Citrus Sinensis ID: 036272

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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---
Protein Sequence
MGAMNSRLDLAEEGSVNRNWGPQGQGGAGYAGGLVAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQEIRRSVNPTFSSSVRNSSNQWNSSLTPSGSKTINLEMIFPIRNLTPIELQRRREQELCYSCDENYTVGHKCKKLFFIEIDEEGEEATGEMYTEETPVISLHALAGIQTPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIENIEAK
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHccccHHHHHHHHHHcccccccHHHHHHHHHHcccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccHHHHHHHHHHccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccEEEEEEcccccccccccccccccccccccccccccccccEEEEEEccEEEEEEEccccccccccHHHHHHHccccEEccccEEEEEcccEEEcccEEcccEEEEccEEEcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcHccccHHHHHHHHHHHcccHHHHHHHHHccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHcccccHHHHHHHHHccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcHHHHHcccccccccccccccccccccccccccccccccccccccHHHcccccEEEEcccccccccccccccEEEEEcccccccccccccccccEEEEEHHHHcccccEEEEEEEEcccEEEEEEEccccccHccHHHHHHccccEEcccccEEEEccccEEEEEcccccEEEEEEcccccccccc
Coil and Loop (DISEMBL)
mgamnsrldlaeegsvnrnwgpqgqggagyagglvapklakldfpcydgsedptlWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYEDSFGdlcklkqtgtvsdyQPQFERLLARagsltdkqEAACFISGLKDglradvraqnpqNLSAAIGLARNYELKAQEIRrsvnptfsssvrnssnqwnssltpsgsktinlemifpirnltpiELQRRREQELCyscdenytvghkckKLFFIEIDEegeeatgemyteetpvISLHalagiqtphtmrvhsqiskipltilidsgsthnylHHRFAkitrikpersCLFSVVVAngerlsspgrckgvrltlqdvpienieak
Flexible Loop (DISEMBL)
MGAMNSRLDLAEEGSVNRNWGPQGQGGAGYAGGLVAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQEIRRSvnptfsssvrnssnqwnssltpsgsktinlemiFPIRNLTPIELQRRREQELCYscdenytvghkcKKLFFIEIDEEGEEATGEMYTEETPVISLHALAGIQTPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAkitrikperSCLFSVVVAngerlsspgrckgvrltlqdvpienieak
Low Complexity Region (SEG)
MGAMNSRLDLAEEGSVNRNWgpqgqggagyaggLVAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDglkagllakfaaTEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQEIRRSVNPTFSSSVRNSSNQWNSSLTPSGSKTINLEMIFPIRNLTPIELQRRREQELCYSCDENYTVGHKCKKLFFIeideegeeatgemyteetPVISLHALAGIQTPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIENIEAK
Disordered region (IsUnstruct)
**************************GAGYAGGLVAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQEAACFISGLKDGLRADVR******LSAAIGLARNYE***********************************TINLEMIFPIRNLTPIELQRRREQELCYSCDENYTVGHKCKKLFFIEIDEEGEEATGEMYTEETPVISLHALAGIQTPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQ**********
Disordered Region (DISOPRED)
******************************************DFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQ*********************************************PIELQRRREQELCYSCDENYTVGHKCKKLFFIEIDEEG********************AGIQTPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE*****
Disordered Region (DISEMBL)
MGAMNSRLDLAEEGSVNRNWGPQGQGGAGYAGGLVAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQEIRRSVNP******************PSGSKTINLEMIFPIRNLTPIELQRRREQELCYSCDENYTVGHKCKKLFFIEIDEEGEEATGEMYTEETPVISLHALAGIQTPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIENIEAK
Disordered Region (DISPRO)
**********************************VAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQEIR*************************************************REQELCYSCDENYTVGHKCKKLFFIEIDEE********Y*EETPVISLHALAGIQTPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIENI***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGAMNSRLDLAEEGSVNRNWGPQGQGGAGYAGGLVAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQEIRRSVNPTFSSSVRNSSNQWNSSLTPSGSKTINLEMIFPIRNLTPIELQRRREQELCYSCDENYTVGHKCKKLFFIEIDEEGEEATGEMYTEETPVISLHALAGIQTPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIENIEAK
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	383
147811718	1365	hypothetical protein VITISV_008352 [Viti	0.783	0.219	0.620	1e-109
147791940	721	hypothetical protein VITISV_026551 [Viti	0.626	0.332	0.687	7e-93
147769575	446	hypothetical protein VITISV_025425 [Viti	0.681	0.585	0.445	4e-62
147774273	1469	hypothetical protein VITISV_026680 [Viti	0.861	0.224	0.351	2e-54
62734405	575	retrotransposon protein, putative, uncla	0.851	0.566	0.379	5e-54
147789424	2822	hypothetical protein VITISV_017554 [Viti	0.887	0.120	0.342	7e-54
224109270	425	predicted protein [Populus trichocarpa]	0.856	0.771	0.361	2e-52
359479937	787	PREDICTED: uncharacterized protein LOC10	0.861	0.419	0.355	2e-51
116309032	1448	OSIGBa0114M03.4 [Oryza sativa Indica Gro	0.874	0.231	0.371	1e-50
147809918	569	hypothetical protein VITISV_025787 [Viti	0.279	0.188	0.831	1e-49

>gi|147811718|emb|CAN77256.1| hypothetical protein VITISV_008352 [Vitis vinifera]

 Score =  401 bits (1030), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 235/379 (62%), Positives = 260/379 (68%), Gaps = 79/379 (20%)

Query: 1   MGAMNSRLDLAEEGSVNRNWGPQGQGGAGYAGGLVAPKLAKLDFPCYDGSEDPTLWICRA 60
           +GAMNSRLDL+EEGSVNRN GP G GGAGY GGLV  KLAKLDFP YDGSEDPTLWICRA
Sbjct: 368 VGAMNSRLDLSEEGSVNRNQGPYGLGGAGYVGGLVVRKLAKLDFPRYDGSEDPTLWICRA 427

Query: 61  EQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYED 120
           EQFFEFQG SLE+QVKLAAYHLE DAQL             W                  
Sbjct: 428 EQFFEFQGISLEDQVKLAAYHLEKDAQL-------------W------------------ 456

Query: 121 SFGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQEAACFISGLKDGLRADVRAQNPQNL 180
                                  LLARA +LTDKQEA CFIS LKDGLRAD         
Sbjct: 457 -----------------------LLARANTLTDKQEAECFISRLKDGLRAD--------- 484

Query: 181 SAAIGLARNYELKAQEIRRSVNPTFSSSVRNSSNQWNSSLTPSGSKTINLEMIFPIRNLT 240
                          E+RR  NPTFSSSV NS+NQWN+S T SG+K  N E I PIR L+
Sbjct: 485 ---------------EVRRPTNPTFSSSVCNSNNQWNTS-TXSGAKDTNPERILPIRKLS 528

Query: 241 PIELQRRREQELCYSCDENYTVGHKCKKLFFIEIDEEGEEATGEMYTEETPVISLHALAG 300
           P ELQRRR+Q LCY+CDE YT+GHKCKKLFFIE++EE EE+  E Y EETP ISLHALAG
Sbjct: 529 PTELQRRRQQRLCYNCDEKYTMGHKCKKLFFIELEEENEESIEEEYVEETPTISLHALAG 588

Query: 301 IQTPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLS 360
           +Q+P TM++HSQI K PLTILIDSGSTHN+LHH+FAKI  +K ERSCLFSVVVANGERLS
Sbjct: 589 VQSPQTMQIHSQIGKTPLTILIDSGSTHNFLHHKFAKIIGLKSERSCLFSVVVANGERLS 648

Query: 361 SPGRCKGVRLTLQDVPIEN 379
           S GRC GV+L LQD+PIE+
Sbjct: 649 SLGRCNGVKLFLQDIPIEH 667

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147791940|emb|CAN72445.1| hypothetical protein VITISV_026551 [Vitis vinifera]

 Score =  347 bits (889), Expect = 7e-93,   Method: Compositional matrix adjust.
 Identities = 187/272 (68%), Positives = 205/272 (75%), Gaps = 32/272 (11%)

Query: 1   MGAMNSRLDLAEEGSVNRNWGPQGQGGAGYAGGLVAPKLAKLDFPCYDGSEDPTLWICRA 60
           +GAMNSRL+L EEG VNRN GP GQGG GYAGGLV PKLAKLDFP YDGS+DPTLWI R 
Sbjct: 32  VGAMNSRLNLQEEGPVNRNQGPHGQGGVGYAGGLVVPKLAKLDFPRYDGSKDPTLWIFRX 91

Query: 61  EQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYED 120
           EQFFEFQGTSLE+QVKLAAYHLE DAQL +++RKNQGHLVT DG+KAGLL          
Sbjct: 92  EQFFEFQGTSLEDQVKLAAYHLEKDAQLXYERRKNQGHLVTXDGMKAGLL---------- 141

Query: 121 SFGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQEAACFISGLKDGLRADVRAQNPQNL 180
                                ERLLARA +L DKQEA C IS LKDGLR DVR QNPQNL
Sbjct: 142 ---------------------ERLLARADTLIDKQEAECLISRLKDGLRXDVRVQNPQNL 180

