Citrus Sinensis ID: 042094

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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-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-----
Protein Sequence
MTIKELEERVEQLSHQFNEKVEVLSQQSNDLQELILSLHDQFIRFQEDRNNNQPLQINNQQPEPAGRIGGALVQPRHIRLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMGNMTWAQFKRALVTQFGTFEDGDAVGTQNLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSNRRIPPRPSMSRPSPPLLNSSPTITKTGGSSQPSLLGPPPPGLPPFRRLSVAEQTERRAKGLCFNCDEQFKPGHRCKAPQLLLLDADIEDKDEQAEALEELPETLEVSLKALTGATPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDSLPPALANHGEINQLLLQEKQGIFFQIMAITTS
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccHHHHHHHHcccccccccccccHHccccccHHHHHHHHHHHccccccccccccccccHHHHHHHHHHccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHccHHHHHHHHHccccccccccEEEEEEcccEEEEEEEcccccccEEcHHHHHHHccccccccccEEEEccccEEEEEEEEEEEEEEEccEEEEEEEEEcccccccEEEcHHHHHHcccEEEEcccEEEEEEEccEEEEEEEccccccccccHHHHHHHHHHHcccEEEEEcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccEccccHHHHHHHHHHHcccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHcccccHHHHccHHHHHHHHHccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccHHcccccEEEEccccccccccccccccEEEEcccccccccccccccccccccEEEEEHHHHcccccEEEEEEEEccEEEEEEEEccccccHccHHHHHHccccEEcccccEEEEccccEEEEEEEcccEEEEEEcccccccEEEEccccccEEEEHHHHHHccccEEEcccEEEEEEEcccEEEEEEEcccccccccccHHcHccHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MTIKELEERVEQLSHQFNEKVEVLSQQSNDLQELILSLHDQFIRFqedrnnnqplqinnqqpepagriggalvqprhIRLDFLvlsgenptsliFRCEQYQRLAALLETDVLSLAIghldgdavpWYHWLEQTMGNMTWAQFKRALVTqfgtfedgdavgtqnlpesFFISCFLSGLREDIKIGVQmlkpasllQTFELARFQEEYAAVsnrripprpsmsrpsppllnssptitktggssqpsllgppppglppfrrlsVAEQTERRAKglcfncdeqfkpghrckapqlllldadieDKDEQAEALEELPETLEVSLKAltgatpqntmrlkgnlkkhgVTILIDsssthiflnsslakqygcpvttttQFQVTvadggvisssgkcshvpvnsqgfqfhldffllpvsgcdivlGAEWLRSLGAILWDFSKLTMQFTWkgqtvqltgydslppalanhgEINQLLLQEKQGIFFQIMAITTS
Flexible Loop (DISEMBL)
MTIKELEERVEQLSHQFNEKVEVLSQQSNDLQELILSLHDQFIRFQEDRNNNQPLQINNQQPEPAGRIGGALVQPRHIRLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMGNMTWAQFKRALVTQFGTFEDGDAVGTQNLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAavsnrripprpsmsrpsppllnSSPTITKTGGSSQPSLLGPPPPGLPPFRRLSVAEQTERRAKGLcfncdeqfkpghrCKAPQLLLLDADIEDKDEQAEALEELPETLEVSLKAltgatpqntmrlkgNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDSLPPALANHGEINQLLLQEKQGIFFQIMAITTS
Low Complexity Region (SEG)
MTIKELEERVEQLSHQFNEKVEVLSQQSNDLQELILSLHDQFIRFQEDRnnnqplqinnqqpepAGRIGGALVQPRHIRLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMGNMTWAQFKRALVTQFGTFEDGDAVGTQNLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVsnrripprpsmsrpsppllnsspTITKTggssqpsllgppppglppFRRLSVAEQTERRAKGLCFNCDEQFKPGHRCKAPQLLLLDADIEDKDeqaealeelpetleVSLKALTGATPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPvttttqfqvtvADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDSLPPALANHGEINQLLLQEKQGIFFQIMAITTS
Disordered region (IsUnstruct)
*******************************QELILSLHDQFIRF**********************IGGALVQPRHIRLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMGNMTWAQFKRALVTQFGTFEDGDAVGTQNLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAA*************************************************************KGLCFNCDEQFKPGHRCKAPQLLLLDAD***********************************LKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDSLPPALANHGEINQLLLQEKQGIFFQIMAI***
Disordered Region (DISOPRED)
*******************************************************************************LDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMGNMTWAQFKRALVTQFGTFEDGDAVGTQNLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSNR***********************************************************LCFNCDEQFKPGHRCKAPQLLLLDADIEDKDEQAEALEELPETLEVSLKALTGATPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTG*********************KQGIFFQIMAIT**
Disordered Region (DISEMBL)
**********EQLSHQFNEKVEVLSQQSNDLQELILSLHDQFIRFQEDRNNNQPLQINNQQPEPAGRIGGALVQPRHIRLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMGNMTWAQFKRALVTQFGTFEDGDAVGTQNLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSNRRIPPRPSMSRPSPPLLNSSPTITKTGGSSQPSLLGPPPPGLPPFRRLSVAEQTERRAKGLCFNCDEQFKPGHRCKAPQLLLLDADIEDKDEQAEALEELPETLEVSLKALTGATPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDSLPPALANHGEINQLLLQEKQGIFFQIMAITTS
Disordered Region (DISPRO)
*******ERVEQLSHQFNEKVEVLSQQSNDLQELILSLHDQF********************************PRHIRLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMGNMTWAQFKRALVTQFGTFEDGDAVGTQNLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSN********************************************************RAKGLCFNCDEQFKPGHRCKAPQLLLLDAD**************PETLEVSLKALTGATPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDSLPP**ANHGEINQLLLQEKQGIFFQIMAITTS
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTxxxxxxxxxxxxxxxxxxxxxLSQQSNDLQELILSLHDQFIRFQEDRNNNQPLQINNQQPEPAGRIGGALVQPRHIRLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMGNMTWAQFKRALVTQFGTFEDGDAVGTQNLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSNRRIPPRPSMSRPSPPLLNSSPTITKTGGSSQPSLLGPPPPGLPPFRRLSVAEQTERRAKGLCFNCDEQFKPGHRCKAPQxxxxxxxxxxxxxxxxxxxxxPETLEVSLKALTGATPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDSLPPALANHGEINQLLLQEKQGIFFQIMAITTS
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

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	485	2.2.26 [Sep-21-2011]
Q7LHG5	1498	Transposon Ty3-I Gag-Pol	yes	no	0.305	0.098	0.251	0.0003

>sp|Q7LHG5|YI31B_YEAST Transposon Ty3-I Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TY3B-I PE=3 SV=2

 Score = 47.0 bits (110), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 41/163 (25%), Positives = 73/163 (44%), Gaps = 15/163 (9%)

Query: 272 LCFNCDEQFKPGHR---CKAPQLLLLDADIEDKDEQAEALEELPETLEVSLKALTGATPQ 328
           LCF C    K GHR   C+A + +L D ++E KD+Q   ++ LP    +++  +   T +
Sbjct: 266 LCFYCK---KEGHRLNECRARKAVLTDLELESKDQQTLFIKTLPIVHYIAIPEMDN-TAE 321

Query: 329 NTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAK--QYGCPVTTTTQFQVTVADGGVISSS 386
            T++++       V  L DS S   F+   + +  +Y    T   +F+  VA    ++S 
Sbjct: 322 KTIKIQNT----KVKTLFDSGSPTSFIRRDIVELLKYEIYETPPLRFRGFVATKSAVTSE 377

Query: 387 GKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAIL 429
                + +N    Q  L  ++L      +++G   LR    IL
Sbjct: 378 AVTIDLKIND--LQITLAAYILDNMDYQLLIGNPILRRYPKIL 418

Integrase (IN) targets the VLP to the nucleus, where a subparticle preintegration complex (PIC) containing at least integrase and the newly synthesized dsDNA copy of the retrotransposon must transit the nuclear membrane. Once in the nucleus, integrase performs the integration of the dsDNA into the host genome.
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)
EC: 3EC: .EC: 1EC: .EC: 2EC: 6EC: .EC: 4

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	485
147774273	1469	hypothetical protein VITISV_026680 [Viti	0.942	0.311	0.311	1e-65
147789424	2822	hypothetical protein VITISV_017554 [Viti	0.861	0.148	0.329	4e-65
147783182	1360	hypothetical protein VITISV_039388 [Viti	0.8	0.285	0.314	1e-57
359479937	787	PREDICTED: uncharacterized protein LOC10	0.752	0.463	0.330	6e-55
147843077	1366	hypothetical protein VITISV_044100 [Viti	0.678	0.240	0.340	1e-54
147860462	1384	hypothetical protein VITISV_014148 [Viti	0.938	0.328	0.284	7e-50
356511037	1863	PREDICTED: uncharacterized protein LOC10	0.806	0.209	0.315	1e-49
147860532	1241	hypothetical protein VITISV_034528 [Viti	0.880	0.344	0.284	6e-49
147838975	566	hypothetical protein VITISV_042364 [Viti	0.861	0.738	0.294	1e-48
89887334	1359	polyprotein [Primula vulgaris]	0.754	0.269	0.321	1e-48

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

 Score =  257 bits (656), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 164/526 (31%), Positives = 266/526 (50%), Gaps = 69/526 (13%)

Query: 2   TIKELEERVEQLSHQFNEKVEVLSQQSNDLQELILSLHDQFIRFQEDRNNNQPLQINNQQ 61
            +K+ +E+ +Q  +   + VE L+ Q     E++ S     ++ +   N+        Q 
Sbjct: 18  AVKQNQEQYQQNHNSLQQVVEGLAHQ----LEVVASNVQTLVQMKTKHNSGDSEGSKRQM 73

Query: 62  PEPAGRIGGALVQPRHIRLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDG 121
             P     G  +Q R +RLDF   +GE+P   ++R +Q+           + LA  H++G
Sbjct: 74  TNPLFEDNGG-IQTRAVRLDFPKFNGEDPNGWVYRADQFFNYHQTNPHHRVLLASFHMEG 132

Query: 122 DAVPWYHWLEQTMGNMTWAQFKRALVTQFGT--FEDG--------------------DAV 159
            A+ W+  +E   G  +W  F RAL T+FG+  +ED                     +A+
Sbjct: 133 KALVWFQDIEAAGGISSWEGFVRALQTRFGSSPYEDPMEALIRLKQTSTVEDYKSQFEAL 192

Query: 160 GTQ--NLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSNR----- 212
             Q   L ES+ +SCFLSGLRE+I+  V+ML P++L   F LA+ QEE  A   R     
Sbjct: 193 SNQLRGLAESYKLSCFLSGLRENIRFMVRMLNPSNLHIAFGLAKMQEENVAALRRTAKLG 252

Query: 213 RIPPRPSMSRPSPPLLNSSPTITKTGGSSQPSLLGPPPPGLPPFRRLSVAEQTERRAKGL 272
            +P R ++  PSPP   +                      + P +RLS ++  ERR KGL
Sbjct: 253 SVPTRLAIGPPSPPEKRA----------------------IVPVQRLSPSQMKERRDKGL 290

Query: 273 CFNCDEQFKPGHRCKAPQLLLLDADIEDKDE----------QAEALEELPET-LE--VSL 319
           C+NCD+++ PGH+CK+ +L +++ D    DE           +++ EE P   +E  +S+
Sbjct: 291 CYNCDDKWAPGHKCKSARLFIMECDESSDDEVPKSEVAEGRASKSKEETPIVEIEPGISI 350

Query: 320 KALTGATPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVAD 379
            AL G+    TMR  G++    V IL+D+ STH F++ S+ ++   P   T    V VA+
Sbjct: 351 HALVGSPNPKTMRFLGHICGRAVVILVDTGSTHNFMDPSVIQRAHLPSNPTEGLSVKVAN 410

Query: 380 GGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQF 439
           G  + S G C+ VP++ QG  + +DF++L + GCDIVLG +WL++LG ILWDFS+L M+F
Sbjct: 411 GQAVRSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIVLGVQWLQTLGPILWDFSRLQMEF 470

Query: 440 TWKGQTVQLTGYDSLPPALANHGEINQLLLQEKQGIFFQIMAITTS 485
           +   +  +L G      +L    +  ++  Q K+G+  Q++    S
Sbjct: 471 SVWDKPRKLQGMSPTGISLVEGEKFGKVSRQNKRGLVIQLIDFENS 516

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  255 bits (651), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 160/485 (32%), Positives = 252/485 (51%), Gaps = 67/485 (13%)

Query: 44  RFQEDRNNNQPLQIN-NQQPEPAGRIGGALVQPRHIRLDFLVLSGENPTSLIFRCEQYQR 102
           ++Q+  N+ Q   +  N++  P+ R GG  +Q R +RLDF   +GE+P+  ++R +Q+  
Sbjct: 21  QYQQXHNSLQQAWLKGNRRTGPSIRNGG--IQTRAVRLDFPKFNGEDPSGWVYRADQFFN 78

Query: 103 LAALLETDVLSLAIGHLDGDAVPWYHWLEQTMGNMTWAQFKRALVTQFG----------- 151
                    + LA  H++G A+ W+  +E   G  +W  F RAL T+FG           
Sbjct: 79  YHQTNPHHRVLLASFHMEGKALVWFQDIEAAGGISSWEGFVRALQTRFGSSPYENPMEAL 138

Query: 152 -------TFEDG----DAVGTQ--NLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFE 198
                  T ED     +A+  Q   L ES+ +SCFLSGLREDI+  V ML P++L   F 
Sbjct: 139 IRLKQTSTVEDYKSQFEALSNQLRGLAESYKLSCFLSGLREDIRFMVCMLNPSNLHIAFG 198

Query: 199 LARFQEEYAAVSNR-----RIPPRPSMSRPSPPLLNSSPTITKTGGSSQPSLLGPPPPGL 253
           LA+ QEE  A   R      +P R ++  PSPP                          +
Sbjct: 199 LAKMQEENVAALRRTAKLGSVPTRLAIGPPSPP----------------------EKRVI 236

Query: 254 PPFRRLSVAEQTERRAKGLCFNCDEQFKPGHRCKAPQLLLLDADIEDKDE---------- 303
            P +RLS ++  ERR KGLC+NCD+++ PGH+CK+ +L +++ D    D+          
Sbjct: 237 VPVQRLSPSQMKERRDKGLCYNCDDKWAPGHKCKSARLFIMECDESSDDKVPKSEVAEGR 296

Query: 304 QAEALEELPET-LE--VSLKALTGATPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLA 360
            +++ EE P   +E  +S+ AL G+    TMR  G++    V IL+D+ STH F++ S+ 
Sbjct: 297 ASKSKEETPIVEIEPGISIHALVGSPNPKTMRFLGHICGRAVVILVDTGSTHNFMDPSVI 356

Query: 361 KQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAE 420
           ++   P   T    V VA+G  + S G C+ VP++ QG  + +DF++L + GCDIVLG +
Sbjct: 357 QRAHLPSNPTEGLSVKVANGQAVCSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIVLGVQ 416

Query: 421 WLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDSLPPALANHGEINQLLLQEKQGIFFQIM 480
           WL++LG ILWDFS+L M+F+   +  +L G      +L       ++  Q K+G+  Q++
Sbjct: 417 WLQTLGPILWDFSRLQMEFSVWDKPQKLQGMAPTGISLVEGENFGKVSRQNKRGLVIQLI 476

Query: 481 AITTS 485
               S
Sbjct: 477 DFENS 481

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147783182|emb|CAN68669.1| hypothetical protein VITISV_039388 [Vitis vinifera]

 Score =  230 bits (587), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 141/448 (31%), Positives = 228/448 (50%), Gaps = 60/448 (13%)

Query: 76  RHIRLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMG 135
           +H++L F   +G++PT  I++ EQY     +     + LA  HL+G A+ W+ WL +  G
Sbjct: 81  QHLKLSFPKFNGDDPTGWIYKAEQYFDFMNITPGQQVQLASFHLEGIALQWHRWLTKFRG 140

Query: 136 NMTWAQFKRALVTQFG--TFEDGDAVGTQ----------------------NLPESFFIS 171
            +TW +F +A+  +FG   +ED     T+                       LPE+F I 
Sbjct: 141 PLTWDEFTKAVQLRFGPTDYEDPSEALTRLKQTTTVAAYQEAFEKLSHRVDGLPENFLIG 200

Query: 172 CFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSNRRIPPRPSMSRPSPPLLNSS 231
           CF++GL+++I+I V++ +P +L  T  +AR  EE   +  +R P + +  +P+     +S
Sbjct: 201 CFIAGLQDEIRIDVKIKQPRTLADTIGVARLIEERNQL--QRKPTQQTRFQPASVTPKAS 258

Query: 232 PTITKTGGSSQPSLLGPPP-----------PGLPPFRRLSVAEQTERRAKGLCFNCDEQF 280
           P  T         +LGPPP           P    F R++  E  ERR KGLC+ CDE+F
Sbjct: 259 PNPTA-------GVLGPPPTQHMNQSSNAQPAT--FHRITNQEARERREKGLCYYCDEKF 309

Query: 281 KPGHRCKAPQLLLLD-------ADIEDKDEQAEALEELPETLEVSLKALTGATPQNTMRL 333
             GHRC+ PQL +++        D+E    + E  E +PE   +   A+ G     T+ +
Sbjct: 310 VAGHRCERPQLFMIEDSPHMNTEDVEGAHPEQEHHEVIPE---IYFHAIAGTEHPQTICV 366

Query: 334 KGNLKKHGVTILIDSSSTHIFLNSSL-AKQYGCPVTTTTQFQVTVADGGVISSSGKCSHV 392
            G LK   V +LID  STH F++ ++   ++G PV    +F+V VA+   I  +G+C  +
Sbjct: 367 MGKLKNKNVMVLIDGGSTHNFIDQAIIVFKFGLPVIRDRKFEVMVANREKIECAGQCRSL 426

Query: 393 PVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYD 452
            +  QG+    D+++LPV+ C +VLG +WL +LG I  D+ +LTM F  +G +    G  
Sbjct: 427 TLTIQGYSVTADYYILPVAACQLVLGVQWLETLGPIEMDYKQLTMNFKMEGTSHTFQGLG 486

Query: 453 SLPPALANHGEINQLLLQEKQGIFFQIM 480
                  ++ E N L   +  G+FFQI+
Sbjct: 487 RTGIEALSNKESNGL---QGTGLFFQII 511

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  221 bits (563), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 142/430 (33%), Positives = 211/430 (49%), Gaps = 65/430 (15%)

Query: 69  GGALVQPRHIRLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYH 128
           G  +V  +  +L+F   SG++PT    R EQ+    +  E   + +A  HL+G+A  W+ 
Sbjct: 43  GRQIVSSKSAKLEFPRFSGDDPTEWFNRVEQFFDYQSTAENQKVPMAAYHLEGEANQWWQ 102

Query: 129 WLEQTMGN----MTWAQFKRALVTQFG--TFEDGDA-------VGT-------------- 161
           WL +T+      ++W +F+  L  +FG    ED D        +GT              
Sbjct: 103 WLHRTLKEEGHVISWEKFEEELWARFGPSGCEDFDEALSRIKQLGTLRDYQREFEKLGNR 162

Query: 162 -QNLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSNRRI---PPR 217
            Q   +   +  F+ GL+ +I   ++M KP SL +   LAR +++  A   R +   P R
Sbjct: 163 VQGWTQKALVGTFMGGLKAEIVDAIRMFKPQSLKEVINLARMRDDQIARQRRFMWLPPVR 222

Query: 218 PSMSRPSPPLLNSSPTITKTGGSSQPSLLGPPPPGLPPFRRLSVAEQTERRAKGLCFNCD 277
             ++ P                  Q + + P  P   P + LS  E   +RA+GLCFNC+
Sbjct: 223 APIALP------------------QATRVDPAIPA-KPIKSLSWEEMQRKRAQGLCFNCN 263

Query: 278 EQFKPGHRCKAPQLLLL-------------DADIEDKDEQAEALE--ELPETLEVSLKAL 322
           E+F  GHRC+ PQLLLL             D    + D   EA E  E    LE++L AL
Sbjct: 264 ERFTAGHRCQKPQLLLLKGHEGNVDCGNGTDQQTWEDDHGGEAAEVQEHEPKLEITLHAL 323

Query: 323 TGATPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV 382
           TG T   TMR+   +  H V +LIDS STH F+++ LA +   PV  T  F V VA+G  
Sbjct: 324 TGWTAPKTMRVTAKMGPHEVMVLIDSGSTHNFISNRLANKLRLPVIPTETFPVWVANGER 383

Query: 383 ISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWK 442
           +   G+   V V  QG +F+L  F LP+SG D+VLG +WL  LG+++ ++ +LTM F W+
Sbjct: 384 LKCQGRYDKVRVELQGTEFYLTLFSLPLSGLDLVLGVQWLEMLGSVVCNWKQLTMDFIWE 443

Query: 443 GQTVQLTGYD 452
            Q  +L G D
Sbjct: 444 NQDRRLQGVD 453

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  220 bits (561), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 134/393 (34%), Positives = 207/393 (52%), Gaps = 64/393 (16%)

Query: 135 GNMTWAQFKRALVTQFGT--FEDG--------------------DAVGTQ--NLPESFFI 170
           G  +W  F RAL T+FG+  +ED                     +A+  Q   L ES+ +
Sbjct: 113 GISSWEGFVRALQTRFGSSPYEDPMEALIRLKQTSTVEDYKSQFEALSNQLRGLAESYKL 172

Query: 171 SCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSNR-----RIPPRPSMSRPSP 225
           SCFLSGLREDI+  V+ML P++L   F LA+ QEE  A   R      +P R ++  PSP
Sbjct: 173 SCFLSGLREDIRFMVRMLNPSNLHIAFGLAKMQEENXAALRRTAKLGSVPTRLAIGPPSP 232

Query: 226 PLLNSSPTITKTGGSSQPSLLGPPPPGLPPFRRLSVAEQTERRAKGLCFNCDEQFKPGHR 285
           P   +                      + P +RLS ++  ERR KGLC+NCD+++ PGH+
Sbjct: 233 PEKRA----------------------IVPVQRLSPSQMKERRDKGLCYNCDDKWAPGHK 270

Query: 286 CKAPQLLLLDADIEDKDE----------QAEALEELPET-LE--VSLKALTGATPQNTMR 332
           CK+ +L +++ D    DE           +++ EE P   +E  +S+ AL G+    TMR
Sbjct: 271 CKSXRLFIMECDESSDDEVPKSEVAEGRASKSKEETPIVEIEPGISIHALVGSPNPKTMR 330

Query: 333 LKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHV 392
             G++    V IL+D+ STH F++ S+ ++   P   T    V VA+G  + S G C+ V
Sbjct: 331 FLGHICGRAVVILVDTGSTHNFMDPSVIQRAHLPSNPTEGLSVKVANGQAVRSEGSCAAV 390

Query: 393 PVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYD 452
           P++ QG  + +DF++L + GCDIVLG +WL++LG ILWDFS+L M+F+   +  +L G  
Sbjct: 391 PLHMQGNLYTIDFYILTLGGCDIVLGVQWLQTLGPILWDFSRLQMEFSVWDKPRKLQGMS 450

Query: 453 SLPPALANHGEINQLLLQEKQGIFFQIMAITTS 485
               +L    +  ++  Q K+G+  Q++    S
Sbjct: 451 PTGISLVEGEKFGKVSRQNKRGLVIQLIDFENS 483

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860462|emb|CAN82562.1| hypothetical protein VITISV_014148 [Vitis vinifera]

 Score =  204 bits (520), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 147/517 (28%), Positives = 240/517 (46%), Gaps = 62/517 (11%)

Query: 6   LEERVEQLSHQFNEKVEVLSQQSNDLQELILSLHDQFIRFQEDRNNNQPLQINNQQPEPA 65
           L++ + ++     +K+  + +  + L E +LS  ++      DRN     ++ N +    
Sbjct: 73  LQDGMSRMELGLTDKLHQMEETIHRLSEALLSNKERSSSNTNDRNG----RVRNNRDNSK 128

Query: 66  GRIGGA--LVQPRHIRLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDA 123
           G++ G   +   +  +L+F   SG +PT    + +Q+     +     +SL   HL+G+A
Sbjct: 129 GQMEGGQQMFLSKLAKLEFPKYSGNDPTEWFNKVDQFFEYQGIPAAQKVSLXSFHLEGEA 188

Query: 124 VPWYHWLEQTMGN----MTWAQFKRALVTQFG--TFEDGDAV------------------ 159
             W+ WL ++       + WA F+  L  +FG    ED D                    
Sbjct: 189 NQWWQWLRRSYSEEGKEVAWADFEEELWARFGPTECEDFDEALSRVKQMSSLRDYQREFE 248

Query: 160 ----GTQNLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSNRRIP 215
                 Q   +   +  F+  L+ +I   ++M KP SL +   LAR +++      R   
Sbjct: 249 KLGNRVQGWTQKALVGTFMGSLKSEIADDIRMFKPKSLKEAIXLARXRDDQLTRQRR--- 305

Query: 216 PRPSMSRPSPPLLNSSPTITKTGGSSQPSLLGPPPPGLPPFRRLSVAEQTERRAKGLCFN 275
                +RP  P  N       T   S+P+         P  +RL+  E  +RRA+GLCFN
Sbjct: 306 ----FTRPLQP--NWPQPDFSTQMKSKPT---------PTMKRLTWEEMQKRRAQGLCFN 350

Query: 276 CDEQFKPGHRCKAPQLLLLDADIEDKDEQAE-------ALEELPETLEVSLKALTGATPQ 328
           CD++F  GH+C+ PQLLLL+ +     E          A+ E  E  E+   ALTG +  
Sbjct: 351 CDDKFTVGHKCRGPQLLLLEGNSSPNKEDDIDEEIEEPAINEQTEP-EIFFHALTGWSTP 409

Query: 329 NTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGK 388
            TMR+   + +H V +LIDS STH F++  +      P   T  F V VA+G  +   G+
Sbjct: 410 KTMRITTKIGQHEVVVLIDSGSTHNFISEKVVDMLHLPXVPTDPFTVKVANGTPLKCQGR 469

Query: 389 CSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQL 448
             HV V  QG  F L  + LP++G D+VLG +WL  LG I+ ++ KLTM+F W+ QT +L
Sbjct: 470 FEHVHVILQGIPFSLTLYSLPLTGLDLVLGVQWLEQLGTIVCNWKKLTMEFQWZNQTHKL 529

Query: 449 TGYDSLPPALANHGEINQLLLQEKQGIFFQIMAITTS 485
            G ++    +A+   +++ L Q +    F I   +TS
Sbjct: 530 QGTNTQTIQVASLKAVSKELRQGRS--MFAICLQSTS 564

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356511037|ref|XP_003524238.1| PREDICTED: uncharacterized protein LOC100782971 [Glycine max]

 Score =  203 bits (517), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 140/444 (31%), Positives = 208/444 (46%), Gaps = 53/444 (11%)

Query: 79  RLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMGNMT 138
           +LD     G +P   IF+  Q+       E + +++A  +LDG A+ W+ W+ Q     +
Sbjct: 31  KLDVPCFDGHDPLGWIFKISQFFEYQGTPEEERITVASFYLDGAALSWFQWMHQNGFITS 90

Query: 139 WAQFKRALVTQFG-TFEDG----------DAVGTQNLPE-------------SFFISCFL 174
           W    +A+ T+F  +F D            A  T+ L E                +SCF+
Sbjct: 91  WPALLQAIETRFAPSFYDDPRGALFKLTQRASVTEYLTEFERLANRIVGLSPPMLLSCFV 150

Query: 175 SGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSNRRIPPRPSMSRPSPPLLNSSPTI 234
           SGL  +I+  VQ  +P SL     LAR QE+   +++RR   R S+  P  P    SP++
Sbjct: 151 SGLNTEIRREVQAFQPVSLPHAMALARLQED--KLNDRRKHSRTSLPPPQTP----SPSL 204

Query: 235 TKTGGSSQPSLLGPPPPGLPPFRRLSVAEQTERRAKGLCFNCDEQFKPGHRCKAPQLLLL 294
           T             PP   PPF + +  E   RR KGLC+NC+E++   HRCK   LL +
Sbjct: 205 TTQHQ---------PPRTKPPFVQRTPEEMAYRREKGLCYNCEEKWSSSHRCKGRVLLFI 255

Query: 295 -DAD---------IEDKDEQAEA----LEELPETLEVSLKALTGATPQNTMRLKGNLKKH 340
            D+D         +ED     +A     +  P    +SL A+ G    +T RL G +   
Sbjct: 256 ADSDEASSMDNPSMEDPAPPTQATLPPFDPTPLLPHISLHAMAGVPATDTFRLYGVINHT 315

Query: 341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQ 400
            VTIL+DS STH F+   +AK  G P+  TT  QV V +G V+     C    +  Q   
Sbjct: 316 RVTILVDSGSTHNFVQPRIAKFLGLPMEDTTSLQVMVGNGSVLECKQSCPATTLLLQQHS 375

Query: 401 FHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDSLPPALAN 460
           F +   +LP+SG D+VLG EWLR+LG I+ D++  TMQFT  GQ + L    +     A+
Sbjct: 376 FTVTLRVLPISGADVVLGVEWLRTLGPIITDYTSFTMQFTHLGQPIILRADVTTCTDTAS 435

Query: 461 HGEINQLLLQEKQGIFFQIMAITT 484
             ++ +LL        F +  + T
Sbjct: 436 AHQVKRLLHTHSLSGLFHLSLLPT 459

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860532|emb|CAN81876.1| hypothetical protein VITISV_034528 [Vitis vinifera]

 Score =  201 bits (511), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 139/488 (28%), Positives = 226/488 (46%), Gaps = 61/488 (12%)

Query: 24  LSQQSNDLQELILSLHDQFIRFQE---DRNNNQPLQINNQQPEPAGRIGGA--LVQPRHI 78
           L+ + + ++E I  L +  +  +E      N++   + N +    G + G   +   +  
Sbjct: 8   LTDKXHQMEETIHRLSEALLSNKEXSSSNTNDRNGXVRNNRDNSKGXMEGGQQMFLSKLA 67

Query: 79  RLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMGN-- 136
           +L+F   SG +PT    + +Q+     +     +SLA  HL+G+A  W+ WL ++     
Sbjct: 68  KLEFPRYSGNDPTEWFNKVDQFFEYQGIPVAQKVSLASFHLEGEANQWWQWLRRSYSEEG 127

Query: 137 --MTWAQFKRALVTQFG--TFEDGDAV----------------------GTQNLPESFFI 170
             + WA F+  L  +FG    ED D                          Q   +   +
Sbjct: 128 KEVXWADFEEELWARFGPTECEDFDEALSRVKQMGSLRDYQREFEKLGNRVQGWTQKALV 187

Query: 171 SCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSNR--RIPPRPSMSRPSPPLL 228
             F+ GL+ +I   ++M KP SL +   LAR +++      R  R              +
Sbjct: 188 GTFMGGLKSEIADXIRMFKPKSLKEAISLARMRDDQLTRQXRFTRPLQPNXPQPBFSTQM 247

Query: 229 NSSPTITKTGGSSQPSLLGPPPPGLPPFRRLSVAEQTERRAKGLCFNCDEQFKPGHRCKA 288
            S PT                    P  +RL+  E  +RRA GL FNCD++F  GH+C+ 
Sbjct: 248 KSKPT--------------------PXMKRLTWEEMQKRRAXGLXFNCDDKFTXGHKCRG 287

Query: 289 PQLLLLDAD-IEDKDEQAEALEELPETLE-----VSLKALTGATPQNTMRLKGNLKKHGV 342
           PQLLLL+ + I +K++  +   E P   E     +S  ALTG +   TMR+   + +H V
Sbjct: 288 PQLLLLEGNSIPNKEDDIDEEIEEPAINEQTKPEISFHALTGWSTPKTMRITAKIGQHKV 347

Query: 343 TILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFH 402
            +LIDS STH F++  +A     PV  T  F V VA+G  +   G+  HV V  QG  F 
Sbjct: 348 VVLIDSGSTHNFISEKVADMLHLPVVPTKPFTVKVANGTPLKCQGRFEHVHVILQGIPFS 407

Query: 403 LDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDSLPPALANHG 462
           L  + LP++G D+VLG +WL  L  ++ ++ KLTM+F W+ QT +L G ++    +A+  
Sbjct: 408 LTLYSLPLTGLDLVLGVQWLEQLETVVCNWKKLTMEFQWENQTHKLQGTNTQTIQVASLK 467

Query: 463 EINQLLLQ 470
            +++ L Q
Sbjct: 468 AVSKELRQ 475

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147838975|emb|CAN68101.1| hypothetical protein VITISV_042364 [Vitis vinifera]

 Score =  200 bits (508), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 140/476 (29%), Positives = 223/476 (46%), Gaps = 58/476 (12%)

Query: 31  LQELILSLHDQFIRFQEDRNNNQPLQINNQQPEPAGRIGGA--LVQPRHIRLDFLVLSGE 88
           L E +LS  +       DRN     ++ N +     ++GG   +   +  +L+F   SG 
Sbjct: 8   LSEALLSNKEGSSSNTNDRNG----RVRNNRDNSKKQMGGGQQMFLSKLAKLEFPRYSGN 63

Query: 89  NPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMGN----MTWAQFKR 144
           +PT    + +Q+     +     +SLA  HL+G+   W+ WL ++       + WA F+ 
Sbjct: 64  DPTEWFNKVDQFFEYQGIPAAQKVSLASFHLEGETNQWWQWLRRSYSEEGKEVAWADFEE 123

Query: 145 ALVTQFGTFEDGD---------AVGT---------------QNLPESFFISCFLSGLRED 180
            L  +FG  E  D          +G+               Q   +   +  F+ GL+ +
Sbjct: 124 ELWARFGPTECEDFDEALSRVKQMGSLRDYQREFEKLGNRVQGWTQKALVGMFMGGLKSE 183

Query: 181 IKIGVQMLKPASLLQTFELARFQEEYAAVSNRRIPPRPSMSRPSPPLLNSSPTITKTGGS 240
           I   ++M KP SL +   LAR +++      R   P    + P P           T   
Sbjct: 184 IADDIRMFKPKSLKEAISLARMRDDQLTCQXRFTRPL-QXNXPQPBF--------STQMK 234

Query: 241 SQPSLLGPPPPGLPPFRRLSVAEQTERRAKGLCFNCDEQFKPGHRCKAPQLLLLDADIE- 299
           S+P+         P  +RL+  E  +RRA GL FNCD++F  GH+C+ PQLLLL+ +   
Sbjct: 235 SKPT---------PTMKRLTWEEMXKRRAXGLXFNCDDKFTXGHKCRGPQLLLLEGNSXP 285

Query: 300 DKDEQAEALEELPETLE-----VSLKALTGATPQNTMRLKGNLKKHGVTILIDSSSTHIF 354
           +K+   +   E P   E     +S  ALTG +   TMR+   + +H V +LIDS STH F
Sbjct: 286 NKENDIDEEIEEPAINEQTEPXISFHALTGWSTPKTMRITTKIAQHEVVVLIDSGSTHNF 345

Query: 355 LNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCD 414
           ++  +A     PV  T  F V VA+G  +    +  HV V  QG  F L  + LP++  D
Sbjct: 346 ISEKVAYMLHLPVVPTKPFTVKVANGTPLKCQWRFEHVHVILQGIPFSLTLYSLPLTXLD 405

Query: 415 IVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDSLPPALANHGEINQLLLQ 470
           +VLG +WL  LG ++ ++ KLTM+F W+ QT +L G ++    +A+   I++ L Q
Sbjct: 406 LVLGVQWLEQLGTVVCNWKKLTMEFQWENQTHKLQGTNTQTIQVASLKAISKELRQ 461

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  200 bits (508), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 131/408 (32%), Positives = 204/408 (50%), Gaps = 42/408 (10%)

Query: 76  RHIRLDFLVLSGENPTSLIFRCEQYQRLAALLETDVLSLAIGHLDGDAVPWYHWLEQTMG 135
           R IRLDF    GEN    +++  Q+  L    ET  + +A  H +G  + WY  LE++  
Sbjct: 18  RTIRLDFPKFYGENVVEWVYKANQFFSLYQTPETQRIKIANLHFEGQPLVWYQNLEKSDL 77

Query: 136 NMTWAQFKRALVTQFG------------TFEDGDAVG------------TQNLPESFFIS 171
             +W      +  +FG              +  ++V              ++L E   ++
Sbjct: 78  ISSWDNLCDQMTKRFGENLNENPLDQLIKLKQRNSVKEYKSDFEIISNRVKDLSEEHKLT 137

Query: 172 CFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAAVSNRRIPPRPSMSRPSPPLLNSS 231
            F+ GL+E+I + V+ML P S+   F +A++QEE   +  +  P   +    +P   N+ 
Sbjct: 138 YFICGLKEEIGLTVKMLFPKSIETAFSIAKYQEEKLHLEKK--PNFRTFQSQAP---NNQ 192

Query: 232 PTITKTGGSSQPSLLGPPPPGLPPFRRLSVAEQTERRAKGLCFNCDEQFKPGHRCKAPQL 291
            T +KT  ++  +        LPP +RL+  E T+RR K LC+NCDE++  GH C  P++
Sbjct: 193 ATFSKTNNTTAIT-------KLPPIKRLTQDELTDRRQKNLCYNCDEKWFRGHVCVKPKI 245

Query: 292 LLLDADIEDKDEQAE-ALEELPETL-----EVSLKALTGATPQNTMRLKGNLKKHGVTIL 345
            LL    E ++E  E ++EE+ E +     E++L+A+TG T   ++R  G LK   V+IL
Sbjct: 246 FLLQNVEEFENEINEESVEEIDENIVGENAEITLQAITGVTNSTSIRFVGKLKGQKVSIL 305

Query: 346 IDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDF 405
           +DS STH F++             +   +V +A+G  I SSG C  V +  Q  QF +DF
Sbjct: 306 VDSGSTHNFIDPKWVPLLKLSNVQSDIMEVKIANGDKIKSSGTCEKVKLLIQENQFEVDF 365

Query: 406 FLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDS 453
            LLP+ G D+VLG  WL  LG I  DF  LTM FT   + V L G ++
Sbjct: 366 LLLPLVGYDLVLGVHWLSQLGVINCDFKNLTMTFTHGNKKVCLKGLNN 413

Source: Primula vulgaris

Species: Primula vulgaris

Genus: Primula

Family: Primulaceae

Order: Ericales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	485
TAIR|locus:2091793	421	AT3G29750 [Arabidopsis thalian	0.253	0.292	0.264	0.00054

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

 Score = 110 (43.8 bits), Expect = 0.00054, Sum P(2) = 0.00054
 Identities = 33/125 (26%), Positives = 50/125 (40%)

Query:   326 TPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPXXXXXXXXXXXADGGVISS 385
             T    MR  G +  H V + IDS +T  F+   LA     P                I S
Sbjct:   119 TRNKGMRFYGFILDHKVVVAIDSGATDNFILVELAFSLKLPTSITNQASVLLGQRQCIQS 178

Query:   386 SGKCSHVPVNSQGFQFHLDFFLLPVS--GCDIVLGAEWLRSLGAILWDFSKLTMQFTWKG 443
              G C  + +  Q  +   +F LL ++    D++LG EWL  LG  + ++      F+   
Sbjct:   179 VGTCLGIRLWVQEVEITENFLLLDLAKTDVDVILGYEWLSKLGETMVNWQNQDFSFSHNQ 238

Query:   444 QTVQL 448
             Q + L
Sbjct:   239 QWITL 243

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: LOC_Os02g01470.1 retrotransposon protein, putative, unclassified (525 aa) (Oryza sativa Japonica)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	485
cd00303	92	cd00303, retropepsin_like, Retropepsins; pepsin-li	3e-18
pfam08284	135	pfam08284, RVP_2, Retroviral aspartyl protease	1e-09
pfam03732	97	pfam03732, Retrotrans_gag, Retrotransposon gag pro	7e-05

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

 Score = 79.3 bits (196), Expect = 3e-18
 Identities = 30/92 (32%), Positives = 48/92 (52%), Gaps = 1/92 (1%)

Query: 333 LKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCP-VTTTTQFQVTVADGGVISSSGKCSH 391
           LKG +    V  L+DS ++  F++ SLAK+ G P     T  +V  A+G  + + G    
Sbjct: 1   LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILP 60

Query: 392 VPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLR 423
           V +   G  F +DF++L +   D++LG  WL 
Sbjct: 61  VTIGIGGKTFTVDFYVLDLLSYDVILGRPWLE 92

The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. Length = 92

>gnl|CDD|116868 pfam08284, RVP_2, Retroviral aspartyl protease

 Score = 56.3 bits (136), Expect = 1e-09
 Identities = 22/82 (26%), Positives = 43/82 (52%)

Query: 343 TILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFH 402
           T+L DS ++H F++ +   ++G P+       +  + GG ++++ +C  V +  QG  F 
Sbjct: 34  TVLFDSGASHSFISQAFVGRHGLPLEALRTPMLVHSPGGDMTATHRCPSVNIEIQGVDFP 93

Query: 403 LDFFLLPVSGCDIVLGAEWLRS 424
            +  LL     D++LG +WL  
Sbjct: 94  ANLILLDSKDLDVILGMDWLAQ 115

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

>gnl|CDD|217701 pfam03732, Retrotrans_gag, Retrotransposon gag protein

 Score = 41.6 bits (98), Expect = 7e-05
 Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 2/48 (4%)

Query: 113 SLAIGHLDGDAVPWYHWLEQTM--GNMTWAQFKRALVTQFGTFEDGDA 158
            LA+ HL+G A+ W+  L         +W + K A + +F      D 
Sbjct: 1   KLAVHHLEGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDL 48

Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved. Length = 97

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	485
PF08284	135	RVP_2: Retroviral aspartyl protease; InterPro: IPR	99.94
cd05479	124	RP_DDI RP_DDI; retropepsin-like domain of DNA dama	99.89
cd05484	91	retropepsin_like_LTR_2 Retropepsins_like_LTR, peps	99.77
PF09668	124	Asp_protease: Aspartyl protease; InterPro: IPR0191	99.7
cd05480	103	NRIP_C NRIP_C; putative nuclear receptor interacti	99.58
PF00077	100	RVP: Retroviral aspartyl protease The Prosite entr	99.57
PF12384	177	Peptidase_A2B: Ty3 transposon peptidase; InterPro:	99.56
TIGR02281	121	clan_AA_DTGA clan AA aspartic protease, TIGR02281	99.53
PF13650	90	Asp_protease_2: Aspartyl protease	99.52
PF02160	201	Peptidase_A3: Cauliflower mosaic virus peptidase (	99.42
cd05483	96	retropepsin_like_bacteria Bacterial aspartate prot	99.42
TIGR03698	107	clan_AA_DTGF clan AA aspartic protease, AF_0612 fa	99.42
cd06095	86	RP_RTVL_H_like Retropepsin of the RTVL_H family of	99.37
KOG0012	380	consensus DNA damage inducible protein [Replicatio	99.36
cd00303	92	retropepsin_like Retropepsins; pepsin-like asparta	99.32
PF13975	72	gag-asp_proteas: gag-polyprotein putative aspartyl	99.28
cd05481	93	retropepsin_like_LTR_1 Retropepsins_like_LTR; peps	99.23
cd06094	89	RP_Saci_like RP_Saci_like, retropepsin family. Ret	99.0
COG3577	215	Predicted aspartyl protease [General function pred	98.96
PF03732	96	Retrotrans_gag: Retrotransposon gag protein ; Inte	98.65
COG5550	125	Predicted aspartyl protease [Posttranslational mod	98.51
cd05482	87	HIV_retropepsin_like Retropepsins, pepsin-like asp	98.49
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.36
PF03564	145	DUF1759: Protein of unknown function (DUF1759); In	98.27
PF05585	164	DUF1758: Putative peptidase (DUF1758); InterPro: I	98.21
PF12382	137	Peptidase_A2E: Retrotransposon peptidase; InterPro	97.99
PF13696	32	zf-CCHC_2: Zinc knuckle	97.03
PF14893	331	PNMA: PNMA	96.64
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	96.45
COG4067	162	Uncharacterized protein conserved in archaea [Post	96.34
PF13917	42	zf-CCHC_3: Zinc knuckle	96.13
smart00343	26	ZnF_C2HC zinc finger.	96.1
PF05618	138	Zn_protease: Putative ATP-dependant zinc protease;	95.4
cd05476	265	pepsin_A_like_plant Chroloplast Nucleoids DNA-bind	95.38
cd06096	326	Plasmepsin_5 Plasmepsins are a class of aspartic p	94.66
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	94.18
cd05477	318	gastricsin Gastricsins, asparate proteases produce	93.55
cd06098	317	phytepsin Phytepsin, a plant homolog of mammalian	93.44
cd05485	329	Cathepsin_D_like Cathepsin_D_like, pepsin family o	93.28
cd05478	317	pepsin_A Pepsin A, aspartic protease produced in g	93.23
COG5222	427	Uncharacterized conserved protein, contains RING Z	92.94
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	92.93
cd05486	316	Cathespin_E Cathepsin E, non-lysosomal aspartic pr	92.42
PF00026	317	Asp: Eukaryotic aspartyl protease The Prosite entr	92.38
cd05474	295	SAP_like SAPs, pepsin-like proteinases secreted fr	92.2
PTZ00368	148	universal minicircle sequence binding protein (UMS	91.91
PF14392	49	zf-CCHC_4: Zinc knuckle	91.86
cd06097	278	Aspergillopepsin_like Aspergillopepsin_like, aspar	91.77
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	91.57
PF02023	95	SCAN: SCAN domain; InterPro: IPR003309 A number of	91.54
PF15288	40	zf-CCHC_6: Zinc knuckle	91.22
cd05472	299	cnd41_like Chloroplast Nucleoids DNA-binding Prote	91.16
cd05488	320	Proteinase_A_fungi Fungal Proteinase A , aspartic	90.02
cd05471	283	pepsin_like Pepsin-like aspartic proteases, biloba	89.96
PTZ00147	453	plasmepsin-1; Provisional	89.5
cd05490	325	Cathepsin_D2 Cathepsin_D2, pepsin family of protei	88.94
PTZ00013	450	plasmepsin 4 (PM4); Provisional	88.26
cd05474	295	SAP_like SAPs, pepsin-like proteinases secreted fr	87.5
PF14223	119	UBN2: gag-polypeptide of LTR copia-type	86.71
cd05487	326	renin_like Renin stimulates production of angioten	86.35
PF00026	317	Asp: Eukaryotic aspartyl protease The Prosite entr	86.03
PF03539	163	Spuma_A9PTase: Spumavirus aspartic protease (A9);	85.98
PTZ00368	148	universal minicircle sequence binding protein (UMS	85.39
cd05470	109	pepsin_retropepsin_like Cellular and retroviral pe	84.17
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	83.9
PLN03146	431	aspartyl protease family protein; Provisional	83.54
PTZ00147	453	plasmepsin-1; Provisional	83.31
PRK04406	75	hypothetical protein; Provisional	83.11
PTZ00013	450	plasmepsin 4 (PM4); Provisional	83.07
PTZ00165	482	aspartyl protease; Provisional	82.46
cd05475	273	nucellin_like Nucellins, plant aspartic proteases	81.5
cd05476	265	pepsin_A_like_plant Chroloplast Nucleoids DNA-bind	81.1
PRK02793	72	phi X174 lysis protein; Provisional	80.99

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

Probab=99.94  E-value=2e-26  Score=190.24  Aligned_cols=117  Identities=30%  Similarity=0.593  Sum_probs=105.2

Q ss_pred             CCCCCeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCcccc-ccceEEEEccCCeeeecceEeeeEEeecceEEEE
Q 042094          325 ATPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTT-TTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHL  403 (485)
Q Consensus       325 ~~~~~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~-~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~  403 (485)
                      ...+.++...+.|++.++.+|||||||||||+.++|.+++++..+ ..++.|..+ |..+.+.+.|..|.+.++|+.+..
T Consensus        16 ~~~~~vi~g~~~I~~~~~~vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~~V~~~-g~~~~~~~~~~~~~~~i~g~~~~~   94 (135)
T PF08284_consen   16 EESPDVITGTFLINSIPASVLIDSGATHSFISSSFAKKLGLPLEPLPRPIVVSAP-GGSINCEGVCPDVPLSIQGHEFVV   94 (135)
T ss_pred             cCCCCeEEEEEEeccEEEEEEEecCCCcEEccHHHHHhcCCEEEEccCeeEEecc-cccccccceeeeEEEEECCeEEEe
Confidence            345678999999999999999999999999999999999999865 467777754 556777888999999999999999


Q ss_pred             EEEEcCCCCCCeeechhHHhhcCCeEEEccCcEEEEEECC
Q 042094          404 DFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKG  443 (485)
Q Consensus       404 ~~~V~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~~~  443 (485)
                      +|+|+++.++|+|||||||.+|+| .|||.+++|+|..+.
T Consensus        95 dl~vl~l~~~DvILGm~WL~~~~~-~IDw~~k~v~f~~p~  133 (135)
T PF08284_consen   95 DLLVLDLGGYDVILGMDWLKKHNP-VIDWATKTVTFNSPS  133 (135)
T ss_pred             eeEEecccceeeEeccchHHhCCC-EEEccCCEEEEeCCC
Confidence            999999999999999999999999 799999999998753

These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases.

