEEEEEEETTEEEEEEEEE
T ss_pred             ceEEEEEEECCEE-EEEEEECCCCccccCHHHHHHcCCCccCCcceEEEEecCCCcccccEEEEEEEEECCEEeceeEEE
Confidence            4578999999995 5799999999999999999999986532111111234554421        1223444  678888


Q ss_pred             eeeCCccceeecchhhhhcccccccceeeeee
Q 041134          195 VKATSPYNAILGRQWIHKMRVVPSTYHQVLCY  226 (267)
Q Consensus       195 vd~~~~yn~iLGrpwLh~~~aipst~hq~vk~  226 (267)
                      ++  .+++.|||..||.++++....-...|.+
T Consensus       104 l~--~~~d~iLG~d~L~~~~~~ID~~~~~l~l  133 (148)
T 2i1a_A          104 LD--TDIDVLIGLDMLKRHLACVDLKENVLRI  133 (148)
T ss_dssp             EC--SSCSEEECHHHHHHTTCEEETTTTEEEE
T ss_pred             ec--CCCCeEecHHHHhhCCEEEECCCCEEEE
Confidence            88  4689999999999998865554444443

>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=95.88  E-value=0.036  Score=42.18  Aligned_cols=85  Identities=19%  Similarity=0.306  Sum_probs=57.1

Q ss_pred             EEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee-------eEEEEEeeeCCc
Q 041134          128 VISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL-------LTDFLVVKATSP  200 (267)
Q Consensus       128 vi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i-------~v~F~Vvd~~~~  200 (267)
                      ++++.|++. ....|+|+|+-.-++.......|+.+....+|  ..+.|..|....---.+       .+.-.|+-..+|
T Consensus        10 ~v~v~I~Gq-~~e~LLDTGAD~TVl~~~~w~~i~lp~~~w~p--~~i~GiGG~i~v~~~~i~i~i~g~~~~gtvlv~~tp   86 (104)
T 1fmb_A           10 TTIVLINDT-PLNVLLDTGADTSVLTTAHYNRLKYRGRKYQG--TGIGGVGGNVETFSTPVTIKKKGRHIKTRMLVADIP   86 (104)
T ss_dssp             EEEEEETTE-EEEEEECTTCSSCEEEHHHHHHCSSCCCCEEC--CCEEETTEEECCEEEEEEEEETTEEEEEEEEEESCS
T ss_pred             EEEEEECCE-EEEEEeccCCCcEEEccccCcccCCCCccCCc--cEEEeCCCeEEeeEeeeEEEECCeEEEEEEEECCCC
Confidence            467999987 56789999999999998888888876532222  56677665321111112       222223336678


Q ss_pred             cceeecchhhhhcccc
Q 041134          201 YNAILGRQWIHKMRVV  216 (267)
Q Consensus       201 yn~iLGrpwLh~~~ai  216 (267)
                      .| |+||.||.++++.
T Consensus        87 ~n-iiGRd~L~qlg~t  101 (104)
T 1fmb_A           87 VT-ILGRDILQDLGAK  101 (104)
T ss_dssp             SC-EECHHHHHHTTCC
T ss_pred             CC-EecHhHHhhcCcE
Confidence            77 8999999988764

>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=93.84  E-value=0.035  Score=44.08  Aligned_cols=87  Identities=21%  Similarity=0.345  Sum_probs=53.6

Q ss_pred             eEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeee--------eccee--eEEEEEee
Q 041134          127 LVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTY--------SDGSL--LTDFLVVK  196 (267)
Q Consensus       127 Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~--------~lG~i--~v~F~Vvd  196 (267)
                      .++++.|++..+ +.|+|+|++.-+|...-+.        +......+.|.+|....        .+|..  ...| +|.
T Consensus        23 P~v~i~I~G~~~-~~LlDTGAd~tVl~~~~~p--------~~~~p~~I~GiGG~i~vr~~~~i~IeI~g~~~~~~~-lV~   92 (132)
T 3slz_A           23 PRITLKVGGQPV-TFLVDTGAQHSVLTQNPGP--------LSDKSAWVQGATGGKRYRWTTDRKVHLATGKVTHSF-LHV   92 (132)
T ss_dssp             SEEEEEETTEEE-EEEECTTCSSCEECSCCCS--------EEEEEEEEECSSCEEEEEEECCEEEEETTEEEEECC-EEC
T ss_pred             CEEEEEECCEEE-EEEEeCCCCeEEEccccCC--------CCCCceEEEccCCEEEEEEEeeeEEEECCeeecceE-EEE
Confidence            357799999765 5789999998888643211        12223567777775331        11111  2233 333