Query: 181 SAAIGLARNYELKAQEIRRSVNPTFSSSVRNSSNQWNSSLTPSGSKTINLEMIFPIRNLT 240
           S AIGLAR YELKAQE+RR  NPTFSSSV NS+NQWN+S TPSG+K  NLE I PI  L+
Sbjct: 181 SVAIGLARTYELKAQEVRRPTNPTFSSSVHNSNNQWNTS-TPSGAKDTNLERILPIHKLS 239

Query: 241 PIELQRRREQELCYSCDENYTVGHKCKKLFFI 272
           P +LQRRR+Q LCY+CDE Y +GHK KKLFFI
Sbjct: 240 PTKLQRRRQQGLCYNCDEKYXMGHKXKKLFFI 271

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147769575|emb|CAN76938.1| hypothetical protein VITISV_025425 [Vitis vinifera]

 Score =  244 bits (624), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 127/285 (44%), Positives = 177/285 (62%), Gaps = 24/285 (8%)

Query: 1   MGAMNSRLDL------------AEEGSVNRNWGPQGQGGAGYAGGLVAPKLAKLDFPCYD 48
           + +MN+RLD             A +G  +R +  +G   +  + G V P++ KLDFP ++
Sbjct: 104 ITSMNTRLDQISGNQSLERGESAHDGGGSRRFNYRGPRDSTESYGAVIPRVTKLDFPRFN 163

Query: 49  GSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAG 108
           GSEDPT WICR EQFFEFQ  + E +V LA YHLE +AQLW+Q  K +G  V W  LK G
Sbjct: 164 GSEDPTSWICRVEQFFEFQKIAEEEKVPLATYHLEGEAQLWYQILKEEGE-VAWLTLKEG 222

Query: 109 LLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQEAACFISGLKDGL 168
           L +++  TE++D FGDL +LKQ G+V +YQ QFE+LL+R G L   Q+ ACFI GL + +
Sbjct: 223 LNSRYGPTEFDDFFGDLTRLKQVGSVREYQSQFEKLLSRVGKLNQSQQVACFIGGLNEDV 282

Query: 169 RADVRAQNPQNLSAAIGLARNYELKAQEIRRSVNPTFSSSVRNSSNQWNSSLTPSGSKTI 228
           R DV+A  P  LSAA+GLAR YE+K  + R S N     +V  +S   +  L+ + +   
Sbjct: 283 RIDVQAMKPPTLSAAVGLARLYEVKYHK-RSSFNLEPKKTVSTNSTVTSRPLSSTPA--- 338

Query: 229 NLEMIFPIRNLTPIELQRRREQELCYSCDENYTVGHKCKKLFFIE 273
                  IR L+P E++ RR++ LC++CDE +  GH+CKKLF IE
Sbjct: 339 -------IRRLSPTEMKERRDKGLCFNCDEKFAPGHRCKKLFLIE 376

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  219 bits (559), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 126/358 (35%), Positives = 190/358 (53%), Gaps = 28/358 (7%)

Query: 33  GLVAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQ 92
           G +  +  +LDFP ++G EDP  W+ RA+QFF +  T+  ++V LA++H+E  A +WFQ 
Sbjct: 82  GGIQTRAVRLDFPKFNG-EDPNGWVYRADQFFNYHQTNPHHRVLLASFHMEGKALVWFQD 140

Query: 93  RKNQGHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAGSLT 152
            +  G + +W+G    L  +F ++ YED    L +LKQT TV DY+ QFE L  +   L 
Sbjct: 141 IEAAGGISSWEGFVRALQTRFGSSPYEDPMEALIRLKQTSTVEDYKSQFEALSNQLRGLA 200

Query: 153 DKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQEIRRSVNPTFSSSVRNS 212
           +  + +CF+SGL++ +R  VR  NP NL  A GLA+  E     +RR        + +  
Sbjct: 201 ESYKLSCFLSGLRENIRFMVRMLNPSNLHIAFGLAKMQEENVAALRR--------TAKLG 252

Query: 213 SNQWNSSLTPSGSKTINLEMIFPIRNLTPIELQRRREQELCYSCDENYTVGHKCK--KLF 270
           S     ++ P          I P++ L+P +++ RR++ LCY+CD+ +  GHKCK  +LF
Sbjct: 253 SVPTRLAIGPPSPP--EKRAIVPVQRLSPSQMKERRDKGLCYNCDDKWAPGHKCKSARLF 310

Query: 271 FIEIDE---------EGEEATGEMYTEETPV------ISLHALAGIQTPHTMRVHSQISK 315
            +E DE         E  E       EETP+      IS+HAL G   P TMR    I  
Sbjct: 311 IMECDESSDDEVPKSEVAEGRASKSKEETPIVEIEPGISIHALVGSPNPKTMRFLGHICG 370

Query: 316 IPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQ 373
             + IL+D+GSTHN++     +   +    +   SV VANG+ + S G C  V L +Q
Sbjct: 371 RAVVILVDTGSTHNFMDPSVIQRAHLPSNPTEGLSVKVANGQAVRSEGSCAAVPLHMQ 428

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|62734405|gb|AAX96514.1| retrotransposon protein, putative, unclassified [Oryza sativa Japonica Group]

 Score =  218 bits (554), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 132/348 (37%), Positives = 185/348 (53%), Gaps = 22/348 (6%)

Query: 32  GGLVAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLW-F 90
            G   P+  KL+FP YD  EDP  W    EQFF  Q T   ++V LA YHL  DAQ W F
Sbjct: 120 AGTGVPRFYKLEFPKYDSKEDPLNWFNHCEQFFRGQKTLDGDRVWLATYHLTGDAQEWYF 179

Query: 91  QQRKNQGHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAGS 150
              ++ G  +            F    + +S G+L +L QT +V+ YQ +F  L +R   
Sbjct: 180 HYEQHHGPRL------------FGPPIHRNSLGELKRLSQTSSVAAYQTKFLALASRTTE 227

Query: 151 -LTDKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQEIRRSVNPTFSSSV 209
            L D Q+   F +GL++ L  DV    P +L  A+GLAR YE KA  +     P   +  
Sbjct: 228 PLMDSQQIQLFTAGLREELAIDVELHQPDDLQEAMGLARAYERKASRLASGTRPALRAPF 287

Query: 210 RNSSNQWNSSLTPSGSKTINLEMI-FPIRNLTPIELQRRREQELCYSCDENYTVGHKCKK 268
           R+     N    P+ +   + E      R L+P EL  RR Q LCY+CDE +  GHKC +
Sbjct: 288 RSGPAAANLPTAPAATTEGSQEQAPRQFRRLSPAELAERRCQGLCYNCDEKFVRGHKCAR 347

Query: 269 LFFIEIDEEGEEATGEMY-TEETPVISLHALAGIQTPHTMRVHSQISKIPLTILIDSGST 327
           LF+IE D+  E   G+M    + P +SL+ LAG+   +TMR+  +I+   +  L+DSGST
Sbjct: 348 LFYIEYDDNVE---GDMEPAPDEPRVSLNVLAGLDGANTMRLPVEIAGERVVALVDSGST 404

Query: 328 HNYLHHRFAK--ITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQ 373
           HN++H   A+     + P R  L+ VVVANG+RL SPGRC  +RL ++
Sbjct: 405 HNFIHTELARHLCLHLSPVRHDLY-VVVANGDRLVSPGRCANLRLRIE 451

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  217 bits (553), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 128/374 (34%), Positives = 196/374 (52%), Gaps = 34/374 (9%)

Query: 17  NRNWGPQGQGGAGYAGGLVAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVK 76
           NR  GP  + G       +  +  +LDFP ++G EDP+ W+ RA+QFF +  T+  ++V 
Sbjct: 37  NRRTGPSIRNGG------IQTRAVRLDFPKFNG-EDPSGWVYRADQFFNYHQTNPHHRVL 89

Query: 77  LAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSD 136
           LA++H+E  A +WFQ  +  G + +W+G    L  +F ++ YE+    L +LKQT TV D
Sbjct: 90  LASFHMEGKALVWFQDIEAAGGISSWEGFVRALQTRFGSSPYENPMEALIRLKQTSTVED 149

Query: 137 YQPQFERLLARAGSLTDKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQE 196
           Y+ QFE L  +   L +  + +CF+SGL++ +R  V   NP NL  A GLA+  E     
Sbjct: 150 YKSQFEALSNQLRGLAESYKLSCFLSGLREDIRFMVCMLNPSNLHIAFGLAKMQEENVAA 209

Query: 197 IRRSVNPTFSSSVRNSSNQWNSSLTPSGSKTINLEMIFPIRNLTPIELQRRREQELCYSC 256
           +RR        + +  S     ++ P         +I P++ L+P +++ RR++ LCY+C
Sbjct: 210 LRR--------TAKLGSVPTRLAIGPPSPP--EKRVIVPVQRLSPSQMKERRDKGLCYNC 259