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

Probab=99.89  E-value=1.6e-22  Score=165.69  Aligned_cols=111  Identities=14%  Similarity=0.217  Sum_probs=97.3

Q ss_pred             CCeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEE
Q 042094          328 QNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFL  407 (485)
Q Consensus       328 ~~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V  407 (485)
                      ...+++.+.|||+++.+||||||++|||+.++|+++|++.....++.+..+++....+.+.+..+.+.+++..+.++|.|
T Consensus        14 ~~~~~v~~~Ing~~~~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~~~~~V   93 (124)
T cd05479          14 VPMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRIHLAQVKIGNLFLPCSFTV   93 (124)
T ss_pred             eeEEEEEEEECCEEEEEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCCCcEEEeEEEEEEEEECCEEeeeEEEE
Confidence            35789999999999999999999999999999999999865555566655654445667878889999999999999999


Q ss_pred             cCCCCCCeeechhHHhhcCCeEEEccCcEEEE
Q 042094          408 LPVSGCDIVLGAEWLRSLGAILWDFSKLTMQF  439 (485)
Q Consensus       408 ~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~  439 (485)
                      ++..++|+|||||||.++++ .|||.+++|+|
T Consensus        94 l~~~~~d~ILG~d~L~~~~~-~ID~~~~~i~~  124 (124)
T cd05479          94 LEDDDVDFLIGLDMLKRHQC-VIDLKENVLRI  124 (124)
T ss_pred             ECCCCcCEEecHHHHHhCCe-EEECCCCEEEC
Confidence            99999999999999999996 89999999874

The family represents the retropepsin-like domain of DNA damage inducible protein. DNA damage inducible protein has a retropepsin-like domain and an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain. This CD represents the retropepsin-like domain of DDI.

>cd05484 retropepsin_like_LTR_2 Retropepsins_like_LTR, pepsin-like aspartate proteases

Probab=99.77  E-value=2.7e-18  Score=133.01  Aligned_cols=90  Identities=19%  Similarity=0.282  Sum_probs=83.6

Q ss_pred             EEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCCC
Q 042094          332 RLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVS  411 (485)
Q Consensus       332 ~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~~  411 (485)
                      ++.+.|||+++.+||||||++|||+++.+.+++++........+.++||+.+.+.|.+ .+.+.+++..+.++|+|++..
T Consensus         2 ~~~~~Ing~~i~~lvDTGA~~svis~~~~~~lg~~~~~~~~~~v~~a~G~~~~~~G~~-~~~v~~~~~~~~~~~~v~~~~   80 (91)
T cd05484           2 TVTLLVNGKPLKFQLDTGSAITVISEKTWRKLGSPPLKPTKKRLRTATGTKLSVLGQI-LVTVKYGGKTKVLTLYVVKNE   80 (91)
T ss_pred             EEEEEECCEEEEEEEcCCcceEEeCHHHHHHhCCCccccccEEEEecCCCEeeEeEEE-EEEEEECCEEEEEEEEEEECC
Confidence            5789999999999999999999999999999999875556889999999999998887 789999999999999999988


Q ss_pred             CCCeeechhHHh
Q 042094          412 GCDIVLGAEWLR  423 (485)
Q Consensus       412 ~~dvILG~dwL~  423 (485)
                       ++.|||+|||+
T Consensus        81 -~~~lLG~~wl~   91 (91)
T cd05484          81 -GLNLLGRDWLD   91 (91)
T ss_pred             -CCCccChhhcC
Confidence             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

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

Probab=99.70  E-value=1.7e-16  Score=126.68  Aligned_cols=101  Identities=18%  Similarity=0.274  Sum_probs=78.0

Q ss_pred             CeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEE-EEccCCeeeecceEeeeEEeecceEEEEEEEE
Q 042094          329 NTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQV-TVADGGVISSSGKCSHVPVNSQGFQFHLDFFL  407 (485)
Q Consensus       329 ~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v-~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V  407 (485)
                      ..+++.+.|||++++|+|||||.+|+||.++|+++||.......+.- ..+-|. ..+.|+...+++.+++..+++.|.|
T Consensus        23 ~mLyI~~~ing~~vkA~VDtGAQ~tims~~~a~r~gL~~lid~r~~g~a~GvG~-~~i~G~Ih~~~l~ig~~~~~~s~~V  101 (124)
T PF09668_consen   23 SMLYINCKINGVPVKAFVDTGAQSTIMSKSCAERCGLMRLIDKRFAGVAKGVGT-QKILGRIHSVQLKIGGLFFPCSFTV  101 (124)
T ss_dssp             ---EEEEEETTEEEEEEEETT-SS-EEEHHHHHHTTGGGGEEGGG-EE--------EEEEEEEEEEEEETTEEEEEEEEE
T ss_pred             ceEEEEEEECCEEEEEEEeCCCCccccCHHHHHHcCChhhccccccccccCCCc-CceeEEEEEEEEEECCEEEEEEEEE
Confidence            46799999999999999999999999999999999997533222222 222243 4567888889999999999999999


Q ss_pred             cCCCCCCeeechhHHhhcCCeEEE
Q 042094          408 LPVSGCDIVLGAEWLRSLGAILWD  431 (485)
Q Consensus       408 ~~~~~~dvILG~dwL~~~~~i~id  431 (485)
                      ++....|+|||.|||.+|.. .||
T Consensus       102 le~~~~d~llGld~L~~~~c-~ID  124 (124)
T PF09668_consen  102 LEDQDVDLLLGLDMLKRHKC-CID  124 (124)
T ss_dssp             ETTSSSSEEEEHHHHHHTT--EEE
T ss_pred             eCCCCcceeeeHHHHHHhCc-ccC
Confidence            99888999999999999998 687

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

>cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein

Probab=99.58  E-value=1.7e-14  Score=107.47  Aligned_cols=99  Identities=9%  Similarity=0.111  Sum_probs=83.2

Q ss_pred             EEEECCeEEEEEEcCCCCccccCHHHHhhcCCccc-cccce-EEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCCC
Q 042094          334 KGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVT-TTTQF-QVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVS  411 (485)
Q Consensus       334 ~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~-~~~~~-~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~~  411 (485)
                      .+++||++++|+|||||.+|+||+.+|+++||... ....+ -+.-.-|+...+.|+...+++.|++..++..|.|++..
T Consensus         2 nCk~nG~~vkAfVDsGaQ~timS~~caercgL~r~v~~~r~~g~A~gvgt~~kiiGrih~~~ikig~~~~~CSftVld~~   81 (103)
T cd05480           2 SCQCAGKELRALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSLPTSVKVIGQIERLVLQLGQLTVECSAQVVDDN   81 (103)
T ss_pred             ceeECCEEEEEEEecCCchhhcCHHHHHHcChHhhhhhccccccccCCCcceeEeeEEEEEEEEeCCEEeeEEEEEEcCC
Confidence            46799999999999999999999999999999743 22121 22323355556789999999999999999999999998


Q ss_pred             CCCeeechhHHhhcCCeEEEcc
Q 042094          412 GCDIVLGAEWLRSLGAILWDFS  433 (485)
Q Consensus       412 ~~dvILG~dwL~~~~~i~id~~  433 (485)
                      ..|++||.|.|.+|.. .||.+
T Consensus        82 ~~d~llGLdmLkrhqc-~IdL~  102 (103)
T cd05480          82 EKNFSLGLQTLKSLKC-VINLE  102 (103)
T ss_pred             CcceEeeHHHHhhcce-eeecc
Confidence            9999999999999998 79865

Proteins in this family have been described as probable nuclear receptor interacting proteins. The C-terminal domain of this family is homologous to the retroviral aspartyl protease domain. The domain is structurally related to one lobe of the pepsin molecule. The conserved active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.

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

Probab=99.57  E-value=1.3e-14  Score=114.80  Aligned_cols=96  Identities=23%  Similarity=0.378  Sum_probs=82.7

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcC
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLP  409 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~  409 (485)
                      ..++.+.++|..+.|||||||++|+|+++.+..++..  ......+..++|.. ...+. ..+.+.+++..+...|+|++
T Consensus         5 rp~i~v~i~g~~i~~LlDTGA~vsiI~~~~~~~~~~~--~~~~~~v~~~~g~~-~~~~~-~~~~v~~~~~~~~~~~~v~~   80 (100)
T PF00077_consen    5 RPYITVKINGKKIKALLDTGADVSIISEKDWKKLGPP--PKTSITVRGAGGSS-SILGS-TTVEVKIGGKEFNHTFLVVP   80 (100)
T ss_dssp             SSEEEEEETTEEEEEEEETTBSSEEESSGGSSSTSSE--EEEEEEEEETTEEE-EEEEE-EEEEEEETTEEEEEEEEESS
T ss_pred             CceEEEeECCEEEEEEEecCCCcceeccccccccccc--ccCCceeccCCCcc-eeeeE-EEEEEEEECccceEEEEecC
Confidence            4578899999999999999999999999999877655  45577888999987 65554 57899999999999999999


Q ss_pred             CCCCCeeechhHHhhcCCeEEE
Q 042094          410 VSGCDIVLGAEWLRSLGAILWD  431 (485)
Q Consensus       410 ~~~~dvILG~dwL~~~~~i~id  431 (485)
                      ....| |||+|||.+++. .|+
T Consensus        81 ~~~~~-ILG~D~L~~~~~-~i~  100 (100)
T PF00077_consen   81 DLPMN-ILGRDFLKKLNA-VIN  100 (100)
T ss_dssp             TCSSE-EEEHHHHTTTTC-EEE
T ss_pred             CCCCC-EeChhHHHHcCC-EEC
Confidence            87778 999999999997 564

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 ....

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

Probab=99.56  E-value=4.3e-14  Score=114.93  Aligned_cols=100  Identities=15%  Similarity=0.239  Sum_probs=88.9

Q ss_pred             CeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEc
Q 042094          329 NTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLL  408 (485)
Q Consensus       329 ~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~  408 (485)
                      ++..+.+.++|..+++|+||||..|||+.+++++|+|+.....+++++++.+...........++|.+++..+.+.+||+
T Consensus        33 ~T~~v~l~~~~t~i~vLfDSGSPTSfIr~di~~kL~L~~~~app~~fRG~vs~~~~~tsEAv~ld~~i~n~~i~i~aYV~  112 (177)
T PF12384_consen   33 KTAIVQLNCKGTPIKVLFDSGSPTSFIRSDIVEKLELPTHDAPPFRFRGFVSGESATTSEAVTLDFYIDNKLIDIAAYVT  112 (177)
T ss_pred             cEEEEEEeecCcEEEEEEeCCCccceeehhhHHhhCCccccCCCEEEeeeccCCceEEEEeEEEEEEECCeEEEEEEEEe
Confidence            57788999999999999999999999999999999999988889999987655444444556789999999999999999


Q ss_pred             CCCCCCeeechhHHhhcCCe
Q 042094          409 PVSGCDIVLGAEWLRSLGAI  428 (485)
Q Consensus       409 ~~~~~dvILG~dwL~~~~~i  428 (485)
                      +..++|+|+|.++|++|..+
T Consensus       113 d~m~~dlIIGnPiL~ryp~l  132 (177)
T PF12384_consen  113 DNMDHDLIIGNPILDRYPTL  132 (177)
T ss_pred             ccCCcceEeccHHHhhhHHH
Confidence            99999999999999999753

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 [].

>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family

Probab=99.53  E-value=2.3e-13  Score=110.60  Aligned_cols=105  Identities=19%  Similarity=0.276  Sum_probs=85.3

Q ss_pred             CCeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCcccc-ccceEEEEccCCeeeecceEeeeEEeecceEEE-EEE
Q 042094          328 QNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTT-TTQFQVTVADGGVISSSGKCSHVPVNSQGFQFH-LDF  405 (485)
Q Consensus       328 ~~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~-~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~-~~~  405 (485)
                      ...+++.+.|||+++.+||||||++++|++++|++||+.... ..+..+.+++|....  ....--.+.+++..+. +.+
T Consensus         9 ~g~~~v~~~InG~~~~flVDTGAs~t~is~~~A~~Lgl~~~~~~~~~~~~ta~G~~~~--~~~~l~~l~iG~~~~~nv~~   86 (121)
T TIGR02281         9 DGHFYATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIKA--ARVTLDRVAIGGIVVNDVDA   86 (121)
T ss_pred             CCeEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCcccCCceEEEEeCCCcEEE--EEEEeCEEEECCEEEeCcEE
Confidence            356899999999999999999999999999999999998643 347788899997542  2223347899999876 899


Q ss_pred             EEcCCC-CCCeeechhHHhhcCCeEEEccC
Q 042094          406 FLLPVS-GCDIVLGAEWLRSLGAILWDFSK  434 (485)
Q Consensus       406 ~V~~~~-~~dvILG~dwL~~~~~i~id~~~  434 (485)
                      .|+|.. ..+.|||||||..+..+++|-..
T Consensus        87 ~v~~~~~~~~~LLGm~fL~~~~~~~~~~~~  116 (121)
T TIGR02281        87 MVAEGGALSESLLGMSFLNRLSRFTVRGGK  116 (121)
T ss_pred             EEeCCCcCCceEcCHHHHhccccEEEECCE
Confidence            999876 35899999999999865666543

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

>PF13650 Asp_protease_2: Aspartyl protease

Probab=99.52  E-value=1.3e-13  Score=106.89  Aligned_cols=87  Identities=22%  Similarity=0.357  Sum_probs=72.9

Q ss_pred             EEEEECCeEEEEEEcCCCCccccCHHHHhhcCCcccccc-ceEEEEccCCeeeecceEeeeEEeecceEE-EEEEEEcC-
Q 042094          333 LKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTT-QFQVTVADGGVISSSGKCSHVPVNSQGFQF-HLDFFLLP-  409 (485)
Q Consensus       333 ~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~-~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~-~~~~~V~~-  409 (485)
                      |++.|||+++.+||||||+.|+|+++++++++++..... ...+..++|........  --.+.+++..+ .+++.|++ 
T Consensus         1 V~v~vng~~~~~liDTGa~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~--~~~i~ig~~~~~~~~~~v~~~   78 (90)
T PF13650_consen    1 VPVKVNGKPVRFLIDTGASISVISRSLAKKLGLKPRPKSVPISVSGAGGSVTVYRGR--VDSITIGGITLKNVPFLVVDL   78 (90)
T ss_pred             CEEEECCEEEEEEEcCCCCcEEECHHHHHHcCCCCcCCceeEEEEeCCCCEEEEEEE--EEEEEECCEEEEeEEEEEECC
Confidence            468899999999999999999999999999999876543 67888999984332332  33799999887 78999999 


Q ss_pred             CCCCCeeechhH
Q 042094          410 VSGCDIVLGAEW  421 (485)
Q Consensus       410 ~~~~dvILG~dw  421 (485)
                      ...+|.|||+||
T Consensus        79 ~~~~~~iLG~df   90 (90)
T PF13650_consen   79 GDPIDGILGMDF   90 (90)
T ss_pred             CCCCEEEeCCcC
Confidence            567999999998

>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=99.42  E-value=1.2e-12  Score=112.58  Aligned_cols=112  Identities=21%  Similarity=0.282  Sum_probs=88.7

Q ss_pred             EEEEEECC---eEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEc
Q 042094          332 RLKGNLKK---HGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLL  408 (485)
Q Consensus       332 ~~~~~i~~---~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~  408 (485)
                      .+.+.+.|   ..+.++|||||+.++++..+.-.-.+. ....++.|.+|||+...+..++..+.+.|++..|.+.+.-.
T Consensus         8 ~~~i~~~gy~~~~~~~~vDTGAt~C~~~~~iiP~e~we-~~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~IP~iYq   86 (201)
T PF02160_consen    8 KVKISFPGYKKFNYHCYVDTGATICCASKKIIPEEYWE-KSKKPIKVKGANGSIIQINKKAKNGKIQIADKIFRIPTIYQ   86 (201)
T ss_pred             EEEEEEcCceeEEEEEEEeCCCceEEecCCcCCHHHHH-hCCCcEEEEEecCCceEEEEEecCceEEEccEEEeccEEEE
Confidence            33444455   468999999999999988765433222 23457899999999888888889999999999999976655


Q ss_pred             CCCCCCeeechhHHhhcCCeEEEccCcEEEEEECC-eEE
Q 042094          409 PVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKG-QTV  446 (485)
Q Consensus       409 ~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~~~-~~~  446 (485)
                      -..+.|+|||++||+.|.| -+.|.. .+.|...+ +++
T Consensus        87 ~~~g~d~IlG~NF~r~y~P-fiq~~~-~I~f~~~~~~~~  123 (201)
T PF02160_consen   87 QESGIDIILGNNFLRLYEP-FIQTED-RIQFHKKGLQKV  123 (201)
T ss_pred             ecCCCCEEecchHHHhcCC-cEEEcc-EEEEEeCCccee
Confidence            5578999999999999999 599975 79999877 444

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

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

Probab=99.42  E-value=1.8e-12  Score=101.72  Aligned_cols=92  Identities=22%  Similarity=0.385  Sum_probs=77.6

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEE-EEEEEc
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFH-LDFFLL  408 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~-~~~~V~  408 (485)
                      .+++++.||++++++||||||++++|+.++++++++.........+..++|........  ...+.+++..+. +.+.|+
T Consensus         2 ~~~v~v~i~~~~~~~llDTGa~~s~i~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~--~~~i~ig~~~~~~~~~~v~   79 (96)
T cd05483           2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAARVR--LDSLQIGGITLRNVPAVVL   79 (96)
T ss_pred             cEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCccCCCcEEEEecCCCccceEEE--cceEEECCcEEeccEEEEe
Confidence            46889999999999999999999999999999999844445677889999987654332  457899998876 789999


Q ss_pred             CCCC--CCeeechhHHh
Q 042094          409 PVSG--CDIVLGAEWLR  423 (485)
Q Consensus       409 ~~~~--~dvILG~dwL~  423 (485)
                      +...  .|.|||+|||+
T Consensus        80 d~~~~~~~gIlG~d~l~   96 (96)
T cd05483          80 PGDALGVDGLLGMDFLR   96 (96)
T ss_pred             CCcccCCceEeChHHhC
Confidence            9887  99999999984

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

>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family

Probab=99.42  E-value=2.1e-12  Score=102.36  Aligned_cols=93  Identities=20%  Similarity=0.319  Sum_probs=76.4

Q ss_pred             CeEEEEEEcCCCCccc-cCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCCCCCCeee
Q 042094          339 KHGVTILIDSSSTHIF-LNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVL  417 (485)
Q Consensus       339 ~~~v~aLiDsGSt~sf-Is~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~~~~dvIL  417 (485)
                      ..++.+||||||+..+ |+.++|++||++...  ...+.+|||......  .....+.++|......+.+.+..+ +++|
T Consensus        14 ~~~v~~LVDTGat~~~~l~~~~a~~lgl~~~~--~~~~~tA~G~~~~~~--v~~~~v~igg~~~~~~v~~~~~~~-~~LL   88 (107)
T TIGR03698        14 FMEVRALVDTGFSGFLLVPPDIVNKLGLPELD--QRRVYLADGREVLTD--VAKASIIINGLEIDAFVESLGYVD-EPLL   88 (107)
T ss_pred             ceEEEEEEECCCCeEEecCHHHHHHcCCCccc--CcEEEecCCcEEEEE--EEEEEEEECCEEEEEEEEecCCCC-ccEe
Confidence            3479999999999997 999999999998643  568999999765543  346789999998766666666666 8999


Q ss_pred             chhHHhhcCCeEEEccCcEE
Q 042094          418 GAEWLRSLGAILWDFSKLTM  437 (485)
Q Consensus       418 G~dwL~~~~~i~id~~~~~~  437 (485)
                      ||.||++++. .|||.++.+
T Consensus        89 G~~~L~~l~l-~id~~~~~~  107 (107)
T TIGR03698        89 GTELLEGLGI-VIDYRNQGL  107 (107)
T ss_pred             cHHHHhhCCE-EEehhhCcC
Confidence            9999999995 899998753

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.

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

Probab=99.37  E-value=3.6e-12  Score=97.22  Aligned_cols=85  Identities=21%  Similarity=0.295  Sum_probs=68.1

Q ss_pred             EEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeee-EEeecceEEEEEEEEcCCC
Q 042094          333 LKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHV-PVNSQGFQFHLDFFLLPVS  411 (485)
Q Consensus       333 ~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v-~v~i~~~~~~~~~~V~~~~  411 (485)
                      +++.|||+++.+||||||+++.|++..++++.   ....+..+.+++|.......  ... .+.+++......+.|++..
T Consensus         1 ~~v~InG~~~~fLvDTGA~~tii~~~~a~~~~---~~~~~~~v~gagG~~~~~v~--~~~~~v~vg~~~~~~~~~v~~~~   75 (86)
T cd06095           1 VTITVEGVPIVFLVDTGATHSVLKSDLGPKQE---LSTTSVLIRGVSGQSQQPVT--TYRTLVDLGGHTVSHSFLVVPNC   75 (86)
T ss_pred             CEEEECCEEEEEEEECCCCeEEECHHHhhhcc---CCCCcEEEEeCCCcccccEE--EeeeEEEECCEEEEEEEEEEcCC
Confidence            36789999999999999999999999999972   23467899999998621111  123 5899999999999999854


Q ss_pred             CCCeeechhHHh
Q 042094          412 GCDIVLGAEWLR  423 (485)
Q Consensus       412 ~~dvILG~dwL~  423 (485)
                       .+.|||||||.
T Consensus        76 -~~~lLG~dfL~   86 (86)
T cd06095          76 -PDPLLGRDLLS   86 (86)
T ss_pred             -CCcEechhhcC
Confidence             59999999984

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

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

Probab=99.36  E-value=2.4e-12  Score=118.02  Aligned_cols=116  Identities=13%  Similarity=0.188  Sum_probs=99.0

Q ss_pred             CeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCcccc-ccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEE
Q 042094          329 NTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTT-TTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFL  407 (485)
Q Consensus       329 ~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~-~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V  407 (485)
                      ..+++.+.|||++|+|+|||||..|.||..+|+++||...- +.-..+.-+.| ..++.|.+..+.++|+...+...|.|
T Consensus       234 ~ML~iN~~ing~~VKAfVDsGaq~timS~~Caer~gL~rlid~r~~g~a~gvg-~~ki~g~Ih~~~lki~~~~l~c~ftV  312 (380)
T KOG0012|consen  234 TMLYINCEINGVPVKAFVDSGAQTTIMSAACAERCGLNRLIDKRFQGEARGVG-TEKILGRIHQAQLKIEDLYLPCSFTV  312 (380)
T ss_pred             eEEEEEEEECCEEEEEEEcccchhhhhhHHHHHHhChHHHhhhhhhccccCCC-cccccceeEEEEEEeccEeeccceEE
Confidence            45799999999999999999999999999999999998632 22222333334 55678888999999999999999999


Q ss_pred             cCCCCCCeeechhHHhhcCCeEEEccCcEEEEEECCeEE
Q 042094          408 LPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTV  446 (485)
Q Consensus       408 ~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~~~~~~  446 (485)
                      ++....|++||.|-|.+|+. .||.+++.+.|...+..+
T Consensus       313 ~d~~~~d~llGLd~Lrr~~c-cIdL~~~~L~ig~~~tei  350 (380)
T KOG0012|consen  313 LDRRDMDLLLGLDMLRRHQC-CIDLKTNVLRIGNTETEI  350 (380)
T ss_pred             ecCCCcchhhhHHHHHhccc-eeecccCeEEecCCCccc
Confidence            99999999999999999999 799999999998776533

>cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases

Probab=99.32  E-value=1.9e-11  Score=93.87  Aligned_cols=90  Identities=32%  Similarity=0.567  Sum_probs=77.1

Q ss_pred             EEEECCeEEEEEEcCCCCccccCHHHHhhcCC-ccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCCCC
Q 042094          334 KGNLKKHGVTILIDSSSTHIFLNSSLAKQYGC-PVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSG  412 (485)
Q Consensus       334 ~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l-~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~~~  412 (485)
                      .+.++|..+.+|+|+||++++++.+++.++++ ......+..+..++|......+.+..+.+.+++..+...|++++...
T Consensus         2 ~~~~~~~~~~~liDtgs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   81 (92)
T cd00303           2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS   81 (92)
T ss_pred             EEEECCEEEEEEEcCCCcccccCHHHHHHcCCCcccCCCceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcCCC
Confidence            45678899999999999999999999999988 44455677888888887666555567888999999999999999999


Q ss_pred             CCeeechhHHh
Q 042094          413 CDIVLGAEWLR  423 (485)
Q Consensus       413 ~dvILG~dwL~  423 (485)
                      +|+|||+|||.
T Consensus        82 ~~~ilG~~~l~   92 (92)
T cd00303          82 YDVILGRPWLE   92 (92)
T ss_pred             cCEEecccccC
Confidence            99999999984

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

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

Probab=99.28  E-value=1.9e-11  Score=89.52  Aligned_cols=64  Identities=30%  Similarity=0.468  Sum_probs=56.8

Q ss_pred             CCCeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCcccccc-ceEEEEccCCeeeecceEe
Q 042094          327 PQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTT-QFQVTVADGGVISSSGKCS  390 (485)
Q Consensus       327 ~~~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~-~~~v~~a~G~~~~~~~~~~  390 (485)
                      .+..+++.+.|+|+.+.+||||||++|||++++|++||++..... +..+.+|||+...+.+...
T Consensus         5 ~~g~~~v~~~I~g~~~~alvDtGat~~fis~~~a~rLgl~~~~~~~~~~v~~a~g~~~~~~g~~~   69 (72)
T PF13975_consen    5 DPGLMYVPVSIGGVQVKALVDTGATHNFISESLAKRLGLPLEKPPSPIRVKLANGSVIEIRGVAE   69 (72)
T ss_pred             cCCEEEEEEEECCEEEEEEEeCCCcceecCHHHHHHhCCCcccCCCCEEEEECCCCccccceEEE
Confidence            456899999999999999999999999999999999999986654 8999999999887766543

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

Probab=99.23  E-value=6.6e-11  Score=91.13  Aligned_cols=84  Identities=19%  Similarity=0.283  Sum_probs=73.8

Q ss_pred             EEECC-eEEEEEEcCCCCccccCHHHHhhcC---CccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCC
Q 042094          335 GNLKK-HGVTILIDSSSTHIFLNSSLAKQYG---CPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPV  410 (485)
Q Consensus       335 ~~i~~-~~v~aLiDsGSt~sfIs~~~~~~l~---l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~  410 (485)
                      ..|++ ..++++|||||++|+|+.+++++|+   .+....+++.+..+||+.+.+.|. ..+.+.+++..+.++|+|++.
T Consensus         3 ~~i~g~~~v~~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~~~G~-~~~~v~~~~~~~~~~f~Vvd~   81 (93)
T cd05481           3 MKINGKQSVKFQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIPVEGG-VKLKCRYRNPKYNLTFQVVKE   81 (93)
T ss_pred             eEeCCceeEEEEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEeeeeEE-EEEEEEECCcEEEEEEEEECC
Confidence            46788 9999999999999999999999998   555566789999999999998887 579999999999999999997


Q ss_pred             CCCCeeechh
Q 042094          411 SGCDIVLGAE  420 (485)
Q Consensus       411 ~~~dvILG~d  420 (485)
                      .. .-|||.+
T Consensus        82 ~~-~~lLG~~   90 (93)
T cd05481          82 EG-PPLLGAK   90 (93)
T ss_pred             CC-CceEccc
Confidence            54 5677865

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

>cd06094 RP_Saci_like RP_Saci_like, retropepsin family

Probab=99.00  E-value=1.6e-09  Score=80.16  Aligned_cols=79  Identities=23%  Similarity=0.413  Sum_probs=65.8

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecce-EEEEEEEEcCCCCCCeeech
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGF-QFHLDFFLLPVSGCDIVLGA  419 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~-~~~~~~~V~~~~~~dvILG~  419 (485)
                      .+++||||||.+|+|.....+..    ....++.+..|||+.+.+-|. ..+.+.+|.. .|.-.|.|.+..  .-|||.
T Consensus         9 ~~~fLVDTGA~vSviP~~~~~~~----~~~~~~~l~AANgt~I~tyG~-~~l~ldlGlrr~~~w~FvvAdv~--~pIlGa   81 (89)
T cd06094           9 GLRFLVDTGAAVSVLPASSTKKS----LKPSPLTLQAANGTPIATYGT-RSLTLDLGLRRPFAWNFVVADVP--HPILGA   81 (89)
T ss_pred             CcEEEEeCCCceEeecccccccc----ccCCceEEEeCCCCeEeeeee-EEEEEEcCCCcEEeEEEEEcCCC--cceecH
Confidence            47899999999999998877752    334577999999999998775 6788999875 889999997765  469999


Q ss_pred             hHHhhcC
Q 042094          420 EWLRSLG  426 (485)
Q Consensus       420 dwL~~~~  426 (485)
                      |||.+|+
T Consensus        82 DfL~~~~   88 (89)
T cd06094          82 DFLQHYG   88 (89)
T ss_pred             HHHHHcC
Confidence            9999986

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

>COG3577 Predicted aspartyl protease [General function prediction only]

Probab=98.96  E-value=5e-09  Score=89.32  Aligned_cols=100  Identities=19%  Similarity=0.303  Sum_probs=81.5

Q ss_pred             CeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCcccc-ccceEEEEccCCeeeecceEeeeEEeecceEE-EEEEE
Q 042094          329 NTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTT-TTQFQVTVADGGVISSSGKCSHVPVNSQGFQF-HLDFF  406 (485)
Q Consensus       329 ~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~-~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~-~~~~~  406 (485)
                      .=+.+.+.|||+.+.+|||||||.-.++++.|+++|+.... .-++.|.+|||...-.  .+.-=.+.|+++.. .++..
T Consensus       104 GHF~a~~~VNGk~v~fLVDTGATsVal~~~dA~RlGid~~~l~y~~~v~TANG~~~AA--~V~Ld~v~IG~I~~~nV~A~  181 (215)
T COG3577         104 GHFEANGRVNGKKVDFLVDTGATSVALNEEDARRLGIDLNSLDYTITVSTANGRARAA--PVTLDRVQIGGIRVKNVDAM  181 (215)
T ss_pred             CcEEEEEEECCEEEEEEEecCcceeecCHHHHHHhCCCccccCCceEEEccCCccccc--eEEeeeEEEccEEEcCchhh
Confidence            34778899999999999999999999999999999998854 5699999999986432  12223688998864 58999


Q ss_pred             EcCCC-CCCeeechhHHhhcCCeEE
Q 042094          407 LLPVS-GCDIVLGAEWLRSLGAILW  430 (485)
Q Consensus       407 V~~~~-~~dvILG~dwL~~~~~i~i  430 (485)
                      |.+.+ -...+|||.||.+++-...
T Consensus       182 V~~~g~L~~sLLGMSfL~rL~~fq~  206 (215)
T COG3577         182 VAEDGALDESLLGMSFLNRLSGFQV  206 (215)
T ss_pred             eecCCccchhhhhHHHHhhccceEe
Confidence            99766 4678899999999986433

>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=98.65  E-value=2.5e-08  Score=77.97  Aligned_cols=67  Identities=27%  Similarity=0.454  Sum_probs=56.6

Q ss_pred             hhhhccccCchHhHhHHhhhcCCC--CCHHHHHHHHHHhhCCCchh-----------------hhhhhcC----------
Q 042094          113 SLAIGHLDGDAVPWYHWLEQTMGN--MTWAQFKRALVTQFGTFEDG-----------------DAVGTQN----------  163 (485)
Q Consensus       113 ~~~~~~L~G~A~~W~~~~~~~~~~--~tw~~f~~~l~~~F~~~~~~-----------------~ey~~~~----------  163 (485)
                      .++..+|+|.|..||..+......  .+|++|+.+|.++|.++...                 .+|+.+|          
T Consensus         1 ~~~~~~L~g~A~~w~~~~~~~~~~~~~~W~~~~~~~~~~f~~~~~~~~~~~~l~~l~Q~~esv~~y~~rf~~l~~~~~~~   80 (96)
T PF03732_consen    1 KLFPSFLKGPARQWYRNLRPNEIRDFITWEEFKDAFRKRFFPPDRKEQARQELNSLRQGNESVREYVNRFRELARRAPPP   80 (96)
T ss_pred             CCchHhccCHHHHHHHHhHhcCCCCCCCHHHHHHHHHHHHhhhhccccchhhhhhhhccCCcHHHHHHHHHHHHHHCCCC
Confidence            367889999999999999875433  49999999999999997655                 5777777          


Q ss_pred             CChHHHHHHHHhhhHH
Q 042094          164 LPESFFISCFLSGLRE  179 (485)
Q Consensus       164 ~~e~~~~~~f~~GL~~  179 (485)
                      ++++.++..|++||++
T Consensus        81 ~~e~~~v~~f~~GL~~   96 (96)
T PF03732_consen   81 MDEEMLVERFIRGLRP   96 (96)
T ss_pred             cCHHHHHHHHHHCCCC
Confidence            5889999999999964

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.

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

Probab=98.51  E-value=1.1e-06  Score=68.91  Aligned_cols=91  Identities=21%  Similarity=0.316  Sum_probs=73.4

Q ss_pred             EEEEEcCCCC-ccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCCCCCCeeechh
Q 042094          342 VTILIDSSST-HIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAE  420 (485)
Q Consensus       342 v~aLiDsGSt-~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~~~~dvILG~d  420 (485)
                      ...|||||.+ -..+.+++++++|++....  ..+..++|+.+.+  ......++++|.+...-+++.+....+ +||++
T Consensus        27 ~~~LiDTGFtg~lvlp~~vaek~~~~~~~~--~~~~~a~~~~v~t--~V~~~~iki~g~e~~~~Vl~s~~~~~~-liG~~  101 (125)
T COG5550          27 YDELIDTGFTGYLVLPPQVAEKLGLPLFST--IRIVLADGGVVKT--SVALATIKIDGVEKVAFVLASDNLPEP-LIGVN  101 (125)
T ss_pred             eeeEEecCCceeEEeCHHHHHhcCCCccCC--hhhhhhcCCEEEE--EEEEEEEEECCEEEEEEEEccCCCccc-chhhh
Confidence            3459999999 8899999999999985433  3456677776654  335678999999888888888888777 99999


Q ss_pred             HHhhcCCeEEEccCcEEE
Q 042094          421 WLRSLGAILWDFSKLTMQ  438 (485)
Q Consensus       421 wL~~~~~i~id~~~~~~~  438 (485)
                      ||+.++- .+|+.++.+.
T Consensus       102 ~lk~l~~-~vn~~~g~LE  118 (125)
T COG5550         102 LLKLLGL-VVNPKTGKLE  118 (125)
T ss_pred             hhhhccE-EEcCCcceEe
Confidence            9999996 8999887764

>cd05482 HIV_retropepsin_like Retropepsins, pepsin-like aspartate proteases

Probab=98.49  E-value=8.6e-07  Score=66.60  Aligned_cols=86  Identities=13%  Similarity=0.030  Sum_probs=63.2

Q ss_pred             EEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCCCCC
Q 042094          334 KGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGC  413 (485)
Q Consensus       334 ~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~~~~  413 (485)
                      .+.|+|+.+.+||||||.+|+|++..+...-  .....+..+...+|. +... .+..+.+++.+......++|.+....
T Consensus         2 ~~~i~g~~~~~llDTGAd~Tvi~~~~~p~~w--~~~~~~~~i~GIGG~-~~~~-~~~~v~i~i~~~~~~g~vlv~~~~~P   77 (87)
T cd05482           2 TLYINGKLFEGLLDTGADVSIIAENDWPKNW--PIQPAPSNLTGIGGA-ITPS-QSSVLLLEIDGEGHLGTILVYVLSLP   77 (87)
T ss_pred             EEEECCEEEEEEEccCCCCeEEcccccCCCC--ccCCCCeEEEeccce-EEEE-EEeeEEEEEcCCeEEEEEEEccCCCc
Confidence            5678999999999999999999975443221  112345677777775 3433 34578999999988889999887444


Q ss_pred             CeeechhHHh
Q 042094          414 DIVLGAEWLR  423 (485)
Q Consensus       414 dvILG~dwL~  423 (485)
                      ..|||+|.|.
T Consensus        78 ~nllGRd~L~   87 (87)
T cd05482          78 VNLWGRDILS   87 (87)
T ss_pred             ccEEccccCC
Confidence            6789999874

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

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.36  E-value=1.6e-07  Score=47.77  Aligned_cols=17  Identities=35%  Similarity=0.770  Sum_probs=15.7

Q ss_pred             ceeecCCCCCCCCcCCC
Q 042094          272 LCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       272 ~Cf~Cg~~GH~a~~C~~  288 (485)
                      .||+||+.||++++||+
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            59999999999999974

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function

Probab=98.27  E-value=2e-06  Score=72.86  Aligned_cols=77  Identities=14%  Similarity=0.132  Sum_probs=63.3

Q ss_pred             ccCCC--hhhHHHHHHHHhHH-hccccccchhhhhccccCchHhHhHHhhhcCCCCCHHHHHHHHHHhhCCCchh-hhhh
Q 042094           85 LSGEN--PTSLIFRCEQYQRL-AALLETDVLSLAIGHLDGDAVPWYHWLEQTMGNMTWAQFKRALVTQFGTFEDG-DAVG  160 (485)
Q Consensus        85 F~G~~--~~~wl~~~e~~~~~-~~~~d~~kv~~~~~~L~G~A~~W~~~~~~~~~~~tw~~f~~~l~~~F~~~~~~-~ey~  160 (485)
                      |+|+.  ...|...|...+.- ..+++.+|..++..+|+|.|+.-+.++..  ...+|+...+.|.++||.+... ..+.
T Consensus         1 F~G~~~~~~~F~~~F~~~v~~n~~~~d~~K~~~L~~~L~G~A~~~i~~~~~--~~~~Y~~a~~~L~~~yg~~~~i~~~~~   78 (145)
T PF03564_consen    1 FDGDPSEWPEFIDQFDSLVHENPDLSDIEKLNYLRSCLKGEAKELIRGLPL--SEENYEEAWELLEERYGNPRRIIQALL   78 (145)
T ss_pred             CCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHhcchHHHHHHcccc--cchhhHHHHHHHHHHhCCchHHHHHHH
Confidence            89943  34667777777777 67899999999999999999999998876  7889999999999999999876 4444


Q ss_pred             hcC
Q 042094          161 TQN  163 (485)
Q Consensus       161 ~~~  163 (485)
                      .++
T Consensus        79 ~~l   81 (145)
T PF03564_consen   79 EEL   81 (145)
T ss_pred             HHH
Confidence            433

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

Probab=98.21  E-value=3.9e-06  Score=72.63  Aligned_cols=71  Identities=21%  Similarity=0.345  Sum_probs=48.3

Q ss_pred             eEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEe--eeEEeecceEEEEEEEEcCCC
Q 042094          340 HGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCS--HVPVNSQGFQFHLDFFLLPVS  411 (485)
Q Consensus       340 ~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~--~v~v~i~~~~~~~~~~V~~~~  411 (485)
                      ..++|||||||..|||++++|++|+|+......+.+.+. |........+.  .+.+.+++..+.+.++|+|..
T Consensus        11 ~~~~~LlDsGSq~SfIt~~la~~L~L~~~~~~~~~~~~~-g~~~~~~~~~~~~~i~~~~~~~~~~i~alvv~~I   83 (164)
T PF05585_consen   11 VEARALLDSGSQRSFITESLANKLNLPGTGEKILVIGTF-GSSSPKSKKCVRVKISSRTSNNSLEIEALVVPKI   83 (164)
T ss_pred             EEEEEEEecCCchhHHhHHHHHHhCCCCCCceEEEEecc-CccCccceeEEEEEEEEecCCCceEEEEEecCcc
Confidence            568999999999999999999999999765554444433 43322222222  344555555678888877644

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

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

Probab=97.99  E-value=1.8e-05  Score=58.76  Aligned_cols=76  Identities=13%  Similarity=0.170  Sum_probs=55.5

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCCCCCCeeec
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLG  418 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~~~~dvILG  418 (485)
                      +-|||||||..|+|.++.++...||+.+-.. .|..++--...+...+..+.+.++|+.+..+|+|+..-+.+.-+.
T Consensus        48 ipclidtgaq~niiteetvrahklptrpw~~-sviyggvyp~kinrkt~kl~i~lngisikteflvvkkfshpaais  123 (137)
T PF12382_consen   48 IPCLIDTGAQVNIITEETVRAHKLPTRPWSQ-SVIYGGVYPNKINRKTIKLNINLNGISIKTEFLVVKKFSHPAAIS  123 (137)
T ss_pred             ceeEEccCceeeeeehhhhhhccCCCCcchh-heEeccccccccccceEEEEEEecceEEEEEEEEEEeccCcceEE
Confidence            4689999999999999999999999866422 222222222234455667889999999999999998765544433

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.