Q ss_pred             eCCccceeecchhhhhcccccccceeeeeeecCCc
Q 041134          197 ATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTIYG  231 (267)
Q Consensus       197 ~~~~yn~iLGrpwLh~~~aipst~hq~vk~~~~~G  231 (267)
                      ...|.| ||||.||.++++.       +.|+.+.+
T Consensus        93 ~~tPvn-LLGrd~Ltqlg~t-------L~fp~~g~  119 (132)
T 3slz_A           93 PDCPYP-LLGRDLLTKLKAQ-------IHFEGSGA  119 (132)
T ss_dssp             TTSSSC-EECHHHHHHHTCE-------EEEETTEE
T ss_pred             CCCCcc-EECHhhHhhCCcE-------EECCCCCc
Confidence            556665 6999999999886       55665433

>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=90.25  E-value=1.1  Score=33.62  Aligned_cols=77  Identities=19%  Similarity=0.372  Sum_probs=44.8

Q ss_pred             EEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCee---------eeccee-eEEEEEeee
Q 041134          128 VISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVT---------YSDGSL-LTDFLVVKA  197 (267)
Q Consensus       128 vi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~---------~~lG~i-~v~F~Vvd~  197 (267)
                      ++++.|++.. ...|+|+|+-..++.     .+.. +...+|  ..+.|..|...         +--|+- .-+|.|  .
T Consensus        10 ~vti~I~Gq~-~e~LLDTGAD~TVl~-----~~~~-Pg~w~p--k~igGiGG~i~v~qy~~i~iei~g~~~~gtvlV--~   78 (99)
T 3ec0_A           10 VVTAYIEGQP-VEVLLDTGADDSIVA-----GIEL-GNNYSP--KIVGGIGGFINTKEYKNVEIEVLNKKVRATIMT--G   78 (99)
T ss_dssp             EEEEEETTEE-EEEEECTTCSSCEES-----SCCC-CSCCEE--EEEEETTEEEEEEEEEEEEEEETTEEEEEEEEE--E
T ss_pred             eEEEEECCEE-EEEEEecCCCceEEc-----Cccc-CCCCCc--eEEEecCCcEeeeEEeeEEEEECCeEEEEEEEe--C
Confidence            5679999965 567899999888873     1221 111222  24556554211         111221 222333  6


Q ss_pred             CCccceeecchhhhhcccc
Q 041134          198 TSPYNAILGRQWIHKMRVV  216 (267)
Q Consensus       198 ~~~yn~iLGrpwLh~~~ai  216 (267)
                      ++|.| |+||.+|.++++.
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            67887 6999999998764

>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=86.06  E-value=2.5  Score=31.60  Aligned_cols=77  Identities=29%  Similarity=0.562  Sum_probs=44.3

Q ss_pred             EEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCee---------eeccee-eEEEEEeee
Q 041134          128 VISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVT---------YSDGSL-LTDFLVVKA  197 (267)
Q Consensus       128 vi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~---------~~lG~i-~v~F~Vvd~  197 (267)
                      ++++.|++.. ...|+|+|+-.-++..     +..+. .-+  ...+.|..|...         +--|+- .-++.|  .
T Consensus        10 ~vtvkI~Gq~-~eaLLDTGAD~TVl~~-----~~~p~-~wk--pk~igGiGG~i~v~qy~qi~iei~g~~~~gtvlV--~   78 (99)
T 2hs1_A           10 LVTIKIGGQL-KEALLDTGADDTIIEE-----MSLPG-RWK--PKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLV--G   78 (99)
T ss_dssp             EEEEEETTEE-EEEEECTTCSSEEESC-----CSSCC-CCE--EEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEE--S
T ss_pred             EEEEEECCEE-EEEEeccCCCcEEEec-----ccCCC-CCC--CcEEEeCCCcEeeeEeccEEEEEeCCEEEEEEEe--C
Confidence            4678998865 5789999998888752     22211 111  124555543211         111111 222333  6


Q ss_pred             CCccceeecchhhhhcccc
Q 041134          198 TSPYNAILGRQWIHKMRVV  216 (267)
Q Consensus       198 ~~~yn~iLGrpwLh~~~ai  216 (267)
                      ++|.| |+||.||.++++.
T Consensus        79 ~tPvn-iiGRd~Ltqlg~t   96 (99)
T 2hs1_A           79 PTPVN-IIGRNLLTQIGAT   96 (99)
T ss_dssp             CCSSC-EECHHHHTTTTCE
T ss_pred             CCccC-chhHhHHHHcCCE
Confidence            67887 8999999988764

---

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	267
d2fmba_	104	EIAV protease {Equine infectious anemia virus [Tax	96.08
d1nsoa_	107	Mason-Pfizer monkey virus protease {Simian retrovi	89.31
d4fiva_	113	Feline immunodeficiency virus (FIV) protease {Feli	82.43

>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=96.08  E-value=0.011  Score=43.23  Aligned_cols=85  Identities=19%  Similarity=0.307  Sum_probs=50.5