Query: 257 DENYTVGHKCK--KLFFIEIDE---------EGEEATGEMYTEETPV------ISLHALA 299
           D+ +  GHKCK  +LF +E DE         E  E       EETP+      IS+HAL 
Sbjct: 260 DDKWAPGHKCKSARLFIMECDESSDDKVPKSEVAEGRASKSKEETPIVEIEPGISIHALV 319

Query: 300 GIQTPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERL 359
           G   P TMR    I    + IL+D+GSTHN++     +   +    +   SV VANG+ +
Sbjct: 320 GSPNPKTMRFLGHICGRAVVILVDTGSTHNFMDPSVIQRAHLPSNPTEGLSVKVANGQAV 379

Query: 360 SSPGRCKGVRLTLQ 373
            S G C  V L +Q
Sbjct: 380 CSEGSCAAVPLHMQ 393

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224109270|ref|XP_002333289.1| predicted protein [Populus trichocarpa] gi|222835888|gb|EEE74309.1| predicted protein [Populus trichocarpa]

 Score =  212 bits (540), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 125/346 (36%), Positives = 190/346 (54%), Gaps = 18/346 (5%)

Query: 34  LVAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQ-- 91
           + + KLAKL+FP Y G+ DPT W  R +QFFE+QGT+   ++ LA++HL+ +A  W+Q  
Sbjct: 82  MFSSKLAKLEFPIYSGN-DPTEWFNRVDQFFEYQGTAETQKMSLASFHLQGEANQWWQWL 140

Query: 92  --QRKNQGHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAG 149
               K++   VTW   +  L A+F   E ED    L +++Q G++ +YQ +FERL  R  
Sbjct: 141 RRAYKDEDREVTWPIFEEELWARFGPPECEDFDEALLRVRQGGSLREYQREFERLGNRVQ 200

Query: 150 SLTDKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQEIRRSVNPTFSSSV 209
             T K     F+ GLK  +   +    P++L  AI LAR  + +    RR+  P    S+
Sbjct: 201 GWTQKALVGTFMGGLKPDIAEGIMMFKPKSLKEAISLARMRDEQLTRQRRNSKPF---SI 257

Query: 210 RNSSNQWNSSLTPSGSKTINLEMIFPIRNLTPIELQRRREQELCYSCDENYTVGHKCKK- 268
            ++     +S +P+ S         P++ L   E+Q+RR Q +C++CDE +T GHKC+K 
Sbjct: 258 NHNPI---ASFSPTKSPAA-----MPMKRLAWDEMQKRRSQGICFNCDEKFTPGHKCQKP 309

Query: 269 -LFFIEIDEEGEEATGEMYTEETPVISLHALAGIQTPHTMRVHSQISKIPLTILIDSGST 327
            L  +E D+E      E +  + P ISLHA+ G     TMR+ ++I    LT+LIDSGST
Sbjct: 310 RLLLLEGDDETSLQDDEEFEGDEPQISLHAITGWSIARTMRIMARIENQDLTVLIDSGST 369

Query: 328 HNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQ 373
           HN++  R A    +    +  F+V VANG  L   GR + + + LQ
Sbjct: 370 HNFISERIANWLHLPVIPTQPFNVKVANGNPLKCQGRFENIHVLLQ 415

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  209 bits (532), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 129/363 (35%), Positives = 190/363 (52%), Gaps = 33/363 (9%)

Query: 34  LVAPKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQ-- 91
           +V+ K AKL+FP + G +DPT W  R EQFF++Q T+   +V +AAYHLE +A  W+Q  
Sbjct: 46  IVSSKSAKLEFPRFSG-DDPTEWFNRVEQFFDYQSTAENQKVPMAAYHLEGEANQWWQWL 104

Query: 92  --QRKNQGHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAG 149
               K +GH+++W+  +  L A+F  +  ED    L ++KQ GT+ DYQ +FE+L  R  
Sbjct: 105 HRTLKEEGHVISWEKFEEELWARFGPSGCEDFDEALSRIKQLGTLRDYQREFEKLGNRVQ 164

Query: 150 SLTDKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQEIRRSVNPTFSSSV 209
             T K     F+ GLK  +   +R   PQ+L   I LAR   ++  +I R     +   V
Sbjct: 165 GWTQKALVGTFMGGLKAEIVDAIRMFKPQSLKEVINLAR---MRDDQIARQRRFMWLPPV 221

Query: 210 RNSSNQWNSSLTPSGSKTINLEMIFPIRNLTPIELQRRREQELCYSCDENYTVGHKCKKL 269
           R           P  ++        PI++L+  E+QR+R Q LC++C+E +T GH+C+K 
Sbjct: 222 RAPIA------LPQATRVDPAIPAKPIKSLSWEEMQRKRAQGLCFNCNERFTAGHRCQKP 275

Query: 270 FFIEI-------------------DEEGEEATGEMYTEETPVISLHALAGIQTPHTMRVH 310
             + +                   D+ G EA      E    I+LHAL G   P TMRV 
Sbjct: 276 QLLLLKGHEGNVDCGNGTDQQTWEDDHGGEAAEVQEHEPKLEITLHALTGWTAPKTMRVT 335

Query: 311 SQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRL 370
           +++    + +LIDSGSTHN++ +R A   R+    +  F V VANGERL   GR   VR+
Sbjct: 336 AKMGPHEVMVLIDSGSTHNFISNRLANKLRLPVIPTETFPVWVANGERLKCQGRYDKVRV 395

Query: 371 TLQ 373
            LQ
Sbjct: 396 ELQ 398

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116309032|emb|CAH66146.1| OSIGBa0114M03.4 [Oryza sativa Indica Group]

 Score =  206 bits (525), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 129/347 (37%), Positives = 188/347 (54%), Gaps = 12/347 (3%)

Query: 37  PKLAKLDFPCYDGSEDPTLWICRAEQFFEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQ 96
           PK  KLDFP YDG  DP ++I R E +F  Q    E +V +A+Y+LE+ AQLW+ Q    
Sbjct: 59  PKFQKLDFPRYDGKSDPLIFINRCESYFHQQRIMEEEKVWMASYNLEDGAQLWYIQVHTD 118

Query: 97  GHLVTWDGLKAGLLAKFAATEYEDSFGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQE 156
               +W   K  L  ++          +L + ++TGTV++YQ +F+ LLARAG L + Q 
Sbjct: 119 EGTPSWRRFKDLLNLRYGPPLRSAPLAELAECRRTGTVAEYQDRFQALLARAGPLEEDQR 178

Query: 157 AACFISGLKDGLRADVRAQNPQNLSAAIGLARNYELKAQEI----RRSVNPTFSSSVRNS 212
              F  GL   L  DVR QNPQ+L+AA+ LAR +EL+ Q      R +  P   +     
Sbjct: 179 VQLFTGGLLPPLSIDVRIQNPQSLAAAMSLARQFELREQYTAPAPRAAHRPLLPAPPPRL 238

Query: 213 SNQWNSSLTPSGSKTINLEMIFPIRNLTPIELQRRREQELCYSCDENYTVGHK--CKKLF 270
           +     +  P+   TI +E    I+ LT  E + RR + LCY+CDE YT GH   C++LF
Sbjct: 239 ALPAPPAPKPATPATITVEGR-QIKRLTQAEQEERRRKGLCYNCDEKYTRGHNRVCQRLF 297

Query: 271 FIEIDEEGE-----EATGEMYTEETPVISLHALAGIQTPHTMRVHSQISKIPLTILIDSG 325
            +E  EE E     E  G+   E+ PV SL A+AG+    TM+V   +    L  L+DSG
Sbjct: 298 LLEGIEEDEDDGTPEDFGDAGAEDAPVFSLQAIAGVSFTDTMQVAVTLGTASLVALLDSG 357

Query: 326 STHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTL 372
           STHN++    A+ + +  ++    + +VANGER++  G  +G  LT+
Sbjct: 358 STHNFISEAAAQRSGLPLQQRPRLTAMVANGERVTCIGVIRGAPLTI 404

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147809918|emb|CAN71623.1| hypothetical protein VITISV_025787 [Vitis vinifera]

 Score =  203 bits (517), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 94/113 (83%), Positives = 99/113 (87%)

Query: 4   MNSRLDLAEEGSVNRNWGPQGQGGAGYAGGLVAPKLAKLDFPCYDGSEDPTLWICRAEQF 63
           MNS LDL EEGSVNRN GP GQGGAGY  GLV PKLAKLDFP YDGSED TLWICRAEQF
Sbjct: 1   MNSXLDLXEEGSVNRNXGPHGQGGAGYTSGLVIPKLAKLDFPRYDGSEDLTLWICRAEQF 60

Query: 64  FEFQGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAAT 116
           FEFQGTSLE+QVKLAAYHLE DAQLW+Q+RKNQGHLVTWDG+ AGLL + A T
Sbjct: 61  FEFQGTSLEDQVKLAAYHLEKDAQLWYQRRKNQGHLVTWDGMDAGLLERLART 113

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	383
TAIR|locus:2091793	421	AT3G29750 [Arabidopsis thalian	0.190	0.173	0.310	0.00013

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

 Score = 85 (35.0 bits), Expect = 0.00013, Sum P(2) = 0.00013
 Identities = 23/74 (31%), Positives = 39/74 (52%)