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=97.03  E-value=0.00025  Score=41.46  Aligned_cols=19  Identities=16%  Similarity=0.382  Sum_probs=17.0

Q ss_pred             CceeecCCCCCCCCcCCCc
Q 042094          271 GLCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~~  289 (485)
                      -.|+.|+++||+..+||.+
T Consensus         9 Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    9 YVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CEeecCCCCCccHhHCCCC
Confidence            5699999999999999864

>PF14893 PNMA: PNMA

Probab=96.64  E-value=0.008  Score=57.24  Aligned_cols=109  Identities=17%  Similarity=0.184  Sum_probs=86.5

Q ss_pred             ccCCCCccCCC-h-------hhHHHHHHHHhHHh-ccccccchhhhhccccCchHhHhHHhhhcCCCCCHHHHHHHHHHh
Q 042094           79 RLDFLVLSGEN-P-------TSLIFRCEQYQRLA-ALLETDVLSLAIGHLDGDAVPWYHWLEQTMGNMTWAQFKRALVTQ  149 (485)
Q Consensus        79 ~~~~p~F~G~~-~-------~~wl~~~e~~~~~~-~~~d~~kv~~~~~~L~G~A~~W~~~~~~~~~~~tw~~f~~~l~~~  149 (485)
                      -.+++.|+|.. |       +.|+.++...+..- .++|.+|...+...|.|.|..+...+...+...+-.+++++|...
T Consensus       163 y~~L~iFSG~~~~~~gee~fe~Wl~~a~~~v~~W~~~~e~ekrrrlle~L~GpA~~~~r~l~~~nP~~t~~~~l~aL~~~  242 (331)
T PF14893_consen  163 YRDLRIFSGREEPAPGEESFESWLEHANEMVKKWNDVSEEEKRRRLLESLRGPALDSRRKLQKKNPKQTAQDCLKALGQV  242 (331)
T ss_pred             hhhhhhhcCCCCCCCCcccHHHHHHHHHHHHHhccCCchhhchhhhHHhcccHHHHHHHHHHhcCCCCCHHHHHHHHHHh
Confidence            35677999974 2       49999998887664 488999999999999999999999998877888999999999999


Q ss_pred             hCCCchhhhhhhcC----CChHHHHHHHHhhhHHHHHHHHHh
Q 042094          150 FGTFEDGDAVGTQN----LPESFFISCFLSGLREDIKIGVQM  187 (485)
Q Consensus       150 F~~~~~~~ey~~~~----~~e~~~~~~f~~GL~~~i~~~v~~  187 (485)
                      |++....++....|    -.+.+.+.-|+..|-.-++..+..
T Consensus       243 Fg~~es~~~~~~kf~~~~Q~~~E~ls~yv~RlE~lLqkav~k  284 (331)
T PF14893_consen  243 FGSSESRETLEAKFLNTFQEPGEKLSAYVKRLESLLQKAVEK  284 (331)
T ss_pred             cCCcccHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHh
Confidence            99999986555555    234445555777777666665544

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A

Probab=96.45  E-value=0.0012  Score=39.45  Aligned_cols=21  Identities=29%  Similarity=0.759  Sum_probs=12.7

Q ss_pred             CCceeecCCCCCCCCcCCCce
Q 042094          270 KGLCFNCDEQFKPGHRCKAPQ  290 (485)
Q Consensus       270 ~~~Cf~Cg~~GH~a~~C~~~~  290 (485)
                      .++|++|++-.|++.+|..+.
T Consensus         2 ~~~CprC~kg~Hwa~~C~sk~   22 (36)
T PF14787_consen    2 PGLCPRCGKGFHWASECRSKT   22 (36)
T ss_dssp             --C-TTTSSSCS-TTT---TC
T ss_pred             CccCcccCCCcchhhhhhhhh
Confidence            378999999999999996653

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

Probab=96.34  E-value=0.013  Score=48.00  Aligned_cols=93  Identities=19%  Similarity=0.228  Sum_probs=64.3

Q ss_pred             CeEEEEEEcCCCCccccCHHHHhhcC------------------Cccc----c-ccceEEEEccCCeeeecceEeeeEEe
Q 042094          339 KHGVTILIDSSSTHIFLNSSLAKQYG------------------CPVT----T-TTQFQVTVADGGVISSSGKCSHVPVN  395 (485)
Q Consensus       339 ~~~v~aLiDsGSt~sfIs~~~~~~l~------------------l~~~----~-~~~~~v~~a~G~~~~~~~~~~~v~v~  395 (485)
                      +..+.|=|||||..|.++..-+....                  ....    + ...++|..++|+... ...+..+.+.
T Consensus        37 ~~~~kAkiDTGA~TSsL~A~dI~~fkRdGe~WVRF~~~~~~~~~~~~~~~e~pvi~~ikvR~s~~~~~e-~RpVV~~~l~  115 (162)
T COG4067          37 KIQLKAKIDTGAVTSSLSASDIERFKRDGERWVRFRLADTDNLDQRSEECEAPVIRKIKVRSSSGSRAE-RRPVVRLTLC  115 (162)
T ss_pred             cceeeeeecccceeeeEEeecceeeeeCCceEEEEEeecccCccccceeeccceEEEEEEecCCCCccc-cccEEEEEEe
Confidence            34578899999999988765433211                  1000    1 124466677777533 3445678999


Q ss_pred             ecceEEEEEEEEcCC--CCCCeeechhHHhhcCCeEEEcc
Q 042094          396 SQGFQFHLDFFLLPV--SGCDIVLGAEWLRSLGAILWDFS  433 (485)
Q Consensus       396 i~~~~~~~~~~V~~~--~~~dvILG~dwL~~~~~i~id~~  433 (485)
                      +||...+++|...+-  ..|++|||..+|.+.+. .+|=.
T Consensus       116 lG~~~~~~E~tLtDR~~m~Yp~LlGrk~l~~~~~-~VDpS  154 (162)
T COG4067         116 LGGRILPIEFTLTDRSNMRYPVLLGRKALRHFGA-VVDPS  154 (162)
T ss_pred             eCCeeeeEEEEeecccccccceEecHHHHhhCCe-EECch
Confidence            999999999999884  56999999999998775 56643

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=96.13  E-value=0.0022  Score=40.51  Aligned_cols=19  Identities=16%  Similarity=0.349  Sum_probs=17.2

Q ss_pred             CCceeecCCCCCCCCcCCC
Q 042094          270 KGLCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       270 ~~~Cf~Cg~~GH~a~~C~~  288 (485)
                      ...|.+|++.||+..+|++
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            4679999999999999984

>smart00343 ZnF_C2HC zinc finger

Probab=96.10  E-value=0.0025  Score=35.99  Aligned_cols=17  Identities=24%  Similarity=0.724  Sum_probs=15.4

Q ss_pred             ceeecCCCCCCCCcCCC
Q 042094          272 LCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       272 ~Cf~Cg~~GH~a~~C~~  288 (485)
                      .||+|++.||++++|+.
T Consensus         1 ~C~~CG~~GH~~~~C~~   17 (26)
T smart00343        1 KCYNCGKEGHIARDCPK   17 (26)
T ss_pred             CCccCCCCCcchhhCCc
Confidence            49999999999999973

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

Probab=95.40  E-value=0.068  Score=44.27  Aligned_cols=92  Identities=16%  Similarity=0.267  Sum_probs=48.6

Q ss_pred             CeEEEEEEcCCCCccccCHHHHhhc---C-------Ccc---ccc----------cceEEEEccCCeeeecceEeeeEEe
Q 042094          339 KHGVTILIDSSSTHIFLNSSLAKQY---G-------CPV---TTT----------TQFQVTVADGGVISSSGKCSHVPVN  395 (485)
Q Consensus       339 ~~~v~aLiDsGSt~sfIs~~~~~~l---~-------l~~---~~~----------~~~~v~~a~G~~~~~~~~~~~v~v~  395 (485)
                      |..+.|=|||||..|-|...-....   |       +..   ...          ....|.-.+|..  -...+..+.+.
T Consensus        14 ~~~~~aKiDTGA~tSSLhA~~I~~ferdg~~~VrF~~~~~~~~~~~~~~~e~p~~~~~~Ik~s~g~~--e~R~VV~~~~~   91 (138)
T PF05618_consen   14 GLTIKAKIDTGAKTSSLHATDIEEFERDGEKWVRFTVHDPDNEEKEGVTFEAPVVRRRKIKSSNGES--ERRPVVETTLC   91 (138)
T ss_dssp             TEEEEEEE-TT-SSEEEE-EEEEEEEETTEEEEEE----EEEETTEEEEEEEEEECEEE-----------CCEEEEEEEE
T ss_pred             CCEEEEEEcCCCcccceeecceEEeeeCCceEEEEecccccCCCcceEEEEEEeEeEEEEEcCCCce--eEeeEEEEEEE
Confidence            4457888899999998865433211   0       000   000          111233334431  12344577899


Q ss_pred             ecceEEEEEEEEcCC--CCCCeeec-hhHHhhcCCeEEEccC
Q 042094          396 SQGFQFHLDFFLLPV--SGCDIVLG-AEWLRSLGAILWDFSK  434 (485)
Q Consensus       396 i~~~~~~~~~~V~~~--~~~dvILG-~dwL~~~~~i~id~~~  434 (485)
                      +++..+.++|.+.+-  ..|+++|| +.||...  +.+|-..
T Consensus        92 lg~~~~~~e~tL~dR~~m~yp~LlGrR~~l~~~--~lVD~s~  131 (138)
T PF05618_consen   92 LGGKTWKIEFTLTDRSNMKYPMLLGRRNFLRGR--FLVDVSR  131 (138)
T ss_dssp             ETTEEEEEEEEEE-S--SS-SEEE-HHHHHHTT--EEEETT-
T ss_pred             ECCEEEEEEEEEcCCCcCcCCEEEEehHHhcCC--EEECCCh
Confidence            999999999999874  56999999 9999854  3577554

; PDB: 2PMA_B.

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

Probab=95.38  E-value=0.098  Score=49.08  Aligned_cols=86  Identities=17%  Similarity=0.173  Sum_probs=54.7

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCC-CCCCeeechh
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPV-SGCDIVLGAE  420 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~-~~~dvILG~d  420 (485)
                      ..++||||++..++.+++.          +.+.+...+|..+.....  ..-+...+....+  -++.. ...-.|||..
T Consensus       177 ~~ai~DTGTs~~~lp~~~~----------P~i~~~f~~~~~~~i~~~--~y~~~~~~~~~C~--~~~~~~~~~~~ilG~~  242 (265)
T cd05476         177 GGTIIDSGTTLTYLPDPAY----------PDLTLHFDGGADLELPPE--NYFVDVGEGVVCL--AILSSSSGGVSILGNI  242 (265)
T ss_pred             CcEEEeCCCcceEcCcccc----------CCEEEEECCCCEEEeCcc--cEEEECCCCCEEE--EEecCCCCCcEEEChh
Confidence            3589999999999988876          356677665554443221  1111111111111  22222 3456899999


Q ss_pred             HHhhcCCeEEEccCcEEEEEEC
Q 042094          421 WLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       421 wL~~~~~i~id~~~~~~~~~~~  442 (485)
                      ||+.+-. ..|+.+++|-|...
T Consensus       243 fl~~~~~-vFD~~~~~iGfa~~  263 (265)
T cd05476         243 QQQNFLV-EYDLENSRLGFAPA  263 (265)
T ss_pred             hcccEEE-EEECCCCEEeeecC
Confidence            9999986 69999999988653

This family contains pepsin like aspartic proteases from plants including Chloroplast Nucleoids DNA-binding Protease and Nucellin. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco and Nucellins are important regulators of nucellar cell's progressive degradation after ovule fertilization. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which

>cd06096 Plasmepsin_5 Plasmepsins are a class of aspartic proteinases produced by the plasmodium parasite

Probab=94.66  E-value=0.11  Score=50.35  Aligned_cols=93  Identities=15%  Similarity=0.151  Sum_probs=59.3

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCCCCCCeeechh
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAE  420 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~~~~dvILG~d  420 (485)
                      ...++||||++.+++.+++.+++.-..   +.+.+.+.+|..+.....  ..-+...+..  . +........-.|||..
T Consensus       231 ~~~aivDSGTs~~~lp~~~~~~l~~~~---P~i~~~f~~g~~~~i~p~--~y~~~~~~~~--c-~~~~~~~~~~~ILG~~  302 (326)
T cd06096         231 GLGMLVDSGSTLSHFPEDLYNKINNFF---PTITIIFENNLKIDWKPS--SYLYKKESFW--C-KGGEKSVSNKPILGAS  302 (326)
T ss_pred             CCCEEEeCCCCcccCCHHHHHHHHhhc---CcEEEEEcCCcEEEECHH--HhccccCCce--E-EEEEecCCCceEEChH
Confidence            345899999999999999998875332   456666665655543211  1111111111  1 1112222235799999


Q ss_pred             HHhhcCCeEEEccCcEEEEEEC
Q 042094          421 WLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       421 wL~~~~~i~id~~~~~~~~~~~  442 (485)
                      ||+.+-. ..|+.+++|.|...
T Consensus       303 flr~~y~-vFD~~~~riGfa~~  323 (326)
T cd06096         303 FFKNKQI-IFDLDNNRIGFVES  323 (326)
T ss_pred             HhcCcEE-EEECcCCEEeeEcC
Confidence            9999986 79999999998743

The family contains a group of aspartic proteinases homologous to plasmepsin 5. Plasmepsins are a class of at least 10 enzymes produced by the plasmodium parasite. Through their haemoglobin-degrading activity, they are an important cause of symptoms in malaria sufferers. This family of enzymes is a potential target for anti-malarial drugs. Plasmepsins are aspartic acid proteases, which means their active site contains two aspartic acid residues. These two aspartic acid residue act respectively as proton donor and proton acceptor, catalyzing the hydrolysis of peptide bond in proteins. Aspartic proteinases are composed of two structurally similar beta barrel lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The catalytic Asp residues are contained in an Asp-Thr-Gly-Ser/thr motif in both N- and C-terminal l

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=94.18  E-value=0.018  Score=49.37  Aligned_cols=22  Identities=27%  Similarity=0.652  Sum_probs=17.4

Q ss_pred             hhhhCCceeecCCCCCCCCcCC
Q 042094          266 ERRAKGLCFNCDEQFKPGHRCK  287 (485)
Q Consensus       266 ~~~~~~~Cf~Cg~~GH~a~~C~  287 (485)
                      .+.....||+||+.||.+++||
T Consensus        56 ~~~~~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          56 IREENPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             ccccccccchhcccCcccccCC
Confidence            3445567999999999999998

>cd05477 gastricsin Gastricsins, asparate proteases produced in gastric mucosa

Probab=93.55  E-value=0.59  Score=45.12  Aligned_cols=94  Identities=14%  Similarity=0.236  Sum_probs=56.1

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCC-eeeecc--eEeeeEEeecceEEEEE-----------E--
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGG-VISSSG--KCSHVPVNSQGFQFHLD-----------F--  405 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~-~~~~~~--~~~~v~v~i~~~~~~~~-----------~--  405 (485)
                      ..++||||++..++..++++.+--......    . ..|. .+.|..  ....+.+.++|..+.+.           +  
T Consensus       202 ~~~iiDSGtt~~~lP~~~~~~l~~~~~~~~----~-~~~~~~~~C~~~~~~p~l~~~f~g~~~~v~~~~y~~~~~~~C~~  276 (318)
T cd05477         202 CQAIVDTGTSLLTAPQQVMSTLMQSIGAQQ----D-QYGQYVVNCNNIQNLPTLTFTINGVSFPLPPSAYILQNNGYCTV  276 (318)
T ss_pred             ceeeECCCCccEECCHHHHHHHHHHhCCcc----c-cCCCEEEeCCccccCCcEEEEECCEEEEECHHHeEecCCCeEEE
Confidence            368999999999999998887532111000    0 0111 111211  11345666666655432           1  


Q ss_pred             EEcC----C--CCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          406 FLLP----V--SGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       406 ~V~~----~--~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      -+.+    .  .....|||..||+.+-. ..|+.+.+|.|..
T Consensus       277 ~i~~~~~~~~~~~~~~ilG~~fl~~~y~-vfD~~~~~ig~a~  317 (318)
T cd05477         277 GIEPTYLPSQNGQPLWILGDVFLRQYYS-VYDLGNNQVGFAT  317 (318)
T ss_pred             EEEecccCCCCCCceEEEcHHHhhheEE-EEeCCCCEEeeee
Confidence            1111    1  12358999999999986 6999999998753

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

>cd06098 phytepsin Phytepsin, a plant homolog of mammalian lysosomal pepsins

Probab=93.44  E-value=0.47  Score=45.78  Aligned_cols=95  Identities=17%  Similarity=0.267  Sum_probs=51.9

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCcc-cc----ccceEEEEccCCeeeecceEeeeEEeecc--e-EEEEEEEEcCC---
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPV-TT----TTQFQVTVADGGVISSSGKCSHVPVNSQG--F-QFHLDFFLLPV---  410 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~-~~----~~~~~v~~a~G~~~~~~~~~~~v~v~i~~--~-~~~~~~~V~~~---  410 (485)
                      ..++||||++..++..++++.+.... ..    .+.+.+.. +|..+.+...  ..-+....  . .....+...+.   
T Consensus       211 ~~aivDTGTs~~~lP~~~~~~i~~~~~C~~~~~~P~i~f~f-~g~~~~l~~~--~yi~~~~~~~~~~C~~~~~~~~~~~~  287 (317)
T cd06098         211 CAAIADSGTSLLAGPTTIVTQINSAVDCNSLSSMPNVSFTI-GGKTFELTPE--QYILKVGEGAAAQCISGFTALDVPPP  287 (317)
T ss_pred             cEEEEecCCcceeCCHHHHHhhhccCCccccccCCcEEEEE-CCEEEEEChH--HeEEeecCCCCCEEeceEEECCCCCC
Confidence            46899999999999999998775221 10    12233333 2332222110  00011000  0 00011111221   


Q ss_pred             CCCCeeechhHHhhcCCeEEEccCcEEEEE
Q 042094          411 SGCDIVLGAEWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       411 ~~~dvILG~dwL~~~~~i~id~~~~~~~~~  440 (485)
                      .+...|||-.||+.+-. ..|+.+++|.|-
T Consensus       288 ~~~~~IlGd~Flr~~y~-VfD~~~~~iGfA  316 (317)
T cd06098         288 RGPLWILGDVFMGAYHT-VFDYGNLRVGFA  316 (317)
T ss_pred             CCCeEEechHHhcccEE-EEeCCCCEEeec
Confidence            12347999999999986 699999999874

Phytepsin, a plant homolog of mammalian lysosomal pepsins, resides in grains, roots, stems, leaves and flowers. Phytepsin may participate in metabolic turnover and in protein processing events. In addition, it highly expressed in several plant tissues undergoing apoptosis. Phytepsin contains an internal region consisting of about 100 residues not present in animal or microbial pepsins. This region is thus called a plant specific insert. The insert is highly similar to saponins, which are lysosomal sphingolipid-activating proteins in mammalian cells. The saponin-like domain may have a role in the vacuolar targeting of phytepsin. Phytepsin, as its animal counterparts, possesses a topology typical of all aspartic proteases. They are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved fro

>cd05485 Cathepsin_D_like Cathepsin_D_like, pepsin family of proteinases

Probab=93.28  E-value=0.3  Score=47.40  Aligned_cols=93  Identities=14%  Similarity=0.248  Sum_probs=54.8

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecc--eEeeeEEeecceEEEEE--------------
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSG--KCSHVPVNSQGFQFHLD--------------  404 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~--~~~~v~v~i~~~~~~~~--------------  404 (485)
                      ..++||||++.+++..++++.+.-..... .  +  .+|.- +.|..  ....+.+.+++..+.+.              
T Consensus       211 ~~~iiDSGtt~~~lP~~~~~~l~~~~~~~-~--~--~~~~~~~~C~~~~~~p~i~f~fgg~~~~i~~~~yi~~~~~~~~~  285 (329)
T cd05485         211 CQAIADTGTSLIAGPVDEIEKLNNAIGAK-P--I--IGGEYMVNCSAIPSLPDITFVLGGKSFSLTGKDYVLKVTQMGQT  285 (329)
T ss_pred             cEEEEccCCcceeCCHHHHHHHHHHhCCc-c--c--cCCcEEEeccccccCCcEEEEECCEEeEEChHHeEEEecCCCCC
Confidence            36999999999999999887653221110 0  0  11111 12211  11345566666554432              


Q ss_pred             -EE--Ec-----CCCCCCeeechhHHhhcCCeEEEccCcEEEEE
Q 042094          405 -FF--LL-----PVSGCDIVLGAEWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       405 -~~--V~-----~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~  440 (485)
                       ++  +.     +..+...|||..||+.+-. ..|+.+++|.|.
T Consensus       286 ~C~~~~~~~~~~~~~~~~~IlG~~fl~~~y~-vFD~~~~~ig~a  328 (329)
T cd05485         286 ICLSGFMGIDIPPPAGPLWILGDVFIGKYYT-EFDLGNNRVGFA  328 (329)
T ss_pred             EEeeeEEECcCCCCCCCeEEEchHHhccceE-EEeCCCCEEeec
Confidence             11  11     1112348999999999986 699999999874

Cathepsin D is the major aspartic proteinase of the lysosomal compartment where it functions in protein catabolism. It is a member of the pepsin family of proteinases. This enzyme is distinguished from other members of the pepsin family by two features that are characteristic of lysosomal hydrolases. First, mature Cathepsin D is found predominantly in a two-chain form due to a posttranslational cleavage event. Second, it contains phosphorylated, N-linked oligosaccharides that target the enzyme to lysosomes via mannose-6-phosphate receptors. Cathepsin D preferentially attacks peptide bonds flanked by bulky hydrophobic amino acids and its pH optimum is between pH 2.8 and 4.0. Two active site aspartic acid residues are essential for the catalytic activity of aspartic proteinases. Like other aspartic proteinases, Cathepsin D is a bilobed molecule; the two evolutionary related lobes are mostly made up of beta-sheets an

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

Probab=93.23  E-value=0.7  Score=44.59  Aligned_cols=100  Identities=16%  Similarity=0.241  Sum_probs=60.2

Q ss_pred             EEECCeEE------EEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCC-eeeecc--eEeeeEEeecceEEEEE-
Q 042094          335 GNLKKHGV------TILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGG-VISSSG--KCSHVPVNSQGFQFHLD-  404 (485)
Q Consensus       335 ~~i~~~~v------~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~-~~~~~~--~~~~v~v~i~~~~~~~~-  404 (485)
                      +.|++..+      .++||||++..++.++.++.+.-.....    . ..+|. .+.|..  ....+.+.++|..+.+. 
T Consensus       194 v~v~g~~~~~~~~~~~iiDTGts~~~lp~~~~~~l~~~~~~~----~-~~~~~~~~~C~~~~~~P~~~f~f~g~~~~i~~  268 (317)
T cd05478         194 VTINGQVVACSGGCQAIVDTGTSLLVGPSSDIANIQSDIGAS----Q-NQNGEMVVNCSSISSMPDVVFTINGVQYPLPP  268 (317)
T ss_pred             EEECCEEEccCCCCEEEECCCchhhhCCHHHHHHHHHHhCCc----c-ccCCcEEeCCcCcccCCcEEEEECCEEEEECH
Confidence            45666544      5899999999999999887753221110    0 01111 112211  12345666666655532 


Q ss_pred             ----------EE--EcCCC-CCCeeechhHHhhcCCeEEEccCcEEEEE
Q 042094          405 ----------FF--LLPVS-GCDIVLGAEWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       405 ----------~~--V~~~~-~~dvILG~dwL~~~~~i~id~~~~~~~~~  440 (485)
                                ++  +.+.. ....|||..||+.+-. ..|+.+++|.|.
T Consensus       269 ~~y~~~~~~~C~~~~~~~~~~~~~IlG~~fl~~~y~-vfD~~~~~iG~A  316 (317)
T cd05478         269 SAYILQDQGSCTSGFQSMGLGELWILGDVFIRQYYS-VFDRANNKVGLA  316 (317)
T ss_pred             HHheecCCCEEeEEEEeCCCCCeEEechHHhcceEE-EEeCCCCEEeec
Confidence                      11  22222 2458999999999986 699999998774

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

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=92.94  E-value=0.048  Score=49.57  Aligned_cols=19  Identities=16%  Similarity=0.483  Sum_probs=16.7

Q ss_pred             CceeecCCCCCCCCcCCCc
Q 042094          271 GLCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~~  289 (485)
                      -.||+||++||+..+||.+
T Consensus       177 Y~CyRCGqkgHwIqnCpTN  195 (427)
T COG5222         177 YVCYRCGQKGHWIQNCPTN  195 (427)
T ss_pred             eeEEecCCCCchhhcCCCC
Confidence            4599999999999999754

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=92.93  E-value=0.045  Score=47.04  Aligned_cols=19  Identities=26%  Similarity=0.660  Sum_probs=16.9

Q ss_pred             CceeecCCCCCCCCcC-CCc
Q 042094          271 GLCFNCDEQFKPGHRC-KAP  289 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C-~~~  289 (485)
                      .+||+||+-||++++| |.+
T Consensus        98 ~~C~~Cg~~GH~~~dC~P~~  117 (190)
T COG5082          98 KKCYNCGETGHLSRDCNPSK  117 (190)
T ss_pred             cccccccccCccccccCccc
Confidence            6899999999999999 554

>cd05486 Cathespin_E Cathepsin E, non-lysosomal aspartic protease

Probab=92.42  E-value=0.45  Score=45.91  Aligned_cols=91  Identities=21%  Similarity=0.279  Sum_probs=53.5

Q ss_pred             EEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecc--eEeeeEEeecceEEEEE---------------
Q 042094          343 TILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSG--KCSHVPVNSQGFQFHLD---------------  404 (485)
Q Consensus       343 ~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~--~~~~v~v~i~~~~~~~~---------------  404 (485)
                      .++||||++..++..+.++.+.-.....      ..+|.. +.|..  ....+.+.++|..+.+.               
T Consensus       200 ~aiiDTGTs~~~lP~~~~~~l~~~~~~~------~~~~~~~~~C~~~~~~p~i~f~f~g~~~~l~~~~y~~~~~~~~~~~  273 (316)
T cd05486         200 QAIVDTGTSLITGPSGDIKQLQNYIGAT------ATDGEYGVDCSTLSLMPSVTFTINGIPYSLSPQAYTLEDQSDGGGY  273 (316)
T ss_pred             EEEECCCcchhhcCHHHHHHHHHHhCCc------ccCCcEEEeccccccCCCEEEEECCEEEEeCHHHeEEecccCCCCE
Confidence            6999999999999998877652111000      011221 12211  12345666666554431               


Q ss_pred             EE--E--cC---CCCCCeeechhHHhhcCCeEEEccCcEEEEE
Q 042094          405 FF--L--LP---VSGCDIVLGAEWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       405 ~~--V--~~---~~~~dvILG~dwL~~~~~i~id~~~~~~~~~  440 (485)
                      ++  +  ++   ..+...|||-.||+.+-. ..|+.+++|-|-
T Consensus       274 C~~~~~~~~~~~~~~~~~ILGd~flr~~y~-vfD~~~~~IGfA  315 (316)
T cd05486         274 CSSGFQGLDIPPPAGPLWILGDVFIRQYYS-VFDRGNNRVGFA  315 (316)
T ss_pred             EeeEEEECCCCCCCCCeEEEchHHhcceEE-EEeCCCCEeecc
Confidence            11  1  11   112247999999999986 699999988763

Cathepsin E is an intracellular, non-lysosomal aspartic protease expressed in a variety of cells and tissues. The protease has proposed physiological roles in antigen presentation by the MHC class II system, in the biogenesis of the vasoconstrictor peptide endothelin, and in neurodegeneration associated with brain ischemia and aging. Cathepsin E is the only A1 aspartic protease that exists as a homodimer with a disulfide bridge linking the two monomers. Like many other aspartic proteases, it is synthesized as a zymogen which is catalytically inactive towards its natural substrates at neutral pH and which auto-activates in an acidic environment. The overall structure follows the general fold of aspartic proteases of the A1 family, it is composed of two structurally similar beta barrel lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The catalyt

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

Probab=92.38  E-value=0.25  Score=47.57  Aligned_cols=94  Identities=15%  Similarity=0.258  Sum_probs=55.9

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecc--eEeeeEEeecceEEEE---------------
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSG--KCSHVPVNSQGFQFHL---------------  403 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~--~~~~v~v~i~~~~~~~---------------  403 (485)
                      ...++||||++...+..+++..+--........     +.-.+.|..  ....+.+.+++..+.+               
T Consensus       199 ~~~~~~Dtgt~~i~lp~~~~~~i~~~l~~~~~~-----~~~~~~c~~~~~~p~l~f~~~~~~~~i~~~~~~~~~~~~~~~  273 (317)
T PF00026_consen  199 GQQAILDTGTSYIYLPRSIFDAIIKALGGSYSD-----GVYSVPCNSTDSLPDLTFTFGGVTFTIPPSDYIFKIEDGNGG  273 (317)
T ss_dssp             EEEEEEETTBSSEEEEHHHHHHHHHHHTTEEEC-----SEEEEETTGGGGSEEEEEEETTEEEEEEHHHHEEEESSTTSS
T ss_pred             ceeeecccccccccccchhhHHHHhhhcccccc-----eeEEEecccccccceEEEeeCCEEEEecchHhcccccccccc
Confidence            368999999999999998877652221100000     111111111  1233445555444321               


Q ss_pred             ----EEEEcC--CCCCCeeechhHHhhcCCeEEEccCcEEEEE
Q 042094          404 ----DFFLLP--VSGCDIVLGAEWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       404 ----~~~V~~--~~~~dvILG~dwL~~~~~i~id~~~~~~~~~  440 (485)
                          .+..++  .....+|||..||+.+-. ..|+.+++|.|-
T Consensus       274 ~C~~~i~~~~~~~~~~~~iLG~~fl~~~y~-vfD~~~~~ig~A  315 (317)
T PF00026_consen  274 YCYLGIQPMDSSDDSDDWILGSPFLRNYYV-VFDYENNRIGFA  315 (317)
T ss_dssp             EEEESEEEESSTTSSSEEEEEHHHHTTEEE-EEETTTTEEEEE
T ss_pred             eeEeeeecccccccCCceEecHHHhhceEE-EEeCCCCEEEEe
Confidence                122211  345789999999999986 799999999875

; InterPro: IPR001461 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to MEROPS peptidase family A1 (pepsin family, clan AA). The type example is pepsin A from Homo sapiens (Human) . More than 70 aspartic peptidases, from all from eukaryotic organisms, have been identified. These include pepsins, cathepsins, and renins. The enzymes are synthesised with signal peptides, and the proenzymes are secreted or passed into the lysosomal/endosomal system, where acidification leads to autocatalytic activation. Most members of the pepsin family specifically cleave bonds in peptides that are at least six residues in length, with hydrophobic residues in both the P1 and P1' positions []. Crystallography has shown the active site to form a groove across the junction of the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors within the active site []. Specificity is determined by several hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. Cysteine residues are well conserved within the pepsin family, pepsin itself containing three disulphide loops. The first loop is found in all but the fungal enzymes, and is usually around five residues in length, but is longer in barrierpepsin and candidapepsin; the second loop is also small and found only in the animal enzymes; and the third loop is the largest, found in all members of the family, except for the cysteine-free polyporopepsin. The loops are spread unequally throughout the two lobes, suggesting that they formed after the initial gene duplication and fusion event []. This family does not include the retroviral nor retrotransposon aspartic proteases which are much smaller and appear to be homologous to the single domain aspartic proteases.; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 1CZI_E 3CMS_A 1CMS_A 4CMS_A 1YG9_A 2NR6_A 3LIZ_A 1FLH_A 3UTL_A 1QRP_E ....

>cd05474 SAP_like SAPs, pepsin-like proteinases secreted from pathogens to degrade host proteins

Probab=92.20  E-value=0.49  Score=45.04  Aligned_cols=95  Identities=19%  Similarity=0.255  Sum_probs=55.3

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccc-cceEEEEccCCeeeecceE-eeeEEeecceEEEEE--------------
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTT-TQFQVTVADGGVISSSGKC-SHVPVNSQGFQFHLD--------------  404 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~-~~~~v~~a~G~~~~~~~~~-~~v~v~i~~~~~~~~--------------  404 (485)
                      ...++||||++..++..++++.+--..... ...    ...-.+.|.... ..+.+.++|..+.+.              
T Consensus       178 ~~~~iiDSGt~~~~lP~~~~~~l~~~~~~~~~~~----~~~~~~~C~~~~~p~i~f~f~g~~~~i~~~~~~~~~~~~~~~  253 (295)
T cd05474         178 NLPALLDSGTTLTYLPSDIVDAIAKQLGATYDSD----EGLYVVDCDAKDDGSLTFNFGGATISVPLSDLVLPASTDDGG  253 (295)
T ss_pred             CccEEECCCCccEeCCHHHHHHHHHHhCCEEcCC----CcEEEEeCCCCCCCEEEEEECCeEEEEEHHHhEeccccCCCC
Confidence            357899999999999999888653221100 000    000011111110 245555555443322              


Q ss_pred             -----EEEcCCCCCCeeechhHHhhcCCeEEEccCcEEEEE
Q 042094          405 -----FFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       405 -----~~V~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~  440 (485)
                           +.+.+......|||..||+.+-. ..|+.+++|.|-
T Consensus       254 ~~~C~~~i~~~~~~~~iLG~~fl~~~y~-vfD~~~~~ig~a  293 (295)
T cd05474         254 DGACYLGIQPSTSDYNILGDTFLRSAYV-VYDLDNNEISLA  293 (295)
T ss_pred             CCCeEEEEEeCCCCcEEeChHHhhcEEE-EEECCCCEEEee
Confidence                 11222222468999999999986 799999999875

SAPs (Secreted aspartic proteinases) are secreted from a group of pathogenic fungi, predominantly Candida species. They are secreted from the pathogen to degrade host proteins. SAP is one of the most significant extracellular hydrolytic enzymes produced by C. albicans. SAP proteins, encoded by a family of 10 SAP genes. All 10 SAP genes of C. albicans encode preproenzymes, approximately 60 amino acid longer than the mature enzyme, which are processed when transported via the secretory pathway. The mature enzymes contain sequence motifs typical for all aspartyl proteinases, including the two conserved aspartate residues other active site and conserved cysteine residues implicated in the maintenance of the three-dimensional structure. Most Sap proteins contain putative N-glycosylation sites, but it remains to be determined which Sap proteins are glycosylated. This family of aspartate proteases

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=91.91  E-value=0.078  Score=44.81  Aligned_cols=16  Identities=25%  Similarity=0.752  Sum_probs=8.2

Q ss_pred             ceeecCCCCCCCCcCC
Q 042094          272 LCFNCDEQFKPGHRCK  287 (485)
Q Consensus       272 ~Cf~Cg~~GH~a~~C~  287 (485)
                      .||+|++.||++++|+
T Consensus       105 ~C~~Cg~~gH~~~~C~  120 (148)
T PTZ00368        105 ACYNCGGEGHISRDCP  120 (148)
T ss_pred             hhcccCcCCcchhcCC
Confidence            3555555555555553

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=91.86  E-value=0.054  Score=35.96  Aligned_cols=19  Identities=21%  Similarity=0.646  Sum_probs=16.7

Q ss_pred             hCCceeecCCCCCCCCcCC
Q 042094          269 AKGLCFNCDEQFKPGHRCK  287 (485)
Q Consensus       269 ~~~~Cf~Cg~~GH~a~~C~  287 (485)
                      -...||+||..||...+|+
T Consensus        30 lp~~C~~C~~~gH~~~~C~   48 (49)
T PF14392_consen   30 LPRFCFHCGRIGHSDKECP   48 (49)
T ss_pred             cChhhcCCCCcCcCHhHcC
Confidence            3466999999999999996

>cd06097 Aspergillopepsin_like Aspergillopepsin_like, aspartic proteases of fungal origin

Probab=91.77  E-value=0.23  Score=46.95  Aligned_cols=79  Identities=20%  Similarity=0.354  Sum_probs=47.8

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCC-eeeecceEeeeEEeecceEEEEEEEEcCCCCCCeeech
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGG-VISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGA  419 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~-~~~~~~~~~~v~v~i~~~~~~~~~~V~~~~~~dvILG~  419 (485)
                      ...++||||++..++..++++.+--...   ........|. .+.|       .-.+-...|.+          ..|||-
T Consensus       198 ~~~~iiDSGTs~~~lP~~~~~~l~~~l~---g~~~~~~~~~~~~~C-------~~~~P~i~f~~----------~~ilGd  257 (278)
T cd06097         198 GFSAIADTGTTLILLPDAIVEAYYSQVP---GAYYDSEYGGWVFPC-------DTTLPDLSFAV----------FSILGD  257 (278)
T ss_pred             CceEEeecCCchhcCCHHHHHHHHHhCc---CCcccCCCCEEEEEC-------CCCCCCEEEEE----------EEEEcc
Confidence            4578999999999999888876632210   0000001111 1122       11122222222          579999


Q ss_pred             hHHhhcCCeEEEccCcEEEEE
Q 042094          420 EWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       420 dwL~~~~~i~id~~~~~~~~~  440 (485)
                      .||+.+-. ..|+.+++|-|-
T Consensus       258 ~fl~~~y~-vfD~~~~~ig~A  277 (278)
T cd06097         258 VFLKAQYV-VFDVGGPKLGFA  277 (278)
T ss_pred             hhhCceeE-EEcCCCceeeec
Confidence            99999987 699999998774

The members of this family are aspartic proteases of fungal origin, including aspergillopepsin, rhizopuspepsin, endothiapepsin, and rodosporapepsin. The various fungal species in this family may be the most economically important genus of fungi. They may serve as virulence factors or as industrial aids. For example, Aspergillopepsin from A. fumigatus is involved in invasive aspergillosis owing to its elastolytic activity and Aspergillopepsins from the mold A. saitoi are used in fermentation industry. Aspartic proteinases are a group of proteolytic enzymes in which the scissile peptide bond is attacked by a nucleophilic water molecule activated by two aspartic residues in a DT(S)G motif at the active site. They have a similar fold composed of two beta-barrel domains. Between the N-terminal and C-terminal domains, each of which contributes one catalytic aspartic residue, there is an extended active-

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=91.57  E-value=0.1  Score=47.65  Aligned_cols=22  Identities=14%  Similarity=0.345  Sum_probs=18.1

Q ss_pred             ceeecCCCCCCCCcCCCceeee
Q 042094          272 LCFNCDEQFKPGHRCKAPQLLL  293 (485)
Q Consensus       272 ~Cf~Cg~~GH~a~~C~~~~~~~  293 (485)
                      .||.||+.||++++||......
T Consensus       162 ~cyrcGkeghwskEcP~~~~~r  183 (346)
T KOG0109|consen  162 GCYRCGKEGHWSKECPVDRTGR  183 (346)
T ss_pred             HheeccccccccccCCccCCCc
Confidence            4999999999999998654433

>PF02023 SCAN: SCAN domain; InterPro: IPR003309 A number of C2H2-zinc finger proteins contain a highly conserved N-terminal motif termed the SCAN domain

Probab=91.54  E-value=0.47  Score=36.50  Aligned_cols=39  Identities=23%  Similarity=0.242  Sum_probs=33.3

Q ss_pred             HHHHHHHHhhhHHHHHHHHHhcCcccHHHHHHHHHHHHH
Q 042094          167 SFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEE  205 (485)
Q Consensus       167 ~~~~~~f~~GL~~~i~~~v~~~~p~tl~~~~~~a~~~e~  205 (485)
                      -..+.+|+..||.+++..|..+.|.+..+++.+|..+..
T Consensus        48 llvlEQFL~~lP~e~~~wV~e~~p~s~~ea~~Lae~~~~   86 (95)
T PF02023_consen   48 LLVLEQFLNILPPEVQTWVRERKPESAEEAVALAEDYQR   86 (95)
T ss_dssp             HHHHHHHHHHS-HHHHHHHHTCS-SSHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHCCHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            357889999999999999999999999999999988754

The SCAN domain may play an important role in the assembly and function of this newly defined subclass of transcriptional regulators [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3LHR_B 4E6S_A 2FI2_A 1Y7Q_A.

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=91.22  E-value=0.13  Score=31.88  Aligned_cols=20  Identities=25%  Similarity=0.295  Sum_probs=16.5

Q ss_pred             CceeecCCCCCCC--CcCCCce
Q 042094          271 GLCFNCDEQFKPG--HRCKAPQ  290 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a--~~C~~~~  290 (485)
                      ..|.+||..||.+  +.||-+.
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~   23 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYC   23 (40)
T ss_pred             ccccccccccccccCccCCCCC
Confidence            4699999999998  6887654

>cd05472 cnd41_like Chloroplast Nucleoids DNA-binding Protease, catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase

Probab=91.16  E-value=1.4  Score=42.10  Aligned_cols=27  Identities=11%  Similarity=0.181  Sum_probs=23.5

Q ss_pred             CeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          414 DIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       414 dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      -.|||..||+.+-. ..|+.+++|.|..
T Consensus       270 ~~ilG~~fl~~~~v-vfD~~~~~igfa~  296 (299)
T cd05472         270 LSIIGNVQQQTFRV-VYDVAGGRIGFAP  296 (299)
T ss_pred             CEEEchHHccceEE-EEECCCCEEeEec
Confidence            47999999999986 6999999998864

Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco. Antisense tobacco with reduced amount of CND41 maintained green leaves and constant protein levels, especially Rubisco. CND41 has DNA-binding as well as aspartic protease activities. The pepsin-like aspartic protease domain is located at the C-terminus of the protein. The enzyme is characterized by having two aspartic protease catalytic site motifs, the Asp-Thr-Gly-Ser in the N-terminal and Asp-Ser-Gly-Ser in the C-terminal region. Aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. This fami

>cd05488 Proteinase_A_fungi Fungal Proteinase A , aspartic proteinase superfamily

Probab=90.02  E-value=1.9  Score=41.71  Aligned_cols=93  Identities=19%  Similarity=0.318  Sum_probs=55.4

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecc--eEeeeEEeecceEEEEE-----------E--
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSG--KCSHVPVNSQGFQFHLD-----------F--  405 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~--~~~~v~v~i~~~~~~~~-----------~--  405 (485)
                      ..++||||++..++..++++.+.-......     ..+|.. +.|..  ....+.+.++|..+.+.           +  
T Consensus       206 ~~~ivDSGtt~~~lp~~~~~~l~~~~~~~~-----~~~~~~~~~C~~~~~~P~i~f~f~g~~~~i~~~~y~~~~~g~C~~  280 (320)
T cd05488         206 TGAAIDTGTSLIALPSDLAEMLNAEIGAKK-----SWNGQYTVDCSKVDSLPDLTFNFDGYNFTLGPFDYTLEVSGSCIS  280 (320)
T ss_pred             CeEEEcCCcccccCCHHHHHHHHHHhCCcc-----ccCCcEEeeccccccCCCEEEEECCEEEEECHHHheecCCCeEEE
Confidence            358999999999999998887532211100     011111 12211  12345666666655432           1  


Q ss_pred             EEcC--C---CCCCeeechhHHhhcCCeEEEccCcEEEEE
Q 042094          406 FLLP--V---SGCDIVLGAEWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       406 ~V~~--~---~~~dvILG~dwL~~~~~i~id~~~~~~~~~  440 (485)
                      .+..  .   .+...|||..||+.+-. ..|+.+.+|.|.
T Consensus       281 ~~~~~~~~~~~~~~~ilG~~fl~~~y~-vfD~~~~~iG~a  319 (320)
T cd05488         281 AFTGMDFPEPVGPLAIVGDAFLRKYYS-VYDLGNNAVGLA  319 (320)
T ss_pred             EEEECcCCCCCCCeEEEchHHhhheEE-EEeCCCCEEeec
Confidence            1111  1   12358999999999886 699999998774

Fungal Proteinase A, a proteolytic enzyme distributed among a variety of organisms, is a member of the aspartic proteinase superfamily. In Saccharomyces cerevisiae, targeted to the vacuole as a zymogen, activation of proteinases A at acidic pH can occur by two different pathways: a one-step process to release mature proteinase A, involving the intervention of proteinase B, or a step-wise pathway via the auto-activation product known as pseudo-proteinase A. Once active, S. cerevisiae proteinase A is essential to the activities of other yeast vacuolar hydrolases, including proteinase B and carboxypeptidase Y. The mature enzyme is bilobal, with each lobe providing one of the two catalytically essential aspartic acid residues in the active site. The crystal structure of free proteinase A shows that flap loop is atypically pointing directly into the S(1) pocket of the enzyme. Proteinase A preferentially hydro

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

Probab=89.96  E-value=0.35  Score=45.58  Aligned_cols=82  Identities=21%  Similarity=0.285  Sum_probs=49.1

Q ss_pred             eEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCCCCCCeeech
Q 042094          340 HGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGA  419 (485)
Q Consensus       340 ~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~~~~dvILG~  419 (485)
                      ....++||||++..++..+++..+--........    ..+...      ..+.-.-.--.+.+.|        ..|||.
T Consensus       201 ~~~~~iiDsGt~~~~lp~~~~~~l~~~~~~~~~~----~~~~~~------~~~~~~~~~p~i~f~f--------~~ilG~  262 (283)
T cd05471         201 GGGGAIVDSGTSLIYLPSSVYDAILKALGAAVSS----SDGGYG------VDCSPCDTLPDITFTF--------LWILGD  262 (283)
T ss_pred             CCcEEEEecCCCCEeCCHHHHHHHHHHhCCcccc----cCCcEE------EeCcccCcCCCEEEEE--------EEEccH
Confidence            3568999999999999999988764332111000    000000      0000000001122222        799999


Q ss_pred             hHHhhcCCeEEEccCcEEEEE
Q 042094          420 EWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       420 dwL~~~~~i~id~~~~~~~~~  440 (485)
                      .||+.+-. ..|+.+++|.|.
T Consensus       263 ~fl~~~y~-vfD~~~~~igfa  282 (283)
T cd05471         263 VFLRNYYT-VFDLDNNRIGFA  282 (283)
T ss_pred             hhhhheEE-EEeCCCCEEeec
Confidence            99999996 699999888774

Pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, renin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (renin, cathepsin D and E, pepsin) or commercially (chymosin) important. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Aspartate residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. Most members of the pepsin family specifically cleave bonds in peptides that are at least six residues in length, with hydrophobic residu

>PTZ00147 plasmepsin-1; Provisional

Probab=89.50  E-value=1.4  Score=44.60  Aligned_cols=97  Identities=16%  Similarity=0.355  Sum_probs=55.1

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeec-ceEeeeEEeecceEEEEE---------------E
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSS-GKCSHVPVNSQGFQFHLD---------------F  405 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~-~~~~~v~v~i~~~~~~~~---------------~  405 (485)
                      ..++||||++..++..+.++.+--....   ..+...++-.+.|. .....+.+.++|..+.+.               +
T Consensus       333 ~~aIiDSGTsli~lP~~~~~ai~~~l~~---~~~~~~~~y~~~C~~~~lP~~~f~f~g~~~~L~p~~yi~~~~~~~~~~C  409 (453)
T PTZ00147        333 ANVIVDSGTSVITVPTEFLNKFVESLDV---FKVPFLPLYVTTCNNTKLPTLEFRSPNKVYTLEPEYYLQPIEDIGSALC  409 (453)
T ss_pred             eeEEECCCCchhcCCHHHHHHHHHHhCC---eecCCCCeEEEeCCCCCCCeEEEEECCEEEEECHHHheeccccCCCcEE
Confidence            5799999999999999988764211100   00000000001111 111234455555443321               1