Q ss_pred             EEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee-------eEEEEEeeeCCc
Q 041134          128 VISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL-------LTDFLVVKATSP  200 (267)
Q Consensus       128 vi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i-------~v~F~Vvd~~~~  200 (267)
                      ++++.|++..+. .|+|+|+-..++...-+..........  ......|..+.....--.+       .+.+.++-.+.|
T Consensus        10 ~~~i~I~Gq~v~-~LLDTGAD~TVI~~~~~p~~~~~~~~~--~~~~igg~g~~~~~~~~~v~i~~~g~~~~~~~lV~p~P   86 (104)
T d2fmba_          10 TTIVLINDTPLN-VLLDTGADTSVLTTAHYNRLKYRGRKY--QGTGIGGVGGNVETFSTPVTIKKKGRHIKTRMLVADIP   86 (104)
T ss_dssp             EEEEEETTEEEE-EEECTTCSSCEEEHHHHHHCSSCCCCE--ECCCEEETTEEECCEEEEEEEEETTEEEEEEEEEESCS
T ss_pred             EEEEEECCEEEE-EEEeCCCCeEEEcccccCccCCCCCCc--ceeEEEEecceEEEEEEEEEEEECCeEEEEEEEECCCC
Confidence            578899998775 889999999999877665432211111  1123333332211111111       333333444588


Q ss_pred             cceeecchhhhhcccc
Q 041134          201 YNAILGRQWIHKMRVV  216 (267)
Q Consensus       201 yn~iLGrpwLh~~~ai  216 (267)
                      .| |+||..|.+|++.
T Consensus        87 vn-LlGRdlL~qlG~~  101 (104)
T d2fmba_          87 VT-ILGRDILQDLGAK  101 (104)
T ss_dssp             SC-EECHHHHHHHTCC
T ss_pred             cc-eecHHHHHHhCCE
Confidence            88 9999999998874

>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=89.31  E-value=0.12  Score=37.47  Aligned_cols=82  Identities=18%  Similarity=0.295  Sum_probs=48.2

Q ss_pred             EEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcC-CCCCCCccEEeeeCCee--eec-------ceeeEEEE--Ee
Q 041134          128 VISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQD-KIKPFEQPLIGFSGIVT--YSD-------GSLLTDFL--VV  195 (267)
Q Consensus       128 vi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~-~L~~~~~~l~gf~g~~~--~~l-------G~i~v~F~--Vv  195 (267)
                      .+++.|++..+ ..|+|+|+-..++...-     .+.+ .+.+....+.|..|...  .+-       +.-...+.  ++
T Consensus        11 ~~~v~I~G~~v-~~LLDTGAD~TVI~~~~-----~p~~wp~~~~~~~~~GiGg~~~~~~~~~~l~~~~~~~~~~~~~p~v   84 (107)
T d1nsoa_          11 SLTLWLDDKMF-TGLINTGADVTIIKLED-----WPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFV   84 (107)
T ss_dssp             CEEEEETTEEE-EECCCSSCSSCBCCGGG-----SCTTSCCCCCEEEECSSSEEEECCCBCCCEEEEETTTEEEEECCBB
T ss_pred             EEEEEECCEEE-EeeecCCCCcEEEeccc-----cCCCCCcCcCccEEEEecCeeeEEEeeeeEEEEeCCCceEEEcceE
Confidence            46788888877 68999999998885442     2222 23444455666544211  010       11011111  12


Q ss_pred             eeCCccceeecchhhhhcccc
Q 041134          196 KATSPYNAILGRQWIHKMRVV  216 (267)
Q Consensus       196 d~~~~yn~iLGrpwLh~~~ai  216 (267)
                      =...|+| |+||..|.+|++.
T Consensus        85 v~~~Pvn-llGRd~L~qlg~~  104 (107)
T d1nsoa_          85 IPNLPVN-LWGRDLLSQMKIM  104 (107)
T ss_dssp             CTTCCCC-BCCHHHHHHHHTS
T ss_pred             CCCCCcC-cccHHHHHHhCCE
Confidence            2356888 9999999999864

>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=82.43  E-value=1  Score=32.70  Aligned_cols=27  Identities=26%  Similarity=0.516  Sum_probs=21.4

Q ss_pred             EEEeeeCCeeeeEEeecCCCccccchHH
Q 041134          128 VISIKIGNCLVRRILIDNGSSVNILDDA  155 (267)
Q Consensus       128 vi~~~I~~~~V~riLvD~GSs~nil~~~  155 (267)
                      .+++.|++..+ +.|+|+|+-..++...
T Consensus        12 ~v~v~I~Gq~v-~~LLDTGAD~TVi~~~   38 (113)
T d4fiva_          12 EILIFVNGYPI-KFLLDTGADITILNRR   38 (113)
T ss_dssp             EEEEEETTEEE-EEEECTTCSSCEEEGG
T ss_pred             eEEEEECCEEE-EEEEcCCCCcEEEecc
Confidence            57888988665 5899999998887543