Query:   307 MRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCK 366
             MR +  I    + + IDSG+T N++    A   ++    +   SV++   + + S G C 
Sbjct:   124 MRFYGFILDHKVVVAIDSGATDNFILVELAFSLKLPTSITNQASVLLGQRQCIQSVGTCL 183

Query:   367 GVRLTLQDVPI-EN 379
             G+RL +Q+V I EN
Sbjct:   184 GIRLWVQEVEITEN 197

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: eugene3.04360003 hypothetical protein (425 aa) (Populus trichocarpa)

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	383
cd00303	92	cd00303, retropepsin_like, Retropepsins; pepsin-li	2e-10
pfam03732	97	pfam03732, Retrotrans_gag, Retrotransposon gag pro	3e-09
pfam13975	72	pfam13975, gag-asp_proteas, gag-polyprotein putati	5e-05
pfam13650	89	pfam13650, Asp_protease_2, Aspartyl protease	7e-05
pfam08284	135	pfam08284, RVP_2, Retroviral aspartyl protease	7e-04

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

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 1/71 (1%)

Query: 309 VHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPER-SCLFSVVVANGERLSSPGRCKG 367
           +  +I+ +P+  L+DSG++ N++    AK   + P        V  ANG  + + G    
Sbjct: 1   LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILP 60

Query: 368 VRLTLQDVPIE 378
           V + +      
Sbjct: 61  VTIGIGGKTFT 71

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|217701 pfam03732, Retrotrans_gag, Retrotransposon gag protein

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 26/97 (26%), Positives = 47/97 (48%), Gaps = 6/97 (6%)

Query: 76  KLAAYHLENDAQLWFQQ--RKNQGHLVTWDGLKAGLLAKFA-ATEYEDSFGDLCKLKQ-T 131
           KLA +HLE  A  W++    ++     +WD LK   L +F  +   +    +L  L+Q T
Sbjct: 1   KLAVHHLEGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLENELRSLRQGT 60

Query: 132 GTVSDYQPQFERLLARA--GSLTDKQEAACFISGLKD 166
            +V +Y  +F+RL  +       ++   + F+ GL+ 
Sbjct: 61  ESVREYVERFKRLARQLPHHGFDEEALISAFLRGLRP 97

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

>gnl|CDD|206145 pfam13975, gag-asp_proteas, gag-polyprotein putative aspartyl protease

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVV-VANGERLSSPGR 364
            + V   I  + +  L+D+G+TH+++    A    +  E     S V +A+G      G 
Sbjct: 8   LVTVEVSIGGVEVKALVDTGATHSFISESLAARLGLPLEADQAPSRVRLADGSVREIQGL 67

This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins. Length = 72

>gnl|CDD|222288 pfam13650, Asp_protease_2, Aspartyl protease

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 3/69 (4%)

Query: 312 QISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRL- 370
            I+  P+  L+D+G++   L    A+   +KP +  +  V  ANG   ++  R   +++ 
Sbjct: 4   TINGKPVRFLLDTGASGTLLSRSLAERLGLKPTKLTIGRVSTANGTVRAALVRLDSLKIG 63

Query: 371 --TLQDVPI 377
             TL++VP 
Sbjct: 64  GITLRNVPA 72

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. Length = 89

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

 Score = 38.9 bits (91), Expect = 7e-04
 Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 14/71 (19%)

Query: 313 ISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPG-------RC 365
           ++ IP T+L DSG++H+++   F     +  E        +     + SPG       RC
Sbjct: 28  VNSIPATVLFDSGASHSFISQAFVGRHGLPLEA-------LRTPMLVHSPGGDMTATHRC 80

Query: 366 KGVRLTLQDVP 376
             V + +Q V 
Sbjct: 81  PSVNIEIQGVD 91

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	383
PF03732	96	Retrotrans_gag: Retrotransposon gag protein ; Inte	99.57
PF08284	135	RVP_2: Retroviral aspartyl protease; InterPro: IPR	99.36
PF13975	72	gag-asp_proteas: gag-polyprotein putative aspartyl	99.3
cd05484	91	retropepsin_like_LTR_2 Retropepsins_like_LTR, peps	99.29
cd05479	124	RP_DDI RP_DDI; retropepsin-like domain of DNA dama	99.21
PF03564	145	DUF1759: Protein of unknown function (DUF1759); In	98.99
PF13650	90	Asp_protease_2: Aspartyl protease	98.95
PF09668	124	Asp_protease: Aspartyl protease; InterPro: IPR0191	98.84
cd05481	93	retropepsin_like_LTR_1 Retropepsins_like_LTR; peps	98.83
TIGR02281	121	clan_AA_DTGA clan AA aspartic protease, TIGR02281	98.76
cd05483	96	retropepsin_like_bacteria Bacterial aspartate prot	98.76
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.66
PF12384	177	Peptidase_A2B: Ty3 transposon peptidase; InterPro:	98.66
cd05480	103	NRIP_C NRIP_C; putative nuclear receptor interacti	98.62
PF00077	100	RVP: Retroviral aspartyl protease The Prosite entr	98.6
cd06095	86	RP_RTVL_H_like Retropepsin of the RTVL_H family of	98.5
COG3577	215	Predicted aspartyl protease [General function pred	98.36
PF14893	331	PNMA: PNMA	98.31
cd00303	92	retropepsin_like Retropepsins; pepsin-like asparta	98.12
TIGR03698	107	clan_AA_DTGF clan AA aspartic protease, AF_0612 fa	98.04
KOG0012	380	consensus DNA damage inducible protein [Replicatio	98.04
PF05585	164	DUF1758: Putative peptidase (DUF1758); InterPro: I	97.9
cd06094	89	RP_Saci_like RP_Saci_like, retropepsin family. Ret	97.73
PF14223	119	UBN2: gag-polypeptide of LTR copia-type	97.69
cd05482	87	HIV_retropepsin_like Retropepsins, pepsin-like asp	97.49
PF12382	137	Peptidase_A2E: Retrotransposon peptidase; InterPro	97.48
PF13696	32	zf-CCHC_2: Zinc knuckle	97.42
PF02160	201	Peptidase_A3: Cauliflower mosaic virus peptidase (	97.23
PF14227	119	UBN2_2: gag-polypeptide of LTR copia-type	96.84
smart00343	26	ZnF_C2HC zinc finger.	96.76
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	96.42
PF13917	42	zf-CCHC_3: Zinc knuckle	96.35
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	95.82
PF02023	95	SCAN: SCAN domain; InterPro: IPR003309 A number of	95.77
PF14244	152	UBN2_3: gag-polypeptide of LTR copia-type	95.67
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	95.37
PF14392	49	zf-CCHC_4: Zinc knuckle	95.31
PF15288	40	zf-CCHC_6: Zinc knuckle	94.59
PTZ00368	148	universal minicircle sequence binding protein (UMS	94.13
COG5550	125	Predicted aspartyl protease [Posttranslational mod	94.11
PF02093	211	Gag_p30: Gag P30 core shell protein; InterPro: IPR	93.81
COG5222	427	Uncharacterized conserved protein, contains RING Z	93.24
PTZ00368	148	universal minicircle sequence binding protein (UMS	91.8
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	89.65
cd07936	85	SCAN SCAN oligomerization domain. The SCAN domain	89.56
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	89.46
smart00431	113	SCAN leucine rich region.	83.8

>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=99.57  E-value=8.2e-15  Score=109.59  Aligned_cols=90  Identities=23%  Similarity=0.469  Sum_probs=81.4

Q ss_pred             HhhhhcccchhhHHHHhhhcCCC--CCHHHHHHHHHhhhcCcccc-cHHHHhhcccc-cccHhhHHHHHHHHHHHhCC-C
Q 036272           77 LAAYHLENDAQLWFQQRKNQGHL--VTWDGLKAGLLAKFAATEYE-DSFGDLCKLKQ-TGTVSDYQPQFERLLARAGS-L  151 (383)
Q Consensus        77 ~~~~~L~g~A~~w~~~~~~~~~~--~~w~~~~~~l~~~F~~~~~~-~~~~~l~~~~q-~~sv~~Y~~~f~~l~~~~~~-~  151 (383)
                      ++..+|+|.|..||..+......  .+|++|++.|.++|.++... .+..+|.+++| +++|.+|+.+|+.|+..++. +
T Consensus         2 ~~~~~L~g~A~~w~~~~~~~~~~~~~~W~~~~~~~~~~f~~~~~~~~~~~~l~~l~Q~~esv~~y~~rf~~l~~~~~~~~   81 (96)
T PF03732_consen    2 LFPSFLKGPARQWYRNLRPNEIRDFITWEEFKDAFRKRFFPPDRKEQARQELNSLRQGNESVREYVNRFRELARRAPPPM   81 (96)
T ss_pred             CchHhccCHHHHHHHHhHhcCCCCCCCHHHHHHHHHHHHhhhhccccchhhhhhhhccCCcHHHHHHHHHHHHHHCCCCc
Confidence            67899999999999998764443  49999999999999998876 57788999999 99999999999999999984 9