Q ss_pred             E--EcC--CCCCCeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          406 F--LLP--VSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       406 ~--V~~--~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                      +  +.+  ......|||..||+.+-. ..|+.+.+|.|-..
T Consensus       410 ~~~i~~~~~~~~~~ILGd~FLr~~Yt-VFD~~n~rIGfA~a  449 (453)
T PTZ00147        410 MLNIIPIDLEKNTFILGDPFMRKYFT-VFDYDNHTVGFALA  449 (453)
T ss_pred             EEEEEECCCCCCCEEECHHHhccEEE-EEECCCCEEEEEEe
Confidence            1  222  222357999999999997 69999999999754

>cd05490 Cathepsin_D2 Cathepsin_D2, pepsin family of proteinases

Probab=88.94  E-value=1.2  Score=43.08  Aligned_cols=93  Identities=12%  Similarity=0.204  Sum_probs=54.1

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCC-eeeecc--eEeeeEEeecceEEEEE--------------
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGG-VISSSG--KCSHVPVNSQGFQFHLD--------------  404 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~-~~~~~~--~~~~v~v~i~~~~~~~~--------------  404 (485)
                      ..++||||++..++..+.++.+.-.....     ...+|. .+.|..  ....+.|.++|..+.+.              
T Consensus       207 ~~aiiDSGTt~~~~p~~~~~~l~~~~~~~-----~~~~~~~~~~C~~~~~~P~i~f~fgg~~~~l~~~~y~~~~~~~~~~  281 (325)
T cd05490         207 CEAIVDTGTSLITGPVEEVRALQKAIGAV-----PLIQGEYMIDCEKIPTLPVISFSLGGKVYPLTGEDYILKVSQRGTT  281 (325)
T ss_pred             CEEEECCCCccccCCHHHHHHHHHHhCCc-----cccCCCEEecccccccCCCEEEEECCEEEEEChHHeEEeccCCCCC
Confidence            47999999999999998887663211100     001111 112211  11234555666544322              


Q ss_pred             -EE--Ec--C---CCCCCeeechhHHhhcCCeEEEccCcEEEEE
Q 042094          405 -FF--LL--P---VSGCDIVLGAEWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       405 -~~--V~--~---~~~~dvILG~dwL~~~~~i~id~~~~~~~~~  440 (485)
                       ++  +.  +   ......|||..||+.+-. ..|+.+++|.|.
T Consensus       282 ~C~~~~~~~~~~~~~~~~~ilGd~flr~~y~-vfD~~~~~IGfA  324 (325)
T cd05490         282 ICLSGFMGLDIPPPAGPLWILGDVFIGRYYT-VFDRDNDRVGFA  324 (325)
T ss_pred             EEeeEEEECCCCCCCCceEEEChHhheeeEE-EEEcCCcEeecc
Confidence             11  11  1   112347999999999986 699999998774

Cathepsin D is the major aspartic proteinase of the lysosomal compartment where it functions in protein catabolism. It is a member of the pepsin family of proteinases. This enzyme is distinguished from other members of the pepsin family by two features that are characteristic of lysosomal hydrolases. First, mature Cathepsin D is found predominantly in a two-chain form due to a posttranslational cleavage event. Second, it contains phosphorylated, N-linked oligosaccharides that target the enzyme to lysosomes via mannose-6-phosphate receptors. Cathepsin D preferentially attacks peptide bonds flanked by bulky hydrophobic amino acids and its pH optimum is between pH 2.8 and 4.0. Two active site aspartic acid residues are essential for the catalytic activity of aspartic proteinases. Like other aspartic proteinases, Cathepsin D is a bilobed molecule; the two evolutionary related lobes are mostly made up of beta-sheets and flank

>PTZ00013 plasmepsin 4 (PM4); Provisional

Probab=88.26  E-value=2.2  Score=43.18  Aligned_cols=95  Identities=19%  Similarity=0.338  Sum_probs=53.6

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCC-eeeec-ceEeeeEEeecceEEEEE---------------
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGG-VISSS-GKCSHVPVNSQGFQFHLD---------------  404 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~-~~~~~-~~~~~v~v~i~~~~~~~~---------------  404 (485)
                      ..|+||||++..++..+.++.+--.....   .+. ..|. .+.|. .....+.+.++|..+.+.               
T Consensus       332 ~~aIlDSGTSli~lP~~~~~~i~~~l~~~---~~~-~~~~y~~~C~~~~lP~i~F~~~g~~~~L~p~~Yi~~~~~~~~~~  407 (450)
T PTZ00013        332 ANVIVDSGTTTITAPSEFLNKFFANLNVI---KVP-FLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYMNPLLDVDDTL  407 (450)
T ss_pred             cceEECCCCccccCCHHHHHHHHHHhCCe---ecC-CCCeEEeecCCCCCCeEEEEECCEEEEECHHHheehhccCCCCe
Confidence            45899999999999998777552111000   000 0110 01111 111234455555433321               


Q ss_pred             --EEEcCC--CCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 --FFLLPV--SGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 --~~V~~~--~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                        +.+.+.  .....|||-.||+.+-. ..|+.+++|-|-.
T Consensus       408 C~~~i~~~~~~~~~~ILGd~FLr~~Y~-VFD~~n~rIGfA~  447 (450)
T PTZ00013        408 CMITMLPVDIDDNTFILGDPFMRKYFT-VFDYDKESVGFAI  447 (450)
T ss_pred             eEEEEEECCCCCCCEEECHHHhccEEE-EEECCCCEEEEEE
Confidence              112222  22358999999999987 6999999998864

>cd05474 SAP_like SAPs, pepsin-like proteinases secreted from pathogens to degrade host proteins

Probab=87.50  E-value=3.3  Score=39.36  Aligned_cols=72  Identities=25%  Similarity=0.353  Sum_probs=48.4

Q ss_pred             EEEEEECC--eEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEE-EEEEEc
Q 042094          332 RLKGNLKK--HGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFH-LDFFLL  408 (485)
Q Consensus       332 ~~~~~i~~--~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~-~~~~V~  408 (485)
                      .+.+.|+.  +.+.++|||||+...|.               ++.+..++|+.+.  |....=.|.+++.... ..|-+.
T Consensus         4 ~~~i~iGtp~q~~~v~~DTgS~~~wv~---------------~~~~~Y~~g~~~~--G~~~~D~v~~g~~~~~~~~fg~~   66 (295)
T cd05474           4 SAELSVGTPPQKVTVLLDTGSSDLWVP---------------DFSISYGDGTSAS--GTWGTDTVSIGGATVKNLQFAVA   66 (295)
T ss_pred             EEEEEECCCCcEEEEEEeCCCCcceee---------------eeEEEeccCCcEE--EEEEEEEEEECCeEecceEEEEE
Confidence            45666765  88999999999999887               5677888876543  4333346777776543 445555


Q ss_pred             CC-CCCCeeechh
Q 042094          409 PV-SGCDIVLGAE  420 (485)
Q Consensus       409 ~~-~~~dvILG~d  420 (485)
                      .. ...|-|||+-
T Consensus        67 ~~~~~~~GilGLg   79 (295)
T cd05474          67 NSTSSDVGVLGIG   79 (295)
T ss_pred             ecCCCCcceeeEC
Confidence            42 3467787754

SAPs (Secreted aspartic proteinases) are secreted from a group of pathogenic fungi, predominantly Candida species. They are secreted from the pathogen to degrade host proteins. SAP is one of the most significant extracellular hydrolytic enzymes produced by C. albicans. SAP proteins, encoded by a family of 10 SAP genes. All 10 SAP genes of C. albicans encode preproenzymes, approximately 60 amino acid longer than the mature enzyme, which are processed when transported via the secretory pathway. The mature enzymes contain sequence motifs typical for all aspartyl proteinases, including the two conserved aspartate residues other active site and conserved cysteine residues implicated in the maintenance of the three-dimensional structure. Most Sap proteins contain putative N-glycosylation sites, but it remains to be determined which Sap proteins are glycosylated. This family of aspartate proteases

>PF14223 UBN2: gag-polypeptide of LTR copia-type

Probab=86.71  E-value=2.7  Score=33.77  Aligned_cols=87  Identities=14%  Similarity=0.024  Sum_probs=54.1

Q ss_pred             hHhHhHHhhhcCCCC------CHHHHHHHHHHh-hCCCchhhhhhhcC-------------CChHHHHHHHHhhhHHHHH
Q 042094          123 AVPWYHWLEQTMGNM------TWAQFKRALVTQ-FGTFEDGDAVGTQN-------------LPESFFISCFLSGLREDIK  182 (485)
Q Consensus       123 A~~W~~~~~~~~~~~------tw~~f~~~l~~~-F~~~~~~~ey~~~~-------------~~e~~~~~~f~~GL~~~i~  182 (485)
                      |..-|..+.......      ....++..|..- +.+.....+|+.++             +++..++..+++|||+...
T Consensus         3 A~e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~g~~i~d~~~v~~iL~~Lp~~y~   82 (119)
T PF14223_consen    3 AKEAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAIGKPISDEDLVSKILRSLPPSYD   82 (119)
T ss_pred             HHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhcCCcccchhHHHHHHhcCCchhH
Confidence            455555554432222      223344444332 24555557777776             6999999999999987654


Q ss_pred             HH---HHhc-Ccc--cHHHHHHHHHHHHHHHhh
Q 042094          183 IG---VQML-KPA--SLLQTFELARFQEEYAAV  209 (485)
Q Consensus       183 ~~---v~~~-~p~--tl~~~~~~a~~~e~~~~~  209 (485)
                      ..   +... ...  ++++++......|.....
T Consensus        83 ~~~~~i~~~~~~~~~t~~el~~~L~~~E~~~~~  115 (119)
T PF14223_consen   83 TFVTAIRNSKDLPKMTLEELISRLLAEEMRLKS  115 (119)
T ss_pred             HHHHHHHhcCCCCcCCHHHHHHHHHHHHHHHHH
Confidence            43   3333 334  799999998888876643

>cd05487 renin_like Renin stimulates production of angiotensin and thus affects blood pressure

Probab=86.35  E-value=2.5  Score=40.91  Aligned_cols=92  Identities=17%  Similarity=0.268  Sum_probs=52.4

Q ss_pred             EEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCC-eeeecc--eEeeeEEeecceEEEEE---------------
Q 042094          343 TILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGG-VISSSG--KCSHVPVNSQGFQFHLD---------------  404 (485)
Q Consensus       343 ~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~-~~~~~~--~~~~v~v~i~~~~~~~~---------------  404 (485)
                      .++||||++..++..+.++.+--.......      .|. .+.|..  ....+.+.+++..+.+.               
T Consensus       209 ~aiiDSGts~~~lP~~~~~~l~~~~~~~~~------~~~y~~~C~~~~~~P~i~f~fgg~~~~v~~~~yi~~~~~~~~~~  282 (326)
T cd05487         209 TAVVDTGASFISGPTSSISKLMEALGAKER------LGDYVVKCNEVPTLPDISFHLGGKEYTLSSSDYVLQDSDFSDKL  282 (326)
T ss_pred             EEEECCCccchhCcHHHHHHHHHHhCCccc------CCCEEEeccccCCCCCEEEEECCEEEEeCHHHhEEeccCCCCCE
Confidence            589999999999999877665211110000      111 112211  11234555555543321               


Q ss_pred             EE--E--cCC---CCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 FF--L--LPV---SGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 ~~--V--~~~---~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      ++  +  .+.   .+...|||..||+.+-. ..|+.+++|-|..
T Consensus       283 C~~~~~~~~~~~~~~~~~ilG~~flr~~y~-vfD~~~~~IGfA~  325 (326)
T cd05487         283 CTVAFHAMDIPPPTGPLWVLGATFIRKFYT-EFDRQNNRIGFAL  325 (326)
T ss_pred             EEEEEEeCCCCCCCCCeEEEehHHhhccEE-EEeCCCCEEeeee
Confidence            11  1  111   11247999999999986 7999999998753

Renin, also known as angiotensinogenase, is a circulating enzyme that participates in the renin-angiotensin system that mediates extracellular volume, arterial vasoconstriction, and consequently mean arterial blood pressure. The enzyme is secreted by the kidneys from specialized juxtaglomerular cells in response to decreases in glomerular filtration rate (a consequence of low blood volume), diminished filtered sodium chloride and sympathetic nervous system innervation. The enzyme circulates in the blood stream and hydrolyzes angiotensinogen secreted from the liver into the peptide angiotensin I. Angiotensin I is further cleaved in the lungs by endothelial bound angiotensin converting enzyme (ACE) into angiotensin II, the final active peptide. Renin is a member of the aspartic protease family. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Aspartate r

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

Probab=86.03  E-value=2.1  Score=41.09  Aligned_cols=86  Identities=22%  Similarity=0.304  Sum_probs=51.4

Q ss_pred             EEEEEEC--CeEEEEEEcCCCCccccCHHHHhhc------CCcc-c-------cccceEEEEccCCeeeecceEeeeEEe
Q 042094          332 RLKGNLK--KHGVTILIDSSSTHIFLNSSLAKQY------GCPV-T-------TTTQFQVTVADGGVISSSGKCSHVPVN  395 (485)
Q Consensus       332 ~~~~~i~--~~~v~aLiDsGSt~sfIs~~~~~~l------~l~~-~-------~~~~~~v~~a~G~~~~~~~~~~~v~v~  395 (485)
                      .+.+.|+  .+.+.++|||||+..+|....+..-      +.-. .       ...++.+..++|. +  .|....=.|.
T Consensus         3 ~~~v~iGtp~q~~~~~iDTGS~~~wv~~~~c~~~~~~~~~~~y~~~~S~t~~~~~~~~~~~y~~g~-~--~G~~~~D~v~   79 (317)
T PF00026_consen    3 YINVTIGTPPQTFRVLIDTGSSDTWVPSSNCNSCSSCASSGFYNPSKSSTFSNQGKPFSISYGDGS-V--SGNLVSDTVS   79 (317)
T ss_dssp             EEEEEETTTTEEEEEEEETTBSSEEEEBTTECSHTHHCTSC-BBGGGSTTEEEEEEEEEEEETTEE-E--EEEEEEEEEE
T ss_pred             EEEEEECCCCeEEEEEEecccceeeeceeccccccccccccccccccccccccceeeeeeeccCcc-c--ccccccceEe
Confidence            4567776  7999999999999998864322211      1110 1       1134566667766 3  3444444788


Q ss_pred             ecceEEE-EEEEEcCC--------CCCCeeechh
Q 042094          396 SQGFQFH-LDFFLLPV--------SGCDIVLGAE  420 (485)
Q Consensus       396 i~~~~~~-~~~~V~~~--------~~~dvILG~d  420 (485)
                      +++.... ..|.++..        ...|=|||+-
T Consensus        80 ig~~~~~~~~f~~~~~~~~~~~~~~~~~GilGLg  113 (317)
T PF00026_consen   80 IGGLTIPNQTFGLADSYSGDPFSPIPFDGILGLG  113 (317)
T ss_dssp             ETTEEEEEEEEEEEEEEESHHHHHSSSSEEEE-S
T ss_pred             eeeccccccceecccccccccccccccccccccc
Confidence            8887655 55555543        2367777766

; InterPro: IPR001461 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to MEROPS peptidase family A1 (pepsin family, clan AA). The type example is pepsin A from Homo sapiens (Human) . More than 70 aspartic peptidases, from all from eukaryotic organisms, have been identified. These include pepsins, cathepsins, and renins. The enzymes are synthesised with signal peptides, and the proenzymes are secreted or passed into the lysosomal/endosomal system, where acidification leads to autocatalytic activation. Most members of the pepsin family specifically cleave bonds in peptides that are at least six residues in length, with hydrophobic residues in both the P1 and P1' positions []. Crystallography has shown the active site to form a groove across the junction of the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors within the active site []. Specificity is determined by several hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. Cysteine residues are well conserved within the pepsin family, pepsin itself containing three disulphide loops. The first loop is found in all but the fungal enzymes, and is usually around five residues in length, but is longer in barrierpepsin and candidapepsin; the second loop is also small and found only in the animal enzymes; and the third loop is the largest, found in all members of the family, except for the cysteine-free polyporopepsin. The loops are spread unequally throughout the two lobes, suggesting that they formed after the initial gene duplication and fusion event []. This family does not include the retroviral nor retrotransposon aspartic proteases which are much smaller and appear to be homologous to the single domain aspartic proteases.; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 1CZI_E 3CMS_A 1CMS_A 4CMS_A 1YG9_A 2NR6_A 3LIZ_A 1FLH_A 3UTL_A 1QRP_E ....

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

Probab=85.98  E-value=3.8  Score=33.67  Aligned_cols=82  Identities=10%  Similarity=0.124  Sum_probs=49.3

Q ss_pred             ECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCCCCCCee
Q 042094          337 LKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIV  416 (485)
Q Consensus       337 i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~~~~dvI  416 (485)
                      |.|..+.+.-||||+++.|-..+...    ..+.....+.+.+|..-.   .+--+.|.++|.....+++.-+.. |-+|
T Consensus         1 ikg~~l~~~wDsga~ITCiP~~fl~~----E~Pi~~~~i~Tihg~~~~---~vYYl~fKi~grkv~aEVi~s~~d-y~li   72 (163)
T PF03539_consen    1 IKGTKLKGHWDSGAQITCIPESFLEE----EQPIGKTLIKTIHGEKEQ---DVYYLTFKINGRKVEAEVIASPYD-YILI   72 (163)
T ss_dssp             ETTEEEEEEE-TT-SSEEEEGGGTTT-------SEEEEEE-SS-EEEE---EEEEEEEEESS-EEEEEEEEESSS-SEEE
T ss_pred             CCCceeeEEecCCCeEEEccHHHhCc----cccccceEEEEecCceec---cEEEEEEEEcCeEEEEEEecCccc-eEEE
Confidence            45788899999999999998887553    134456678888887643   333478999998776666655532 2222


Q ss_pred             --echhHHhhcC
Q 042094          417 --LGAEWLRSLG  426 (485)
Q Consensus       417 --LG~dwL~~~~  426 (485)
                        .-.+|+.+..
T Consensus        73 ~p~diPw~~~~p   84 (163)
T PF03539_consen   73 SPSDIPWYKKKP   84 (163)
T ss_dssp             -TTT-HHHHS--
T ss_pred             cccccccccCCC
Confidence              1568998765

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

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=85.39  E-value=0.45  Score=40.18  Aligned_cols=19  Identities=21%  Similarity=0.630  Sum_probs=12.0

Q ss_pred             CceeecCCCCCCCCcCCCc
Q 042094          271 GLCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~~  289 (485)
                      ..||+|++.||++++||.+
T Consensus        28 ~~C~~Cg~~GH~~~~Cp~~   46 (148)
T PTZ00368         28 RPCYKCGEPGHLSRECPSA   46 (148)
T ss_pred             ccCccCCCCCcCcccCcCC
Confidence            4566666666666666543

>cd05470 pepsin_retropepsin_like Cellular and retroviral pepsin-like aspartate proteases

Probab=84.17  E-value=4.2  Score=31.87  Aligned_cols=27  Identities=15%  Similarity=0.322  Sum_probs=20.5

Q ss_pred             EEEECC--eEEEEEEcCCCCccccCHHHH
Q 042094          334 KGNLKK--HGVTILIDSSSTHIFLNSSLA  360 (485)
Q Consensus       334 ~~~i~~--~~v~aLiDsGSt~sfIs~~~~  360 (485)
                      .+.|+.  +.+.++|||||+...|..+-+
T Consensus         2 ~i~vGtP~q~~~~~~DTGSs~~Wv~~~~c   30 (109)
T cd05470           2 EIGIGTPPQTFNVLLDTGSSNLWVPSVDC   30 (109)
T ss_pred             EEEeCCCCceEEEEEeCCCCCEEEeCCCC
Confidence            345554  789999999999998876543

This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=83.90  E-value=0.45  Score=44.45  Aligned_cols=18  Identities=28%  Similarity=0.704  Sum_probs=16.5

Q ss_pred             CceeecCCCCCCCCcCCC
Q 042094          271 GLCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~  288 (485)
                      ..||+||+.||+.++|+.
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~  161 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPE  161 (261)
T ss_pred             CccCCCCcCCcchhhCCC
Confidence            569999999999999984

>PLN03146 aspartyl protease family protein; Provisional

Probab=83.54  E-value=2.2  Score=43.10  Aligned_cols=28  Identities=14%  Similarity=0.083  Sum_probs=23.9

Q ss_pred             CeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          414 DIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       414 dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                      ..|||..+++.+.. ..|..+++|.|...
T Consensus       399 ~~IlG~~~q~~~~v-vyDl~~~~igFa~~  426 (431)
T PLN03146        399 IAIFGNLAQMNFLV-GYDLESKTVSFKPT  426 (431)
T ss_pred             ceEECeeeEeeEEE-EEECCCCEEeeecC
Confidence            37999999998885 79999999998753

>PTZ00147 plasmepsin-1; Provisional

Probab=83.31  E-value=5.4  Score=40.51  Aligned_cols=89  Identities=19%  Similarity=0.318  Sum_probs=54.4

Q ss_pred             eEEEEEEEC--CeEEEEEEcCCCCccccCHHHHhhcCCc-----------c--ccccceEEEEccCCeeeecceEeeeEE
Q 042094          330 TMRLKGNLK--KHGVTILIDSSSTHIFLNSSLAKQYGCP-----------V--TTTTQFQVTVADGGVISSSGKCSHVPV  394 (485)
Q Consensus       330 ~~~~~~~i~--~~~v~aLiDsGSt~sfIs~~~~~~l~l~-----------~--~~~~~~~v~~a~G~~~~~~~~~~~v~v  394 (485)
                      .....+.|+  .+.+.++|||||+...|...-|..-+..           +  ....++.+..++|+ +  .|....=.|
T Consensus       139 ~Y~~~I~IGTP~Q~f~Vi~DTGSsdlWVps~~C~~~~C~~~~~yd~s~SsT~~~~~~~f~i~Yg~Gs-v--sG~~~~DtV  215 (453)
T PTZ00147        139 MSYGEAKLGDNGQKFNFIFDTGSANLWVPSIKCTTEGCETKNLYDSSKSKTYEKDGTKVEMNYVSGT-V--SGFFSKDLV  215 (453)
T ss_pred             EEEEEEEECCCCeEEEEEEeCCCCcEEEeecCCCcccccCCCccCCccCcceEECCCEEEEEeCCCC-E--EEEEEEEEE
Confidence            346677886  7899999999999999865433211110           0  01235677777775 2  344333357


Q ss_pred             eecceEEEEEEEEcC----------CCCCCeeechhH
Q 042094          395 NSQGFQFHLDFFLLP----------VSGCDIVLGAEW  421 (485)
Q Consensus       395 ~i~~~~~~~~~~V~~----------~~~~dvILG~dw  421 (485)
                      .+++......|..+.          ....|=|||+-|
T Consensus       216 tiG~~~v~~qF~~~~~~~~f~~~~~~~~~DGILGLG~  252 (453)
T PTZ00147        216 TIGNLSVPYKFIEVTDTNGFEPFYTESDFDGIFGLGW  252 (453)
T ss_pred             EECCEEEEEEEEEEEeccCcccccccccccceecccC
Confidence            888876655554432          123688999876

>PRK04406 hypothetical protein; Provisional

Probab=83.11  E-value=6.6  Score=28.63  Aligned_cols=44  Identities=30%  Similarity=0.327  Sum_probs=29.7

Q ss_pred             cHHHHHHHHHHhhhhhh-------hhHHHHHHhhhhHHHHHhhhhhhhhhh
Q 042094            2 TIKELEERVEQLSHQFN-------EKVEVLSQQSNDLQELILSLHDQFIRF   45 (485)
Q Consensus         2 ~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~   45 (485)
                      ||..|++|++.||..+.       +.+++..+++.++..+...++....+.
T Consensus         5 ~~~~le~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl   55 (75)
T PRK04406          5 TIEQLEERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKV   55 (75)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57778888888877665       566677777777666666655544443

>PTZ00013 plasmepsin 4 (PM4); Provisional

Probab=83.07  E-value=4.8  Score=40.81  Aligned_cols=88  Identities=20%  Similarity=0.386  Sum_probs=53.0

Q ss_pred             EEEEEEEC--CeEEEEEEcCCCCccccCHHHHhhcCC------ccc-------cccceEEEEccCCeeeecceEeeeEEe
Q 042094          331 MRLKGNLK--KHGVTILIDSSSTHIFLNSSLAKQYGC------PVT-------TTTQFQVTVADGGVISSSGKCSHVPVN  395 (485)
Q Consensus       331 ~~~~~~i~--~~~v~aLiDsGSt~sfIs~~~~~~l~l------~~~-------~~~~~~v~~a~G~~~~~~~~~~~v~v~  395 (485)
                      .+..+.|+  ++.+.++|||||+...|...-|...+.      ...       ....+.+..++|+ +  .|....=.|.
T Consensus       139 Yy~~i~IGTP~Q~f~vi~DTGSsdlWV~s~~C~~~~C~~~~~yd~s~SsT~~~~~~~~~i~YG~Gs-v--~G~~~~Dtv~  215 (450)
T PTZ00013        139 FYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCDSIGCSIKNLYDSSKSKSYEKDGTKVDITYGSGT-V--KGFFSKDLVT  215 (450)
T ss_pred             EEEEEEECCCCeEEEEEEeCCCCceEEecccCCccccccCCCccCccCcccccCCcEEEEEECCce-E--EEEEEEEEEE
Confidence            45566775  789999999999999986544332111      000       1124677777775 3  3433333677


Q ss_pred             ecceEEEEEEEEcC----------CCCCCeeechhH
Q 042094          396 SQGFQFHLDFFLLP----------VSGCDIVLGAEW  421 (485)
Q Consensus       396 i~~~~~~~~~~V~~----------~~~~dvILG~dw  421 (485)
                      +++......|.++.          ....|=|||+-|
T Consensus       216 iG~~~~~~~f~~~~~~~~~~~~~~~~~~dGIlGLg~  251 (450)
T PTZ00013        216 LGHLSMPYKFIEVTDTDDLEPIYSSSEFDGILGLGW  251 (450)
T ss_pred             ECCEEEccEEEEEEeccccccceecccccceecccC
Confidence            78876554444332          123688999875

>PTZ00165 aspartyl protease; Provisional

Probab=82.46  E-value=7.3  Score=39.92  Aligned_cols=28  Identities=18%  Similarity=0.338  Sum_probs=24.6

Q ss_pred             CeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          414 DIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       414 dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                      ..|||-.||+.+-. ..|..+++|-|...
T Consensus       419 ~~ILGd~Flr~yy~-VFD~~n~rIGfA~a  446 (482)
T PTZ00165        419 LFVLGNNFIRKYYS-IFDRDHMMVGLVPA  446 (482)
T ss_pred             eEEEchhhheeEEE-EEeCCCCEEEEEee
Confidence            47999999999987 69999999999743

>cd05475 nucellin_like Nucellins, plant aspartic proteases specifically expressed in nucellar cells during degradation

Probab=81.50  E-value=2.8  Score=39.40  Aligned_cols=85  Identities=16%  Similarity=0.276  Sum_probs=49.7

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccC---CeeeecceEeeeEEee-cceEEEEEEEEcCCC----CC
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADG---GVISSSGKCSHVPVNS-QGFQFHLDFFLLPVS----GC  413 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G---~~~~~~~~~~~v~v~i-~~~~~~~~~~V~~~~----~~  413 (485)
                      ..++||||++.+++..+..    +     +++.+.+.++   ..+.....  ..-+.. ++.   .-+.++...    .-
T Consensus       178 ~~~ivDTGTt~t~lp~~~y----~-----p~i~~~f~~~~~~~~~~l~~~--~y~~~~~~~~---~Cl~~~~~~~~~~~~  243 (273)
T cd05475         178 LEVVFDSGSSYTYFNAQAY----F-----KPLTLKFGKGWRTRLLEIPPE--NYLIISEKGN---VCLGILNGSEIGLGN  243 (273)
T ss_pred             ceEEEECCCceEEcCCccc----c-----ccEEEEECCCCceeEEEeCCC--ceEEEcCCCC---EEEEEecCCCcCCCc
Confidence            4689999999999988765    2     2455555433   12222111  000000 111   112223221    12


Q ss_pred             CeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          414 DIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       414 dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      ..|||-.||+.+-. ..|+.+++|-|..
T Consensus       244 ~~ilG~~~l~~~~~-vfD~~~~riGfa~  270 (273)
T cd05475         244 TNIIGDISMQGLMV-IYDNEKQQIGWVR  270 (273)
T ss_pred             eEEECceEEEeeEE-EEECcCCEeCccc
Confidence            47999999999986 6999999998864

Nucellins are important regulators of nucellar cell's progressive degradation after ovule fertilization. This degradation is a characteristic of programmed cell death. Nucellins are plant aspartic proteases specifically expressed in nucellar cells during degradation. The enzyme is characterized by having two aspartic protease catalytic site motifs, the Asp-Thr-Gly-Ser in the N-terminal and Asp-Ser-Gly-Ser in the C-terminal region, and two other regions nearly identical to two regions of plant aspartic proteases. Aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. Although the three-dimensional structures of the two lobes are very similar, the amino acid sequences are more d

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

Probab=81.10  E-value=6.1  Score=36.91  Aligned_cols=75  Identities=15%  Similarity=0.207  Sum_probs=48.0

Q ss_pred             EEEEEEC--CeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecce--EE-EEEEE
Q 042094          332 RLKGNLK--KHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGF--QF-HLDFF  406 (485)
Q Consensus       332 ~~~~~i~--~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~--~~-~~~~~  406 (485)
                      .+.+.|+  .+.+.++|||||+...|..             ..+.+..++|+.+.  |....=.|.+++.  .. ...|-
T Consensus         3 ~~~i~iGtP~q~~~v~~DTGSs~~wv~~-------------~~~~~~Y~dg~~~~--G~~~~D~v~~g~~~~~~~~~~Fg   67 (265)
T cd05476           3 LVTLSIGTPPQPFSLIVDTGSDLTWTQC-------------CSYEYSYGDGSSTS--GVLATETFTFGDSSVSVPNVAFG   67 (265)
T ss_pred             EEEEecCCCCcceEEEecCCCCCEEEcC-------------CceEeEeCCCceee--eeEEEEEEEecCCCCccCCEEEE
Confidence            3556665  5789999999999998853             35667777776543  4433335677765  22 23454


Q ss_pred             EcCCC------CCCeeechhH
Q 042094          407 LLPVS------GCDIVLGAEW  421 (485)
Q Consensus       407 V~~~~------~~dvILG~dw  421 (485)
                      ++...      ..|=|||+-+
T Consensus        68 ~~~~~~~~~~~~~~GIlGLg~   88 (265)
T cd05476          68 CGTDNEGGSFGGADGILGLGR   88 (265)
T ss_pred             ecccccCCccCCCCEEEECCC
Confidence            44432      4788888765

This family contains pepsin like aspartic proteases from plants including Chloroplast Nucleoids DNA-binding Protease and Nucellin. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco and Nucellins are important regulators of nucellar cell's progressive degradation after ovule fertilization. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which

>PRK02793 phi X174 lysis protein; Provisional

Probab=80.99  E-value=9.5  Score=27.59  Aligned_cols=45  Identities=18%  Similarity=0.196  Sum_probs=29.8

Q ss_pred             CcHHHHHHHHHHhhhhhh-------hhHHHHHHhhhhHHHHHhhhhhhhhhh
Q 042094            1 MTIKELEERVEQLSHQFN-------EKVEVLSQQSNDLQELILSLHDQFIRF   45 (485)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~   45 (485)
                      ||...+++|+..||..+.       +.+++..++..++..+...+.....+.
T Consensus         1 m~~~~~e~Ri~~LE~~lafQe~tIe~Ln~~v~~Qq~~I~~L~~~l~~L~~rl   52 (72)
T PRK02793          1 MQDSSLEARLAELESRLAFQEITIEELNVTVTAHEMEMAKLRDHLRLLTEKL   52 (72)
T ss_pred             CChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            677778888888877665       566676777766666665555444443

---

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	485
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	9e-15
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	4e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06

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

 Score = 70.5 bits (172), Expect = 9e-15
 Identities = 20/151 (13%), Positives = 43/151 (28%), Gaps = 11/151 (7%)

Query: 305 AEALEELPETLEVSLKALTGATPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYG 364
             +   +P                  + +   +  H +   +DS +    ++ + A++  
Sbjct: 9   HHSSGLVPRGSGQV----------TMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCN 58

Query: 365 CPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAEWLRS 424
                  ++       G     G+     +  +G      F +L     D++LG + LR 
Sbjct: 59  IMRLVDRRWAGVAKGVGTQRIIGRVHLAQIQIEGDFLQCSFSILEDQPMDMLLGLDMLRR 118

Query: 425 LGAILWDFSKLTMQFTWKGQTVQLTGYDSLP 455
                 D  K  +     G          LP
Sbjct: 119 HQCS-IDLKKNVLVIGTTGTQTYFLPEGELP 148

>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 = 62.8 bits (152), Expect = 4e-12
 Identities = 25/155 (16%), Positives = 51/155 (32%), Gaps = 15/155 (9%)

Query: 302 DEQAE-ALEELPETLEVSLKALTGATPQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLA 360
           DEQ   A+E  PE                 + +   +  + V   +D+ +    +++ LA
Sbjct: 7   DEQLRNAIEYTPEMFTQV----------PMLYINIEINNYPVKAFVDTGAQTTIMSTRLA 56

Query: 361 KQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSGCDIVLGAE 420
           K+ G       +F       G     G+     V  +       F +L  +  D+++G +
Sbjct: 57  KKTGLSRMIDKRFIGEARGVGTGKIIGRIHQAQVKIETQYIPCSFTVLD-TDIDVLIGLD 115

Query: 421 WLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDSLP 455
            L+   A + D  +  +                +P
Sbjct: 116 MLKRHLACV-DLKENVL--RIAEVETSFLSEAEIP 147

>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 = 48.3 bits (114), Expect = 5e-06
 Identities = 69/440 (15%), Positives = 120/440 (27%), Gaps = 112/440 (25%)

Query: 2   TIKELEERVEQLSHQFNEKVEVLSQQSNDLQELILSLHDQFIRFQEDRNNNQPLQI--NN 59
           + + + E +++L +Q +      S  S++++  I S+  +  R  + +     L +  N 
Sbjct: 194 SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV 253

Query: 60  QQPEPAG------RIGGALVQPRHIRL-DFLVLSGENPTSLIFRC------EQYQRLAAL 106
           Q  +         +I   L+  R  ++ DFL  +     SL          E    L   
Sbjct: 254 QNAKAWNAFNLSCKI---LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKY 310

Query: 107 LETDVLSLA-------------IGHLDGDAVPWYHWLEQTMGNMTWAQFKRALVTQFGT- 152
           L+     L              I     D            G  TW  +K     +  T 
Sbjct: 311 LDCRPQDLPREVLTTNPRRLSIIAESIRD------------GLATWDNWKHVNCDKLTTI 358

Query: 153 ----FEDGDAVGTQNLPESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEEYAA 208
                   +    + + +   +            I      P  LL        + +   
Sbjct: 359 IESSLNVLEPAEYRKMFDRLSV------FPPSAHI------PTILLSLIWFDVIKSDVMV 406

Query: 209 VSNRRIPPRPSMSRPSPPLLNSSPTITKTGGSSQPSL---LGPPPPGLPPFRRLSVAEQT 265
           V N        + + S  L+   P   K    S PS+   L           R  V    
Sbjct: 407 VVN-------KLHKYS--LVEKQP---KESTISIPSIYLELKVKLENEYALHRSIV---- 450

Query: 266 ERRAKGLCFNCDEQFKP----------GHRCKA----------PQLLL----LDADIEDK 301
           +       F+ D+   P          GH  K             + L    L+  I   
Sbjct: 451 DHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHD 510

Query: 302 DEQAEALEELPETL---EVSLKALTGATPQNTMR---LKGNLKKHGVTILIDSSSTHIFL 355
                A   +  TL   +     +    P+       +   L K     LI S  T + L
Sbjct: 511 STAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIE-ENLICSKYTDL-L 568

Query: 356 NSSLAKQYGCPVTTTTQFQV 375
             +L  +    +      QV
Sbjct: 569 RIALMAEDE-AIFEEAHKQV 587

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	485
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	99.87
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	99.77
1fmb_A	104	EIAV protease; hydrolase (acid proteinase), RNA-di	99.19
3slz_A	132	GAG-Pro-POL polyprotein; beta sheet and dimer, pro	99.13
3ec0_A	99	Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1	99.0
2hs1_A	99	HIV-1 protease; ultra-high resolution active site	98.9
2hah_A	116	Protease, retropepsin; retroviral, aspartyl, hydro	98.63
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	98.55
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	98.24
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.22
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.14
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.14
3sqf_A	114	Protease; folded monomer, retropepsin, D-type retr	98.08
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.88
2rsp_A	124	RSV protease; hydrolase(aspartyl proteinase); 2.00	97.77
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.38
3liy_A	116	Protease; hydrolase, hydrolase-hydrolase inhibitor	97.25
2pma_A	146	Uncharacterized protein; APC86035.2, protein LPG00	97.2
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.04
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.0
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	96.99
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	96.99
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	96.97
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	96.97
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	96.88
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	96.83
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	96.76
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	96.74
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	96.73
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	96.68
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	96.53
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	96.52
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	96.5
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	96.28
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	96.25
2jys_A	107	Protease/reverse transcriptase; retroviral proteas	95.4
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	95.13
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	95.12
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	95.05
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	94.83
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	92.96
3cms_A	323	Chymosin B; hydrolase, acid proteinase; 2.00A {Bos	92.58
1am5_A	324	Pepsin, acid proteinase; aspartyl protease, hydrol	92.56
3qvc_A	451	Histo-aspartic protease; HAP, plasmepsin, zymogen,	92.53
1dpj_A	329	Proteinase A; proteinase A, hydrolase-hydrolase in	92.28
1lya_B	241	Cathepsin D; lysosomal aspartic protease; HET: NAG	92.12
1yg9_A	330	Aspartic protease BLA G 2; allegren, hydrolase, al	91.92
2apr_A	325	Rhizopuspepsin; hydrolase (aspartic proteinase); 1	91.9
2x0b_A	383	Renin; hydrolase-hormone complex, hydrolase hormon	91.55
1tzs_A	351	Cathepsin E; hydrolase, aspartic protease, activat	91.32
4aa9_A	320	Chymosin; hydrolase, aspartic peptidase, rennet; H	91.03
1izd_A	323	Aspartic proteinase; sugar binding, acid protease,	90.85
3k1w_A	341	Renin; protease, alternative splicing, aspartyl pr	90.82
1wkr_A	340	Polyporopepsin; hydrolase, hydrolase-hydrolase inh	90.48
2bju_A	453	Plasmepsin II; aspartic proteinase, drug design, m	90.46
1miq_A	375	Plasmepsin; aspartic proteinase zymogen, domain op	90.14
3fv3_A	339	SAPP1P-secreted aspartic protease 1; secreted aspa	90.13
3pvk_A	342	Candidapepsin-2; hydrolase; 1.27A {Candida albican	90.02
1j71_A	334	Candidapepsin, aspartic proteinase; candida tropic	89.8
1htr_B	329	Gastricsin; aspartyl protease; 1.62A {Homo sapiens	89.15
1bxo_A	323	Protein (penicillopepsin); hydrolase, phosphonate	89.08
2qzx_A	342	Candidapepsin-5; aspartic proteinase, aspartyl pro	88.99
1ibq_A	325	Aspergillopepsin; aspartic proteinase, hydrolase;	88.29
3aup_A	403	SBG7S, BG, basic 7S globulin; pepsin-like fold, pl	88.23
1mpp_A	361	Pepsin; hydrolase(acid proteinase); 2.00A {Rhizomu	87.83
3psg_A	370	Pepsinogen; hydrolase(acid proteinase zymogen); 1.	87.31
1oew_A	329	Endothiapepsin; hydrolase, aspartic proteinase mec	85.97
1t6e_X	381	Xylanase inhibitor; two beta-barrel domain structu	84.94
3lpj_A	455	Beta-secretase 1; alzheimer'S, aspartyl protease,	84.41
3c9x_A	329	Trichoderma reesei aspartic protease; aspartic pro	83.85
3vf3_A	402	Beta-secretase 1; structure-based drug design, hyd	83.01
2ewy_A	383	Beta-secretase 2; BACE2, aspartic protease, hydrol	82.63
2fi2_A	94	Zinc finger protein 42; SCAN domain, ZNF-42, MZF-1	80.93
2qp8_A	395	Beta-secretase 1; BACE1, protease, alternative spl	80.67
1bxo_A	323	Protein (penicillopepsin); hydrolase, phosphonate	80.11

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

Probab=99.87  E-value=8.2e-22  Score=164.51  Aligned_cols=125  Identities=14%  Similarity=0.184  Sum_probs=101.8

Q ss_pred             CCeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEE
Q 042094          328 QNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFL  407 (485)
Q Consensus       328 ~~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V  407 (485)
                      ...+++.+.|||+++++||||||++|||+.++|+++|+.......+.....+.....+.+.+..++++|++..+.++|.|
T Consensus        22 ~~~l~v~~~Ing~~v~~LVDTGAs~s~Is~~~A~rlGL~~~~~~~~~~~a~g~G~~~~~g~v~~~~I~Ig~~~~~~~~~V  101 (148)
T 3s8i_A           22 VTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIIGRVHLAQIQIEGDFLQCSFSI  101 (148)
T ss_dssp             CCCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHTTCGGGEEGGGCEECCC---CEEEEEEEEEEEEETTEEEEEEEEE
T ss_pred             cCEEEEEEEECCEEEEEEEeCCCCcEeeCHHHHHHcCCccccCcceeEEEEcCCccEEEEEEEEEEEEECCEEEEEEEEE
Confidence            45789999999999999999999999999999999999764222222222222233446677778999999999999999


Q ss_pred             cCCCCCCeeechhHHhhcCCeEEEccCcEEEEEECCeEEEEeecCC
Q 042094          408 LPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDS  453 (485)
Q Consensus       408 ~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~~~~~~~~~~~~~  453 (485)
                      ++...+|+|||||||.+++. .|||+++++.|...++.+.|-+..+
T Consensus       102 le~~~~d~LLGmD~L~~~~~-~ID~~~~~L~l~~~~~~~pfl~~~~  146 (148)
T 3s8i_A          102 LEDQPMDMLLGLDMLRRHQC-SIDLKKNVLVIGTTGTQTYFLPEGE  146 (148)
T ss_dssp             ETTCSSSEEECHHHHHHTTC-EEETTTTEEECTTTCCEEECCCGGG
T ss_pred             eCCCCcCeeccHHHHHhCCE-EEEcCCCEEEEccCCeEEeecCccc
Confidence            99989999999999999997 7999999999998777787766543

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

Probab=99.77  E-value=3.8e-18  Score=144.27  Aligned_cols=120  Identities=14%  Similarity=0.214  Sum_probs=94.2

Q ss_pred             CCeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceE--EEEccCCeeeecceEeeeEEeecceEEEEEE
Q 042094          328 QNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQ--VTVADGGVISSSGKCSHVPVNSQGFQFHLDF  405 (485)
Q Consensus       328 ~~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~--v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~  405 (485)
                      .+.+++.+.|||+++++||||||++|+|+.++|+++|+.......+.  +..++|..  ..+.+..+++.+++..+.++|
T Consensus        24 ~~~~~v~v~InG~~~~~LvDTGAs~s~is~~~a~~lgl~~~~~~~~~~~a~g~g~~~--~~~~~~~~~i~ig~~~~~~~~  101 (148)
T 2i1a_A           24 VPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGK--IIGRIHQAQVKIETQYIPCSF  101 (148)
T ss_dssp             CCCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHHTGGGGCBCCCC-------------CEEEEEEEEEETTEEEEEEE
T ss_pred             cceEEEEEEECCEEEEEEEECCCCccccCHHHHHHcCCCccCCcceEEEEecCCCcc--cccEEEEEEEEECCEEeceeE
Confidence            45689999999999999999999999999999999999764433332  23333432  245555678999999999999


Q ss_pred             EEcCCCCCCeeechhHHhhcCCeEEEccCcEEEEEECCeEEEEeecCC
Q 042094          406 FLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWKGQTVQLTGYDS  453 (485)
Q Consensus       406 ~V~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~~~~~~~~~~~~~  453 (485)
                      .|++ .++|.|||+|||.+++. .|||.++++.|.  ++.+.|.+...
T Consensus       102 ~vl~-~~~d~iLG~d~L~~~~~-~ID~~~~~l~l~--~~~~~f~~~~~  145 (148)
T 2i1a_A          102 TVLD-TDIDVLIGLDMLKRHLA-CVDLKENVLRIA--EVETSFLSEAE  145 (148)
T ss_dssp             EEEC-SSCSEEECHHHHHHTTC-EEETTTTEEEET--TEEEECCCTTT
T ss_pred             EEec-CCCCeEecHHHHhhCCE-EEECCCCEEEEc--cEEEecCChhh
Confidence            9999 67899999999999997 899999999986  47777666554

>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=99.19  E-value=1.2e-10  Score=89.62  Aligned_cols=97  Identities=13%  Similarity=0.184  Sum_probs=78.0

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcC
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLP  409 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~  409 (485)
                      ...+.++|+|+.+.+||||||..|+|+...+.+++++...-.+..+.. -|..+.+.  +..+.+++.|+.....++|-+
T Consensus         8 RP~v~v~I~Gq~~e~LLDTGAD~TVl~~~~w~~i~lp~~~w~p~~i~G-iGG~i~v~--~~~i~i~i~g~~~~gtvlv~~   84 (104)
T 1fmb_A            8 RPTTIVLINDTPLNVLLDTGADTSVLTTAHYNRLKYRGRKYQGTGIGG-VGGNVETF--STPVTIKKKGRHIKTRMLVAD   84 (104)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHCSSCCCCEECCCEEE-TTEEECCE--EEEEEEEETTEEEEEEEEEES
T ss_pred             CCEEEEEECCEEEEEEeccCCCcEEEccccCcccCCCCccCCccEEEe-CCCeEEee--EeeeEEEECCeEEEEEEEECC
Confidence            457889999999999999999999999999999999865223444444 45556655  578999999999988888866