Q ss_pred             CHHHHHHHHHhhcch
Q 036272          152 TDKQEAACFISGLKD  166 (383)
Q Consensus       152 ~e~~~~~~f~~gL~~  166 (383)
                      +++.++.+|++||+|
T Consensus        82 ~e~~~v~~f~~GL~~   96 (96)
T PF03732_consen   82 DEEMLVERFIRGLRP   96 (96)
T ss_pred             CHHHHHHHHHHCCCC
Confidence            999999999999975

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

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

Probab=99.36  E-value=3.3e-12  Score=100.56  Aligned_cols=77  Identities=31%  Similarity=0.454  Sum_probs=69.3

Q ss_pred             CCCcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          302 QTPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       302 ~~~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      ..+..+...+.|++.++.+|||||||+|||+.++|.+++++..+.....++.++|+.+.+.+.|..+++.++|+.|.
T Consensus        17 ~~~~vi~g~~~I~~~~~~vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~~V~~~g~~~~~~~~~~~~~~~i~g~~~~   93 (135)
T PF08284_consen   17 ESPDVITGTFLINSIPASVLIDSGATHSFISSSFAKKLGLPLEPLPRPIVVSAPGGSINCEGVCPDVPLSIQGHEFV   93 (135)
T ss_pred             CCCCeEEEEEEeccEEEEEEEecCCCcEEccHHHHHhcCCEEEEccCeeEEecccccccccceeeeEEEEECCeEEE
Confidence            35678999999999999999999999999999999999999998876666667788888999999999999999875

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.

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

Probab=99.30  E-value=1.3e-11  Score=86.20  Aligned_cols=65  Identities=28%  Similarity=0.431  Sum_probs=59.0

Q ss_pred             CCcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCC-ceEEEEeCCCeEecCceeec
Q 036272          303 TPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSC-LFSVVVANGERLSSPGRCKG  367 (383)
Q Consensus       303 ~~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~-~~~v~~~~g~~~~~~~~~~~  367 (383)
                      .+..+++.+.|+|..+.+||||||++|||++++|++|+++..... ...+.++||+.....|....
T Consensus         5 ~~g~~~v~~~I~g~~~~alvDtGat~~fis~~~a~rLgl~~~~~~~~~~v~~a~g~~~~~~g~~~~   70 (72)
T PF13975_consen    5 DPGLMYVPVSIGGVQVKALVDTGATHNFISESLAKRLGLPLEKPPSPIRVKLANGSVIEIRGVAEN   70 (72)
T ss_pred             cCCEEEEEEEECCEEEEEEEeCCCcceecCHHHHHHhCCCcccCCCCEEEEECCCCccccceEEEe
Confidence            346789999999999999999999999999999999999998877 89999999999999887643

>cd05484 retropepsin_like_LTR_2 Retropepsins_like_LTR, pepsin-like aspartate proteases

Probab=99.29  E-value=2e-11  Score=89.94  Aligned_cols=70  Identities=19%  Similarity=0.194  Sum_probs=63.5

Q ss_pred             EEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          308 RVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       308 ~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      .+.+.|||+++.+||||||++|||+++.+.+++.+........+..++|..+...|.+ .+.+.++|.++.
T Consensus         2 ~~~~~Ing~~i~~lvDTGA~~svis~~~~~~lg~~~~~~~~~~v~~a~G~~~~~~G~~-~~~v~~~~~~~~   71 (91)
T cd05484           2 TVTLLVNGKPLKFQLDTGSAITVISEKTWRKLGSPPLKPTKKRLRTATGTKLSVLGQI-LVTVKYGGKTKV   71 (91)
T ss_pred             EEEEEECCEEEEEEEcCCcceEEeCHHHHHHhCCCccccccEEEEecCCCEeeEeEEE-EEEEEECCEEEE
Confidence            5778999999999999999999999999999998876556789999999999999998 699999999754

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

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

Probab=99.21  E-value=7e-11  Score=92.17  Aligned_cols=74  Identities=12%  Similarity=0.191  Sum_probs=62.7

Q ss_pred             cceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          305 HTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       305 ~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      ..+++.+.|||.++.+||||||++|||+.++|+++|++........+..+.+......|.+..+++.|+|+.|.
T Consensus        15 ~~~~v~~~Ing~~~~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~   88 (124)
T cd05479          15 PMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRIHLAQVKIGNLFLP   88 (124)
T ss_pred             eEEEEEEEECCEEEEEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCCCcEEEeEEEEEEEEECCEEee
Confidence            56889999999999999999999999999999999998765444555555545577788888899999999875

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.

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

Probab=98.99  E-value=3.9e-09  Score=85.07  Aligned_cols=124  Identities=12%  Similarity=0.141  Sum_probs=99.8

Q ss_pred             ccCCCChHHHHHHHH---HHHHH-hCCchhhHHHHhhhhcccchhhHHHHhhhcCCCCCHHHHHHHHHhhhcCcccc--c
Q 036272           47 YDGSEDPTLWICRAE---QFFEF-QGTSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYE--D  120 (383)
Q Consensus        47 F~G~~d~~~w~~~~e---~~~~~-~~~~d~~k~~~~~~~L~g~A~~w~~~~~~~~~~~~w~~~~~~l~~~F~~~~~~--~  120 (383)
                      |+|  |+.+|..+.+   ..... ..++|..|..+|..+|+|+|+.-+.++..  ...+|...++.|.++|+.+...  .
T Consensus         1 F~G--~~~~~~~F~~~F~~~v~~n~~~~d~~K~~~L~~~L~G~A~~~i~~~~~--~~~~Y~~a~~~L~~~yg~~~~i~~~   76 (145)
T PF03564_consen    1 FDG--DPSEWPEFIDQFDSLVHENPDLSDIEKLNYLRSCLKGEAKELIRGLPL--SEENYEEAWELLEERYGNPRRIIQA   76 (145)
T ss_pred             CCC--CHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHhcchHHHHHHcccc--cchhhHHHHHHHHHHhCCchHHHHH
Confidence            899  7866555444   44444 57899999999999999999999998864  4579999999999999999853  4


Q ss_pred             HHHHhhcccc-----cccHhhHHHHHHHHHHHhC----CCCHHHHHHHHHhhcchhHHhHccc
Q 036272          121 SFGDLCKLKQ-----TGTVSDYQPQFERLLARAG----SLTDKQEAACFISGLKDGLRADVRA  174 (383)
Q Consensus       121 ~~~~l~~~~q-----~~sv~~Y~~~f~~l~~~~~----~~~e~~~~~~f~~gL~~~l~~~l~~  174 (383)
                      ...+|.++..     .+.+..++..++.+...+.    ..++..++..++..||+.++..|..
T Consensus        77 ~~~~l~~l~~~~~~d~~~L~~~~~~v~~~i~~L~~lg~~~~~~~l~~~i~~KLp~~~~~~w~~  139 (145)
T PF03564_consen   77 LLEELRNLPPISNDDPEALRSLVDKVNNCIRALKALGVNVDDPLLISIILSKLPPEIREKWEE  139 (145)
T ss_pred             HHHHHhccccccchhHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHCCHHHHHHHHH
Confidence            6677877774     5677888888888877762    3467789999999999999998864

>PF13650 Asp_protease_2: Aspartyl protease

Probab=98.95  E-value=4.7e-09  Score=77.13  Aligned_cols=72  Identities=25%  Similarity=0.373  Sum_probs=58.2

Q ss_pred             EEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCC-ceEEEEeCCCeEecCceeeceEEEecCeeeeeeec
Q 036272          309 VHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSC-LFSVVVANGERLSSPGRCKGVRLTLQDVPIENIEA  382 (383)
Q Consensus       309 ~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~-~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~~~~~  382 (383)
                      |.+.+||+++.+||||||+.++|+++++++++++..+.. ...+..++|......+.  .-.++|++.++.++.+
T Consensus         1 V~v~vng~~~~~liDTGa~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~--~~~i~ig~~~~~~~~~   73 (90)
T PF13650_consen    1 VPVKVNGKPVRFLIDTGASISVISRSLAKKLGLKPRPKSVPISVSGAGGSVTVYRGR--VDSITIGGITLKNVPF   73 (90)
T ss_pred             CEEEECCEEEEEEEcCCCCcEEECHHHHHHcCCCCcCCceeEEEEeCCCCEEEEEEE--EEEEEECCEEEEeEEE
Confidence            357899999999999999999999999999999887764 56777888884443333  3489999999987654

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

Probab=98.84  E-value=1.1e-08  Score=78.23  Aligned_cols=75  Identities=15%  Similarity=0.225  Sum_probs=50.8

Q ss_pred             CcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          304 PHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       304 ~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      ...+++.+.+||++++|+|||||.+|+||.++|+++||...-.....-....-....+.|..-.+++.|++..++
T Consensus        22 v~mLyI~~~ing~~vkA~VDtGAQ~tims~~~a~r~gL~~lid~r~~g~a~GvG~~~i~G~Ih~~~l~ig~~~~~   96 (124)
T PF09668_consen   22 VSMLYINCKINGVPVKAFVDTGAQSTIMSKSCAERCGLMRLIDKRFAGVAKGVGTQKILGRIHSVQLKIGGLFFP   96 (124)
T ss_dssp             ----EEEEEETTEEEEEEEETT-SS-EEEHHHHHHTTGGGGEEGGG-EE-------EEEEEEEEEEEEETTEEEE
T ss_pred             cceEEEEEEECCEEEEEEEeCCCCccccCHHHHHHcCChhhccccccccccCCCcCceeEEEEEEEEEECCEEEE
Confidence            357999999999999999999999999999999999995432222222222225667888888899999997664

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.