Q ss_pred             CCCCCeeechhHHhhcCCeEEEc
Q 042094          410 VSGCDIVLGAEWLRSLGAILWDF  432 (485)
Q Consensus       410 ~~~~dvILG~dwL~~~~~i~id~  432 (485)
                      .  ..-|||+|||.+.|. .+||
T Consensus        85 t--p~niiGRd~L~qlg~-tLnf  104 (104)
T 1fmb_A           85 I--PVTILGRDILQDLGA-KLVL  104 (104)
T ss_dssp             C--SSCEECHHHHHHTTC-CCCC
T ss_pred             C--CCCEecHhHHhhcCc-EEeC
Confidence            4  357899999999997 6765

>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=99.13  E-value=1.1e-10  Score=93.61  Aligned_cols=97  Identities=22%  Similarity=0.222  Sum_probs=73.1

Q ss_pred             CCCeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEE
Q 042094          327 PQNTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFF  406 (485)
Q Consensus       327 ~~~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~  406 (485)
                      ......+.++|+|+.+.+||||||+.+++++..+.      ....+..+.+++|... . .....+.+++++......++
T Consensus        19 ~~~RP~v~i~I~G~~~~~LlDTGAd~tVl~~~~~p------~~~~p~~I~GiGG~i~-v-r~~~~i~IeI~g~~~~~~~l   90 (132)
T 3slz_A           19 PPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGP------LSDKSAWVQGATGGKR-Y-RWTTDRKVHLATGKVTHSFL   90 (132)
T ss_dssp             CCCSSEEEEEETTEEEEEEECTTCSSCEECSCCCS------EEEEEEEEECSSCEEE-E-EEECCEEEEETTEEEEECCE
T ss_pred             ccCCCEEEEEECCEEEEEEEeCCCCeEEEccccCC------CCCCceEEEccCCEEE-E-EEEeeeEEEECCeeecceEE
Confidence            34556788999999999999999999999875333      2224678888998754 2 33345789999988877777


Q ss_pred             EcCCCCCCeeechhHHhhcCCeEEEcc
Q 042094          407 LLPVSGCDIVLGAEWLRSLGAILWDFS  433 (485)
Q Consensus       407 V~~~~~~dvILG~dwL~~~~~i~id~~  433 (485)
                      |++.. ...|||+|||.+++. .+||-
T Consensus        91 V~~~t-PvnLLGrd~Ltqlg~-tL~fp  115 (132)
T 3slz_A           91 HVPDC-PYPLLGRDLLTKLKA-QIHFE  115 (132)
T ss_dssp             ECTTS-SSCEECHHHHHHHTC-EEEEE
T ss_pred             EECCC-CccEECHhhHhhCCc-EEECC
Confidence            75433 357899999999998 56654

>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=99.00  E-value=5.8e-09  Score=78.63  Aligned_cols=92  Identities=12%  Similarity=0.164  Sum_probs=70.6

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcC
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLP  409 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~  409 (485)
                      ...+.++|+|+.+.+|+||||.+|+|+     ..+++.... +. ...+-|..+.+.. +..+.+++.|+.....++|-|
T Consensus         8 RP~vti~I~Gq~~e~LLDTGAD~TVl~-----~~~~Pg~w~-pk-~igGiGG~i~v~q-y~~i~iei~g~~~~gtvlV~~   79 (99)
T 3ec0_A            8 RPVVTAYIEGQPVEVLLDTGADDSIVA-----GIELGNNYS-PK-IVGGIGGFINTKE-YKNVEIEVLNKKVRATIMTGD   79 (99)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEES-----SCCCCSCCE-EE-EEEETTEEEEEEE-EEEEEEEETTEEEEEEEEEEC
T ss_pred             CCeEEEEECCEEEEEEEecCCCceEEc-----CcccCCCCC-ce-EEEecCCcEeeeE-EeeEEEEECCeEEEEEEEeCC
Confidence            356789999999999999999999996     345553322 32 4556677777655 467999999999888888855


Q ss_pred             CCCCCeeechhHHhhcCCeEEEc
Q 042094          410 VSGCDIVLGAEWLRSLGAILWDF  432 (485)
Q Consensus       410 ~~~~dvILG~dwL~~~~~i~id~  432 (485)
                      ..  --|||+|+|.++|. .++|
T Consensus        80 tP--vniiGRnlLtqlG~-tLnf   99 (99)
T 3ec0_A           80 TP--INIFGRNILTALGM-SLNL   99 (99)
T ss_dssp             CS--SCEECHHHHHHHTC-EEEC
T ss_pred             CC--cCeeehhhHhhcCc-EEeC
Confidence            33  37899999999997 7876

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

Probab=98.90  E-value=9e-09  Score=77.92  Aligned_cols=92  Identities=14%  Similarity=0.192  Sum_probs=69.9

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcC
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLP  409 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~  409 (485)
                      ...+.++|+|+.+.||+||||..|+|++     .+++... .|. ...+-|..+.+.. +..+++++.|+.....++|-|
T Consensus         8 rP~vtvkI~Gq~~eaLLDTGAD~TVl~~-----~~~p~~w-kpk-~igGiGG~i~v~q-y~qi~iei~g~~~~gtvlV~~   79 (99)
T 2hs1_A            8 RPLVTIKIGGQLKEALLDTGADDTIIEE-----MSLPGRW-KPK-MIGGIGGFIKVRQ-YDQIIIEIAGHKAIGTVLVGP   79 (99)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSEEESC-----CSSCCCC-EEE-EEEETTEEEEEEE-EEEEEEEETTEEEEEEEEESC
T ss_pred             CCEEEEEECCEEEEEEeccCCCcEEEec-----ccCCCCC-CCc-EEEeCCCcEeeeE-eccEEEEEeCCEEEEEEEeCC
Confidence            3567899999999999999999999985     3555322 233 3444566666544 468999999999999998855


Q ss_pred             CCCCCeeechhHHhhcCCeEEEc
Q 042094          410 VSGCDIVLGAEWLRSLGAILWDF  432 (485)
Q Consensus       410 ~~~~dvILG~dwL~~~~~i~id~  432 (485)
                      ..  --|||+|||.+.|. .+||
T Consensus        80 tP--vniiGRd~Ltqlg~-tLnf   99 (99)
T 2hs1_A           80 TP--VNIIGRNLLTQIGA-TLNF   99 (99)
T ss_dssp             CS--SCEECHHHHTTTTC-EEEC
T ss_pred             Cc--cCchhHhHHHHcCC-EEeC
Confidence            43  35899999999997 7775

>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=98.63  E-value=1.7e-07  Score=73.16  Aligned_cols=93  Identities=14%  Similarity=0.094  Sum_probs=65.0

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceE-----EEEE
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQ-----FHLD  404 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~-----~~~~  404 (485)
                      ...+ ++|+|+.+.+||||||..|+|++.-+..  .+......+.+. +-|..+.+. .+..+.+++.+..     ....
T Consensus        14 rP~v-ikI~Gq~~eaLLDTGAD~TVi~~~~~~~--~p~~wkpk~~ig-GiGG~i~v~-qy~qv~iei~g~~~~~~~~~gt   88 (116)
T 2hah_A           14 PEIL-IFVNGYPIKFLLDTGADITVLNRRDFQV--KNSIENGRQMIG-GIGGFIRGT-NYINVHLEIRDENYKTQCIFGN   88 (116)
T ss_dssp             CEEE-EEETTEEEEEEECTTCSSCEEEGGGCCC--TTCEEEEEEEEE-ETTEEEEEE-EEEEEEEEECCTTSCCEEEEEE
T ss_pred             CCEE-EEECCEEEEEEecCCCCcEEEccccccc--CCCCCCCceEEe-cCCCceeee-EEccEEEEEeCCCCCcceeEEE
Confidence            3456 9999999999999999999998643211  032222222244 445555554 4467899999887     7788


Q ss_pred             EEEcC-CCCCCeeechhHHhhcCC
Q 042094          405 FFLLP-VSGCDIVLGAEWLRSLGA  427 (485)
Q Consensus       405 ~~V~~-~~~~dvILG~dwL~~~~~  427 (485)
                      ++|.| ...---|||+|+|.+.|.
T Consensus        89 vlV~p~tP~~vniiGRd~Ltqlg~  112 (116)
T 2hah_A           89 VCVLEDNSTPVNILGRDNMIKFNI  112 (116)
T ss_dssp             EEEETTCCCSSEEECHHHHTTTTC
T ss_pred             EEECCCCCccccEecHHHHhHcCC
Confidence            88988 332237899999999996

>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=98.55  E-value=7.3e-07  Score=76.59  Aligned_cols=93  Identities=14%  Similarity=0.176  Sum_probs=71.8

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcC
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLP  409 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~  409 (485)
                      ...++++|+|+.+.+||||||.+|+|.     .++++.. -.|..+ .+-|..+.+.. +..+++++.|+.....++|-+
T Consensus         8 RP~vtv~I~Gq~~e~LLDTGAD~TVl~-----~~~lpg~-w~pk~i-gGIGG~i~vrq-y~~i~iei~g~~~~gtvlVg~   79 (203)
T 3ka2_A            8 RPLVTIRIGGQLKEALLDTGADDTVIE-----ELNLPGX-WKPKLI-GGIAGFIKVRQ-YDQIPVEIXGHKAIGTVLVGP   79 (203)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEC-----SCCCSSC-EEEEEE-EETTEEEEEEE-EEEEEEEETTEEEEEEEEESC
T ss_pred             CCeEEEEECCEEEEEEEecCCCceEEe-----cccCCCC-CCceEE-EEccCcEEEEE-EcceeEEEcCeEEEEEEeeCC
Confidence            457789999999999999999999998     3666642 123334 44566666544 457899999999888888865


Q ss_pred             CCCCCeeechhHHhhcCCeEEEcc
Q 042094          410 VSGCDIVLGAEWLRSLGAILWDFS  433 (485)
Q Consensus       410 ~~~~dvILG~dwL~~~~~i~id~~  433 (485)
                      .  ..-|||+|.|.++|. .+||.
T Consensus        80 t--PvnIiGRd~LtqlG~-tLnf~  100 (203)
T 3ka2_A           80 T--PVNIIGRNLLTQIGX-TLNFX  100 (203)
T ss_dssp             C--SSCEECHHHHTTTTC-EEEGG
T ss_pred             C--CcCccchhhhhhcCc-eEEec
Confidence            3  456899999999997 89987

>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=98.24  E-value=1.4e-05  Score=68.67  Aligned_cols=92  Identities=15%  Similarity=0.192  Sum_probs=70.0

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcC
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLP  409 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~  409 (485)
                      ...+.++|+|+.+.+|+||||.+|+|.     ..+++... +|..+ .+-|..+.+... ..+++++.|+.....++|-|
T Consensus       112 rP~~~iki~Gq~~e~LlDTGAD~TVl~-----~~~lpg~w-~pk~i-gGiGg~i~v~qy-~~i~iei~g~~~~~tvlVgp  183 (203)
T 3ka2_A          112 RPLVTIRIGGQLKEALLDTGADDTVIE-----ELNLPGXW-KPKLI-GGIGGFIKVRQY-DQIPVEIXGHKAIGTVLVGP  183 (203)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEC-----SCCCCSCC-EEEEE-EETTEEEEEEEE-EEEEEEETTEEEEEEEEESC
T ss_pred             CCcEEEEECCEEEeeeecccCCceeee-----cccCCCCC-CceEE-eeccceEEEEEe-ccEEEEECCeEEEEEEEECC
Confidence            456889999999999999999999995     45555322 23333 445666665443 67899999998888888877


Q ss_pred             CCCCCeeechhHHhhcCCeEEEc
Q 042094          410 VSGCDIVLGAEWLRSLGAILWDF  432 (485)
Q Consensus       410 ~~~~dvILG~dwL~~~~~i~id~  432 (485)
                      .  .--|+|+|.|.++|. .++|
T Consensus       184 t--PvniiGRn~LtqlG~-tl~f  203 (203)
T 3ka2_A          184 T--PVNIIGRNLLTQIGX-TLNF  203 (203)
T ss_dssp             C--SSCEECHHHHGGGTC-EEEC
T ss_pred             C--CcCeechhhHHHhCC-eeeC
Confidence            5  356789999999997 7775

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=98.14  E-value=7.2e-07  Score=54.90  Aligned_cols=21  Identities=19%  Similarity=0.430  Sum_probs=18.5

Q ss_pred             CCceeecCCCCCCCCcCCCce
Q 042094          270 KGLCFNCDEQFKPGHRCKAPQ  290 (485)
Q Consensus       270 ~~~Cf~Cg~~GH~a~~C~~~~  290 (485)
                      ...||+||+.||++++||.+.
T Consensus        10 ~~~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSC
T ss_pred             CCeeeECCCCCcchhhCcCCc
Confidence            467999999999999998764

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=98.14  E-value=4.7e-07  Score=52.01  Aligned_cols=21  Identities=29%  Similarity=0.749  Sum_probs=18.0

Q ss_pred             hCCceeecCCCCCCCCcCCCc
Q 042094          269 AKGLCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       269 ~~~~Cf~Cg~~GH~a~~C~~~  289 (485)
                      +...||+||+.||++++|+.+
T Consensus         5 ~~~~C~nCgk~GH~ar~C~~p   25 (29)
T 1nc8_A            5 KVIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSS
T ss_pred             CCCEEEECCccccCHhHCccc
Confidence            346799999999999999654

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

Probab=98.08  E-value=4.7e-06  Score=64.27  Aligned_cols=100  Identities=12%  Similarity=0.026  Sum_probs=59.1

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCcccccc--ceEEEEccCCeeeecceEeeeEEe--ecceEEEEEE
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTT--QFQVTVADGGVISSSGKCSHVPVN--SQGFQFHLDF  405 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~--~~~v~~a~G~~~~~~~~~~~v~v~--i~~~~~~~~~  405 (485)
                      ...+.++|+|+.+.+||||||..++|..     .+++..-..  ..+...+=|..+.+... ..+...  +.|+......
T Consensus         9 RP~vti~I~Gq~~eaLLDTGADdTVi~~-----~~lpg~W~p~~~~k~igGIGG~i~v~qy-~~~~~~~~i~g~k~i~tv   82 (114)
T 3sqf_A            9 KPSLTLWLDDKMFTGLINTGADVTIIKL-----EDWPPNWPITDTLTNLRGIGQSNNPKQS-SKYLTWRDKENNSGLIKP   82 (114)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEEG-----GGSCTTSCEEECCCCCTTCCGGGCCEEE-SSCEEEECTTCCEEEECC
T ss_pred             CCeEEEEECCEEEEEEEccCCCceEEec-----ccCCCCcccCcCceEEEeccceEEEEEe-ccceEEEecCCCEEEEEE
Confidence            3467799999999999999999999974     345432111  11222333445554432 333333  6788777777


Q ss_pred             EEcCCCCCCeeechhHHhhcCCeEEEccCcEE
Q 042094          406 FLLPVSGCDIVLGAEWLRSLGAILWDFSKLTM  437 (485)
Q Consensus       406 ~V~~~~~~dvILG~dwL~~~~~i~id~~~~~~  437 (485)
                      +|.+... --|+|+|.|.++|. .++|-+..+
T Consensus        83 lV~~ptP-vNIiGRn~LtqlG~-tLnfp~~~~  112 (114)
T 3sqf_A           83 FVIPNLP-VNLWGRDLLSQMKI-MMASPNDIV  112 (114)
T ss_dssp             EEETTCS-SCEECHHHHTTSCC----------
T ss_pred             EECCCCc-ccEEchhhHhhcCc-EEECCCccc
Confidence            8873222 45689999999997 677765443

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=97.88  E-value=3e-06  Score=56.49  Aligned_cols=21  Identities=19%  Similarity=0.430  Sum_probs=18.4

Q ss_pred             CCceeecCCCCCCCCcCCCce
Q 042094          270 KGLCFNCDEQFKPGHRCKAPQ  290 (485)
Q Consensus       270 ~~~Cf~Cg~~GH~a~~C~~~~  290 (485)
                      ...||+||+.||++++||.+.
T Consensus        23 ~~~C~~Cge~GH~ardCp~~~   43 (56)
T 1u6p_A           23 RDQCAYCKEKGHWAKDCPKKP   43 (56)
T ss_dssp             TTBCSSSCCBSSCGGGCTTCC
T ss_pred             CCcceeCCCCCcccccCcCCc
Confidence            467999999999999998764

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

Probab=97.77  E-value=3.3e-05  Score=60.82  Aligned_cols=85  Identities=19%  Similarity=0.262  Sum_probs=52.8

Q ss_pred             ECCeEEEEEEcCCCCccccCHHHHhhcCCccccc----cceEEEEccCCeeeecceEe-eeEEeecce--EEEEEEEEcC
Q 042094          337 LKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTT----TQFQVTVADGGVISSSGKCS-HVPVNSQGF--QFHLDFFLLP  409 (485)
Q Consensus       337 i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~----~~~~v~~a~G~~~~~~~~~~-~v~v~i~~~--~~~~~~~V~~  409 (485)
                      |+|+.+.+||||||..++|.+     ..++....    ....+...+|- +.+.. +. .+.+++.|.  .....++|.|
T Consensus        27 i~gq~~eaLLDTGAD~TVl~~-----~~lP~~W~k~~~~~~~igGIGG~-i~v~q-y~~~i~iei~g~~g~~~~tvlV~P   99 (124)
T 2rsp_A           27 QRSVYITALLDSGADITIISE-----EDWPTDWPVMEAANPQIHGIGGG-IPMRK-SRDMIELGVINRDGSLERPLLLFP   99 (124)
T ss_dssp             CSEEEEEEEECTTCSSCEEET-----TTSCTTSCEEECC---------C-CCEEE-ESSCEEEEEECTTSCBCCCEEECC
T ss_pred             CCCEEEEEEecCCCCcEEEec-----ccCCCcceeeccccceeeecCce-EeeEE-eCCceEEEEeCCCCcEEEEEEECc
Confidence            899999999999999999984     34443211    11125555553 44333 33 677878776  5556677777


Q ss_pred             CC--CCCeeechhHHhhcCCe
Q 042094          410 VS--GCDIVLGAEWLRSLGAI  428 (485)
Q Consensus       410 ~~--~~dvILG~dwL~~~~~i  428 (485)
                      ..  .---|+|+|.|.++|..
T Consensus       100 ~~~~tPvnIiGRdlLtqlG~t  120 (124)
T 2rsp_A          100 AVAMVRGSILGRDCLQGLGLR  120 (124)
T ss_dssp             EEESCSSEEECHHHHHHTTCE
T ss_pred             CCCCCceeEECHhHHhhCCcE
Confidence            31  12468999999999973

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.38  E-value=4e-05  Score=50.83  Aligned_cols=19  Identities=21%  Similarity=0.446  Sum_probs=16.8

Q ss_pred             CceeecCCCCCCCCcCCCc
Q 042094          271 GLCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~~  289 (485)
                      ..||+||++||++++||..
T Consensus         8 ~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            8 YTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             CCCTTTCCTTSCGGGCSGG
T ss_pred             CccccCCCcCcccccCCCC
Confidence            5699999999999999743

>3liy_A Protease; hydrolase, hydrolase-hydrolase inhibitor complex; HET: STA; 1.86A {Human t-lymphotropic virus 1} PDB: 2b7f_A* 3liq_A* 3lit_A* 3liv_A* 3lix_A* 3lin_A*

Probab=97.25  E-value=0.00052  Score=52.40  Aligned_cols=90  Identities=16%  Similarity=0.122  Sum_probs=56.8

Q ss_pred             EEEEEEEC-----CeEEEEEEcCCCCccccCHHHHhhcCCcccc--ccceEEEEccCCeeeecceEeeeEEeecc----e
Q 042094          331 MRLKGNLK-----KHGVTILIDSSSTHIFLNSSLAKQYGCPVTT--TTQFQVTVADGGVISSSGKCSHVPVNSQG----F  399 (485)
Q Consensus       331 ~~~~~~i~-----~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~--~~~~~v~~a~G~~~~~~~~~~~v~v~i~~----~  399 (485)
                      ..+.++|+     |+.+.||+||||..++|.+     .+++...  ... ++..+.|..+.. .....+++.+-.    .
T Consensus        11 PlvtikI~~~~~~Gq~~eaLLDTGADdTVl~~-----~~lPg~Wkp~~t-kiiGGiGg~~~~-~qs~~~pv~i~lpfr~~   83 (116)
T 3liy_A           11 PVIKAQVDTQTSHPKTIEALLDTGADMTVIPI-----ALFSSNTPLKNT-SVLGAGGQTQDH-FKLTSLPVLIRLPFRTT   83 (116)
T ss_dssp             CEEEEEEECSSSCCEEEEEEECTTBSSCEEEG-----GGSCTTCCEEEC-CEEETTEEESSS-EEEESSCEEEECTTCCS
T ss_pred             CeEEEEEccccCCCeEeEEEeccCCCccEEec-----ccCCCCCccccc-ceEeecccceee-eEecCCCeEEEeccCCc
Confidence            46788888     9999999999999999974     4554321  112 455555555443 233456665554    2


Q ss_pred             EEEEEEEEcCCCCCCeeechhHHhhcCC
Q 042094          400 QFHLDFFLLPVSGCDIVLGAEWLRSLGA  427 (485)
Q Consensus       400 ~~~~~~~V~~~~~~dvILG~dwL~~~~~  427 (485)
                      ...+....++..+.=.|||+|-|.+.+.
T Consensus        84 pv~l~~~lv~~~~~w~iigRd~l~q~q~  111 (116)
T 3liy_A           84 PIVLTSCLVDTKNNWAIIGRDALQQCQG  111 (116)
T ss_dssp             CEEESSCEEETTSCCCEECHHHHHHTTC
T ss_pred             ceeeceEEEcCCCceeEechhHHhhhcc
Confidence            2333333334443456889999999986

>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=97.20  E-value=0.00041  Score=56.40  Aligned_cols=95  Identities=8%  Similarity=0.054  Sum_probs=59.3

Q ss_pred             CeEEEEEEcCCCCccccCHHHHhhcC----------Cc-------cc-c-ccceEEEEccCCe------e-eecceEeee
Q 042094          339 KHGVTILIDSSSTHIFLNSSLAKQYG----------CP-------VT-T-TTQFQVTVADGGV------I-SSSGKCSHV  392 (485)
Q Consensus       339 ~~~v~aLiDsGSt~sfIs~~~~~~l~----------l~-------~~-~-~~~~~v~~a~G~~------~-~~~~~~~~v  392 (485)
                      |..+.|=|||||..|-|+..-++...          +.       .+ + .....|...+|..      . .-...+...
T Consensus        17 g~~~~AKiDTGA~TSSLhA~dI~~Ferdg~~wVrF~~~~~~~~~~~e~pv~~~~~Ik~s~g~~~~~~~~~~~e~R~VV~~   96 (146)
T 2pma_A           17 NLTLSAKLDTGAKSASLHAVNITEIEKKGIPYLRFTVPTKTGDYSFEGEYVGKVKIKVRSSETNPGLLRTTPIKRPVVLL   96 (146)
T ss_dssp             TEEEEEEECTTCSSEEEECEEEEEEEETTEEEEEEEEEETTEEEEEEEEEEEEEEC---------------CCEEEEEEE
T ss_pred             CCEEEEEecCCcCcceecceeEEEeeeCCCcEEEEEEecCCCCceEEEEeEEEEEEecCCCccccccccCCcccccEEEE
Confidence            55688999999999988765443211          10       00 0 0122334444541      0 112345567


Q ss_pred             EEeecceEEEEEEEEcCC--CCCCeeechhHHhhcCCeEEEccC
Q 042094          393 PVNSQGFQFHLDFFLLPV--SGCDIVLGAEWLRSLGAILWDFSK  434 (485)
Q Consensus       393 ~v~i~~~~~~~~~~V~~~--~~~dvILG~dwL~~~~~i~id~~~  434 (485)
                      .+.+|+....++|.+.+-  ..|+++||++||...+. .+|-..
T Consensus        97 ~i~lG~~~~~ie~tLtdRs~m~ypmLLGR~~L~~~~~-lVD~s~  139 (146)
T 2pma_A           97 NIKLGDKVRTIKVNLTNRKRFLYPLLLGRDAIIDFNG-AVDPAL  139 (146)
T ss_dssp             EEEETTEEEEEEEEEECCCCCSCSEEECHHHHHHTTE-EEETTC
T ss_pred             EEEECCEEEEEEEEEcCCCcCCCCEEechhHHhhCCE-EECCch
Confidence            899999999999999984  56999999999988776 577553

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=97.04  E-value=0.00021  Score=44.13  Aligned_cols=18  Identities=22%  Similarity=0.534  Sum_probs=15.3

Q ss_pred             CceeecCCCCCCCCcCCC
Q 042094          271 GLCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~  288 (485)
                      ..||+||+.||++++||+
T Consensus        22 ~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A           22 EGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             SSCTTTCCSSSCTTTSCC
T ss_pred             CccccCCCCCCccCcCcC
Confidence            569999999999999963

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=97.00  E-value=0.00026  Score=43.10  Aligned_cols=16  Identities=31%  Similarity=0.924  Sum_probs=9.4

Q ss_pred             eeecCCCCCCCCcCCC
Q 042094          273 CFNCDEQFKPGHRCKA  288 (485)
Q Consensus       273 Cf~Cg~~GH~a~~C~~  288 (485)
                      ||+|++.||++++|+.
T Consensus         3 C~~Cg~~GH~~~~C~~   18 (37)
T 2bl6_A            3 CYNCGKPGHLSSQCRA   18 (37)
T ss_dssp             BSSSCCSSCCTTTSSC
T ss_pred             ccccCCCCcchhhCcC
Confidence            5666666666666643

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=96.99  E-value=0.0002  Score=46.79  Aligned_cols=18  Identities=28%  Similarity=0.772  Sum_probs=11.1

Q ss_pred             CceeecCCCCCCCCcCCC
Q 042094          271 GLCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~  288 (485)
                      ..||+||+.||++++|+.
T Consensus         7 ~~C~~Cg~~GH~a~~C~~   24 (49)
T 2ec7_A            7 IRCWNCGKEGHSARQCRA   24 (49)
T ss_dssp             CBCTTTCCBTCCTTTCCC
T ss_pred             CeeeecCCCCcChhhCcC
Confidence            446666666666666654

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=96.99  E-value=0.00021  Score=44.12  Aligned_cols=18  Identities=33%  Similarity=0.927  Sum_probs=16.4

Q ss_pred             ceeecCCCCCCCCcCCCc
Q 042094          272 LCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       272 ~Cf~Cg~~GH~a~~C~~~  289 (485)
                      .||+|++.||++++|+.+
T Consensus         2 ~C~~Cg~~GH~a~~C~~~   19 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQP   19 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSC
T ss_pred             eeeccCCCCcccccCCCC
Confidence            599999999999999764

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=96.97  E-value=0.0002  Score=43.63  Aligned_cols=18  Identities=22%  Similarity=0.794  Sum_probs=16.4

Q ss_pred             CceeecCCCCCCCCcCCC
Q 042094          271 GLCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~  288 (485)
                      ..||+|++.||++++||+
T Consensus        20 ~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A           20 KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             TTCSSCCCTTGGGGTTCC
T ss_pred             CeEccCCCcCCccCcCcC
Confidence            579999999999999974

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=96.97  E-value=0.00024  Score=46.33  Aligned_cols=20  Identities=20%  Similarity=0.468  Sum_probs=18.0

Q ss_pred             CceeecCCCCCCCCcCCCce
Q 042094          271 GLCFNCDEQFKPGHRCKAPQ  290 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~~~  290 (485)
                      ..||+||+.||++++||.++
T Consensus        28 ~~C~~Cg~~GH~~~~C~~~~   47 (49)
T 2ec7_A           28 QGCWKCGKTGHVMAKCPERQ   47 (49)
T ss_dssp             CSCSSSCCSSCCGGGCCSSC
T ss_pred             CeeCcCCCcCCccCCCcCCC
Confidence            57999999999999998764

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=96.88  E-value=0.00027  Score=51.61  Aligned_cols=24  Identities=25%  Similarity=0.517  Sum_probs=20.2

Q ss_pred             hCCceeecCCCCCCCCcCCCceee
Q 042094          269 AKGLCFNCDEQFKPGHRCKAPQLL  292 (485)
Q Consensus       269 ~~~~Cf~Cg~~GH~a~~C~~~~~~  292 (485)
                      ....||+||+.||++++|+..+..
T Consensus        45 ~~~~CYnCG~~GH~~rdC~~~r~s   68 (83)
T 3nyb_B           45 HTIYCYNCGGKGHFGDDCKEKRSS   68 (83)
T ss_dssp             CCCBCSSSSCBSSCGGGCSSCCSC
T ss_pred             CCCeecccCCCCcCcccCCccccC
Confidence            347799999999999999877643

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=96.83  E-value=0.00042  Score=47.48  Aligned_cols=22  Identities=27%  Similarity=0.593  Sum_probs=18.7

Q ss_pred             hCCceeecCCCCCCCCcCCCce
Q 042094          269 AKGLCFNCDEQFKPGHRCKAPQ  290 (485)
Q Consensus       269 ~~~~Cf~Cg~~GH~a~~C~~~~  290 (485)
                      ....||+|++.||++++|+.+.
T Consensus        29 ~~~~C~~Cg~~GH~ar~C~~~~   50 (60)
T 1cl4_A           29 VPGLCPRCKRGKHWANECKSKT   50 (60)
T ss_dssp             CCCSCSSCSSCSSCSTTCCCTT
T ss_pred             CCcceeECCCCCCccCcCCCcc
Confidence            3478999999999999997653

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=96.76  E-value=0.00036  Score=47.92  Aligned_cols=21  Identities=14%  Similarity=0.452  Sum_probs=17.6

Q ss_pred             CCceeecCCCCCCCCcCCCce
Q 042094          270 KGLCFNCDEQFKPGHRCKAPQ  290 (485)
Q Consensus       270 ~~~Cf~Cg~~GH~a~~C~~~~  290 (485)
                      ...||+|++.||++++|+.++
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~   50 (61)
T 2ihx_A           30 RERCQLCNGMGHNAKQCRKRD   50 (61)
T ss_dssp             CSBCTTTCCBSSCGGGCCCCC
T ss_pred             CCeeCCCCCCCCCcCCCcCCC
Confidence            367999999999999997765

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=96.74  E-value=0.00036  Score=46.88  Aligned_cols=17  Identities=18%  Similarity=0.581  Sum_probs=8.6

Q ss_pred             ceeecCCCCCCCCcCCC
Q 042094          272 LCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       272 ~Cf~Cg~~GH~a~~C~~  288 (485)
                      .||+||+.||++++||.
T Consensus        35 ~C~~Cg~~GH~~~~C~~   51 (55)
T 1a1t_A           35 GCWKCGKEGHQMKDCTE   51 (55)
T ss_dssp             BCTTTCCBSSCGGGCSS
T ss_pred             EeCCCCCcCCccCCCcC
Confidence            45555555555555543

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=96.73  E-value=0.00037  Score=47.85  Aligned_cols=21  Identities=29%  Similarity=0.735  Sum_probs=18.0

Q ss_pred             hCCceeecCCCCCCCCcCCCc
Q 042094          269 AKGLCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       269 ~~~~Cf~Cg~~GH~a~~C~~~  289 (485)
                      ....||+|++.||++++|+..
T Consensus         3 ~~~~C~~Cg~~GH~a~~C~~~   23 (61)
T 2ihx_A            3 ARGLCYTCGSPGHYQAQCPKK   23 (61)
T ss_dssp             CTTBCSSSCCBTCCGGGCTTT
T ss_pred             CCCcccccCCCCeehhhCcCC
Confidence            346799999999999999764

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=96.68  E-value=0.00048  Score=46.24  Aligned_cols=22  Identities=36%  Similarity=0.821  Sum_probs=18.7

Q ss_pred             hhCCceeecCCCCCCCCcCCCc
Q 042094          268 RAKGLCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       268 ~~~~~Cf~Cg~~GH~a~~C~~~  289 (485)
                      ++...||+|++.||++++|+..
T Consensus        10 ~~~~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           10 RKTVKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             GGTCBCTTTCCBSSCGGGCSSC
T ss_pred             CCCcceeeeCCCCcChhhcCCC
Confidence            3456799999999999999764

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=96.53  E-value=0.0004  Score=47.62  Aligned_cols=19  Identities=26%  Similarity=0.739  Sum_probs=0.0

Q ss_pred             CceeecCCCCCCCCcCCCc
Q 042094          271 GLCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~~  289 (485)
                      +.||+|++.||++++|+..
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~~   20 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHEH   20 (60)
T ss_dssp             -------------------
T ss_pred             CccccCCCCCcCHhhCcCC
Confidence            3599999999999999764

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.52  E-value=0.0007  Score=46.77  Aligned_cols=21  Identities=14%  Similarity=0.243  Sum_probs=16.1

Q ss_pred             CCceeecCCCCCCCCcCCCce
Q 042094          270 KGLCFNCDEQFKPGHRCKAPQ  290 (485)
Q Consensus       270 ~~~Cf~Cg~~GH~a~~C~~~~  290 (485)
                      ...||+|++.||++++||.+.
T Consensus        29 ~~~C~~Cg~~GH~ar~Cp~~~   49 (63)
T 2cqf_A           29 PKKCHFCQSISHMVASCPLKA   49 (63)
T ss_dssp             SSCCTTTCCSSSCTTTCTGGG
T ss_pred             CCccCCcCCcCCccCcCCCcc
Confidence            356888888888888887543

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.50  E-value=0.00095  Score=46.08  Aligned_cols=18  Identities=28%  Similarity=0.695  Sum_probs=16.5

Q ss_pred             CceeecCCCCCCCCcCCC
Q 042094          271 GLCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~  288 (485)
                      ..||+|++.||++++|+.
T Consensus         8 ~~C~~Cg~~GH~a~~C~~   25 (63)
T 2cqf_A            8 DRCYNCGGLDHHAKECKL   25 (63)
T ss_dssp             CCCSSSCCSSSCTTTCCS
T ss_pred             CcccccCCCCcChhhCCC
Confidence            569999999999999975

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=96.28  E-value=0.0011  Score=47.24  Aligned_cols=17  Identities=18%  Similarity=0.348  Sum_probs=8.3

Q ss_pred             ceeecCCCCCCCCcCCC
Q 042094          272 LCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       272 ~Cf~Cg~~GH~a~~C~~  288 (485)
                      .||+|++.||++++|+.
T Consensus        48 ~C~~Cg~~GH~ar~Cp~   64 (74)
T 2li8_A           48 KCHFCQSISHMVASCPL   64 (74)
T ss_dssp             CCTTTCCTTSCGGGCTT
T ss_pred             ccCCcCCcCCccCcCcC
Confidence            35555555555555543

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=96.25  E-value=0.0012  Score=47.04  Aligned_cols=20  Identities=25%  Similarity=0.600  Sum_probs=17.4

Q ss_pred             hCCceeecCCCCCCCCcCCC
Q 042094          269 AKGLCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       269 ~~~~Cf~Cg~~GH~a~~C~~  288 (485)
                      ....||+||+.||++++|+.
T Consensus        23 r~~~C~~Cg~~GH~a~~C~~   42 (74)
T 2li8_A           23 KGDRCYNCGGLDHHAKECKL   42 (74)
T ss_dssp             TTSCCTTTCCSSSCTTTCSS
T ss_pred             CCCcccccCCcCcCcccCCC
Confidence            34679999999999999974

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

Probab=95.40  E-value=0.16  Score=36.74  Aligned_cols=86  Identities=13%  Similarity=0.184  Sum_probs=61.2

Q ss_pred             EEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcCCCC
Q 042094          333 LKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLPVSG  412 (485)
Q Consensus       333 ~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~~~~  412 (485)
                      +.+.|.|..+++.-||||+++.|-..+...    ..+.....+.+.+|..-.   .+--+.|.++|.....+++--+.. 
T Consensus        10 L~vEiKg~kLkg~WDsGA~ITCiP~~fL~~----E~PI~~~~I~TIHG~k~q---~vYYl~fKv~GRKveaEVi~sp~d-   81 (107)
T 2jys_A           10 LEAEIKGTKLKAHWDSGATITCVPEAFLED----ERPIQTMLIKTIHGEKQQ---DVYYLTFKVQGRKVEAEVLASPYD-   81 (107)
T ss_dssp             EEEEETTEEEEEEECTTCSSEEEEGGGTTT----CCCSEEEEEECSSCEEEE---EEEEEEEEESSCEEEEEEEEESSS-
T ss_pred             eeEEEeCcEEEEEecCCCeEEEcchHHhcc----cccccceEEEEecCceec---eEEEEEEEEcCeEEEEEEecCccc-
Confidence            678899999999999999999999887653    134456678888987643   223478999999777666655532 


Q ss_pred             CCee--echhHHhhcC
Q 042094          413 CDIV--LGAEWLRSLG  426 (485)
Q Consensus       413 ~dvI--LG~dwL~~~~  426 (485)
                      |-+|  --.+|+.+.+
T Consensus        82 Yvli~P~DiPW~~~~p   97 (107)
T 2jys_A           82 YILLNPSDVPWLMKKP   97 (107)
T ss_dssp             SEEECTTTCHHHHSCC
T ss_pred             EEEEcCcCccccccCc
Confidence            2122  1468988654

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=95.13  E-value=0.0058  Score=50.26  Aligned_cols=17  Identities=29%  Similarity=0.759  Sum_probs=10.3

Q ss_pred             CceeecCCCCCCCCcCC
Q 042094          271 GLCFNCDEQFKPGHRCK  287 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~  287 (485)
                      ..||+||+.||++++|+
T Consensus        98 ~~C~~Cg~~GH~a~~C~  114 (148)
T 3ts2_A           98 DRCYNCGGLDHHAKECK  114 (148)
T ss_dssp             CCCTTTCCSSCCGGGCC
T ss_pred             CcccEeCCccchhhhCC
Confidence            34666666666666664

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=95.12  E-value=0.0059  Score=48.74  Aligned_cols=20  Identities=30%  Similarity=0.675  Sum_probs=17.8

Q ss_pred             hCCceeecCCCCCCCCcCCC
Q 042094          269 AKGLCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       269 ~~~~Cf~Cg~~GH~a~~C~~  288 (485)
                      ....||+|++.||++++||.
T Consensus       104 ~~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A          104 HTIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CCCCTTTTSSSCTTTTTSCC
T ss_pred             CCCCcCCCCCCCcCcccCcC
Confidence            35789999999999999985

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=95.05  E-value=0.0054  Score=44.68  Aligned_cols=20  Identities=25%  Similarity=0.491  Sum_probs=16.2

Q ss_pred             CCceeecCCCCCCCCcCCCc
Q 042094          270 KGLCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       270 ~~~Cf~Cg~~GH~a~~C~~~  289 (485)
                      ...||+|++.||++++||..
T Consensus         5 ~~~C~~Cg~~GH~~~~Cp~~   24 (83)
T 3nyb_B            5 KVQCTLCKSKKHSKERCPSI   24 (83)
T ss_dssp             --CCSSSCCSSSCGGGCGGG
T ss_pred             cCCCCCCCCCCCccccCCCc
Confidence            46799999999999999754

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=94.83  E-value=0.0072  Score=49.67  Aligned_cols=17  Identities=18%  Similarity=0.372  Sum_probs=16.0

Q ss_pred             eeecCCCCCCCCcCCCc
Q 042094          273 CFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       273 Cf~Cg~~GH~a~~C~~~  289 (485)
                      ||+|++.||++++||.+
T Consensus       122 C~~Cg~~GH~~r~Cp~~  138 (148)
T 3ts2_A          122 CHFCQSINHMVASCPLK  138 (148)
T ss_dssp             CTTTCCSSCCGGGCTTT
T ss_pred             ccccCCcCCEeccCcCC
Confidence            99999999999999865

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=92.96  E-value=0.036  Score=44.11  Aligned_cols=17  Identities=18%  Similarity=0.526  Sum_probs=9.1

Q ss_pred             ceeecCCC-CCCCCcCCC
Q 042094          272 LCFNCDEQ-FKPGHRCKA  288 (485)
Q Consensus       272 ~Cf~Cg~~-GH~a~~C~~  288 (485)
                      .||+||+. ||++++||.
T Consensus        24 ~C~~Cg~~~gH~~~~C~~   41 (124)
T 2lli_A           24 ICSYCGATDDHYSRHCPK   41 (124)
T ss_dssp             CCTTTCCTTTCCTTTGGG
T ss_pred             cCcCCCCcCCccCcccCC
Confidence            45555555 555555543

>3cms_A Chymosin B; hydrolase, acid proteinase; 2.00A {Bos taurus} SCOP: b.50.1.2 PDB: 4cms_A 1czi_E* 1cms_A

Probab=92.58  E-value=0.71  Score=43.29  Aligned_cols=101  Identities=13%  Similarity=0.126  Sum_probs=61.8

Q ss_pred             EEECCeE------EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeec--ceEeeeEEeecceEEEEE-
Q 042094          335 GNLKKHG------VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSS--GKCSHVPVNSQGFQFHLD-  404 (485)
Q Consensus       335 ~~i~~~~------v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~--~~~~~v~v~i~~~~~~~~-  404 (485)
                      +.|++..      ..++||||++..++..++++.+.-.....     ...+|.. +.|.  .....+.|.++|..+.+. 
T Consensus       198 i~v~~~~~~~~~~~~aiiDSGTt~~~lP~~~~~~l~~~~~~~-----~~~~g~~~~~C~~~~~~P~i~f~f~g~~~~i~~  272 (323)
T 3cms_A          198 VTISGVVVACEGGCQAILDTGTSKLVGPSSDILNIQQAIGAT-----QNQYGEFDIDCDNLSYMPTVVFEINGKMYPLTP  272 (323)
T ss_dssp             EEETTEEEESTTCEEEEECTTCCSEEECHHHHHHHHHHHTCE-----EETTTEEEECTTCTTTSCCEEEEETTEEEEECH
T ss_pred             EEECCEEeecCCCcEEEEecCCccEeCCHHHHHHHHHHhCCe-----ecCCCcEEEECCCCccCceEEEEECCEEEEECH
Confidence            4556654      47999999999999998887663221110     0011211 1221  112356677777665432 


Q ss_pred             ----------EE--EcCC-CCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 ----------FF--LLPV-SGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 ----------~~--V~~~-~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                                ++  +.+. .+...|||..||+.+-. ..|+.+++|-|..
T Consensus       273 ~~y~~~~~~~C~~~i~~~~~~~~~iLG~~fl~~~y~-vfD~~~~~igfA~  321 (323)
T 3cms_A          273 SAYTSQDQGFCTSGFQSENHSQKWILGDVFIREYYS-VFDRANNLVGLAK  321 (323)
T ss_dssp             HHHEEEETTEEEESEEEC---CCEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             HHhccCCCCEEEEEEEeCCCCCcEEECHHHhhceEE-EEECCCCEEEEEE
Confidence                      22  2222 23468999999999986 7999999998864

>1am5_A Pepsin, acid proteinase; aspartyl protease, hydrolase; 2.16A {Gadus morhua} SCOP: b.50.1.2

Probab=92.56  E-value=0.23  Score=46.74  Aligned_cols=93  Identities=13%  Similarity=0.168  Sum_probs=58.6

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecc--eEeeeEEeecceEEEEE-----------EE-
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSG--KCSHVPVNSQGFQFHLD-----------FF-  406 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~--~~~~v~v~i~~~~~~~~-----------~~-  406 (485)
                      ..++||||++..++..++++.+.-.....      ..+|.. +.|..  ....+.|.++|..+.+.           ++ 
T Consensus       209 ~~aiiDSGTt~~~lp~~~~~~l~~~~~~~------~~~g~~~~~C~~~~~~P~i~f~f~g~~~~i~~~~y~~~~~~~C~~  282 (324)
T 1am5_A          209 CQAIVDTGTSKIVAPVSALANIMKDIGAS------ENQGEMMGNCASVQSLPDITFTINGVKQPLPPSAYIEGDQAFCTS  282 (324)
T ss_dssp             EEEEECTTCSSEEECTTTHHHHHHHHTCE------ECCCCEECCTTSSSSSCCEEEEETTEEEEECHHHHEEESSSCEEE
T ss_pred             ceEEEecCCccEECCHHHHHHHHHHhCCc------ccCCcEEEeCCCcccCCcEEEEECCEEEEECHHHhcccCCCeEEE
Confidence            67999999999999988877653221110      122321 12211  12356677777665431           22 


Q ss_pred             -EcCC-----CCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          407 -LLPV-----SGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       407 -V~~~-----~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                       +.+.     .+...|||..||+.+-. ..|+.+++|.|..
T Consensus       283 ~~~~~~~~~~~~~~~ilG~~fl~~~y~-vfD~~~~~igfa~  322 (324)
T 1am5_A          283 GLGSSGVPSNTSELWIFGDVFLRNYYT-IYDRTNNKVGFAP  322 (324)
T ss_dssp             CEEECCSCCSSSCEEEECHHHHHHEEE-EEETTTTEEEEEE
T ss_pred             EEEECccCCCCCCcEEEChHHhccEEE-EEECCCCEEEEEE
Confidence             2222     13468999999999986 7999999998864

>3qvc_A Histo-aspartic protease; HAP, plasmepsin, zymogen, hydrolase; 2.10A {Plasmodium falciparum} PDB: 3qvi_A* 3fns_A 3fnt_A* 3fnu_A*

Probab=92.53  E-value=0.28  Score=48.47  Aligned_cols=102  Identities=15%  Similarity=0.245  Sum_probs=64.2