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

Probab=98.83  E-value=1.3e-08  Score=74.69  Aligned_cols=68  Identities=16%  Similarity=0.214  Sum_probs=59.1

Q ss_pred             EEEEcC-eEEEEEeeCCCcchhccHHHHHHhC---CccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          310 HSQISK-IPLTILIDSGSTHNYLHHRFAKITR---IKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       310 ~~~i~~-~~v~~LiDsGAt~s~Is~~~~~~l~---l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      .+.++| .+++++|||||++|+|+.+++++|+   .+....+...+..++|+.+...|. ..+.+.+++..+.
T Consensus         2 ~~~i~g~~~v~~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~~~G~-~~~~v~~~~~~~~   73 (93)
T cd05481           2 DMKINGKQSVKFQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIPVEGG-VKLKCRYRNPKYN   73 (93)
T ss_pred             ceEeCCceeEEEEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEeeeeEE-EEEEEEECCcEEE
Confidence            356788 9999999999999999999999998   555566678999999999999999 4699999988754

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

>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family

Probab=98.76  E-value=6.4e-08  Score=74.90  Aligned_cols=77  Identities=18%  Similarity=0.261  Sum_probs=61.5

Q ss_pred             CcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCC-ceEEEEeCCCeEecCceeeceEEEecCeeeeeeec
Q 036272          304 PHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSC-LFSVVVANGERLSSPGRCKGVRLTLQDVPIENIEA  382 (383)
Q Consensus       304 ~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~-~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~~~~~  382 (383)
                      ...+.+.+.|||.++.+||||||++++|+.++|++|++...... ...+..++|....  .....-.|.|+++.++++.+
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            35688999999999999999999999999999999999765433 4667778886442  33344678999999888765

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).

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

Probab=98.76  E-value=5.4e-08  Score=72.35  Aligned_cols=74  Identities=19%  Similarity=0.266  Sum_probs=59.9

Q ss_pred             ceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeeeeee
Q 036272          306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIENIE  381 (383)
Q Consensus       306 ~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~~~~  381 (383)
                      .+.+.+.+|+.++.+||||||++++|++.+++++++...+.....+..++|........  .-.|.|++..|.++.
T Consensus         2 ~~~v~v~i~~~~~~~llDTGa~~s~i~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~--~~~i~ig~~~~~~~~   75 (96)
T cd05483           2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAARVR--LDSLQIGGITLRNVP   75 (96)
T ss_pred             cEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCccCCCcEEEEecCCCccceEEE--cceEEECCcEEeccE
Confidence            36788999999999999999999999999999998744444566777788876665544  567899999887764

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.

>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=98.66  E-value=8.8e-09  Score=50.18  Aligned_cols=17  Identities=29%  Similarity=0.866  Sum_probs=16.0

Q ss_pred             cccccCCCcccccccce
Q 036272          252 LCYSCDENYTVGHKCKK  268 (383)
Q Consensus       252 ~Cf~C~~~GH~a~~Cp~  268 (383)
                      .||+|++.||++++||+
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            69999999999999985

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 ....

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

Probab=98.66  E-value=1.7e-07  Score=73.43  Aligned_cols=75  Identities=13%  Similarity=0.205  Sum_probs=64.6

Q ss_pred             CcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          304 PHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       304 ~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      ..+..+++.++|.++.+|+||||-.|||+.+.+++|+|+....++..++..-+.........+.+++.+++..+.
T Consensus        32 g~T~~v~l~~~~t~i~vLfDSGSPTSfIr~di~~kL~L~~~~app~~fRG~vs~~~~~tsEAv~ld~~i~n~~i~  106 (177)
T PF12384_consen   32 GKTAIVQLNCKGTPIKVLFDSGSPTSFIRSDIVEKLELPTHDAPPFRFRGFVSGESATTSEAVTLDFYIDNKLID  106 (177)
T ss_pred             CcEEEEEEeecCcEEEEEEeCCCccceeehhhHHhhCCccccCCCEEEeeeccCCceEEEEeEEEEEEECCeEEE
Confidence            356778888999999999999999999999999999999999999999977655555556667799999998875

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 [].

>cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein

Probab=98.62  E-value=8.9e-08  Score=68.66  Aligned_cols=70  Identities=17%  Similarity=0.156  Sum_probs=53.6

Q ss_pred             EEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccc-cC-CceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          309 VHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPE-RS-CLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       309 ~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~-~~-~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      +.+++||.+++|+|||||.+|+||+..|+++||... .. ..--+..+-|...+.+|..-.+++.|++..++
T Consensus         1 vnCk~nG~~vkAfVDsGaQ~timS~~caercgL~r~v~~~r~~g~A~gvgt~~kiiGrih~~~ikig~~~~~   72 (103)
T cd05480           1 VSCQCAGKELRALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSLPTSVKVIGQIERLVLQLGQLTVE   72 (103)
T ss_pred             CceeECCEEEEEEEecCCchhhcCHHHHHHcChHhhhhhccccccccCCCcceeEeeEEEEEEEEeCCEEee
Confidence            357899999999999999999999999999998633 22 11122223455578889988999999987654

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=98.60  E-value=5.5e-08  Score=72.97  Aligned_cols=71  Identities=15%  Similarity=0.159  Sum_probs=55.8

Q ss_pred             cceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeeee
Q 036272          305 HTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIEN  379 (383)
Q Consensus       305 ~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~~  379 (383)
                      ....+.+.++|.++.|||||||++|+|+++.+..+...  +.....+..++|.. ...|.. .+.+.+++..+.+
T Consensus         4 ~rp~i~v~i~g~~i~~LlDTGA~vsiI~~~~~~~~~~~--~~~~~~v~~~~g~~-~~~~~~-~~~v~~~~~~~~~   74 (100)
T PF00077_consen    4 NRPYITVKINGKKIKALLDTGADVSIISEKDWKKLGPP--PKTSITVRGAGGSS-SILGST-TVEVKIGGKEFNH   74 (100)
T ss_dssp             SSSEEEEEETTEEEEEEEETTBSSEEESSGGSSSTSSE--EEEEEEEEETTEEE-EEEEEE-EEEEEETTEEEEE
T ss_pred             CCceEEEeECCEEEEEEEecCCCcceeccccccccccc--ccCCceeccCCCcc-eeeeEE-EEEEEEECccceE
Confidence            34678889999999999999999999999988877654  33345565566666 666654 6999999998876

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 ....

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

Probab=98.50  E-value=5.3e-07  Score=65.39  Aligned_cols=65  Identities=14%  Similarity=0.228  Sum_probs=48.2

Q ss_pred             EEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeece-EEEecCeeeee
Q 036272          310 HSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGV-RLTLQDVPIEN  379 (383)
Q Consensus       310 ~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~-~v~i~~~~~~~  379 (383)
                      .+.|||.++.+||||||+.++|+...++++.   .......+..++|........  .+ .|.++++++.+
T Consensus         2 ~v~InG~~~~fLvDTGA~~tii~~~~a~~~~---~~~~~~~v~gagG~~~~~v~~--~~~~v~vg~~~~~~   67 (86)
T cd06095           2 TITVEGVPIVFLVDTGATHSVLKSDLGPKQE---LSTTSVLIRGVSGQSQQPVTT--YRTLVDLGGHTVSH   67 (86)
T ss_pred             EEEECCEEEEEEEECCCCeEEECHHHhhhcc---CCCCcEEEEeCCCcccccEEE--eeeEEEECCEEEEE
Confidence            4679999999999999999999999999972   233567777788876212222  23 47888887764

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

>COG3577 Predicted aspartyl protease [General function prediction only]

Probab=98.36  E-value=1.9e-06  Score=70.40  Aligned_cols=76  Identities=20%  Similarity=0.287  Sum_probs=63.5

Q ss_pred             cceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCC-ceEEEEeCCCeEecCceeeceEEEecCeeeeeeec
Q 036272          305 HTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSC-LFSVVVANGERLSSPGRCKGVRLTLQDVPIENIEA  382 (383)
Q Consensus       305 ~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~-~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~~~~~  382 (383)
                      ..+.+.+.|||+.+.+|||||||...++++.|+++|+..-+.. +..+.++||......=  +.=.|.|+++.+.+++|
T Consensus       104 GHF~a~~~VNGk~v~fLVDTGATsVal~~~dA~RlGid~~~l~y~~~v~TANG~~~AA~V--~Ld~v~IG~I~~~nV~A  180 (215)
T COG3577         104 GHFEANGRVNGKKVDFLVDTGATSVALNEEDARRLGIDLNSLDYTITVSTANGRARAAPV--TLDRVQIGGIRVKNVDA  180 (215)
T ss_pred             CcEEEEEEECCEEEEEEEecCcceeecCHHHHHHhCCCccccCCceEEEccCCccccceE--EeeeEEEccEEEcCchh
Confidence            4688899999999999999999999999999999999887765 6888889998654432  23567888888888876