Q ss_pred             EEECCe---EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeec-ceEeeeEEeecceEEEEEE----
Q 042094          335 GNLKKH---GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSS-GKCSHVPVNSQGFQFHLDF----  405 (485)
Q Consensus       335 ~~i~~~---~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~-~~~~~v~v~i~~~~~~~~~----  405 (485)
                      +.|++.   ...++||||++..++..++++.+.-.....    .....|.. +.|. .....+.+.++|..+.+..    
T Consensus       322 I~Vgg~~~~~~~aiiDSGTt~i~lP~~~~~~i~~~i~a~----~~~~~g~y~v~C~~~~~P~itf~fgg~~i~lp~~~yi  397 (451)
T 3qvc_A          322 VHFGNVSSKKANVILDSATSVITVPTEFFNQFVESASVF----KVPFLSLYVTTCGNTKLPTLEYRSPNKVYTLEPKQYL  397 (451)
T ss_dssp             EEETTEEEEEEEEEECTTBSSEEECHHHHHHHHTTTTCE----ECTTSSCEEEETTCTTCCCEEEEETTEEEEECHHHHE
T ss_pred             EEECCccCCCceEEEeCCCccccCCHHHHHHHHHHcCCe----ecCCCCeEEeeCCcCcCCcEEEEECCEEEEEcHHHhe
Confidence            556663   567999999999999999988774332110    00011221 2222 1224567777777655421    


Q ss_pred             -----------E--EcCCC--CCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          406 -----------F--LLPVS--GCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       406 -----------~--V~~~~--~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                                 +  +.+..  ....|||..||+.+-. ..|+.+++|.|-.
T Consensus       398 ~~~~~~~~~~C~~~i~~~~~~~~~~ILG~~FLr~~Yv-VfD~~n~rIGfA~  447 (451)
T 3qvc_A          398 EPLENIFSALCMLNIVPIDLEKNTFVLGDPFMRKYFT-VYDYDNHTVGFAL  447 (451)
T ss_dssp             EECTTTSTTEEEECEEECCCSTTEEEECHHHHHHEEE-EEETTTTEEEEEE
T ss_pred             eecccCCCCeEEEEEEeCCCCCCCEEECHHHhhcEEE-EEECCCCEEEEEE
Confidence                       1  11222  2458999999999996 7999999998864

>1dpj_A Proteinase A; proteinase A, hydrolase-hydrolase inhibitor COM; HET: BMA MAN NAG; 1.80A {Saccharomyces cerevisiae} SCOP: b.50.1.2 PDB: 1dp5_A* 1fmu_A* 1fmx_A* 1fq5_A* 1fq4_A* 1fq6_A* 1fq7_A* 1fq8_A* 2jxr_A* 1g0v_A*

Probab=92.28  E-value=0.52  Score=44.34  Aligned_cols=101  Identities=18%  Similarity=0.268  Sum_probs=60.0

Q ss_pred             EEECCeE-----EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCee-eecc--eEeeeEEeecceEEEEE--
Q 042094          335 GNLKKHG-----VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVI-SSSG--KCSHVPVNSQGFQFHLD--  404 (485)
Q Consensus       335 ~~i~~~~-----v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~-~~~~--~~~~v~v~i~~~~~~~~--  404 (485)
                      +.|++..     ..++||||++..++..++++.+.-.....     ...+|... .|..  ....+.|.++|..+.+.  
T Consensus       201 i~v~~~~~~~~~~~aiiDSGTt~~~lP~~~~~~l~~~~~~~-----~~~~g~~~~~C~~~~~~P~i~f~f~g~~~~i~~~  275 (329)
T 1dpj_A          201 IGLGDEYAELESHGAAIDTGTSLITLPSGLAEMINAEIGAK-----KGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPY  275 (329)
T ss_dssp             EEETTEEEECSSCEEEECTTCSCEEECHHHHHHHHHHHTCE-----ECTTSSEEECGGGGGGCCCEEEEETTEEEEECTT
T ss_pred             EEECCeEecCCCccEEeeCCCCcEECCHHHHHHHHHHhCCc-----cCCCCeEEEECCCCCcCCcEEEEECCEEEEECHH
Confidence            4555544     36999999999999999888663221100     01122111 1211  11345566665544321  


Q ss_pred             ---------EE--EcCC-----CCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 ---------FF--LLPV-----SGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 ---------~~--V~~~-----~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                               ++  +.+.     .+...|||..||+.+-. ..|+.+++|-|..
T Consensus       276 ~y~~~~~~~C~~~~~~~~~~~~~~~~~iLG~~fl~~~y~-vfD~~~~~igfA~  327 (329)
T 1dpj_A          276 DYTLEVSGSCISAITPMDFPEPVGPLAIVGDAFLRKYYS-IYDLGNNAVGLAK  327 (329)
T ss_dssp             TSEEEETTEEEECEEECCCCTTTCSEEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             HhEecCCCEEEEEEEecccCCCCCCcEEEChHHhcceEE-EEECCCCEEEEEE
Confidence                     22  2222     23468999999999986 7999999998864

>1lya_B Cathepsin D; lysosomal aspartic protease; HET: NAG BMA MAN; 2.50A {Homo sapiens} SCOP: b.50.1.2 PDB: 1lyb_B* 1lyw_B*

Probab=92.12  E-value=0.34  Score=43.28  Aligned_cols=94  Identities=12%  Similarity=0.199  Sum_probs=56.8

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecc--eEeeeEEeecceEEEE---------------
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSG--KCSHVPVNSQGFQFHL---------------  403 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~--~~~~v~v~i~~~~~~~---------------  403 (485)
                      ..++||||++..++..++++.+.-.....    . ..+|.. +.|..  ....+.+.++|..+.+               
T Consensus       121 ~~aiiDSGTt~~~lP~~~~~~l~~~~~~~----~-~~~g~~~~~C~~~~~~p~i~f~f~g~~~~l~~~~y~~~~~~~~~~  195 (241)
T 1lya_B          121 CEAIVDTGTSLMVGPVDEVRELQKAIGAV----P-LIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKT  195 (241)
T ss_dssp             EEEEECTTCSSEEECHHHHHHHHHHHTCE----E-EETTEEEEEGGGGGGSCCEEEEETTEEEEECTTTSEEEETTTTSS
T ss_pred             CEEEEECCCccccCCHHHHHHHHHHhCCe----e-ccCCcEEEECCCCccCCeEEEEECCEEEEECHHHhEEEccCCCCC
Confidence            57999999999999999888663221100    0 012211 12211  1234556666654432               


Q ss_pred             EEE--EcCC-----CCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          404 DFF--LLPV-----SGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       404 ~~~--V~~~-----~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      .++  +.+.     .....|||..||+.+-. ..|+.+++|-|..
T Consensus       196 ~C~~~~~~~~~~~~~~~~~ilG~~fl~~~y~-vfD~~~~~igfA~  239 (241)
T 1lya_B          196 LCLSGFMGMDIPPPSGPLWILGDVFIGRYYT-VFDRDNNRVGFAE  239 (241)
T ss_dssp             EEEESEEECCCCTTTCCCEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             eeEEEEEecccCCCCCCeEEechHHhcceEE-EEECCCCEEEEEE
Confidence            122  2221     23468999999999986 7999999998864

>1yg9_A Aspartic protease BLA G 2; allegren, hydrolase, allergen; HET: NAG; 1.30A {Blattella germanica} PDB: 2nr6_A* 3liz_A*

Probab=91.92  E-value=0.35  Score=45.58  Aligned_cols=101  Identities=13%  Similarity=0.187  Sum_probs=64.3

Q ss_pred             EEECCeE-----EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccC--C--eeeecc--eEeeeEEeecceEEEE
Q 042094          335 GNLKKHG-----VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADG--G--VISSSG--KCSHVPVNSQGFQFHL  403 (485)
Q Consensus       335 ~~i~~~~-----v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G--~--~~~~~~--~~~~v~v~i~~~~~~~  403 (485)
                      +.|++..     ..++||||++..++..++++.+.-.....   .  ..+|  .  .+.|..  ....+.|.++|..+.+
T Consensus       202 i~v~~~~~~~~~~~aiiDSGTs~~~lP~~~~~~l~~~~~~~---~--~~~g~~~~~~~~C~~~~~~p~i~f~fgg~~~~l  276 (330)
T 1yg9_A          202 VKIGDTTVAPAGTQAIIDTSKAIIVGPKAYVNPINEAIGCV---V--EKTTTRRICKLDCSKIPSLPDVTFVINGRNFNI  276 (330)
T ss_dssp             EEETTEEEECTTCEEEECTTCSSEEEEHHHHHHHHHHHTCE---E--EECSSCEEEEECGGGGGGSCCEEEEETTEEEEE
T ss_pred             EEECCEEEcCCCcEEEEecCCccccCCHHHHHHHHHHhCCc---c--cCCCceEEEEEECCCccccCcEEEEECCEEEEE
Confidence            4455544     47999999999999999888763322110   0  1233  1  223321  2345777888876654


Q ss_pred             E-----------EE--EcCC-CCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          404 D-----------FF--LLPV-SGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       404 ~-----------~~--V~~~-~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      .           ++  +.+. .+...|||..||+.+-. ..|+.+++|-|..
T Consensus       277 ~~~~y~~~~~~~C~~~i~~~~~~~~~ilG~~fl~~~y~-vfD~~~~riGfA~  327 (330)
T 1yg9_A          277 SSQYYIQQNGNLCYSGFQPCGHSDHFFIGDFFVDHYYS-EFNWENKTMGFGR  327 (330)
T ss_dssp             CHHHHEEEETTEEEESEEEETTCSSEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             CHHHhcccCCCcEEEEEEeCCCCCeEEecHHHhhheEE-EEECCCCEEEEEE
Confidence            2           22  1221 23468999999999986 7999999998875

>2apr_A Rhizopuspepsin; hydrolase (aspartic proteinase); 1.80A {Rhizopus microsporus var} SCOP: b.50.1.2 PDB: 3apr_E* 4apr_E* 5apr_E* 6apr_E* 1uh9_A 1uh8_A 1uh7_A

Probab=91.90  E-value=0.46  Score=44.66  Aligned_cols=93  Identities=14%  Similarity=0.212  Sum_probs=54.5

Q ss_pred             EEEEEEcCCCCccccCHH----HHhhcCCccccccceEEEEccCCeeeecce-EeeeEEeecceEEEE------------
Q 042094          341 GVTILIDSSSTHIFLNSS----LAKQYGCPVTTTTQFQVTVADGGVISSSGK-CSHVPVNSQGFQFHL------------  403 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~----~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~-~~~v~v~i~~~~~~~------------  403 (485)
                      ...++||||++..++..+    +++.+.-.........        +.|... ...+.|.++|..+.+            
T Consensus       212 ~~~~iiDSGTs~~~lP~~~~~~~~~~~~~~~~~~g~~~--------~~C~~~~~p~i~f~f~g~~~~ip~~~~~~~~~~~  283 (325)
T 2apr_A          212 SFDGILDTGTTLLILPNNIAASVARAYGASDNGDGTYT--------ISCDTSAFKPLVFSINGASFQVSPDSLVFEEFQG  283 (325)
T ss_dssp             CEEEEECTTCSSEEEEHHHHHHHHHHHTCEECSSSCEE--------ECSCGGGCCCEEEEETTEEEEECGGGGEEEEETT
T ss_pred             CceEEEecCCccEECCHHHHHHHHHHHhcccCCCCeEE--------EECCCCCCCcEEEEECCEEEEECHHHEEEcCCCC
Confidence            357999999999999999    6666653321100111        111111 123444444332221            


Q ss_pred             EEE--EcCCCCCCeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          404 DFF--LLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       404 ~~~--V~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                      .++  +.+...-..|||..||+.+-. ..|+.+++|-|...
T Consensus       284 ~C~~~i~~~~~~~~iLG~~fl~~~y~-vfD~~~~~igfA~~  323 (325)
T 2apr_A          284 QCIAGFGYGNWGFAIIGDTFLKNNYV-VFNQGVPEVQIAPV  323 (325)
T ss_dssp             EEEESEEEESSSSEEECHHHHTTEEE-EEETTTTEEEEEEB
T ss_pred             eEEEEEEcCCCCCEEECHHHhcceEE-EEECCCCEEEEEec
Confidence            111  111113458999999999986 79999999998753

>2x0b_A Renin; hydrolase-hormone complex, hydrolase hormone complex, vasoconstrictor, glycoprotein, hypertension, serpins; 4.33A {Homo sapiens}

Probab=91.55  E-value=0.5  Score=45.55  Aligned_cols=94  Identities=15%  Similarity=0.196  Sum_probs=59.7

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecc--eEeeeEEeecceEEEEE-------------
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSG--KCSHVPVNSQGFQFHLD-------------  404 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~--~~~~v~v~i~~~~~~~~-------------  404 (485)
                      ...|+||||++..++..++++.+.-.....    .  .+|.. +.|..  ....+.|.++|..+.+.             
T Consensus       263 ~~~aiiDTGTs~~~lP~~~~~~i~~~i~a~----~--~~g~~~v~C~~~~~~P~i~f~~~g~~~~l~~~~yi~~~~~~~~  336 (383)
T 2x0b_A          263 GCLALVDTGASYISGSTSSIEKLMEALGAK----K--RLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSK  336 (383)
T ss_dssp             CEEEEECTTCSSEEECHHHHHHHHHHHTCE----E--CSSCEEEEGGGTTTCCCEEEEETTEEEEECHHHHBCCCCCCTT
T ss_pred             CcEEEEcCCCceEEcCHHHHHHHHHHhCCc----c--cCCcEEEeccccccCceEEEEECCEEEEECHHHhEeeccCCCC
Confidence            368999999999999998887663222110    0  23322 12221  12456777777665431             


Q ss_pred             --EE--EcCC-----CCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 --FF--LLPV-----SGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 --~~--V~~~-----~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                        ++  +.+.     .+...|||..||+.+-. ..|+.+++|-|..
T Consensus       337 ~~C~~~~~~~~~~~~~~~~~ILGd~Fl~~~y~-vfD~~~~rIGfA~  381 (383)
T 2x0b_A          337 KLCTLAIHAMDIPPPTGPTWALGATFIRKFYT-EFDRRNNRIGFAL  381 (383)
T ss_dssp             SEEEBSEEECCCCTTTCSCEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             CeEEEEEEecccCCCCCCcEEEChHHhcceEE-EEECCCCEEeEEE
Confidence              22  1111     23468999999999986 7999999998864

>1tzs_A Cathepsin E; hydrolase, aspartic protease, activation intermediate; 2.35A {Homo sapiens}

Probab=91.32  E-value=0.63  Score=44.22  Aligned_cols=101  Identities=14%  Similarity=0.165  Sum_probs=59.2

Q ss_pred             EEECCeE------EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecc--eEeeeEEeecceEEEE--
Q 042094          335 GNLKKHG------VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSG--KCSHVPVNSQGFQFHL--  403 (485)
Q Consensus       335 ~~i~~~~------v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~--~~~~v~v~i~~~~~~~--  403 (485)
                      +.|++..      ..++||||++..++..++++.+.-..... ..    . |.. +.|..  ....+.|.++|..+.+  
T Consensus       210 i~v~~~~~~~~~~~~aiiDSGTs~~~lP~~~~~~l~~~~~~~-~~----~-g~~~~~C~~~~~~P~i~f~f~g~~~~i~~  283 (351)
T 1tzs_A          210 IQVGGTVMFCSEGCQAIVDTGTSLITGPSDKIKQLQNAIGAA-PV----D-GEYAVECANLNVMPDVTFTINGVPYTLSP  283 (351)
T ss_dssp             EEETTEEEECTTCEEEEECTTCSSEEECHHHHHHHHHHHTCE-EC----S-SSEEECGGGGGGSCCEEEEETTEEEEECT
T ss_pred             EEECCceEEcCCCceEEeccCCcceeCCHHHHHHHHHHhCCc-cc----C-CeEEEeCCCCccCCcEEEEECCEEEEECH
Confidence            4556654      47999999999999998887653211100 00    0 111 11111  1123445555544322  


Q ss_pred             -------------EEE--EcCC-----CCCCeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          404 -------------DFF--LLPV-----SGCDIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       404 -------------~~~--V~~~-----~~~dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                                   .++  +.+.     .....|||..||+.+-. ..|+.+++|.|...
T Consensus       284 ~~yi~~~~~~~~~~C~~~~~~~~~~~~~~~~~iLG~~fl~~~y~-vfD~~~~rigfA~~  341 (351)
T 1tzs_A          284 TAYTLLDFVDGMQFCSSGFQGLDIHPPAGPLWILGDVFIRQFYS-VFDRGNNRVGLAPA  341 (351)
T ss_dssp             TTSEECC-----CCEEESEEECCCCTTTCSCEEECHHHHHHEEE-EEETTTTEEEEEEB
T ss_pred             HHhEeeccCCCCCeEEEEEEECCCCCCCCCeEEEChHHhhheEE-EEECCCCEEEEEEC
Confidence                         121  2221     23468999999999986 79999999999754

>4aa9_A Chymosin; hydrolase, aspartic peptidase, rennet; HET: NAG; 1.60A {Camelus dromedarius} PDB: 4aa8_A 1czi_E* 1cms_A 4cms_A 3cms_A

Probab=91.03  E-value=0.42  Score=44.76  Aligned_cols=94  Identities=14%  Similarity=0.175  Sum_probs=57.8

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecc--eEeeeEEeecceEEEEE-----------EE-
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSG--KCSHVPVNSQGFQFHLD-----------FF-  406 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~--~~~~v~v~i~~~~~~~~-----------~~-  406 (485)
                      ..++||||++..++..++++.+.-.....     ...+|.. +.|..  ....+.|.++|..+.+.           ++ 
T Consensus       208 ~~~iiDsGtt~~~lP~~~~~~i~~~~~~~-----~~~~g~~~~~C~~~~~~p~i~f~f~g~~~~l~~~~y~~~~~~~C~~  282 (320)
T 4aa9_A          208 CQAILDTGTSVLFGPSSDILKIQMAIGAT-----ENRYGEFDVNCGNLRSMPTVVFEINGRDYPLSPSAYTSKDQGFCTS  282 (320)
T ss_dssp             EEEEECTTCSSEEEEHHHHHHHHHHTTCE-----ECTTSCEEECGGGGGGCCCEEEEETTEEEEECHHHHEEEETTEEEE
T ss_pred             cEEEEECCCCcEECCHHHHHHHHHHhCCc-----ccCCCcEEEeCCCCCcCceEEEEECCEEEEECHHHhccCCCCeEEE
Confidence            57999999999999998877663221110     0011221 12211  12346667777655432           11 


Q ss_pred             -EcC-CCCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          407 -LLP-VSGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       407 -V~~-~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                       +.+ ..+...|||..||+.+-. ..|+.+++|.|-.
T Consensus       283 ~i~~~~~~~~~ilG~~fl~~~y~-vfD~~~~~igfA~  318 (320)
T 4aa9_A          283 GFQGDNNSELWILGDVFIREYYS-VFDRANNRVGLAK  318 (320)
T ss_dssp             SEEEETTCCCEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             EEEcCCCCCcEEEChHHhcceEE-EEECCCCEEEEEe
Confidence             112 122358999999999986 7999999998863

>1izd_A Aspartic proteinase; sugar binding, acid protease, hydrolase; HET: MAN; 1.90A {Aspergillus oryzae} SCOP: b.50.1.2 PDB: 1ize_A*

Probab=90.85  E-value=0.67  Score=43.46  Aligned_cols=98  Identities=21%  Similarity=0.286  Sum_probs=59.6

Q ss_pred             eEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCC-eeeecceEeeeEEeecceEEEEE-------------E
Q 042094          340 HGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGG-VISSSGKCSHVPVNSQGFQFHLD-------------F  405 (485)
Q Consensus       340 ~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~-~~~~~~~~~~v~v~i~~~~~~~~-------------~  405 (485)
                      ....++||||++..++..++++.+.-.....   .....+|. .+.|......+.|.++|..+.+.             +
T Consensus       207 ~~~~aiiDSGTs~~~lp~~~~~~i~~~i~ga---~~~~~~g~~~~~C~~~~P~i~f~fgg~~~~i~~~~~~~~~~~~~~C  283 (323)
T 1izd_A          207 DSITGIADTGTTLLLLDDSIVDAYYEQVNGA---SYDSSQGGYVFPSSASLPDFSVTIGDYTATVPGEYISFADVGNGQT  283 (323)
T ss_dssp             CCEEEEECTTCCSEEECHHHHHHHHTTSTTC---EEETTTTEEEEETTCCCCCEEEEETTEEEEECHHHHEEEECSTTEE
T ss_pred             CCceEEEeCCCcceeCCHHHHHHHHHhCCCc---EEcCcCCEEEEECCCCCceEEEEECCEEEecCHHHeEEecCCCCeE
Confidence            3467999999999999999988764332100   00001121 11222222346666666654431             2


Q ss_pred             E--EcCCC-CCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          406 F--LLPVS-GCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       406 ~--V~~~~-~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      +  +.+.. ....|||..||+.+-. ..|+.+++|-|..
T Consensus       284 ~~~i~~~~~~~~~IlG~~fl~~~y~-vfD~~~~riGfA~  321 (323)
T 1izd_A          284 FGGIQSNSGIGFSIFGDVFLKSQYV-VFDASGPRLGFAA  321 (323)
T ss_dssp             EESEEECTTTSSEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             EEEEEcCCCCCcEEEChHHhcCEEE-EEECCCCEEEEee
Confidence            1  12222 2468999999999986 7999999998864

>3k1w_A Renin; protease, alternative splicing, aspartyl protease, cleavage on PAIR of basic residues, disease mutation, disulfide bond, glycoprotein; HET: BFX NDG HSQ; 1.50A {Homo sapiens} SCOP: b.50.1.2 PDB: 3d91_A* 3g70_A* 3g6z_A* 3own_A* 2iko_A* 1bbs_A* 1rne_A* 2bkt_A* 2bks_A* 2iku_A* 2il2_A* 2ren_A* 2v0z_C* 2v10_C* 2v11_C* 2v12_C* 2v13_A* 2v16_C* 3g72_A* 3oot_A* ...

Probab=90.82  E-value=0.39  Score=45.44  Aligned_cols=94  Identities=15%  Similarity=0.170  Sum_probs=58.3

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecc--eEeeeEEeecceEEEEE---------------
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSG--KCSHVPVNSQGFQFHLD---------------  404 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~--~~~~v~v~i~~~~~~~~---------------  404 (485)
                      ..++||||++..++..++++.+.-.....    . ..+|-.+.|..  ....+.|.++|..+.+.               
T Consensus       221 ~~~iiDsGtt~~~lP~~~~~~i~~~~~~~----~-~~~g~~~~C~~~~~~p~i~f~f~g~~~~l~~~~~~~~~~~~~~~~  295 (341)
T 3k1w_A          221 CLALVDTGASYISGSTSSIEKLMEALGAK----K-RLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKL  295 (341)
T ss_dssp             EEEEECTTCSSEEECHHHHHHHHHHHTCE----E-CSSCEEEEGGGGGGCCCEEEEETTEEEEECHHHHBCCSCCCTTSE
T ss_pred             CEEEEECCCChhcCCHHHHHHHHHHcCCe----e-cCCCeEEeCCCCCcCCcEEEEECCEEEEECHHHheeEccCCCCCe
Confidence            57999999999999998887763221100    0 11221122221  12356677777655432               


Q ss_pred             EE--EcC-----CCCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 FF--LLP-----VSGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 ~~--V~~-----~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      ++  +.+     ..+...|||..||+.+-. ..|+.+++|.|..
T Consensus       296 C~~~i~~~~~~~~~~~~~iLG~~fl~~~y~-vfD~~~~~igfA~  338 (341)
T 3k1w_A          296 CTLAIHAMDIPPPTGPTWALGATFIRKFYT-EFDRRNNRIGFAL  338 (341)
T ss_dssp             EEBSEEECCCCTTTCSCEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             EEeEEEecccCCCCCCeEEEChHHhcceEE-EEeCCCCEEEEEE
Confidence            11  111     113468999999999986 7999999998864

>1wkr_A Polyporopepsin; hydrolase, hydrolase-hydrolase inhibitor complex; HET: STA; 1.30A {Irpex lacteus} SCOP: b.50.1.2

Probab=90.48  E-value=0.43  Score=45.16  Aligned_cols=104  Identities=13%  Similarity=0.205  Sum_probs=60.4

Q ss_pred             EEEECC-eEE----EEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCC-eeeec--ceEeeeEEeecceEEEEE-
Q 042094          334 KGNLKK-HGV----TILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGG-VISSS--GKCSHVPVNSQGFQFHLD-  404 (485)
Q Consensus       334 ~~~i~~-~~v----~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~-~~~~~--~~~~~v~v~i~~~~~~~~-  404 (485)
                      .+.|++ ..+    .++||||++..++..++++.+.-....    ......|. .+.|.  .....+.+.++|..+.+. 
T Consensus       194 ~i~v~~~~~l~~~~~aiiDSGTt~~~lP~~~~~~l~~~~~a----~~~~~~g~~~~~C~~~~~~p~i~f~f~g~~~~i~~  269 (340)
T 1wkr_A          194 SIRYGSSTSILSSTAGIVDTGTTLTLIASDAFAKYKKATGA----VADNNTGLLRLTTAQYANLQSLFFTIGGQTFELTA  269 (340)
T ss_dssp             EEEETTTEEEEEEEEEEECTTBCSEEECHHHHHHHHHHHTC----EECTTTSSEEECHHHHHTCCCEEEEETTEEEEECT
T ss_pred             eEEECCCeEccCCCeEEEeCCcccccCCHHHHHHHHHhhCC----EEcCCCCeEEeeccccccCCcEEEEECCEEEEEcH
Confidence            355665 443    799999999999999988876211110    00000111 11111  111345555666544431 


Q ss_pred             -------------------E--EEcCCC-----CCCeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          405 -------------------F--FLLPVS-----GCDIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       405 -------------------~--~V~~~~-----~~dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                                         +  .+.++.     +...|||..||+.+-. ..|+.+++|.|...
T Consensus       270 ~~yi~~~~~~~~~g~~~~~c~~~~~~~~~~~~~~~~~iLG~~fl~~~y~-vfD~~~~~igfA~~  332 (340)
T 1wkr_A          270 NAQIWPRNLNTAIGGSASSVYLIVGDLGSDSGEGLDFINGLTFLERFYS-VYDTTNKRLGLATT  332 (340)
T ss_dssp             GGGBCCGGGGGGGTCCSSCEEBCEEECSSCTTSSCCEEECHHHHTSEEE-EEETTTTEEEEEEC
T ss_pred             HHhccccccccccCCCCceEEEEEecCCCCCCCCcceEeChHhhhheEE-EEeCCCCeEEEEec
Confidence                               1  111211     2348999999999986 79999999999753

>2bju_A Plasmepsin II; aspartic proteinase, drug design, malaria, aspartyl protease, glycoprotein, hydrolase, signal, zymogen; HET: IH4; 1.56A {Plasmodium falciparum} SCOP: b.50.1.2 PDB: 1pfz_A 1xdh_A* 1lf3_A 1w6h_A* 1w6i_A* 1lf4_A* 1lf2_A* 1lee_A* 1m43_A* 2igx_A* 1sme_A* 1me6_A* 1xe6_A* 1xe5_A* 2igy_A* 2r9b_A 3f9q_A 3qrv_A 3qs1_A* 2anl_A* ...

Probab=90.46  E-value=1.2  Score=43.78  Aligned_cols=102  Identities=11%  Similarity=0.184  Sum_probs=63.9

Q ss_pred             EEECCe---EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccC-Ce-eeecc-eEeeeEEeecceEEEEE----
Q 042094          335 GNLKKH---GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADG-GV-ISSSG-KCSHVPVNSQGFQFHLD----  404 (485)
Q Consensus       335 ~~i~~~---~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G-~~-~~~~~-~~~~v~v~i~~~~~~~~----  404 (485)
                      +.|++.   ...++||||++.+++..++++.+.-.....     ...+| .. +.|.. ....+.+.++|..+.+.    
T Consensus       323 I~Vgg~~~~~~~aIiDSGTsl~~lP~~~~~~l~~~i~~~-----~~~~g~~~~v~C~~~~~P~itf~fgg~~~~l~~~~y  397 (453)
T 2bju_A          323 AHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVI-----KVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYY  397 (453)
T ss_dssp             EEETTEEEEEEEEEECTTCCSEEECHHHHHHHTTTSSCE-----ECTTSSCEEEETTCTTCCCEEEECSSCEEEECHHHH
T ss_pred             EEECcEEeccccEEEcCCCCeEecCHHHHHHHHHHhCCc-----ccCCCceEEEecCCCCCCcEEEEECCEEEEECHHHh
Confidence            455663   357999999999999999999875433211     11222 11 12211 12346667776655431    


Q ss_pred             -----------EE--EcCCC--CCCeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          405 -----------FF--LLPVS--GCDIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       405 -----------~~--V~~~~--~~dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                                 ++  +.+..  ....|||..||+.+-. ..|+.+.+|.|...
T Consensus       398 i~~~~~~g~~~C~~~~~~~~~~~~~~ILGd~Flr~~yv-VFD~~n~rIGfA~~  449 (453)
T 2bju_A          398 LQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFT-VFDYDNHSVGIALA  449 (453)
T ss_dssp             EEECTTTSTTEEEECEEECCCSSCEEEECHHHHHHEEE-EEETTTTEEEEEEE
T ss_pred             EeecccCCCceEEEEEEeCCCCCCCEEECHHHhhcEEE-EEECCCCEEEEEEc
Confidence                       21  12222  2368999999999986 79999999998753

>1miq_A Plasmepsin; aspartic proteinase zymogen, domain opening, hydrolase; 2.50A {Plasmodium vivax} SCOP: b.50.1.2 PDB: 1ls5_A*

Probab=90.14  E-value=1.1  Score=42.94  Aligned_cols=102  Identities=17%  Similarity=0.270  Sum_probs=59.9

Q ss_pred             EEECCe---EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecc-eEeeeEEeecceEEEE------
Q 042094          335 GNLKKH---GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSG-KCSHVPVNSQGFQFHL------  403 (485)
Q Consensus       335 ~~i~~~---~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~-~~~~v~v~i~~~~~~~------  403 (485)
                      +.|++.   ...++||||++..++..++++.+.-.....    ....+|.. +.|.. ....+.|.++|..+.+      
T Consensus       247 i~v~g~~~~~~~aiiDSGTs~~~lP~~~~~~l~~~~~~~----~~~~~g~~~~~C~~~~~P~i~f~f~g~~~~l~~~~yi  322 (375)
T 1miq_A          247 VHFGKQTMEKANVIVDSGTTTITAPSEFLNKFFANLNVI----KVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYM  322 (375)
T ss_dssp             EEETTEEEEEEEEEECTTBSSEEECHHHHHHHHHHHTCE----ECTTSSCEEEETTCTTCCCEEEECSSCEEEECGGGSE
T ss_pred             EEECCEEcccceEEecCCCccEEcCHHHHHHHHHHhCCc----ccCCCCeEEEECCCCCCCcEEEEECCEEEEECHHHhE
Confidence            667775   468999999999999998887652211100    00011111 11111 1233455555544332      


Q ss_pred             ---------EEE--EcCCC--CCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          404 ---------DFF--LLPVS--GCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       404 ---------~~~--V~~~~--~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                               .++  +.+..  ....|||..||+.+-. ..|+.+++|-|..
T Consensus       323 ~~~~~~g~~~C~~~~~~~~~~~~~~ILG~~fl~~~yv-vfD~~~~riGfA~  372 (375)
T 1miq_A          323 NPILEVDDTLCMITMLPVDIDSNTFILGDPFMRKYFT-VFDYDKESVGFAI  372 (375)
T ss_dssp             EESSSSSCSEEEESEEECCSSSSEEEECHHHHHHEEE-EEETTTTEEEEEE
T ss_pred             eeccCCCCCeEEEEEEECCCCCCcEEECHHHhccEEE-EEECCCCEEEEEE
Confidence                     111  12222  2468999999999986 7999999999864

>3fv3_A SAPP1P-secreted aspartic protease 1; secreted aspartic protease, virulence factor, H; HET: STA; 1.85A {Candida parapsilosis} SCOP: b.50.1.0 PDB: 3tne_A*

Probab=90.13  E-value=1.4  Score=41.53  Aligned_cols=106  Identities=21%  Similarity=0.220  Sum_probs=59.2

Q ss_pred             EEECCeE----EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCC-eeeecc-eEeeeEEeec-ceEEEEE--E
Q 042094          335 GNLKKHG----VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGG-VISSSG-KCSHVPVNSQ-GFQFHLD--F  405 (485)
Q Consensus       335 ~~i~~~~----v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~-~~~~~~-~~~~v~v~i~-~~~~~~~--~  405 (485)
                      +.|++..    ..++||||++..++..++++.+.-....... ......|. .+.|.. ....+.|.++ |..+.+.  -
T Consensus       204 i~v~g~~~~~~~~~iiDSGtt~~~lP~~~~~~i~~~~~~~~~-~~~~~~~~~~~~C~~~~~p~i~f~f~~g~~~~v~~~~  282 (339)
T 3fv3_A          204 VNLKGSSFSFGDGALLDSGTTLTYFPSDFAAQLADKAGARLV-QVARDQYLYFIDCNTDTSGTTVFNFGNGAKITVPNTE  282 (339)
T ss_dssp             EEESSCEEEEEEEEEECTTBSSEEECHHHHHHHHHHHTCEEE-EEETTEEEEEECTTCCCCSEEEEEETTSCEEEEEGGG
T ss_pred             EEECCEeecCCccEEEeCCCCCEecCHHHHHHHHHHcCCEEc-cccccCceEEEecCCCCCCcEEEEECCCCEEEECHHH
Confidence            4455554    3599999999999999988876322210000 00000111 111111 1234556663 4444332  1


Q ss_pred             EEcCC---C-------CCCeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          406 FLLPV---S-------GCDIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       406 ~V~~~---~-------~~dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                      ++++.   .       .-..|||..||+.+-. ..|+.+++|.|...
T Consensus       283 ~~~~~~~~~C~~~i~~~~~~ilG~~fl~~~y~-vfD~~~~~igfA~~  328 (339)
T 3fv3_A          283 YVYQNGDGTCLWGIQPSDDTILGDNFLRHAYL-LYNLDANTISIAQV  328 (339)
T ss_dssp             GEEECSSSCEEESEEECSSCEECHHHHTTEEE-EEETTTTEEEEEEB
T ss_pred             heeeCCCCeEEEEEEeCCcEEeChHHHhCEEE-EEECCCCEEEEEec
Confidence            11110   0       1247999999999986 79999999999753

>3pvk_A Candidapepsin-2; hydrolase; 1.27A {Candida albicans} SCOP: b.50.1.2 PDB: 1eag_A 3q70_A* 1zap_A* 2qzw_A 2h6t_A* 2h6s_A*

Probab=90.02  E-value=0.57  Score=44.33  Aligned_cols=103  Identities=18%  Similarity=0.227  Sum_probs=57.0

Q ss_pred             EEECCeE-----EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCC---eeeecceEeeeEEeec-ceEEEEE-
Q 042094          335 GNLKKHG-----VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGG---VISSSGKCSHVPVNSQ-GFQFHLD-  404 (485)
Q Consensus       335 ~~i~~~~-----v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~---~~~~~~~~~~v~v~i~-~~~~~~~-  404 (485)
                      +.|++..     ..++||||++..++..++++.+.-.....   ......|.   .+.|.. ...+.|.++ |..+.+. 
T Consensus       201 i~v~g~~~~~~~~~~iiDSGtt~~~lP~~~~~~i~~~~~~~---~~~~~~~~~~~~~~C~~-~p~i~f~f~~g~~~~vp~  276 (342)
T 3pvk_A          201 VEVSGKTINTDNVDVLLDSGTTITYLQQDLADQIIKAFNGK---LTQDSNGNSFYEVDCNL-SGDVVFNFSKNAKISVPA  276 (342)
T ss_dssp             EEETTEEEEEEEEEEEECTTCSSEEECHHHHHHHHHHTTCE---EEECTTSCEEEEECSCC-CSEEEEEESTTCEEEEEG
T ss_pred             EEECCEEecCCCceEEEeCCCCCeecCHHHHHHHHHHcCCe---ecccCCCceEEEEecCC-CCceEEEECCCCEEEEcH
Confidence            4556654     57999999999999999887663221100   00000110   011111 123344443 3322221 


Q ss_pred             -EEEcC---------------C-CCCCeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          405 -FFLLP---------------V-SGCDIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       405 -~~V~~---------------~-~~~dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                       -++++               . ..-..|||..||+.+-. ..|+.+++|.|...
T Consensus       277 ~~~~~~~~~~~g~~~~~C~~~i~~~~~~ilG~~fl~~~y~-vfD~~~~~igfA~~  330 (342)
T 3pvk_A          277 SEFAASLQGDDGQPYDKCQLLFDVNDANILGDNFLRSAYI-VYDLDDNEISLAQV  330 (342)
T ss_dssp             GGGEEC----------CEEESEEECTTCEECHHHHTTEEE-EEETTTTEEEEEEB
T ss_pred             HHheeeccccCCCcCCeeEEEEeeCCCeEeCHHHHhcEEE-EEECCCCEEEEEec
Confidence             01111               0 01357999999999986 79999999999753

>1j71_A Candidapepsin, aspartic proteinase; candida tropicalis aspartic protease, SAPT1, hydrolase; 1.80A {Candida tropicalis} SCOP: b.50.1.2

Probab=89.80  E-value=0.68  Score=43.64  Aligned_cols=98  Identities=18%  Similarity=0.244  Sum_probs=56.7

Q ss_pred             EEECCeE----EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccC-Ce--eeecceEeeeEEee-cceEEEEE--
Q 042094          335 GNLKKHG----VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADG-GV--ISSSGKCSHVPVNS-QGFQFHLD--  404 (485)
Q Consensus       335 ~~i~~~~----v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G-~~--~~~~~~~~~v~v~i-~~~~~~~~--  404 (485)
                      +.|++..    ..++||||++..++..++++.+.-.....    .. ..+ ..  +.|.. ...+.|.+ +|..+.+.  
T Consensus       202 i~v~g~~~~~~~~~iiDSGTt~~~lP~~~~~~l~~~~~~~----~~-~~~~~~~~~~C~~-~p~i~f~f~~g~~~~i~~~  275 (334)
T 1j71_A          202 INFDGTSVSTNADVVLDSGTTITYFSQSTADKFARIVGAT----WD-SRNEIYRLPSCDL-SGDAVFNFDQGVKITVPLS  275 (334)
T ss_dssp             EEETTEEEEEEEEEEECTTCSSEEECHHHHHHHHHHHTCE----EE-TTTTEEECSSSCC-CSEEEEEESTTCEEEEEGG
T ss_pred             EEECCEeccCCccEEEeCCCCcEecCHHHHHHHHHHcCCc----cc-CCCceEEEEcCCC-CCceEEEEcCCcEEEECHH
Confidence            4556654    46899999999999999887652211100    00 111 00  11111 12344444 34433321  


Q ss_pred             -----------EE--EcCCCCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 -----------FF--LLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 -----------~~--V~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                                 ++  +.+.  ...|||..||+.+-. ..|+.+++|.|..
T Consensus       276 ~y~~~~~~~~~C~~~i~~~--~~~iLG~~fl~~~y~-vfD~~~~~igfA~  322 (334)
T 1j71_A          276 ELILKDSDSSICYFGISRN--DANILGDNFLRRAYI-VYDLDDKTISLAQ  322 (334)
T ss_dssp             GGEEECSSSSCEEESEEEC--TTCEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             HheeecCCCCeeEEEEeEC--CCcEEChHhhccEEE-EEECCCCEEEEEe
Confidence                       11  1111  258999999999986 7999999999975

>1htr_B Gastricsin; aspartyl protease; 1.62A {Homo sapiens} SCOP: b.50.1.2 PDB: 1avf_A

Probab=89.15  E-value=0.44  Score=44.88  Aligned_cols=94  Identities=15%  Similarity=0.245  Sum_probs=57.7

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecc--eEeeeEEeecceEEEEE-----------EE-
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSG--KCSHVPVNSQGFQFHLD-----------FF-  406 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~--~~~~v~v~i~~~~~~~~-----------~~-  406 (485)
                      ..++||||++..++..++++.+.-.....     ...+|.. +.|..  ....+.|.++|..+.+.           ++ 
T Consensus       212 ~~aiiDSGTt~~~lp~~~~~~l~~~~~~~-----~~~~g~~~~~C~~~~~~P~i~f~f~g~~~~i~~~~y~~~~~g~C~~  286 (329)
T 1htr_B          212 CQAIVDTGTSLLTVPQQYMSALLQATGAQ-----EDEYGQFLVNCNSIQNLPSLTFIINGVEFPLPPSSYILSNNGYCTV  286 (329)
T ss_dssp             EEEEECTTCCSEEEEGGGHHHHHHHHTCE-----ECTTSCEEECGGGGGGSCCEEEEETTEEEEECHHHHEEECSSCEEE
T ss_pred             ceEEEecCCccEECCHHHHHHHHHHhCCe-----ecCCCeEEEeCCCcccCCcEEEEECCEEEEECHHHhcccCCCEEEE
Confidence            57999999999999998887663221100     0112221 12211  12346677777655432           22 


Q ss_pred             -EcCC-----CCC-CeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          407 -LLPV-----SGC-DIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       407 -V~~~-----~~~-dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                       +.+.     .+. ..|||..||+.+-. ..|+.+++|-|..
T Consensus       287 ~~~~~~~~~~~~~~~~iLG~~fl~~~yv-vfD~~~~~igfa~  327 (329)
T 1htr_B          287 GVEPTYLSSQNGQPLWILGDVFLRSYYS-VYDLGNNRVGFAT  327 (329)
T ss_dssp             SEEEECCCCTTSSCEEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             EEEECCCCCCCCCceEEEChHHhccEEE-EEECCCCEEEEEe
Confidence             2121     122 58999999999986 7999999998864

>1bxo_A Protein (penicillopepsin); hydrolase, phosphonate inhibitors, macrocycle; HET: MAN PP7; 0.95A {Penicillium janthinellum} SCOP: b.50.1.2 PDB: 1apu_E* 1apv_E* 1apw_E* 1apt_E* 1bxq_A* 1ppk_E* 1ppl_E* 1ppm_E* 2wea_A* 2web_A* 2wec_A* 2wed_A* 3app_A

Probab=89.08  E-value=0.73  Score=43.19  Aligned_cols=98  Identities=20%  Similarity=0.286  Sum_probs=59.4

Q ss_pred             eEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecceEeeeEEeecceEEEEE--------------
Q 042094          340 HGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSGKCSHVPVNSQGFQFHLD--------------  404 (485)
Q Consensus       340 ~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~~~~~v~v~i~~~~~~~~--------------  404 (485)
                      ....++||||++..++..++++.+.-.....   .....+|.. +.|......+.|.++|..+.+.              
T Consensus       206 ~~~~aiiDSGTs~~~lP~~~~~~l~~~i~~a---~~~~~~g~~~~~C~~~~P~i~f~fgg~~~~l~~~~~~~~~~~~~~~  282 (323)
T 1bxo_A          206 DGFSGIADTGTTLLLLDDSVVSQYYSQVSGA---QQDSNAGGYVFDCSTNLPDFSVSISGYTATVPGSLINYGPSGDGST  282 (323)
T ss_dssp             EEEEEEECTTCSSEEECHHHHHHHHTTSTTC---EEETTTTEEEECTTCCCCCEEEEETTEEEEECHHHHEEEECSSSSC
T ss_pred             CCceEEEeCCCCceeCCHHHHHHHHHhCCCc---eEcCcCCEEEEECCCCCceEEEEECCEEEEECHHHeEEeccCCCCe
Confidence            3467999999999999999988764322100   001111211 1222222346666666654431              


Q ss_pred             EE--EcCCC-CCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 FF--LLPVS-GCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 ~~--V~~~~-~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      ++  +.+.. ....|||..||+.+-. ..|+.+++|-|..
T Consensus       283 C~~~i~~~~~~~~~ILG~~fl~~~y~-vfD~~~~riGfA~  321 (323)
T 1bxo_A          283 CLGGIQSNSGIGFSIFGDIFLKSQYV-VFDSDGPQLGFAP  321 (323)
T ss_dssp             EEESEEECTTCSSEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             EEEEEECCCCCCcEEEChHHHcCEEE-EEECCCCEEEEec
Confidence            11  11111 2358999999999986 7999999998864

>2qzx_A Candidapepsin-5; aspartic proteinase, aspartyl protease, CL PAIR of basic residues, glycoprotein, protease, secreted; HET: STA; 2.50A {Candida albicans}

Probab=88.99  E-value=0.46  Score=44.99  Aligned_cols=104  Identities=15%  Similarity=0.288  Sum_probs=58.7

Q ss_pred             EEECCeE----EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccC-C-eeeecceEeeeEEee-cceEEEEE--E
Q 042094          335 GNLKKHG----VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADG-G-VISSSGKCSHVPVNS-QGFQFHLD--F  405 (485)
Q Consensus       335 ~~i~~~~----v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G-~-~~~~~~~~~~v~v~i-~~~~~~~~--~  405 (485)
                      +.|++..    ..++||||++..++..++++.+.-.....  ....-..+ . .+.|.. ...+.|.+ +|..+.+.  -
T Consensus       202 i~v~g~~~~~~~~aiiDSGTt~~~lP~~~~~~l~~~~~~~--~~~~~~~~~~~~~~C~~-~p~i~f~f~~g~~~~i~~~~  278 (342)
T 2qzx_A          202 VNVRGRNVDANTNVLLDSGTTISYFTRSIVRNILYAIGAQ--MKFDSAGNKVYVADCKT-SGTIDFQFGNNLKISVPVSE  278 (342)
T ss_dssp             EEETTEEEEEEEEEEECTTCSSEEECHHHHHHHHHHHTCE--EEECTTSCEEEEECTTC-CCEEEEEETTTEEEEEEGGG
T ss_pred             EEECCEecCCCcCEEEeCCCCCEEcCHHHHHHHHHHhCCe--eeeccCCCcEEEEECCC-CCcEEEEECCCcEEEEcHHH
Confidence            4556654    46899999999999999888653221100  00000000 0 111111 23445555 45444332  1