>PF14893 PNMA: PNMA

Probab=98.31  E-value=1.1e-05  Score=72.75  Aligned_cols=135  Identities=21%  Similarity=0.270  Sum_probs=104.8

Q ss_pred             CCCCCCCCccCCCCh-------HHHHHHHHHHHHHhC-CchhhHHHHhhhhcccchhhHHHHhhhcCCCCCHHHHHHHHH
Q 036272           39 LAKLDFPCYDGSEDP-------TLWICRAEQFFEFQG-TSLENQVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLL  110 (383)
Q Consensus        39 ~~~~~~p~F~G~~d~-------~~w~~~~e~~~~~~~-~~d~~k~~~~~~~L~g~A~~w~~~~~~~~~~~~w~~~~~~l~  110 (383)
                      +.-.+++.|+|...+       +.|+.++...+..-. ++|.++...+...|.|+|..+.+.+....+..+-.++++.|.
T Consensus       161 ~~y~~L~iFSG~~~~~~gee~fe~Wl~~a~~~v~~W~~~~e~ekrrrlle~L~GpA~~~~r~l~~~nP~~t~~~~l~aL~  240 (331)
T PF14893_consen  161 IAYRDLRIFSGREEPAPGEESFESWLEHANEMVKKWNDVSEEEKRRRLLESLRGPALDSRRKLQKKNPKQTAQDCLKALG  240 (331)
T ss_pred             hhhhhhhhhcCCCCCCCCcccHHHHHHHHHHHHHhccCCchhhchhhhHHhcccHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence            334567799997433       479999987776544 789999999999999999999999877677789999999999


Q ss_pred             hhhcCcccc-cHHHHhhcccc--cccHhhHHHHHHHHHHHh---CCC----CHHHHHHHHHhh-c-chhHHhHcc
Q 036272          111 AKFAATEYE-DSFGDLCKLKQ--TGTVSDYQPQFERLLARA---GSL----TDKQEAACFISG-L-KDGLRADVR  173 (383)
Q Consensus       111 ~~F~~~~~~-~~~~~l~~~~q--~~sv~~Y~~~f~~l~~~~---~~~----~e~~~~~~f~~g-L-~~~l~~~l~  173 (383)
                      ..|+++... +...++.+..|  +|++.+|+.+++.+...+   +.+    .+...+..++.+ . ...++.+++
T Consensus       241 ~~Fg~~es~~~~~~kf~~~~Q~~~E~ls~yv~RlE~lLqkav~k~a~~p~~adq~rl~q~l~~a~~~e~lq~klr  315 (331)
T PF14893_consen  241 QVFGSSESRETLEAKFLNTFQEPGEKLSAYVKRLESLLQKAVEKGAIKPSEADQVRLRQVLSGAVLSESLQDKLR  315 (331)
T ss_pred             HhcCCcccHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHhcCCCccccCHHHHHHHHccCCCCHHHHHHHH
Confidence            999999986 57778878777  999999999999998885   222    345555565544 3 444555443

>cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases

Probab=98.12  E-value=2.3e-05  Score=56.36  Aligned_cols=69  Identities=22%  Similarity=0.330  Sum_probs=54.5

Q ss_pred             EEEEcCeEEEEEeeCCCcchhccHHHHHHhCC-ccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          310 HSQISKIPLTILIDSGSTHNYLHHRFAKITRI-KPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       310 ~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l-~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      .+.+++..+.+|+|+||++++++..++.++++ .........+...+|......+.+..+.+.+.+.++.
T Consensus         2 ~~~~~~~~~~~liDtgs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~   71 (92)
T cd00303           2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFT   71 (92)
T ss_pred             EEEECCEEEEEEEcCCCcccccCHHHHHHcCCCcccCCCceEEEecCCCEeccCcEEEEEEEEeCCEEEE
Confidence            35578899999999999999999999999987 4444456677778888777777766788888876654

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

>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family

Probab=98.04  E-value=2.6e-05  Score=58.89  Aligned_cols=59  Identities=12%  Similarity=0.153  Sum_probs=47.2

Q ss_pred             CeEEEEEeeCCCcchh-ccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeee
Q 036272          315 KIPLTILIDSGSTHNY-LHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPI  377 (383)
Q Consensus       315 ~~~v~~LiDsGAt~s~-Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~  377 (383)
                      ..++.+||||||+..+ |+.+.|++||++...  ...+.++||......-  ....|.++|+..
T Consensus        14 ~~~v~~LVDTGat~~~~l~~~~a~~lgl~~~~--~~~~~tA~G~~~~~~v--~~~~v~igg~~~   73 (107)
T TIGR03698        14 FMEVRALVDTGFSGFLLVPPDIVNKLGLPELD--QRRVYLADGREVLTDV--AKASIIINGLEI   73 (107)
T ss_pred             ceEEEEEEECCCCeEEecCHHHHHHcCCCccc--CcEEEecCCcEEEEEE--EEEEEEECCEEE
Confidence            3489999999999997 999999999997754  5689999997555543  357788888765

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.

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

Probab=98.04  E-value=7.7e-06  Score=72.39  Aligned_cols=73  Identities=15%  Similarity=0.257  Sum_probs=57.7

Q ss_pred             cceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCC-ceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          305 HTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSC-LFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       305 ~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~-~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      ..++|++.|||++|+|+|||||..|+||..+|+++||...=.+ -.-+.-+-| ..+++|..-.++|.|.+..++
T Consensus       234 ~ML~iN~~ing~~VKAfVDsGaq~timS~~Caer~gL~rlid~r~~g~a~gvg-~~ki~g~Ih~~~lki~~~~l~  307 (380)
T KOG0012|consen  234 TMLYINCEINGVPVKAFVDSGAQTTIMSAACAERCGLNRLIDKRFQGEARGVG-TEKILGRIHQAQLKIEDLYLP  307 (380)
T ss_pred             eEEEEEEEECCEEEEEEEcccchhhhhhHHHHHHhChHHHhhhhhhccccCCC-cccccceeEEEEEEeccEeec
Confidence            4689999999999999999999999999999999998554322 222222333 778889888999999877653

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

Probab=97.90  E-value=2.2e-05  Score=64.52  Aligned_cols=45  Identities=16%  Similarity=0.278  Sum_probs=33.9

Q ss_pred             eEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEec
Q 036272          316 IPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSS  361 (383)
Q Consensus       316 ~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~  361 (383)
                      .++++|+||||+.|||+++++++|+|+..+.....+ ...|.....
T Consensus        11 ~~~~~LlDsGSq~SfIt~~la~~L~L~~~~~~~~~~-~~~g~~~~~   55 (164)
T PF05585_consen   11 VEARALLDSGSQRSFITESLANKLNLPGTGEKILVI-GTFGSSSPK   55 (164)
T ss_pred             EEEEEEEecCCchhHHhHHHHHHhCCCCCCceEEEE-eccCccCcc
Confidence            478999999999999999999999998877653333 333443333

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

>cd06094 RP_Saci_like RP_Saci_like, retropepsin family

Probab=97.73  E-value=5.2e-05  Score=53.84  Aligned_cols=59  Identities=22%  Similarity=0.313  Sum_probs=46.0

Q ss_pred             CeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCe-eee
Q 036272          315 KIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDV-PIE  378 (383)
Q Consensus       315 ~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~-~~~  378 (383)
                      ...+.+||||||.+|+|.....+..    ....+..+..+||..+.+-|.. .+.|.++.+ +|+
T Consensus         7 ~s~~~fLVDTGA~vSviP~~~~~~~----~~~~~~~l~AANgt~I~tyG~~-~l~ldlGlrr~~~   66 (89)
T cd06094           7 TSGLRFLVDTGAAVSVLPASSTKKS----LKPSPLTLQAANGTPIATYGTR-SLTLDLGLRRPFA   66 (89)
T ss_pred             CCCcEEEEeCCCceEeecccccccc----ccCCceEEEeCCCCeEeeeeeE-EEEEEcCCCcEEe
Confidence            3457899999999999999877653    2334578999999999999964 588888764 554

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

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

Probab=97.69  E-value=0.0003  Score=54.39  Aligned_cols=93  Identities=13%  Similarity=0.178  Sum_probs=72.9

Q ss_pred             HHHHHHHhhhcCccc---c---cHHHHhhcccc--cccHhhHHHHHHHHHHHhC----CCCHHHHHHHHHhhcchhHHhH
Q 036272          104 GLKAGLLAKFAATEY---E---DSFGDLCKLKQ--TGTVSDYQPQFERLLARAG----SLTDKQEAACFISGLKDGLRAD  171 (383)
Q Consensus       104 ~~~~~l~~~F~~~~~---~---~~~~~l~~~~q--~~sv~~Y~~~f~~l~~~~~----~~~e~~~~~~f~~gL~~~l~~~  171 (383)
                      ++++.|...|.....   .   .+..+|.+++.  ++++.+|+.+|..++..+.    .+++..++..+++|||+.....
T Consensus         5 e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~g~~i~d~~~v~~iL~~Lp~~y~~~   84 (119)
T PF14223_consen    5 EAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAIGKPISDEDLVSKILRSLPPSYDTF   84 (119)
T ss_pred             HHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhcCCcccchhHHHHHHhcCCchhHHH
Confidence            566677778887765   3   35678888884  9999999999999998882    5789999999999999876655