Q ss_pred             EEcC---------------C-CCCCeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          406 FLLP---------------V-SGCDIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       406 ~V~~---------------~-~~~dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                      ++++               . .....|||..||+.+-. ..|+.+++|.|...
T Consensus       279 ~~~~~~~~~~~~~~~C~~~i~~~~~~iLG~~fl~~~y~-vfD~~~~~igfA~~  330 (342)
T 2qzx_A          279 FLFQTYYTSGKPFPKCEVRIRESEDNILGDNFLRSAYV-VYNLDDKKISMAPV  330 (342)
T ss_dssp             GEECCBCTTSCBCSSEEESEEECSSCEECHHHHTTEEE-EEETTTTEEEEEEB
T ss_pred             hcccccccCCCCCCccEEEEecCCCcEeChHhhhcEEE-EEECCCCEEEEEee
Confidence            1111               0 01258999999999986 79999999999753

>1ibq_A Aspergillopepsin; aspartic proteinase, hydrolase; HET: MAN; 2.14A {Aspergillus phoenicis} SCOP: b.50.1.2

Probab=88.29  E-value=1.3  Score=41.44  Aligned_cols=96  Identities=20%  Similarity=0.275  Sum_probs=57.5

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCcc-ccccceEEEEccCC-eeeecceEeeeEEeecceEEEEE--------------
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPV-TTTTQFQVTVADGG-VISSSGKCSHVPVNSQGFQFHLD--------------  404 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~-~~~~~~~v~~a~G~-~~~~~~~~~~v~v~i~~~~~~~~--------------  404 (485)
                      ...++||||++..++..++++.+.-.. .....    ..+|. .+.|......+.|.++|..+.+.              
T Consensus       208 ~~~aiiDSGTt~~~lP~~~~~~i~~~i~~a~~~----~~~g~~~~~C~~~~P~i~f~fgg~~~~i~~~~~~~~~~~~~~~  283 (325)
T 1ibq_A          208 GFSAIADTGTTLILLDDEIVSAYYEQVSGAQES----YEAGGYVFSCSTDLPDFTVVIGDYKAVVPGKYINYAPVSTGSS  283 (325)
T ss_dssp             CEEEEECTTCCSEEECHHHHHHHHTTSTTCBCC----SSSSSCEEETTCCCCCEEEEETTEEEEECHHHHEEEESSTTCS
T ss_pred             CceEEEeCCCCcEeCCHHHHHHHHHhCCCceEc----CcCCeEEEEcCCCCCcEEEEECCEEEEECHHHhcccccCCCCC
Confidence            467999999999999999888763322 10000    00111 11222122345556666544321              


Q ss_pred             -EE--EcCCC-CCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 -FF--LLPVS-GCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 -~~--V~~~~-~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                       ++  +.+.. ....|||..||+.+-. ..|+.+++|-|..
T Consensus       284 ~C~~~i~~~~~~~~~iLG~~fl~~~y~-vfD~~~~~igfA~  323 (325)
T 1ibq_A          284 TCYGGIQSNSGLGLSILGDVFLKSQYV-VFNSEGPKLGFAA  323 (325)
T ss_dssp             EEEESEEECTTTCSEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             eEEEEEEcCCCCCceEEChHHhcCEEE-EEECCCCEEEeee
Confidence             11  11211 2358999999999986 7999999998864

>3aup_A SBG7S, BG, basic 7S globulin; pepsin-like fold, plant protein; 1.91A {Glycine max}

Probab=88.23  E-value=1  Score=43.67  Aligned_cols=25  Identities=28%  Similarity=0.480  Sum_probs=22.8

Q ss_pred             CeeechhHHhhcCCeEEEccCcEEEE
Q 042094          414 DIVLGAEWLRSLGAILWDFSKLTMQF  439 (485)
Q Consensus       414 dvILG~dwL~~~~~i~id~~~~~~~~  439 (485)
                      ..|||..||+.+-. ..|..+++|-|
T Consensus       358 ~~ILG~~fl~~~yv-vfD~~~~rIGf  382 (403)
T 3aup_A          358 EITLGARQLEENLV-VFDLARSRVGF  382 (403)
T ss_dssp             SEEECHHHHTTSCE-EEETTTTEEEE
T ss_pred             cEEEChHHhcCeEE-EEECCCCEEEE
Confidence            57999999999986 79999999988

>1mpp_A Pepsin; hydrolase(acid proteinase); 2.00A {Rhizomucor pusillus} SCOP: b.50.1.2 PDB: 2asi_A* 2rmp_A*

Probab=87.83  E-value=1  Score=42.94  Aligned_cols=96  Identities=19%  Similarity=0.290  Sum_probs=54.5

Q ss_pred             EEEE-EcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecc--eE-eeeEEee--c-----ceEEEEE-----
Q 042094          342 VTIL-IDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSG--KC-SHVPVNS--Q-----GFQFHLD-----  404 (485)
Q Consensus       342 v~aL-iDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~--~~-~~v~v~i--~-----~~~~~~~-----  404 (485)
                      ..++ ||||++..++..++++.+.-.....  .  ...+|.. +.|..  .. ..+.|.+  +     |..+.+.     
T Consensus       231 ~~ai~iDSGTt~~~lP~~~~~~l~~~~~~~--~--~~~~g~~~~~C~~~~~~~p~i~f~f~~g~~~~~g~~~~i~~~~y~  306 (361)
T 1mpp_A          231 AQAFTIDTGTNFFIAPSSFAEKVVKAALPD--A--TESQQGYTVPCSKYQDSKTTFSLVLQKSGSSSDTIDVSVPISKML  306 (361)
T ss_dssp             EEEEEEETTCCSEEEEHHHHHHHHHHHCTT--C--EEETTEEEEEHHHHTTCCCEEEEEEECTTCSSCEEEEEEEGGGGE
T ss_pred             CEEEEECCCCCceeCCHHHHHHHHHHhCCc--c--cCCCCcEEEECCCcccCCCcEEEEEEcCCcCCCCeEEEECHHHhE
Confidence            4689 9999999999998877652211110  0  0011111 11111  11 2344444  4     3333221     


Q ss_pred             ---------EE--EcCCCCCCeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          405 ---------FF--LLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       405 ---------~~--V~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                               ++  +.+..+...|||..||+.+-. ..|+.+++|.|...
T Consensus       307 ~~~~~~~~~C~~~i~~~~~~~~iLG~~fl~~~yv-vfD~~~~~igfa~~  354 (361)
T 1mpp_A          307 LPVDKSGETCMFIVLPDGGNQFIVGNLFLRFFVN-VYDFGKNRIGFAPL  354 (361)
T ss_dssp             EECSSSSCEEEESEEEESSSCCEEEHHHHTTEEE-EEETTTTEEEEEEB
T ss_pred             EecCCCCCeeEEEEEeCCCCCEEEChHHhccEEE-EEECCCCEEEEEEc
Confidence                     11  122223468999999999986 79999999999753

>3psg_A Pepsinogen; hydrolase(acid proteinase zymogen); 1.65A {Sus scrofa} SCOP: b.50.1.2 PDB: 2psg_A 4pep_A* 3pep_A* 1f34_A* 1psa_A* 1yx9_A 5pep_A 1flh_A 1qrp_E* 1psn_A* 1pso_E* 3utl_A

Probab=87.31  E-value=1.1  Score=42.86  Aligned_cols=95  Identities=18%  Similarity=0.280  Sum_probs=58.6

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecc--eEeeeEEeecceEEEEE-----------EE
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSG--KCSHVPVNSQGFQFHLD-----------FF  406 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~--~~~~v~v~i~~~~~~~~-----------~~  406 (485)
                      ...|+||||++..++..++++.+.-.....     ...+|.. +.|..  ....+.|.++|..+.+.           ++
T Consensus       253 ~~~aiiDTGTs~~~lP~~~~~~i~~~i~a~-----~~~~g~~~v~C~~~~~lP~i~f~~~g~~~~l~~~~yi~~~~~~C~  327 (370)
T 3psg_A          253 GCQAIVDTGTSLLTGPTSAIANIQSDIGAS-----ENSDGEMVISCSSIDSLPDIVFTIDGVQYPLSPSAYILQDDDSCT  327 (370)
T ss_dssp             CEEEEECTTCCSEEEEHHHHHHHHHHTTCE-----ECTTCCEECCGGGGGGCCCEEEEETTEEEEECHHHHEEECSSCEE
T ss_pred             CceEEEcCCCCcEECCHHHHHHHHHHhCCc-----ccCCCcEEEECCCcccCCcEEEEECCEEEEECHHHhcccCCCEEE
Confidence            357999999999999998887763221110     0122221 12211  12356777777765542           11


Q ss_pred             --E--cCC--CCC-CeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          407 --L--LPV--SGC-DIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       407 --V--~~~--~~~-dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                        +  .+.  ..- -.|||..||+.+-. ..|+.+++|-|-.
T Consensus       328 ~~~~~~~~~~~~~~~~ILG~~Fl~~~y~-vfD~~~~riGfA~  368 (370)
T 3psg_A          328 SGFEGMDVPTSSGELWILGDVFIRQYYT-VFDRANNKVGLAP  368 (370)
T ss_dssp             ESEEEECCCTTSCCEEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             EEEEeCCCCCCCCCcEEeChHHhcceEE-EEECCCCEEEEEE
Confidence              1  111  112 38999999999986 7999999998864

>1oew_A Endothiapepsin; hydrolase, aspartic proteinase mechanism, atomic resolution, succinimide, anisotropic refinement; HET: SUI; 0.9A {Cryphonectria parasitica} SCOP: b.50.1.2 PDB: 1gkt_A* 1gvt_A* 1gvv_A* 1gvw_A* 1gvx_A* 1gvu_A* 1oex_A* 2jji_A* 2jjj_A* 2vs2_A* 3uri_A* 3urj_A* 3url_A* 3pww_A* 1e80_E* 1e81_E* 1e82_E* 1e5o_E* 1eed_P* 1epl_E* ...

Probab=85.97  E-value=2.4  Score=39.71  Aligned_cols=97  Identities=13%  Similarity=0.207  Sum_probs=57.7

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecceEeeeEEeecceEEEEE---------------
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSGKCSHVPVNSQGFQFHLD---------------  404 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~~~~~v~v~i~~~~~~~~---------------  404 (485)
                      ...++||||++..++..++++.+.-.....   .....+|.. +.|......+.|.++|..+.+.               
T Consensus       212 ~~~aiiDSGTt~~~lP~~~~~~l~~~i~~a---~~~~~~g~~~~~C~~~~P~i~f~fgg~~~~ip~~~~~~~~~~~~~~~  288 (329)
T 1oew_A          212 SIDGIADTGTTLLYLPATVVSAYWAQVSGA---KSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSS  288 (329)
T ss_dssp             EEEEEECTTCCSEEECHHHHHHHHTTSTTC---EEETTTTEEEEETTCCCCCEEEEETTEEEEECHHHHEEEESSTTCSE
T ss_pred             CceEEEeCCCCCEECCHHHHHHHHHhCCCc---EEcCCCCEEEEECCCCCCcEEEEECCEEEEECHHHeeeeecCCCCCe
Confidence            457999999999999999988764322100   000011111 1222222345566666554321               


Q ss_pred             EE--EcCCC-CCCeeechhHHhhcCCeEEEc-cCcEEEEEE
Q 042094          405 FF--LLPVS-GCDIVLGAEWLRSLGAILWDF-SKLTMQFTW  441 (485)
Q Consensus       405 ~~--V~~~~-~~dvILG~dwL~~~~~i~id~-~~~~~~~~~  441 (485)
                      ++  +.+.. ....|||..||+.+-. ..|+ .+++|-|..
T Consensus       289 C~~~i~~~~~~~~~iLG~~fl~~~y~-vfD~~~~~riGfA~  328 (329)
T 1oew_A          289 CFGGIQSSAGIGINIFGDVALKAAFV-VFNGATTPTLGFAS  328 (329)
T ss_dssp             EEESEEESTTTSSEEECHHHHTTEEE-EEECSSSCEEEEEE
T ss_pred             EEEEEEeCCCCCceEEChHHhcCEEE-EEECCCCceEEEec
Confidence            11  11111 2468999999999986 7999 999998864

>1t6e_X Xylanase inhibitor; two beta-barrel domain structure, hydrolase inhibitor; 1.70A {Triticum aestivum} SCOP: b.50.1.2 PDB: 1t6g_A 2b42_A 3hd8_A

Probab=84.94  E-value=4.2  Score=38.90  Aligned_cols=28  Identities=18%  Similarity=0.348  Sum_probs=24.8

Q ss_pred             CeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          414 DIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       414 dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                      -.|||..||+.+-. ..|..+++|-|...
T Consensus       345 ~~ILGd~fl~~~yv-vfD~~~~riGfA~~  372 (381)
T 1t6e_X          345 AVILGGAQMEDFVL-DFDMEKKRLGFSRL  372 (381)
T ss_dssp             SEEECHHHHTTEEE-EEETTTTEEEEEEC
T ss_pred             eEEEChHHhCCcEE-EEECCCCEEEEecc
Confidence            48999999999986 79999999999854

>3lpj_A Beta-secretase 1; alzheimer'S, aspartyl protease, hydrolase; HET: TLA Z75; 1.79A {Homo sapiens} PDB: 3lpi_A* 3lpk_A* 3ohf_A* 3ohh_A* 3r2f_A* 3skf_A* 3skg_A* 4fse_A* 2hiz_A* 2p83_A* 2va7_A* 2va5_A* 2va6_A*

Probab=84.41  E-value=0.43  Score=47.25  Aligned_cols=28  Identities=18%  Similarity=0.324  Sum_probs=25.0

Q ss_pred             CCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          413 CDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       413 ~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      ...|||..||+.+-. ..|+.+++|-|..
T Consensus       391 ~~~ILG~~fl~~~yv-vfD~~~~rIGfA~  418 (455)
T 3lpj_A          391 TGTVMGAVIMEGFYV-VFDRARKRIGFAV  418 (455)
T ss_dssp             SCEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             CcEEEChHHhCCeEE-EEECCCCEEEEEe
Confidence            468999999999996 7999999999974

>3c9x_A Trichoderma reesei aspartic protease; aspartic proteinase, aspartyl protease, hydrolase; 1.70A {Trichoderma reesei} PDB: 3c9y_A* 3emy_A*

Probab=83.85  E-value=3.8  Score=38.32  Aligned_cols=97  Identities=14%  Similarity=0.212  Sum_probs=56.8

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecceEeeeEEeecceEEEEE---------------
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSGKCSHVPVNSQGFQFHLD---------------  404 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~~~~~v~v~i~~~~~~~~---------------  404 (485)
                      ...++||||++..++..++++.+.-.....   .....+|.. +.|......+.|.++|..+.+.               
T Consensus       213 ~~~aiiDSGTt~~~lp~~~~~~i~~~i~~a---~~~~~~~~~~~~C~~~~P~i~f~f~g~~~~ip~~~~~~~~~~~~~~~  289 (329)
T 3c9x_A          213 SIDGIADTGTTLLLLDDNVVDAYYANVQSA---QYDNQQEGVVFDCDEDLPSFSFGVGSSTITIPGDLLNLTPLEEGSST  289 (329)
T ss_dssp             CEEEEECTTCCSEEECHHHHHHHHTTCTTC---EEETTTTEEEEETTCCCCCEEEEETTEEEEECGGGGEEEESSTTCSE
T ss_pred             CceEEEECCCCcEeCCHHHHHHHHHhCCCc---EEcCCCCEEEEECCCCCCcEEEEECCEEEEECHHHeeeeccCCCCCe
Confidence            468999999999999999888764322100   000011111 1222112345555555443321               


Q ss_pred             EE--EcCCC-CCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 FF--LLPVS-GCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 ~~--V~~~~-~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      ++  +.+.. ....|||..||+.+-. ..|+.+++|-|..
T Consensus       290 C~~~i~~~~~~~~~ILG~~fl~~~y~-vfD~~~~riGfA~  328 (329)
T 3c9x_A          290 CFGGLQSSSGIGINIFGDVALKAALV-VFDLGNERLGWAQ  328 (329)
T ss_dssp             EEESEEECTTTTSEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             EEEEEEcCCCCCcEEEChHHhccEEE-EEECCCCEEeEec
Confidence            11  11221 2458999999999986 7999999998864

>3vf3_A Beta-secretase 1; structure-based drug design, hydrolase-hydrolase inhibitor C; HET: 0GS; 1.48A {Homo sapiens} PDB: 2f3e_A* 2f3f_A* 1ym2_A* 3dv1_A* 3dv5_A* 3k5c_A* 3k5f_A* 3k5g_A* 3pi5_A* 3qbh_A* 3duy_A* 3veu_A* 3vg1_A* 4d83_A* 4d88_A* 4d89_A* 4d8c_A* 3msk_A* 3k5d_A* 1ym4_A* ...

Probab=83.01  E-value=0.5  Score=45.91  Aligned_cols=28  Identities=18%  Similarity=0.324  Sum_probs=25.0

Q ss_pred             CCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          413 CDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       413 ~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      ...|||..||+.+-. ..|+.+++|-|..
T Consensus       345 ~~~ILG~~fl~~~yv-vfD~~~~rIGfA~  372 (402)
T 3vf3_A          345 TGTVMGAVIMEGFYV-VFDRARKRIGFAV  372 (402)
T ss_dssp             SCEEECHHHHTTEEE-EEEGGGTEEEEEE
T ss_pred             CcEEEChHHhCCeEE-EEECCCCEEEEEe
Confidence            468999999999996 7999999999975

>2ewy_A Beta-secretase 2; BACE2, aspartic protease, hydrolase; HET: DBO; 3.10A {Homo sapiens}

Probab=82.63  E-value=2.2  Score=40.93  Aligned_cols=29  Identities=17%  Similarity=0.321  Sum_probs=25.4

Q ss_pred             CCeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          413 CDIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       413 ~dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                      ...|||..||+.+-. ..|+.+++|.|...
T Consensus       326 ~~~ILG~~fl~~~yv-vfD~~~~rIGfA~~  354 (383)
T 2ewy_A          326 NALVIGATVMEGFYV-IFDRAQKRVGFAAS  354 (383)
T ss_dssp             SCEEECHHHHTTEEE-EEETTTTEEEEEEC
T ss_pred             CcEEEChHHhCCeeE-EEECCCCeEEEEec
Confidence            358999999999986 79999999999753

>2fi2_A Zinc finger protein 42; SCAN domain, ZNF-42, MZF-1, homodimer, transcription factor, structural genomics, PSI, protein structure initiative; NMR {Homo sapiens} SCOP: a.28.3.2

Probab=80.93  E-value=1.7  Score=31.93  Aligned_cols=40  Identities=25%  Similarity=0.244  Sum_probs=34.7

Q ss_pred             ChHHHHHHHHhhhHHHHHHHHHhcCcccHHHHHHHHHHHH
Q 042094          165 PESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQE  204 (485)
Q Consensus       165 ~e~~~~~~f~~GL~~~i~~~v~~~~p~tl~~~~~~a~~~e  204 (485)
                      -|-..+.+|+.-||.+++..|..+.|.+-++++.++..+.
T Consensus        50 lElLVLEQFL~iLP~eiq~wV~~~~P~s~eeav~lvEdl~   89 (94)
T 2fi2_A           50 LELLVLEQFLGALPPEIQARVQGQRPGSPEEAAALVDGLR   89 (94)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHCCCSHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCcHHHHHHHHhcCCCcHHHHHHHHHHHH
Confidence            3445688999999999999999999999999999877654

>2qp8_A Beta-secretase 1; BACE1, protease, alternative splicing, aspartyl protease, glycoprotein, hydrolase, membrane, transmembrane, zymogen; HET: TAR SC7; 1.50A {Homo sapiens} SCOP: b.50.1.2 PDB: 2qk5_A* 2qmf_A* 2qmg_A* 2qmd_A* 4djx_A* 3l59_A* 3l5b_A* 3l5c_A* 3l58_A* 3l5d_A* 3l5f_A* 4dju_A* 4djv_A* 4djw_A* 3l5e_A* 4djy_A* 2zhv_A 2zhs_A 2zhr_A 2zhu_A ...

Probab=80.67  E-value=1.5  Score=42.39  Aligned_cols=28  Identities=18%  Similarity=0.324  Sum_probs=24.9

Q ss_pred             CCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          413 CDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       413 ~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      ...|||..||+.+-. ..|+.+++|-|..
T Consensus       338 ~~~ILG~~fl~~~yv-vfD~~~~rIGfA~  365 (395)
T 2qp8_A          338 TGTVMGAVIMEGFYV-VFDRARKRIGFAV  365 (395)
T ss_dssp             SCEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             CcEEEChHHhCCeeE-EEECCCCEEEEEe
Confidence            458999999999986 7999999999975

>1bxo_A Protein (penicillopepsin); hydrolase, phosphonate inhibitors, macrocycle; HET: MAN PP7; 0.95A {Penicillium janthinellum} SCOP: b.50.1.2 PDB: 1apu_E* 1apv_E* 1apw_E* 1apt_E* 1bxq_A* 1ppk_E* 1ppl_E* 1ppm_E* 2wea_A* 2web_A* 2wec_A* 2wed_A* 3app_A

Probab=80.11  E-value=3.5  Score=38.41  Aligned_cols=91  Identities=14%  Similarity=0.147  Sum_probs=55.0

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHh-----hcCCc-cc------cccceEEEEccCCeeeecceEeeeEEeec
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAK-----QYGCP-VT------TTTQFQVTVADGGVISSSGKCSHVPVNSQ  397 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~-----~l~l~-~~------~~~~~~v~~a~G~~~~~~~~~~~v~v~i~  397 (485)
                      ...+.+.|+.+.+.++|||||+...|...-+.     ..+.- ..      ...++.+..++|+.+.  |....=.|.++
T Consensus        16 ~Y~~~i~iG~Q~~~v~~DTGSs~lWv~~~~C~~~~c~~~~~y~~~~Ss~~~~~~~~~i~Yg~Gs~~~--G~~~~D~v~ig   93 (323)
T 1bxo_A           16 EYITPVTIGGTTLNLNFDTGSADLWVFSTELPASQQSGHSVYNPSATGKELSGYTWSISYGDGSSAS--GNVFTDSVTVG   93 (323)
T ss_dssp             CEEEEEEETTEEEEEEEETTCCCEEECBTTSCHHHHTTSCCBCHHHHCEEEEEEEEEEECTTSCEEE--EEEEEEEEEET
T ss_pred             EEEEEEEECCEEEEEEEeCCCcceEEecCCCCchhccCCCCCCcccCCcccCCCeEEEEeCCCCeEE--EEEEEEEEEEC
Confidence            46788889999999999999999988643221     11110 00      1235667777887443  33333357777


Q ss_pred             ceEEE-EEEEEcCC--------CCCCeeechhHH
Q 042094          398 GFQFH-LDFFLLPV--------SGCDIVLGAEWL  422 (485)
Q Consensus       398 ~~~~~-~~~~V~~~--------~~~dvILG~dwL  422 (485)
                      +.... ..|-+...        ...|=|||+-+-
T Consensus        94 ~~~v~~~~fg~~~~~~~~~~~~~~~~GilGLg~~  127 (323)
T 1bxo_A           94 GVTAHGQAVQAAQQISAQFQQDTNNDGLLGLAFS  127 (323)
T ss_dssp             TEEEEEEEEEEEEEECHHHHTCTTCSEEEECSCG
T ss_pred             CEEECcEEEEEEEecCcccccCCCCceEEEeCcc
Confidence            76533 33443321        357889987663

---

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	485
d2fmba_	104	EIAV protease {Equine infectious anemia virus [Tax	99.02
d2nmza1	99	Human immunodeficiency virus type 1 protease {Huma	98.61
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.54
d4fiva_	113	Feline immunodeficiency virus (FIV) protease {Feli	98.52
d1hvca_	203	Human immunodeficiency virus type 1 protease {Huma	98.45
d3ecga1	99	Human immunodeficiency virus type 2 (HIV-2) protea	98.38
d1nsoa_	107	Mason-Pfizer monkey virus protease {Simian retrovi	98.23
d2rspa_	124	Rous sarcoma virus protease {Rous sarcoma virus, s	97.77
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	97.77
d1hvca_	203	Human immunodeficiency virus type 1 protease {Huma	97.69
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.37
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.36
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	97.12
d2pmaa1	141	Uncharacterized protein LPG0085 {Legionella pneumo	96.94
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	95.76
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	95.33
d1izea_	323	Acid protease {Fungus (Aspergillus oryzae) [TaxId:	93.74
d1wkra_	340	Acid protease {Irpex lacteus (Polyporus tulipifera	93.22
d1bxoa_	323	Acid protease {Fungus (Penicillium janthinellum),	93.14
d1miqa_	373	Plasmepsin (a hemoglobin-degrading enzyme) {Plasmo	92.89
d1oewa_	330	Endothiapepsin {Chestnut blight fungus (Endothia p	92.42
d1eaga_	342	Acid protease {Yeast (Candida albicans) [TaxId: 54	92.4
d2bjua1	329	Plasmepsin (a hemoglobin-degrading enzyme) {Plasmo	92.38
d2fi2a1	92	Zinc finger protein 42 {Human (Homo sapiens) [TaxI	91.81
d1am5a_	324	Pepsin(ogen) {Atlantic cod (Gadus morhua) [TaxId:	91.43
d1y7qa1	96	Zinc finger protein 174 {Human (Homo sapiens) [Tax	91.01
d1j71a_	334	Acid protease {Yeast (Candida tropicalis) [TaxId:	90.86
d1t6ex_	381	Xylanase inhibitor TAXI-I {Wheat (Triticum aestivu	90.08
d3cmsa_	323	Chymosin (synonym: renin) {Cow (Bos taurus) [TaxId	90.07
d1dpja_	329	Acid protease {Baker's yeast (Saccharomyces cerevi	89.26
d3psga_	370	Pepsin(ogen) {Pig (Sus scrofa) [TaxId: 9823]}	88.89
g1htr.1	372	Pepsin(ogen) {Human (Homo sapiens), progastricsin	88.47
d1hrna_	337	Chymosin (synonym: renin) {Human (Homo sapiens) [T	86.42
d1smra_	335	Chymosin (synonym: renin) {Mouse (Mus musculus) [T	86.31
d2apra_	325	Acid protease {Bread mold (Rhizopus chinensis) [Ta	85.88
g1lya.1	338	Cathepsin D {Human (Homo sapiens) [TaxId: 9606]}	83.5
d1mppa_	357	Pepsin {Mucor pusillus [TaxId: 4840]}	82.28
d1qdma2	337	Plant acid proteinase, phytepsin {Barley (Hordeum	81.18
d2qp8a1	387	beta-secretase (memapsin) {Human (Homo sapiens) [T	80.47

>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=99.02  E-value=1.6e-09  Score=81.78  Aligned_cols=94  Identities=14%  Similarity=0.222  Sum_probs=70.6

Q ss_pred             CeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEc
Q 042094          329 NTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLL  408 (485)
Q Consensus       329 ~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~  408 (485)
                      +...+.++|+|+.+.+|+||||.+|+|+..-+...........+..+ .+.|..+..  ....+.+.+.|......++|.
T Consensus         7 ~RP~~~i~I~Gq~v~~LLDTGAD~TVI~~~~~p~~~~~~~~~~~~~i-gg~g~~~~~--~~~~v~i~~~g~~~~~~~lV~   83 (104)
T d2fmba_           7 KRPTTIVLINDTPLNVLLDTGADTSVLTTAHYNRLKYRGRKYQGTGI-GGVGGNVET--FSTPVTIKKKGRHIKTRMLVA   83 (104)
T ss_dssp             SCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHCSSCCCCEECCCE-EETTEEECC--EEEEEEEEETTEEEEEEEEEE
T ss_pred             cCeEEEEEECCEEEEEEEeCCCCeEEEcccccCccCCCCCCcceeEE-EEecceEEE--EEEEEEEEECCeEEEEEEEEC
Confidence            34578899999999999999999999999998876544333333333 334444433  234588899998888899998


Q ss_pred             CCCCCCeeechhHHhhcCC
Q 042094          409 PVSGCDIVLGAEWLRSLGA  427 (485)
Q Consensus       409 ~~~~~dvILG~dwL~~~~~  427 (485)
                      |..  .-|||+|.|.++|.
T Consensus        84 p~P--vnLlGRdlL~qlG~  100 (104)
T d2fmba_          84 DIP--VTILGRDILQDLGA  100 (104)
T ss_dssp             SCS--SCEECHHHHHHHTC
T ss_pred             CCC--cceecHHHHHHhCC
Confidence            832  34999999999996

>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=98.61  E-value=3.4e-07  Score=65.25  Aligned_cols=92  Identities=14%  Similarity=0.216  Sum_probs=71.5

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcC
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLP  409 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~  409 (485)
                      ...++++|+|+.+.||+||||..+++.     .++|+... .|-.+. +-|..+.+.. +..+.+++.|+...-+++|-|
T Consensus         8 RP~vtvkIgGq~~eaLLDTGADdTVle-----ei~lpg~W-kPk~Ig-GIGGfikVrq-Yd~i~iei~g~k~~gtVLVgp   79 (99)
T d2nmza1           8 RPLVTIKIGGQLKEALLDTGADDTVIE-----EMSLPGRW-KPKMIG-GIGGFIKVRQ-YDQIIIEIAGHKAIGTVLVGP   79 (99)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEE-----SCCCCSCC-EEEEEE-ETTEEEEEEE-EEEEEEEETTEEEEEEEEEES
T ss_pred             CCeEEEEECCEEEEEeeccCCCceEEe-----cccCCCCC-CceEEE-eccceEEEEE-eCceEEEECCcEEEEEEEECC
Confidence            356889999999999999999999984     46776433 333344 4455666544 468999999999999999998


Q ss_pred             CCCCCeeechhHHhhcCCeEEEc
Q 042094          410 VSGCDIVLGAEWLRSLGAILWDF  432 (485)
Q Consensus       410 ~~~~dvILG~dwL~~~~~i~id~  432 (485)
                      ..  =-|+|++.|.++|. .+||
T Consensus        80 TP--vNIiGRN~Ltq~Gc-tLnf   99 (99)
T d2nmza1          80 TP--ANIIGRNLLTQIGA-TLNF   99 (99)
T ss_dssp             CS--SCEECHHHHTTTTC-EEEC
T ss_pred             CC--ccEEcccchhhcCc-eecC
Confidence            42  45789999999997 7876

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=98.54  E-value=7.2e-09  Score=54.52  Aligned_cols=22  Identities=32%  Similarity=0.786  Sum_probs=18.3

Q ss_pred             hhCCceeecCCCCCCCCcCCCc
Q 042094          268 RAKGLCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       268 ~~~~~Cf~Cg~~GH~a~~C~~~  289 (485)
                      ++...|||||+.||.+++|+.+
T Consensus         4 r~~ikCfNCGkeGH~ar~CrAP   25 (29)
T d1nc8a_           4 RKVIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCCCBCTTTSCBSSCGGGCCSS
T ss_pred             cceeEeecCCccchhhhhccCc
Confidence            3457799999999999999544

>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=98.52  E-value=2.1e-07  Score=70.56  Aligned_cols=95  Identities=11%  Similarity=0.071  Sum_probs=63.5

Q ss_pred             CeEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceE-----EEE
Q 042094          329 NTMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQ-----FHL  403 (485)
Q Consensus       329 ~~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~-----~~~  403 (485)
                      +...+.++|+|+.+.+||||||.+|+|+..-+....-  .+..+..+... |..+... .+..+.+++.+..     ...
T Consensus         9 ~RP~v~v~I~Gq~v~~LLDTGAD~TVi~~~d~p~~~~--~~~~~~~~~GI-GG~~~v~-~~~~v~i~~~~~~~~gtvl~g   84 (113)
T d4fiva_           9 KRPEILIFVNGYPIKFLLDTGADITILNRRDFQVKNS--IENGRQNMIGV-GGGKRGT-NYINVHLEIRDENYKTQCIFG   84 (113)
T ss_dssp             SCCEEEEEETTEEEEEEECTTCSSCEEEGGGCCCTTC--EEEEEEEEECS-SCEEEEE-EEEEEEEEECCTTSCCCEEEE
T ss_pred             cCCeEEEEECCEEEEEEEcCCCCcEEEeccccCCCCC--CCCCCCeEEec-CeEEeee-EEceEEEEEcCCeEeEEEEEc
Confidence            3467889999999999999999999998765443211  11122344444 4445543 3467888887654     334


Q ss_pred             EEEEcCCCCCC-eeechhHHhhcCC
Q 042094          404 DFFLLPVSGCD-IVLGAEWLRSLGA  427 (485)
Q Consensus       404 ~~~V~~~~~~d-vILG~dwL~~~~~  427 (485)
                      .+.|+|...++ -|||+|+|.++|.
T Consensus        85 ~~pvlp~~~~p~nllGRd~LtqlG~  109 (113)
T d4fiva_          85 NVCVLEDNSLIQPLLGRDNMIKFNI  109 (113)
T ss_dssp             EEEEETTCCCSSCEECHHHHHHTTC
T ss_pred             cccccCCCCCcCCEEChhhhHHhCC
Confidence            55566655443 6899999999996

>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=98.45  E-value=6.9e-07  Score=72.15  Aligned_cols=107  Identities=14%  Similarity=0.179  Sum_probs=79.5

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcC
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLP  409 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~  409 (485)
                      ...+.++|+|+.+.||+||||.++++.     .++++... .|..+... |..+.+.. +..+.+++.|+....+++|.|
T Consensus         8 RP~VtVkIgGQ~~eaLLDTGADDTVLe-----~inLpG~W-kPkiIGGI-GGfIkVrq-Y~~V~IeI~gkk~~gTVLVgP   79 (203)
T d1hvca_           8 RPLVTIRIGGQLKEALLDTGADDTVLE-----EMNLPGKW-KPKMIGGI-GGFIKVRQ-YDQILIEICGHKAIGTVLVGP   79 (203)
T ss_dssp             CCEEEEESSSCEEEEEECTTCSSEEEE-----CCCCSSCE-EEEEEEET-TEEEEEEE-EEEEEEEETTEEEEEEEEEES
T ss_pred             CCeEEEEECCEEEEEEecCCCCceEEe-----cccCCCCC-cccEEEec-CceEEEEE-eCCEEEEECCcEEEEEEEECC
Confidence            457889999999999999999999984     36666433 34344444 45556544 468999999999999999999


Q ss_pred             CCCCCeeechhHHhhcCCeEEEcc-----------CcEEEEEECCeEEE
Q 042094          410 VSGCDIVLGAEWLRSLGAILWDFS-----------KLTMQFTWKGQTVQ  447 (485)
Q Consensus       410 ~~~~dvILG~dwL~~~~~i~id~~-----------~~~~~~~~~~~~~~  447 (485)
                      .  .--|||+|.|.++|. .++|.           .-.++.+.+|+...
T Consensus        80 T--PvNIIGRNlLtqlG~-tLnFpG~dGP~i~~wqrp~vt~ki~gq~~e  125 (203)
T d1hvca_          80 T--PVNIIGRNLLTQIGC-TLNFGGSSGPQITLWQRPLVTIKIGGQLKE  125 (203)
T ss_dssp             C--SSCEECHHHHGGGTC-EEECTTTTSSEECSSSCCEEEEEETTEEEE
T ss_pred             C--Cccccchhhhhhhhh-eeecccCCCCceeecccceEEEecchhHHH
Confidence            3  356789999999997 88872           34455566666543

>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=98.38  E-value=3.5e-06  Score=59.79  Aligned_cols=91  Identities=13%  Similarity=0.161  Sum_probs=70.0

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcC
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLP  409 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~  409 (485)
                      ...+.++|+|+.+.||+||||..+++.     .++|+... .|-.+. .-|..+.+.. +..+++++.|+...-+++|-|
T Consensus         8 RP~vtvkIgGq~~eaLLDTGADdTVle-----~i~lpg~W-kPk~iG-GIGGfikVrq-Yd~i~Ieicg~k~~gtVLvgp   79 (99)
T d3ecga1           8 RPVVTAYIEGQPVEVLLDTGADDSIVA-----GIELGNNY-SPKIVG-GIGGFINTKE-YKNVEIEVLNKKVRATIMTGD   79 (99)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEC-----SCCCCSCC-EEEEEE-ETTEEEEEEE-EEEEEEEETTEEEEEEEEEEC
T ss_pred             CCeEEEEECCEEeeeecccCCCceeee-----ccCCCCCC-cceEEE-EeeeeEEEEE-eCcEEEEECCcEEEEEEEeCC
Confidence            356889999999999999999999984     56776433 343444 4455666544 567999999999999999977


Q ss_pred             CCCCCeeechhHHhhcCCeEEE
Q 042094          410 VSGCDIVLGAEWLRSLGAILWD  431 (485)
Q Consensus       410 ~~~~dvILG~dwL~~~~~i~id  431 (485)
                      ..  =-|+|++.|.+.|. .+|
T Consensus        80 TP--vNIiGRNlLtqlGc-tLn   98 (99)
T d3ecga1          80 TP--INIFGRNILTALGM-SLN   98 (99)
T ss_dssp             CS--SCEECHHHHHHTTC-EEE
T ss_pred             CC--ceEEccchhhhhCc-ccC
Confidence            54  45789999999997 665

>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=98.23  E-value=5.9e-07  Score=67.64  Aligned_cols=92  Identities=15%  Similarity=0.092  Sum_probs=56.0

Q ss_pred             EEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecc--eEEEEEEEEc
Q 042094          331 MRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQG--FQFHLDFFLL  408 (485)
Q Consensus       331 ~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~--~~~~~~~~V~  408 (485)
                      ..+.+.|+|+.+.+||||||.+|+|+..-+.. +.+.. ..+..+... |....+... ..+.....+  ....+..+|+
T Consensus        10 P~~~v~I~G~~v~~LLDTGAD~TVI~~~~~p~-~wp~~-~~~~~~~Gi-Gg~~~~~~~-~~~l~~~~~~~~~~~~~p~vv   85 (107)
T d1nsoa_          10 PSLTLWLDDKMFTGLINTGADVTIIKLEDWPP-NWPIT-DTLTNLRGI-GQSNNPKQS-SKYLTWRDKENNSGLIKPFVI   85 (107)
T ss_dssp             SCEEEEETTEEEEECCCSSCSSCBCCGGGSCT-TSCCC-CCEEEECSS-SEEEECCCB-CCCEEEEETTTEEEEECCBBC
T ss_pred             cEEEEEECCEEEEeeecCCCCcEEEeccccCC-CCCcC-cCccEEEEe-cCeeeEEEe-eeeEEEEeCCCceEEEcceEC
Confidence            45678899999999999999999998775432 22211 122333333 444443332 334334333  3344444566


Q ss_pred             CCCCCCeeechhHHhhcCC
Q 042094          409 PVSGCDIVLGAEWLRSLGA  427 (485)
Q Consensus       409 ~~~~~dvILG~dwL~~~~~  427 (485)
                      +..... |||+|.|.++|.
T Consensus        86 ~~~Pvn-llGRd~L~qlg~  103 (107)
T d1nsoa_          86 PNLPVN-LWGRDLLSQMKI  103 (107)
T ss_dssp             TTCCCC-BCCHHHHHHHHT
T ss_pred             CCCCcC-cccHHHHHHhCC
Confidence            644443 899999999985

>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=97.77  E-value=1.2e-05  Score=61.58  Aligned_cols=92  Identities=20%  Similarity=0.188  Sum_probs=48.4

Q ss_pred             EECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCee-eecceEeeeEEeec----ceEEEEEEEEcCC
Q 042094          336 NLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVI-SSSGKCSHVPVNSQ----GFQFHLDFFLLPV  410 (485)
Q Consensus       336 ~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~-~~~~~~~~v~v~i~----~~~~~~~~~V~~~  410 (485)
                      +++|+.+.+|+||||..|+|+..-+.. ..+..+..+..+.+.+|..- ........+.+...    +..+.+..+|.+.
T Consensus        26 k~~g~~i~~LLDTGAD~TVI~~~dwp~-~Wp~~~~~~~~i~GIGg~~~v~~~~~~~~~~~~~~~~~~~~~~~~~p~V~~t  104 (124)
T d2rspa_          26 KQRSVYITALLDSGADITIISEEDWPT-DWPVMEAANPQIHGIGGGIPMRKSRDMIELGVINRDGSLERPLLLFPAVAMV  104 (124)
T ss_dssp             SCSEEEEEEEECTTCSSCEEETTTSCT-TSCEEECC---------CCCEEEESSCEEEEEECTTSCBCCCEEECCEEESC
T ss_pred             eeCCEEEEEEEcCCCCeEEEcCCccCC-CCccCCCCCCEEEEcCCceeeEEeeeeEEEeeEecCCceeeeEEEecCCCCC
Confidence            346788999999999999998765432 22333333334544444322 11111122223221    1234444555544


Q ss_pred             CCCCeeechhHHhhcCCeEEE
Q 042094          411 SGCDIVLGAEWLRSLGAILWD  431 (485)
Q Consensus       411 ~~~dvILG~dwL~~~~~i~id  431 (485)
                      .  .-|+|+|.|.++|. .+.
T Consensus       105 P--vni~GRdiL~qlG~-tLt  122 (124)
T d2rspa_         105 R--GSILGRDCLQGLGL-RLT  122 (124)
T ss_dssp             S--SEEECHHHHHHTTC-EEE
T ss_pred             c--ccEECHhHHHHhCC-EEe
Confidence            3  46999999999997 453

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=97.77  E-value=3.2e-06  Score=42.14  Aligned_cols=19  Identities=26%  Similarity=0.677  Sum_probs=16.7

Q ss_pred             CceeecCCCCCCCCcCCCc
Q 042094          271 GLCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~~  289 (485)
                      ..||.||+.||+.++|+..
T Consensus         3 pvcfscgktghikkdck~e   21 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CEEEecCCcccchhhhhhh
Confidence            4699999999999999653

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

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

Probab=97.69  E-value=0.00026  Score=56.91  Aligned_cols=92  Identities=14%  Similarity=0.198  Sum_probs=71.8

Q ss_pred             eEEEEEEECCeEEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeecceEeeeEEeecceEEEEEEEEcC
Q 042094          330 TMRLKGNLKKHGVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLDFFLLP  409 (485)
Q Consensus       330 ~~~~~~~i~~~~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~~~V~~  409 (485)
                      ...++++|+|+...||+||||..+++     +.++|+-. -.|-.+. .-|..+.+.. +..+++++-|+...-+++|-|
T Consensus       112 rp~vt~ki~gq~~ealldtgaddtv~-----e~~~lpgr-wkpk~ig-giggfikvrq-y~~v~iei~g~k~~gtvlvgp  183 (203)
T d1hvca_         112 RPLVTIKIGGQLKEALLDTGADDTVL-----EEMSLPGR-WKPKMIG-GIGGFIKVRQ-YDQILIEICGHKAIGTVLVGP  183 (203)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEE-----ESCCCSSC-CEEEEEE-ETTEEEEEEE-EEEEEEEETTEEEEEEEEEEC
T ss_pred             cceEEEecchhHHHHHhcccCCceEE-----ecccCCCC-CcceEEE-Eeccccceee-EccEEEEECCCEEEEEEEECC
Confidence            45789999999999999999999987     45777743 2343343 4455666544 578999999999999999988


Q ss_pred             CCCCCeeechhHHhhcCCeEEEc
Q 042094          410 VSGCDIVLGAEWLRSLGAILWDF  432 (485)
Q Consensus       410 ~~~~dvILG~dwL~~~~~i~id~  432 (485)
                      ..  =-|+|++.|.+.|. .+||
T Consensus       184 tp--~niigrn~ltq~g~-tlnf  203 (203)
T d1hvca_         184 TP--VNIIGRNLLTQIGC-TLNF  203 (203)
T ss_dssp             CS--SCEECHHHHTTTTC-EEEC
T ss_pred             CC--ceEEcccchhhcCc-cccC
Confidence            54  45789999999997 7776

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=97.37  E-value=2.6e-05  Score=47.29  Aligned_cols=17  Identities=35%  Similarity=0.944  Sum_probs=9.6

Q ss_pred             ceeecCCCCCCCCcCCC
Q 042094          272 LCFNCDEQFKPGHRCKA  288 (485)
Q Consensus       272 ~Cf~Cg~~GH~a~~C~~  288 (485)
                      .||+||+.||++++||.
T Consensus         3 ~C~~Cg~~GH~~~~Cp~   19 (42)
T d2exfa1           3 KCFNCGKEGHTARNCRA   19 (42)
T ss_dssp             CCTTTCCSSSCTTTCSS
T ss_pred             ccccCCCcCcCcccCcC
Confidence            45555555555555544

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=97.36  E-value=3.2e-05  Score=46.90  Aligned_cols=20  Identities=20%  Similarity=0.506  Sum_probs=17.5

Q ss_pred             CceeecCCCCCCCCcCCCce
Q 042094          271 GLCFNCDEQFKPGHRCKAPQ  290 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~~~  290 (485)
                      ..||+||+.||++++||.++
T Consensus        23 ~~C~~Cg~~GH~~~~Cp~rq   42 (42)
T d2exfa1          23 KGCWKCGKEGHQMKDCTERQ   42 (42)
T ss_dssp             SSCSSSCCSSSCTTTCCSSC
T ss_pred             CccccCCCCCeecccCCCCC
Confidence            45999999999999998763

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=97.12  E-value=8.9e-05  Score=41.98  Aligned_cols=20  Identities=20%  Similarity=0.406  Sum_probs=17.4

Q ss_pred             CceeecCCCCCCCCcCCCce
Q 042094          271 GLCFNCDEQFKPGHRCKAPQ  290 (485)
Q Consensus       271 ~~Cf~Cg~~GH~a~~C~~~~  290 (485)
                      ..|-+|.++||++++||.+.
T Consensus        11 DQCAyCke~GHW~~dCPkkp   30 (40)
T d1a6bb_          11 DQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             SSCSSSCCTTCCTTSCSSSC
T ss_pred             hhhHHHhhcCchhhhCccCC
Confidence            45999999999999998653

>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=96.94  E-value=0.00083  Score=52.82  Aligned_cols=46  Identities=9%  Similarity=-0.023  Sum_probs=38.0

Q ss_pred             ceEeeeEEeecceEEEEEEEEcCC--CCCCeeechhHHhhcCCeEEEcc
Q 042094          387 GKCSHVPVNSQGFQFHLDFFLLPV--SGCDIVLGAEWLRSLGAILWDFS  433 (485)
Q Consensus       387 ~~~~~v~v~i~~~~~~~~~~V~~~--~~~dvILG~dwL~~~~~i~id~~  433 (485)
                      ..+..+.+.++|..+.++|.+.+-  ..|+++||++||...+. .+|=.
T Consensus        88 RpvV~~~i~ig~~~~~ie~tL~dR~~m~yp~LiGR~~L~~~~~-~VD~s  135 (141)
T d2pmaa1          88 RPVVLLNIKLGDKVRTIKVNLTNRKRFLYPLLLGRDAIIDFNG-AVDPA  135 (141)
T ss_dssp             EEEEEEEEEETTEEEEEEEEEECCCCCSCSEEECHHHHHHTTE-EEETT
T ss_pred             eeEEEEEEEECCEEEEEEEEECCCCCCCCCEEECHHHHhcCCE-EECCc
Confidence            345567899999999999999985  46999999999998885 57754

>d1cl4a_ g.40.1.1 (A:) Nucleocapsid protein from mason-pfizer monkey virus (MPMV) {Mason-pfizer monkey virus [TaxId: 11855]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleocapsid protein from mason-pfizer monkey virus (MPMV)
species: Mason-pfizer monkey virus [TaxId: 11855]

Probab=95.76  E-value=0.0023  Score=34.55  Aligned_cols=20  Identities=30%  Similarity=0.650  Sum_probs=17.8

Q ss_pred             CCceeecCCCCCCCCcCCCc
Q 042094          270 KGLCFNCDEQFKPGHRCKAP  289 (485)
Q Consensus       270 ~~~Cf~Cg~~GH~a~~C~~~  289 (485)
                      .++|-+|++--|++++|+++
T Consensus         2 P~lCPrC~kG~HWa~~Crsk   21 (32)
T d1cl4a_           2 PGLCPRCKRGKHWANECKSK   21 (32)
T ss_dssp             CCSCSSCSSCSSCSTTCCCT
T ss_pred             CccCccccCcchHHHHhhhh
Confidence            37899999999999999765

>d1dsva_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=95.33  E-value=0.0032  Score=33.83  Aligned_cols=21  Identities=29%  Similarity=0.676  Sum_probs=18.3

Q ss_pred             CCceeecCCCCCCCCcCCCce
Q 042094          270 KGLCFNCDEQFKPGHRCKAPQ  290 (485)
Q Consensus       270 ~~~Cf~Cg~~GH~a~~C~~~~  290 (485)
                      .++|-+|++--|++++|+++-
T Consensus         2 p~lCPrC~kG~HWa~~Crsk~   22 (31)
T d1dsva_           2 PGLCPRCKKGYHWKSECKSKF   22 (31)
T ss_dssp             CCBCTTTCSSBSCTTTCCCSE
T ss_pred             CccCccccCcchHHHHhhhhh
Confidence            378999999999999998763

>d1izea_ b.50.1.2 (A:) Acid protease {Fungus (Aspergillus oryzae) [TaxId: 5062]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Fungus (Aspergillus oryzae) [TaxId: 5062]

Probab=93.74  E-value=0.045  Score=49.17  Aligned_cols=97  Identities=21%  Similarity=0.258  Sum_probs=56.6

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeecceEeeeEEeecceEEEEE-------------E-
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSSGKCSHVPVNSQGFQFHLD-------------F-  405 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~~~~~~v~v~i~~~~~~~~-------------~-  405 (485)
                      ...++||||++.+++..++++.+--...   ........+.. +.+......+.+.++|..+.+.             + 
T Consensus       208 ~~~~ivDSGts~~~lp~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~p~i~f~f~g~~~~ip~~~~~~~~~~~~~C~  284 (323)
T d1izea_         208 SITGIADTGTTLLLLDDSIVDAYYEQVN---GASYDSSQGGYVFPSSASLPDFSVTIGDYTATVPGEYISFADVGNGQTF  284 (323)
T ss_dssp             CEEEEECTTCCSEEECHHHHHHHHTTST---TCEEETTTTEEEEETTCCCCCEEEEETTEEEEECHHHHEEEECSTTEEE
T ss_pred             CceEEeccCCccccCCHHHHHHHHHHcC---CccccCCCCcEEeecccCCceEEEEECCEEEEcChHHEEEEeCCCCEEE
Confidence            3578999999999999999887632211   01111111110 1111112345566666543321             1 


Q ss_pred             -EEcCCCC-CCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          406 -FLLPVSG-CDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       406 -~V~~~~~-~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                       .+.+..+ -..|||..||+.+-. ..|+.+++|-|-.
T Consensus       285 ~~i~~~~~~~~~iLG~~flr~~y~-vfD~~~~~IGfA~  321 (323)
T d1izea_         285 GGIQSNSGIGFSIFGDVFLKSQYV-VFDASGPRLGFAA  321 (323)
T ss_dssp             ESEEECTTTSSEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             EEEECCCCCCCEEECHHHhCCEEE-EEECCCCEEEEcc
Confidence             1112222 346999999999986 7999999998853

>d1wkra_ b.50.1.2 (A:) Acid protease {Irpex lacteus (Polyporus tulipiferae), Polyporopepsin [TaxId: 5319]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Irpex lacteus (Polyporus tulipiferae), Polyporopepsin [TaxId: 5319]

Probab=93.22  E-value=0.045  Score=49.68  Aligned_cols=95  Identities=15%  Similarity=0.234  Sum_probs=57.3

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCe-eeec--ceEeeeEEeecceEEEEE--EEE---------
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGV-ISSS--GKCSHVPVNSQGFQFHLD--FFL---------  407 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~-~~~~--~~~~~v~v~i~~~~~~~~--~~V---------  407 (485)
                      ..|+||||++.+++..++++.+.-....    .....+|.. +.+.  .....+.|.++|..+.+.  .+|         
T Consensus       207 ~~aiiDSGtt~~~lP~~~~~~l~~~~~~----~~~~~~~~~~~~c~~~~~~P~i~f~f~g~~~~i~~~~yi~~~~~~~~~  282 (340)
T d1wkra_         207 TAGIVDTGTTLTLIASDAFAKYKKATGA----VADNNTGLLRLTTAQYANLQSLFFTIGGQTFELTANAQIWPRNLNTAI  282 (340)
T ss_dssp             EEEEECTTBCSEEECHHHHHHHHHHHTC----EECTTTSSEEECHHHHHTCCCEEEEETTEEEEECTGGGBCCGGGGGGG
T ss_pred             cceEEecCCccEeccHHHHHHHHHHhCc----cccCCceEEEEeccccCCCCceEEEECCEEEEEChHHeEeeccCceee
Confidence            4689999999999999887766322110    000011111 1111  112356777777665543  111         


Q ss_pred             -------------cC---CCCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          408 -------------LP---VSGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       408 -------------~~---~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                                   +.   .....+|||..||+.+-. ..|..+++|.|-.
T Consensus       283 ~~~~~~~~~~~~~~~~~~~~~~~~ILG~~fl~~~yv-vfD~~~~~iGfA~  331 (340)
T d1wkra_         283 GGSASSVYLIVGDLGSDSGEGLDFINGLTFLERFYS-VYDTTNKRLGLAT  331 (340)
T ss_dssp             TCCSSCEEBCEEECSSCTTSSCCEEECHHHHTSEEE-EEETTTTEEEEEE
T ss_pred             cCccceEEEEEecccCCCCCCCCEEechHHhCCEEE-EEECCCCEEEEEE
Confidence                         11   112457999999999985 6999999999864

>d1bxoa_ b.50.1.2 (A:) Acid protease {Fungus (Penicillium janthinellum), penicillopepsin [TaxId: 5079]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Fungus (Penicillium janthinellum), penicillopepsin [TaxId: 5079]

Probab=93.14  E-value=0.11  Score=46.39  Aligned_cols=96  Identities=22%  Similarity=0.348  Sum_probs=56.4

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCee-eecceEeeeEEeecceEEEEE--------------E
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVI-SSSGKCSHVPVNSQGFQFHLD--------------F  405 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~-~~~~~~~~v~v~i~~~~~~~~--------------~  405 (485)
                      ...++||||++..++..++++++--.....   ....-.+..+ .+......+.+.++|..+.+.              +
T Consensus       207 ~~~aiiDSGTs~~~lp~~~~~~l~~~i~~~---~~~~~~~~~~~~c~~~~p~itf~f~g~~~~i~~~~~~~~~~~~~~~C  283 (323)
T d1bxoa_         207 GFSGIADTGTTLLLLDDSVVSQYYSQVSGA---QQDSNAGGYVFDCSTNLPDFSVSISGYTATVPGSLINYGPSGDGSTC  283 (323)
T ss_dssp             EEEEEECTTCSSEEECHHHHHHHHTTSTTC---EEETTTTEEEECTTCCCCCEEEEETTEEEEECHHHHEEEECSSSSCE
T ss_pred             CcceEEecccccccCCHHHHHHHHHHhCCc---cccCCCCcEEEeccCCCCcEEEEECCEEEEEChHHeEEEEcCCCCEE
Confidence            467999999999999999999873221100   0000001100 111122345555566544321              1


Q ss_pred             --EEcCCCCCC-eeechhHHhhcCCeEEEccCcEEEEE
Q 042094          406 --FLLPVSGCD-IVLGAEWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       406 --~V~~~~~~d-vILG~dwL~~~~~i~id~~~~~~~~~  440 (485)
                        .+.+..+.+ .|||..||+.+-. ..|+.+++|-|-
T Consensus       284 ~~~i~~~~~~~~~ILG~~flr~~y~-vfD~~~~~IGfA  320 (323)
T d1bxoa_         284 LGGIQSNSGIGFSIFGDIFLKSQYV-VFDSDGPQLGFA  320 (323)
T ss_dssp             EESEEECTTCSSEEECHHHHTTEEE-EEETTTTEEEEE
T ss_pred             EEEEECCCCCCcEEECHHHhCCEEE-EEECCCCEEeEE
Confidence              112223333 6899999999986 799999999885

>d1miqa_ b.50.1.2 (A:) Plasmepsin (a hemoglobin-degrading enzyme) {Plasmodium vivax [TaxId: 5855]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Plasmepsin (a hemoglobin-degrading enzyme)
species: Plasmodium vivax [TaxId: 5855]

Probab=92.89  E-value=0.37  Score=43.86  Aligned_cols=103  Identities=18%  Similarity=0.351  Sum_probs=59.5

Q ss_pred             EEEEEECCe---EEEEEEcCCCCccccCHHHHhhcCCcc----ccccceEEEEccCCeeeecceEeeeEEeecceEEEEE
Q 042094          332 RLKGNLKKH---GVTILIDSSSTHIFLNSSLAKQYGCPV----TTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLD  404 (485)
Q Consensus       332 ~~~~~i~~~---~v~aLiDsGSt~sfIs~~~~~~l~l~~----~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~  404 (485)
                      .+.+.+++.   ...++||||++..++..+.++.+--..    .......+...+.      .....+.|.++|..+.+.
T Consensus       242 ~l~~~~~~~~~~~~~~iiDTGTs~~~lP~~~~~~l~~~i~~~~~~~~~~~~~~~~~------~~~P~itf~f~g~~~~l~  315 (373)
T d1miqa_         242 DLDVHFGKQTMEKANVIVDSGTTTITAPSEFLNKFFANLNVIKVPFLPFYVTTCDN------KEMPTLEFKSANNTYTLE  315 (373)
T ss_dssp             EEEEEETTEEEEEEEEEECTTBSSEEECHHHHHHHHHHHTCEECTTSSCEEEETTC------TTCCCEEEECSSCEEEEC
T ss_pred             EEEEEECcEecCCcceEeccCCceeccCHHHHHHHHHHhCCeeccCCCeeEecccc------CCCceEEEEECCEEEEEC
Confidence            344445443   457999999999999998877652111    1111111111110      111334555555544321


Q ss_pred             -------------------EEEcCCCCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 -------------------FFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 -------------------~~V~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                                         +...+....-.|||..||+.+-. ..|+.+.+|-|-.
T Consensus       316 p~~y~~~~~~~~~~~C~~~~~~~~~~~~~~ILG~~fl~~~y~-vfD~~~~rIGfA~  370 (373)
T d1miqa_         316 PEYYMNPILEVDDTLCMITMLPVDIDSNTFILGDPFMRKYFT-VFDYDKESVGFAI  370 (373)
T ss_dssp             GGGSEEESSSSSCSEEEESEEECCSSSSEEEECHHHHHHEEE-EEETTTTEEEEEE
T ss_pred             HHHeeEEEEeCCCCEEEEEEEECCCCCCCEEEcHHhhCcEEE-EEECCCCEEEEEE
Confidence                               11122223336999999999986 6999999998863

>d1oewa_ b.50.1.2 (A:) Endothiapepsin {Chestnut blight fungus (Endothia parasitica) [TaxId: 5116]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Endothiapepsin
species: Chestnut blight fungus (Endothia parasitica) [TaxId: 5116]

Probab=92.42  E-value=0.17  Score=45.37  Aligned_cols=96  Identities=16%  Similarity=0.268  Sum_probs=54.6

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCC-eeeecceEeeeEEeecceEEEEE---------------
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGG-VISSSGKCSHVPVNSQGFQFHLD---------------  404 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~-~~~~~~~~~~v~v~i~~~~~~~~---------------  404 (485)
                      ...+|||||++..++..++++.+--....   .....-.|. .+.|......+.+.++|..+.+.               
T Consensus       213 ~~~~iiDSGts~~~lp~~~~~~i~~~~~~---~~~~~~~~~~~~~C~~~~P~i~f~f~g~~~~lp~~~~~~~~~~~~~~~  289 (330)
T d1oewa_         213 SIDGIADTGTTLLYLPATVVSAYWAQVSG---AKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSS  289 (330)
T ss_dssp             EEEEEECTTCCSEEECHHHHHHHHTTSTT---CEEETTTTEEEEETTCCCCCEEEEETTEEEEECHHHHEEEESSTTCSE
T ss_pred             CcceeeccccccccCCHHHHHHHHHHccC---cccCcccceEEecccCCCCcEEEEECCEEEecCHHHeeEEEecCCCCE
Confidence            35689999999999999998877322110   000000111 11222222345666666654431               


Q ss_pred             EE--EcCCCCC-CeeechhHHhhcCCeEEEc-cCcEEEEE
Q 042094          405 FF--LLPVSGC-DIVLGAEWLRSLGAILWDF-SKLTMQFT  440 (485)
Q Consensus       405 ~~--V~~~~~~-dvILG~dwL~~~~~i~id~-~~~~~~~~  440 (485)
                      ++  +.+..+. ..|||..||+.+-. ..|+ .+.+|-|-
T Consensus       290 C~~~i~~~~~~~~~ILG~~flr~~y~-vfD~~~~~~IGfA  328 (330)
T d1oewa_         290 CFGGIQSSAGIGINIFGDVALKAAFV-VFNGATTPTLGFA  328 (330)
T ss_dssp             EEESEEESTTTSSEEECHHHHTTEEE-EEECSSSCEEEEE
T ss_pred             EEEEEECCCCCCCEEECHHHhCCEEE-EEECCCCCEEEEe
Confidence            11  1112222 36899999999986 6998 45578774

>d1eaga_ b.50.1.2 (A:) Acid protease {Yeast (Candida albicans) [TaxId: 5476]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Yeast (Candida albicans) [TaxId: 5476]

Probab=92.40  E-value=0.063  Score=48.69  Aligned_cols=26  Identities=23%  Similarity=0.425  Sum_probs=23.1

Q ss_pred             eeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          415 IVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       415 vILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      .|||..||+.+-. ..|+.+++|-|-.
T Consensus       304 ~ILG~~fl~~~y~-vfD~~~~~iGfA~  329 (342)
T d1eaga_         304 NILGDNFLRSAYI-VYDLDDNEISLAQ  329 (342)
T ss_dssp             CEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             cEECHHhhCcEEE-EEECCCCEEEEEE
Confidence            3799999999996 6999999999964

>d2bjua1 b.50.1.2 (A:1-329) Plasmepsin (a hemoglobin-degrading enzyme) {Plasmodium falciparum, plasmepsin II [TaxId: 5833]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Plasmepsin (a hemoglobin-degrading enzyme)
species: Plasmodium falciparum, plasmepsin II [TaxId: 5833]

Probab=92.38  E-value=0.21  Score=44.52  Aligned_cols=95  Identities=15%  Similarity=0.264  Sum_probs=57.3

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccc----cccceEEEEccCCeeeecceEeeeEEeecceEEEE-------------
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVT----TTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHL-------------  403 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~----~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~-------------  403 (485)
                      ...++||||++..++..++++++--...    ......+..-+-      .....+.+.+++..+.+             
T Consensus       208 ~~~~~iDSGt~~~~lp~~~~~~l~~~~~~~~~~~~~~~~~~~~~------~~~p~~~f~~~g~~~~i~p~~y~~~~~~~~  281 (329)
T d2bjua1         208 KANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNN------SKLPTFEFTSENGKYTLEPEYYLQHIEDVG  281 (329)
T ss_dssp             EEEEEECTTCCSEEECHHHHHHHTTTSSCEECTTSSCEEEETTC------TTCCCEEEECSSCEEEECHHHHEEECTTTS
T ss_pred             CCcccccccccceeCCHHHHHHHHHHhCCeecCCCCeeEeeccc------CCCCceeEEeCCEEEEECHHHhEEEeecCC
Confidence            4678999999999999999998743221    111111111111      11123344444443332             


Q ss_pred             ------EEEEcCCCCCCeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          404 ------DFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       404 ------~~~V~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                            -+...+......|||..||+.+-. ..|+.+++|.|-..
T Consensus       282 ~~~C~~~i~~~~~~~~~~IlG~~fl~~~y~-vfD~~~~~iGfA~a  325 (329)
T d2bjua1         282 PGLCMLNIIGLDFPVPTFILGDPFMRKYFT-VFDYDNHSVGIALA  325 (329)
T ss_dssp             TTEEEECEEECCCSSCEEEECHHHHHHEEE-EEETTTTEEEEEEE
T ss_pred             CCEEEEEEEECCCCCCCEEEchHhhCcEEE-EEECCCCEEEEEEe
Confidence                  111222233446899999999986 79999999999754

>d2fi2a1 a.28.3.2 (A:37-128) Zinc finger protein 42 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Acyl carrier protein-like
superfamily: Retrovirus capsid dimerization domain-like
family: SCAN domain
domain: Zinc finger protein 42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.81  E-value=0.086  Score=37.22  Aligned_cols=39  Identities=26%  Similarity=0.247  Sum_probs=34.7

Q ss_pred             ChHHHHHHHHhhhHHHHHHHHHhcCcccHHHHHHHHHHH
Q 042094          165 PESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQ  203 (485)
Q Consensus       165 ~e~~~~~~f~~GL~~~i~~~v~~~~p~tl~~~~~~a~~~  203 (485)
                      -+-..+.+|+..||.+++..|..+.|.+..+++.+|..+
T Consensus        48 lelLVLEQFl~~lP~e~~~~V~e~~p~s~~eav~L~Edl   86 (92)
T d2fi2a1          48 LELLVLEQFLGALPPEIQARVQGQRPGSPEEAAALVDGL   86 (92)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHCCCSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            345678999999999999999999999999999998854

>d1am5a_ b.50.1.2 (A:) Pepsin(ogen) {Atlantic cod (Gadus morhua) [TaxId: 8049]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Pepsin(ogen)
species: Atlantic cod (Gadus morhua) [TaxId: 8049]

Probab=91.43  E-value=0.13  Score=46.02  Aligned_cols=96  Identities=14%  Similarity=0.128  Sum_probs=54.6

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCcccc-ccceEEEEccCCeeeecceEeeeEEeecceEEEEE---------------
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTT-TTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLD---------------  404 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~-~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~---------------  404 (485)
                      ...++||||++.+++..+++.++--.... ........... .   ......+.+.++|..+.+.               
T Consensus       208 ~~~~iiDsGts~~~lp~~~~~~l~~~i~~~~~~~~~~~~~~-~---~~~~P~i~f~f~g~~~~l~~~~y~~~~~~~c~~~  283 (324)
T d1am5a_         208 GCQAIVDTGTSKIVAPVSALANIMKDIGASENQGEMMGNCA-S---VQSLPDITFTINGVKQPLPPSAYIEGDQAFCTSG  283 (324)
T ss_dssp             CEEEEECTTCSSEEECTTTHHHHHHHHTCEECCCCEECCTT-S---SSSSCCEEEEETTEEEEECHHHHEEESSSCEEEC
T ss_pred             CcceeeccCcccccCCHHHHHHHHHHhCCcccCCccccccc-c---cccCCceEEEECCEEEEECHHHhEecCCCeEEEE
Confidence            46789999999999999887765211100 00000000000 0   0112345556666554321               


Q ss_pred             EEEcCC--C-CCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 FFLLPV--S-GCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 ~~V~~~--~-~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      +...+.  . ..-.|||..||+.+-. ..|..+++|.|..
T Consensus       284 i~~~~~~~~~~~~~ILG~~fl~~~y~-vfD~~~~~igfA~  322 (324)
T d1am5a_         284 LGSSGVPSNTSELWIFGDVFLRNYYT-IYDRTNNKVGFAP  322 (324)
T ss_dssp             EEECCSCCSSSCEEEECHHHHHHEEE-EEETTTTEEEEEE
T ss_pred             EEecCcCCCCCCCEEECHHhhcCEEE-EEECCCCEEEEEE
Confidence            122221  1 2235899999999996 6999999998864

>d1y7qa1 a.28.3.2 (A:37-132) Zinc finger protein 174 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Acyl carrier protein-like
superfamily: Retrovirus capsid dimerization domain-like
family: SCAN domain
domain: Zinc finger protein 174
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.01  E-value=0.089  Score=37.31  Aligned_cols=40  Identities=23%  Similarity=0.151  Sum_probs=35.6

Q ss_pred             hHHHHHHHHhhhHHHHHHHHHhcCcccHHHHHHHHHHHHH
Q 042094          166 ESFFISCFLSGLREDIKIGVQMLKPASLLQTFELARFQEE  205 (485)
Q Consensus       166 e~~~~~~f~~GL~~~i~~~v~~~~p~tl~~~~~~a~~~e~  205 (485)
                      +-..+.+|+..||.+++..|..+.|.+.++++.+|..+..
T Consensus        51 elLVLEQFl~~lP~e~q~wV~e~~p~s~eeav~L~Edl~~   90 (96)
T d1y7qa1          51 ELLVMEQFLTILPEEIQARVRHRCLMSSKEIVTLVEDFHR   90 (96)
T ss_dssp             HHHHHHHHHHHSCTHHHHHHHTSCCCCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            3467899999999999999999999999999999987653

>d1j71a_ b.50.1.2 (A:) Acid protease {Yeast (Candida tropicalis) [TaxId: 5482]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Yeast (Candida tropicalis) [TaxId: 5482]

Probab=90.86  E-value=0.47  Score=42.46  Aligned_cols=102  Identities=15%  Similarity=0.218  Sum_probs=56.4

Q ss_pred             EEEECCeE----EEEEEcCCCCccccCHHHHhhcC----Ccc-----------c-cccceEEEEccCCeeeecceEeeeE
Q 042094          334 KGNLKKHG----VTILIDSSSTHIFLNSSLAKQYG----CPV-----------T-TTTQFQVTVADGGVISSSGKCSHVP  393 (485)
Q Consensus       334 ~~~i~~~~----v~aLiDsGSt~sfIs~~~~~~l~----l~~-----------~-~~~~~~v~~a~G~~~~~~~~~~~v~  393 (485)
                      .+.|++..    ..|+||||++.+++..++++++-    ...           . ....+.+.+.+|..+.+...  ..-
T Consensus       201 ~i~v~g~~~~~~~~aiiDSGt~~~~lp~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~p~i~f~f~~g~~~~i~~~--~y~  278 (334)
T d1j71a_         201 SINFDGTSVSTNADVVLDSGTTITYFSQSTADKFARIVGATWDSRNEIYRLPSCDLSGDAVFNFDQGVKITVPLS--ELI  278 (334)
T ss_dssp             EEEETTEEEEEEEEEEECTTCSSEEECHHHHHHHHHHHTCEEETTTTEEECSSSCCCSEEEEEESTTCEEEEEGG--GGE
T ss_pred             eEEECCEEecccccccccCCCcceeccHHHHHHHHHHhCCEEcCCCCeeeccccccCCCceEEeCCCEEEEEChH--HeE
Confidence            34566654    45999999999999999988762    110           0 11223333333333322111  111


Q ss_pred             EeecceEEEEEEEEcCCCCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          394 VNSQGFQFHLDFFLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       394 v~i~~~~~~~~~~V~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      +..++..+-. +.+.+  .-..|||..||+.+-. ..|+.+++|.|-.
T Consensus       279 ~~~~~~~~C~-~~i~~--~~~~ILG~~fl~~~y~-vfD~~n~~iGfA~  322 (334)
T d1j71a_         279 LKDSDSSICY-FGISR--NDANILGDNFLRRAYI-VYDLDDKTISLAQ  322 (334)
T ss_dssp             EECSSSSCEE-ESEEE--CTTCEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             EecCCCCEEE-EEecC--CCCcEECHHhhCcEEE-EEECCCCEEEEEE
Confidence            1111110000 01111  1245899999999986 6999999999963

>d1t6ex_ b.50.1.2 (X:) Xylanase inhibitor TAXI-I {Wheat (Triticum aestivum) [TaxId: 4565]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Xylanase inhibitor TAXI-I
species: Wheat (Triticum aestivum) [TaxId: 4565]

Probab=90.08  E-value=0.47  Score=43.17  Aligned_cols=28  Identities=18%  Similarity=0.336  Sum_probs=24.9

Q ss_pred             CCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          413 CDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       413 ~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      ...|||..||+.+-. ..|..+++|-|..
T Consensus       344 ~~~ILG~~flr~~y~-vfD~~~~~IGfA~  371 (381)
T d1t6ex_         344 PAVILGGAQMEDFVL-DFDMEKKRLGFSR  371 (381)
T ss_dssp             CSEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             CcEEECHHHhCcEEE-EEECCCCEEEEEE
Confidence            468999999999986 6999999999875

>d3cmsa_ b.50.1.2 (A:) Chymosin (synonym: renin) {Cow (Bos taurus) [TaxId: 9913]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Chymosin (synonym: renin)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=90.07  E-value=0.31  Score=43.14  Aligned_cols=95  Identities=12%  Similarity=0.120  Sum_probs=54.7

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCcccc--ccceEEEEccCCeeeecceEeeeEEeecceEEEEE-------------E
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTT--TTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLD-------------F  405 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~--~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~-------------~  405 (485)
                      ...++||||++.+++.+++++.+--....  .......... .   .......+.+.++|..+.+.             +
T Consensus       210 ~~~~iiDSGtt~~~lp~~~~~~l~~~~~~~~~~~~~~~~~~-~---~~~~~p~i~f~f~g~~~~l~~~~y~~~~~~~c~~  285 (323)
T d3cmsa_         210 GCQAILDTGTSKLVGPSSDILNIQQAIGATQNQYGEFDIDC-D---NLSYMPTVVFEINGKMYPLTPSAYTSQDQGFCTS  285 (323)
T ss_dssp             CEEEEECTTCCSEEECHHHHHHHHHHHTCEEETTTEEEECT-T---CTTTSCCEEEEETTEEEEECHHHHEEEETTEEEE
T ss_pred             CeeEEEecCcceEEecHHHHHHHHHHhCceeccCCceeEec-c---ccCCCCeEEEEECCEEEEECHHHeEEcCCCEEEE
Confidence            46799999999999999998866322110  0000000000 0   00111244555555543321             1


Q ss_pred             EEcCCCC-CCeeechhHHhhcCCeEEEccCcEEEEE
Q 042094          406 FLLPVSG-CDIVLGAEWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       406 ~V~~~~~-~dvILG~dwL~~~~~i~id~~~~~~~~~  440 (485)
                      -+.+... ...|||..||+.+-. ..|+.+.+|.|.
T Consensus       286 ~i~~~~~~~~~iLG~~~l~~~yv-vfD~~~~~igfa  320 (323)
T d3cmsa_         286 GFQSENHSQKWILGDVFIREYYS-VFDRANNLVGLA  320 (323)
T ss_dssp             SEEEC---CCEEECHHHHTTEEE-EEETTTTEEEEE
T ss_pred             EEEeCCCCCCEEEcHHhhCcEEE-EEECCCCEEEEE
Confidence            1222222 357999999999986 799999999885

>d1dpja_ b.50.1.2 (A:) Acid protease {Baker's yeast (Saccharomyces cerevisiae), proteinase A [TaxId: 4932]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Baker's yeast (Saccharomyces cerevisiae), proteinase A [TaxId: 4932]

Probab=89.26  E-value=0.57  Score=41.56  Aligned_cols=92  Identities=17%  Similarity=0.278  Sum_probs=53.5

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccc----cccceEEEEccCCeeeecceEeeeEEeecceEEEE--------------
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVT----TTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHL--------------  403 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~----~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~--------------  403 (485)
                      ..++||||++.+++..++++++.-...    ......+..-.      ......+.|.++|..+.+              
T Consensus       213 ~~~iiDSGts~~~lp~~~~~~l~~~~~~~~~~~~~~~~~c~~------~~~~P~i~f~f~g~~~~l~p~~y~~~~~~~c~  286 (329)
T d1dpja_         213 HGAAIDTGTSLITLPSGLAEMINAEIGAKKGWTGQYTLDCNT------RDNLPDLIFNFNGYNFTIGPYDYTLEVSGSCI  286 (329)
T ss_dssp             CEEEECTTCSCEEECHHHHHHHHHHHTCEECTTSSEEECGGG------GGGCCCEEEEETTEEEEECTTTSEEEETTEEE
T ss_pred             cccccCcccceeeCCHHHHHHHHHHhCCccccceeEEEeccc------cCccceEEEEECCEEEEECHHHeEEecCCcEE
Confidence            468999999999999999887632211    00111111000      011123445555544332              


Q ss_pred             -EEEEcCC--CC-CCeeechhHHhhcCCeEEEccCcEEEEE
Q 042094          404 -DFFLLPV--SG-CDIVLGAEWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       404 -~~~V~~~--~~-~dvILG~dwL~~~~~i~id~~~~~~~~~  440 (485)
                       .+..+..  .. .-.|||..||+.+-. ..|+.+++|.|-
T Consensus       287 ~~~~~~~~~~~~~~~~iLG~~fl~~~y~-vfD~~~~~igfA  326 (329)
T d1dpja_         287 SAITPMDFPEPVGPLAIVGDAFLRKYYS-IYDLGNNAVGLA  326 (329)
T ss_dssp             ECEEECCCCTTTCSEEEECHHHHTTEEE-EEETTTTEEEEE
T ss_pred             EEEEECccCCCCCCcEEEcHHhhCcEEE-EEECCCCEEEEE
Confidence             1112221  11 226899999999986 699999999885

>d3psga_ b.50.1.2 (A:) Pepsin(ogen) {Pig (Sus scrofa) [TaxId: 9823]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Pepsin(ogen)
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=88.89  E-value=0.4  Score=43.64  Aligned_cols=93  Identities=18%  Similarity=0.294  Sum_probs=58.0

Q ss_pred             EEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCee-eec--ceEeeeEEeecceEEEEE--------------
Q 042094          342 VTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVI-SSS--GKCSHVPVNSQGFQFHLD--------------  404 (485)
Q Consensus       342 v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~-~~~--~~~~~v~v~i~~~~~~~~--------------  404 (485)
                      ..++||||++.+++..+++..+--.....     ...+|... .|.  .....+.|.++|..+.+.              
T Consensus       254 ~~aiiDSGTs~~~lp~~~~~~i~~~l~~~-----~~~~~~~~~~C~~~~~~P~l~f~f~g~~~~l~~~~yi~~~~~~c~~  328 (370)
T d3psga_         254 CQAIVDTGTSLLTGPTSAIANIQSDIGAS-----ENSDGEMVISCSSIDSLPDIVFTIDGVQYPLSPSAYILQDDDSCTS  328 (370)
T ss_dssp             EEEEECTTCCSEEEEHHHHHHHHHHTTCE-----ECTTCCEECCGGGGGGCCCEEEEETTEEEEECHHHHEEECSSCEEE
T ss_pred             ccEEEecCCceEeCCHHHHHHHHHHhCCe-----eecCCcEEEeccccCCCceEEEEECCEEEEEChHHeEEEcCCeEEE
Confidence            58899999999999999988763221100     01122211 111  122456777777765431              


Q ss_pred             -EEEcCC--C-CCCeeechhHHhhcCCeEEEccCcEEEEE
Q 042094          405 -FFLLPV--S-GCDIVLGAEWLRSLGAILWDFSKLTMQFT  440 (485)
Q Consensus       405 -~~V~~~--~-~~dvILG~dwL~~~~~i~id~~~~~~~~~  440 (485)
                       |..++.  . +.-.|||..||+.+-. ..|..+.+|-|-
T Consensus       329 ~~~~~~~~~~~~~~~ILG~~flr~~y~-vfD~~~~~IGfA  367 (370)
T d3psga_         329 GFEGMDVPTSSGELWILGDVFIRQYYT-VFDRANNKVGLA  367 (370)
T ss_dssp             SEEEECCCTTSCCEEEECHHHHTTEEE-EEETTTTEEEEE
T ss_pred             EEEEcccCCCCCCcEEECHHhhcCEEE-EEECCCCEEEEE
Confidence             122221  1 2237999999999986 699999999885

>d1hrna_ b.50.1.2 (A:) Chymosin (synonym: renin) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Chymosin (synonym: renin)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.42  E-value=0.65  Score=41.33  Aligned_cols=95  Identities=16%  Similarity=0.221  Sum_probs=56.6

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCccccccceEEEEccCCeeeec--ceEeeeEEeecceEEEEEE--EEcC-------
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPVTTTTQFQVTVADGGVISSS--GKCSHVPVNSQGFQFHLDF--FLLP-------  409 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~~~~~~~~v~~a~G~~~~~~--~~~~~v~v~i~~~~~~~~~--~V~~-------  409 (485)
                      ...++||||++.+++...+++.+--.....     ...++-.+.+.  .....+.|.++|..+.+..  ++++       
T Consensus       217 ~~~~iiDSGtt~~~lp~~~~~~l~~~~~~~-----~~~~~~~~~c~~~~~~P~l~f~f~g~~~~l~p~~yl~~~~~~~~~  291 (337)
T d1hrna_         217 GCLALVDTGASYISGSTSSIEKLMEALGAK-----KRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKK  291 (337)
T ss_dssp             CEEEEECTTCSSEEECHHHHHHHHHHHTCE-----ECSSCEEEETTTGGGCCCEEEEETTEEEEECHHHHBCCCCCCTTS
T ss_pred             CcceEEeCCCcceeccHHHHHHHHHHhCCc-----ccccceeeeccccCCCCceeEEECCEEEEEChHHeEEEecCCCCC
Confidence            357899999999999999888763221100     00011111111  1124566777776655421  1111       


Q ss_pred             -------------CCCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          410 -------------VSGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       410 -------------~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                                   ..+.-.|||..||+.+-. ..|..+++|-|-.
T Consensus       292 ~C~~~i~~~~~~~~~~~~~ILG~~fl~~~y~-vfD~~~~~IGfA~  335 (337)
T d1hrna_         292 LCTLAIHAMDIPPPTGPTWALGATFIRKFYT-EFDRRNNRIGFAL  335 (337)
T ss_dssp             EEEBSEEECCCCTTTCSCEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             EEEEEEEcCCcCCCCCCCEEECHHhhCCEEE-EEECCCCEEEEEE
Confidence                         111225899999999986 6999999998853

>d1smra_ b.50.1.2 (A:) Chymosin (synonym: renin) {Mouse (Mus musculus) [TaxId: 10090]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Chymosin (synonym: renin)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.31  E-value=0.41  Score=42.71  Aligned_cols=94  Identities=19%  Similarity=0.288  Sum_probs=54.7

Q ss_pred             EEEEEEcCCCCccccCHHHHhhcCCcc----ccccceEEEEccCCeeeecceEeeeEEeecceEEEEE------------
Q 042094          341 GVTILIDSSSTHIFLNSSLAKQYGCPV----TTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLD------------  404 (485)
Q Consensus       341 ~v~aLiDsGSt~sfIs~~~~~~l~l~~----~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~------------  404 (485)
                      ...++||||++.+++..++++.+--..    .......+...+      ......+.+.++|..+.+.            
T Consensus       214 ~~~~iiDSGtt~~~lp~~~~~~l~~~~~~~~~~~~~~~~~c~~------~~~~P~i~f~f~g~~~~l~~~~y~~~~~~~~  287 (335)
T d1smra_         214 GCEVVVDTGSSFISAPTSSLKLIMQALGAKEKRLHEYVVSCSQ------VPTLPDISFNLGGRAYTLSSTDYVLQYPNRR  287 (335)
T ss_dssp             CEEEEECTTBSSEEECHHHHHHHHHHHTCEEEETTEEEEEGGG------GGGSCCEEEEETTEEEEECHHHHBTT----C
T ss_pred             CceEEEeCCCCcccCCHHHHHHHHHHhCCeeccCCceeecccc------cCCCCccEEEECCeEEEEChHHeEEEeccCC
Confidence            367899999999999999988773211    000011111000      0111234555555543322            


Q ss_pred             -------EEEcC---CCCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 -------FFLLP---VSGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 -------~~V~~---~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                             +..++   ..+.-.|||..||+.+-. ..|+.+.+|.|-.
T Consensus       288 ~~~C~~~~~~~~~~~~~~~~~ILG~~fl~~~yv-vfD~~~~~iGfA~  333 (335)
T d1smra_         288 DKLCTVALHAMDIPPPTGPVWVLGATFIRKFYT-EFDRHNNRIGFAL  333 (335)
T ss_dssp             CCEEEBSEEECCCCTTTCSCEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             CCEEEEEEEecCcCCCCCCcEEECHHHhCcEEE-EEECCCCEEEEEE
Confidence                   11111   112236999999999986 6999999998853

>d2apra_ b.50.1.2 (A:) Acid protease {Bread mold (Rhizopus chinensis) [TaxId: 4843]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Acid protease
species: Bread mold (Rhizopus chinensis) [TaxId: 4843]

Probab=85.88  E-value=0.5  Score=41.99  Aligned_cols=98  Identities=9%  Similarity=0.123  Sum_probs=55.5

Q ss_pred             EEECCeE----EEEEEcCCCCccccCHHHHhhcCCcc----ccccceEEEEccCCeeeec-ceEeeeEEeecceEEEEE-
Q 042094          335 GNLKKHG----VTILIDSSSTHIFLNSSLAKQYGCPV----TTTTQFQVTVADGGVISSS-GKCSHVPVNSQGFQFHLD-  404 (485)
Q Consensus       335 ~~i~~~~----v~aLiDsGSt~sfIs~~~~~~l~l~~----~~~~~~~v~~a~G~~~~~~-~~~~~v~v~i~~~~~~~~-  404 (485)
                      +.+++..    ..++||||++..++..++++++--..    .......+.        |. .....+.+.++|..+.+. 
T Consensus       202 i~i~~~~~~~~~~~iiDSGt~~~~lp~~~~~~l~~~~~~~~~~~~~~~~~--------C~~~~~p~i~f~f~g~~~~i~~  273 (325)
T d2apra_         202 ATVGTSTVASSFDGILDTGTTLLILPNNIAASVARAYGASDNGDGTYTIS--------CDTSAFKPLVFSINGASFQVSP  273 (325)
T ss_dssp             EEETTEEEECCEEEEECTTCSSEEEEHHHHHHHHHHHTCEECSSSCEEEC--------SCGGGCCCEEEEETTEEEEECG
T ss_pred             EEECCEeecceeeeeccCCCccccCCHHHHHHHHHHhCCcccCCCceeec--------ccCCCCCcEEEEECCEEEEECh
Confidence            3445543    47999999999999998887662111    100011111        10 001223444444433321 


Q ss_pred             -----------E--EEcCCCCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 -----------F--FLLPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 -----------~--~V~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                                 +  .+.+...--.|||..||+.+-. ..|..+++|.|-.
T Consensus       274 ~~y~~~~~~~~C~~~i~~~~~~~~iLG~~flr~~y~-vfD~~~~~IGfAp  322 (325)
T d2apra_         274 DSLVFEEFQGQCIAGFGYGNWGFAIIGDTFLKNNYV-VFNQGVPEVQIAP  322 (325)
T ss_dssp             GGGEEEEETTEEEESEEEESSSSEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             HHeEEecCCCEEEEEEccCCCCCEEECHHHhCcEEE-EEECCCCEEeEEE
Confidence                       1  1112222347999999999986 6999999998853

>d1mppa_ b.50.1.2 (A:) Pepsin {Mucor pusillus [TaxId: 4840]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Pepsin
species: Mucor pusillus [TaxId: 4840]

Probab=82.28  E-value=0.43  Score=43.09  Aligned_cols=33  Identities=30%  Similarity=0.548  Sum_probs=26.4

Q ss_pred             cCCCCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          408 LPVSGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       408 ~~~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                      .+..+...|||..||+.+-. ..|+.+++|.|-.
T Consensus       317 ~~~~~~~~ILG~~fl~~~yv-vfD~~~~~iGfA~  349 (357)
T d1mppa_         317 LPDGGNQFIVGNLFLRFFVN-VYDFGKNRIGFAP  349 (357)
T ss_dssp             EEESSSCCEEEHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             cCCCCCCEEechHHhCCEEE-EEECCCCEEEEEE
Confidence            34444557999999999985 6999999999863

>d1qdma2 b.50.1.2 (A:2-247,A:248-338) Plant acid proteinase, phytepsin {Barley (Hordeum vulgare) [TaxId: 4513]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: Plant acid proteinase, phytepsin
species: Barley (Hordeum vulgare) [TaxId: 4513]

Probab=81.18  E-value=1.8  Score=38.03  Aligned_cols=95  Identities=16%  Similarity=0.278  Sum_probs=55.5

Q ss_pred             eEEEEEEcCCCCccccCHHHHhhcCC----ccccccceEEEEccCCeeeecceEeeeEEeecceEEEEE-----------
Q 042094          340 HGVTILIDSSSTHIFLNSSLAKQYGC----PVTTTTQFQVTVADGGVISSSGKCSHVPVNSQGFQFHLD-----------  404 (485)
Q Consensus       340 ~~v~aLiDsGSt~sfIs~~~~~~l~l----~~~~~~~~~v~~a~G~~~~~~~~~~~v~v~i~~~~~~~~-----------  404 (485)
                      ....++||||.+.+.+..+++..+--    .........+...+      ......+.+.++|..+.+.           
T Consensus       215 ~~~~~iiDtgt~~~~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~------~~~~p~itf~f~g~~~~l~~~~~~~~~~~~  288 (337)
T d1qdma2         215 GGCAAIADSGTSLLAGPTAIITEINEKIGAAGSPMGESAVDCGS------LGSMPDIEFTIGGKKFALKPEEYILKVGEG  288 (337)
T ss_dssp             TCEEEEECSSCCSEEECHHHHHHHHHHHTCCCCSSSCCEECGGG------GTTCCCEEEEETTEEEEECHHHHEEECSCG
T ss_pred             CCceEEeeccCcceecchHHHHHHHHHhccccccCCcccccccc------cCCCCceEEEECCEEEEEChHHeEEEeccC
Confidence            34679999999999999988776522    11111111111000      1112334555555544321           


Q ss_pred             ----EE--E--cC---CCCCCeeechhHHhhcCCeEEEccCcEEEEEE
Q 042094          405 ----FF--L--LP---VSGCDIVLGAEWLRSLGAILWDFSKLTMQFTW  441 (485)
Q Consensus       405 ----~~--V--~~---~~~~dvILG~dwL~~~~~i~id~~~~~~~~~~  441 (485)
                          ++  +  ++   ......|||..||+.+-. ..|+.+++|.|..
T Consensus       289 ~~~~C~~~i~~~~~~~~~~~~~IlG~~fl~~~y~-vfD~~~~~igfA~  335 (337)
T d1qdma2         289 AAAQCISGFTAMDIPPPRGPLWILGDVFMGPYHT-VFDYGKLRIGFAK  335 (337)
T ss_dssp             GGCCEEESEEECCCCTTSCSEEEECHHHHTTEEE-EEETTTTEEEEEE
T ss_pred             CCCEEEEEEEecCcCCCCCCcEEEhHHhhcCEEE-EEECCCCEEEEEE
Confidence                11  1  11   122457999999999986 7999999998863

>d2qp8a1 b.50.1.2 (A:60-446) beta-secretase (memapsin) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Acid proteases
superfamily: Acid proteases
family: Pepsin-like
domain: beta-secretase (memapsin)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.47  E-value=1.7  Score=39.39  Aligned_cols=30  Identities=17%  Similarity=0.308  Sum_probs=25.8

Q ss_pred             CCCeeechhHHhhcCCeEEEccCcEEEEEEC
Q 042094          412 GCDIVLGAEWLRSLGAILWDFSKLTMQFTWK  442 (485)
Q Consensus       412 ~~dvILG~dwL~~~~~i~id~~~~~~~~~~~  442 (485)
                      ....|||..||+.+-. ..|+.+++|-|...
T Consensus       330 ~~~~ILG~~Flr~~y~-vfD~~~~~IGfA~a  359 (387)
T d2qp8a1         330 STGTVMGAVIMEGFYV-VFDRARKRIGFAVS  359 (387)
T ss_dssp             SSCEEECHHHHTTEEE-EEETTTTEEEEEEE
T ss_pred             CCCEEEhHHhhCcEEE-EEECCCCEEEEEEC
Confidence            4567999999999986 69999999999754