Q ss_pred             cc---cc-CCC--CHHHHHHHHHHHHHHHhh
Q 036272          172 VR---AQ-NPQ--NLSAAIGLARNYELKAQE  196 (383)
Q Consensus       172 l~---~~-~~~--~l~~~~~~a~~~e~~~~~  196 (383)
                      +.   .. +..  ++++++......|.....
T Consensus        85 ~~~i~~~~~~~~~t~~el~~~L~~~E~~~~~  115 (119)
T PF14223_consen   85 VTAIRNSKDLPKMTLEELISRLLAEEMRLKS  115 (119)
T ss_pred             HHHHHhcCCCCcCCHHHHHHHHHHHHHHHHH
Confidence            54   22 334  899999999998876543

>cd05482 HIV_retropepsin_like Retropepsins, pepsin-like aspartate proteases

Probab=97.49  E-value=0.00042  Score=49.71  Aligned_cols=63  Identities=11%  Similarity=-0.011  Sum_probs=41.8

Q ss_pred             EEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCee
Q 036272          310 HSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVP  376 (383)
Q Consensus       310 ~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~  376 (383)
                      .+.++|+.+.+|+||||++++|++..+...   .........+.+-|..+...... .+.+++++..
T Consensus         2 ~~~i~g~~~~~llDTGAd~Tvi~~~~~p~~---w~~~~~~~~i~GIGG~~~~~~~~-~v~i~i~~~~   64 (87)
T cd05482           2 TLYINGKLFEGLLDTGADVSIIAENDWPKN---WPIQPAPSNLTGIGGAITPSQSS-VLLLEIDGEG   64 (87)
T ss_pred             EEEECCEEEEEEEccCCCCeEEcccccCCC---CccCCCCeEEEeccceEEEEEEe-eEEEEEcCCe
Confidence            467889999999999999999998543221   10111235555666655555443 5888888753

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

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

Probab=97.48  E-value=0.00022  Score=50.75  Aligned_cols=61  Identities=11%  Similarity=0.172  Sum_probs=41.2

Q ss_pred             EEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          317 PLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       317 ~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      .+-+||||||.+++|.+..++.++|+..|.....+. +.--....-.+...+.+.++|+.+.
T Consensus        47 sipclidtgaq~niiteetvrahklptrpw~~sviy-ggvyp~kinrkt~kl~i~lngisik  107 (137)
T PF12382_consen   47 SIPCLIDTGAQVNIITEETVRAHKLPTRPWSQSVIY-GGVYPNKINRKTIKLNINLNGISIK  107 (137)
T ss_pred             cceeEEccCceeeeeehhhhhhccCCCCcchhheEe-ccccccccccceEEEEEEecceEEE
Confidence            446899999999999999999999999887543222 2111222333344566677776553

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=97.42  E-value=5e-05  Score=42.43  Aligned_cols=18  Identities=17%  Similarity=0.438  Sum_probs=16.9

Q ss_pred             ccccccCCCcccccccce
Q 036272          251 ELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ..|+.|+++||+.++||.
T Consensus         9 Y~C~~C~~~GH~i~dCP~   26 (32)
T PF13696_consen    9 YVCHRCGQKGHWIQDCPT   26 (32)
T ss_pred             CEeecCCCCCccHhHCCC
Confidence            679999999999999996

>PF02160 Peptidase_A3: Cauliflower mosaic virus peptidase (A3); InterPro: IPR000588 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=97.23  E-value=0.00067  Score=56.31  Aligned_cols=62  Identities=15%  Similarity=0.147  Sum_probs=48.3

Q ss_pred             eEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          316 IPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       316 ~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      ..+.++|||||+++++++..+-.-...- ...+..|..+|++......++..+.+.|.|..|.
T Consensus        19 ~~~~~~vDTGAt~C~~~~~iiP~e~we~-~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~   80 (201)
T PF02160_consen   19 FNYHCYVDTGATICCASKKIIPEEYWEK-SKKPIKVKGANGSIIQINKKAKNGKIQIADKIFR   80 (201)
T ss_pred             EEEEEEEeCCCceEEecCCcCCHHHHHh-CCCcEEEEEecCCceEEEEEecCceEEEccEEEe
Confidence            4678999999999998887652211111 1125789999999999999999999999998885

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

>PF14227 UBN2_2: gag-polypeptide of LTR copia-type

Probab=96.84  E-value=0.015  Score=44.85  Aligned_cols=93  Identities=18%  Similarity=0.226  Sum_probs=72.2

Q ss_pred             HHHHHHHHhhhcCcccc---cHHHHhhcccc--cccHhhHHHHHHHHHHHhC----CCCHHHHHHHHHhhcchhHHhHcc
Q 036272          103 DGLKAGLLAKFAATEYE---DSFGDLCKLKQ--TGTVSDYQPQFERLLARAG----SLTDKQEAACFISGLKDGLRADVR  173 (383)
Q Consensus       103 ~~~~~~l~~~F~~~~~~---~~~~~l~~~~q--~~sv~~Y~~~f~~l~~~~~----~~~e~~~~~~f~~gL~~~l~~~l~  173 (383)
                      .++++.|...|......   ...++|..++.  +.++.+|+.+|+.+...+.    .++++.++..++.+||+.....+.
T Consensus         5 ~~~W~~L~~~y~~~~~~~~~~l~~kl~~~k~~~~~~v~~hi~~~~~l~~~L~~~g~~i~d~~~~~~lL~sLP~sy~~~~~   84 (119)
T PF14227_consen    5 KEMWDKLKKKYEKKSFANKIYLLRKLYSLKMDEGGSVRDHINEFRSLVNQLKSLGVPIDDEDKVIILLSSLPPSYDSFVT   84 (119)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHhHhccchhHHHHHHHHHHHHHhhccccccchHHHHHHHHHHcCCHhHHHHHH
Confidence            35667788888887763   35678888876  7899999999999999983    468999999999999998776663


Q ss_pred             c--c----CCCCHHHHHHHHHHHHHHHh
Q 036272          174 A--Q----NPQNLSAAIGLARNYELKAQ  195 (383)
Q Consensus       174 ~--~----~~~~l~~~~~~a~~~e~~~~  195 (383)
                      .  .    ...++++++......|....
T Consensus        85 ~l~~~~~~~~~tl~~v~~~L~~ee~~~~  112 (119)
T PF14227_consen   85 ALLYSKPEDELTLEEVKSKLLQEEERRK  112 (119)
T ss_pred             HHHccCCCCCcCHHHHHHHHHHHHHHHH
Confidence            2  2    34688888888877665443

>smart00343 ZnF_C2HC zinc finger

Probab=96.76  E-value=0.00055  Score=36.98  Aligned_cols=17  Identities=29%  Similarity=0.907  Sum_probs=15.6

Q ss_pred             cccccCCCcccccccce
Q 036272          252 LCYSCDENYTVGHKCKK  268 (383)
Q Consensus       252 ~Cf~C~~~GH~a~~Cp~  268 (383)
                      .||+|++.||++++||.
T Consensus         1 ~C~~CG~~GH~~~~C~~   17 (26)
T smart00343        1 KCYNCGKEGHIARDCPK   17 (26)
T ss_pred             CCccCCCCCcchhhCCc
Confidence            49999999999999984

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

Probab=96.42  E-value=0.001  Score=37.99  Aligned_cols=22  Identities=18%  Similarity=0.510  Sum_probs=13.1

Q ss_pred             CccccccCCCcccccccceeEE
Q 036272          250 QELCYSCDENYTVGHKCKKLFF  271 (383)
Q Consensus       250 ~~~Cf~C~~~GH~a~~Cp~~~~  271 (383)
                      .++|++|++..|.+++|....-
T Consensus         2 ~~~CprC~kg~Hwa~~C~sk~d   23 (36)
T PF14787_consen    2 PGLCPRCGKGFHWASECRSKTD   23 (36)
T ss_dssp             --C-TTTSSSCS-TTT---TCC
T ss_pred             CccCcccCCCcchhhhhhhhhc
Confidence            3689999999999999986543

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=96.35  E-value=0.0015  Score=39.43  Aligned_cols=19  Identities=16%  Similarity=0.424  Sum_probs=17.2

Q ss_pred             CccccccCCCcccccccce
Q 036272          250 QELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       250 ~~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ...|.+|++.||+..+|++
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            3679999999999999994

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

Probab=95.82  E-value=0.0032  Score=51.44  Aligned_cols=22  Identities=27%  Similarity=0.779  Sum_probs=18.2

Q ss_pred             hhhcCccccccCCCcccccccc
Q 036272          246 RRREQELCYSCDENYTVGHKCK  267 (383)
Q Consensus       246 ~~~~~~~Cf~C~~~GH~a~~Cp  267 (383)
                      .+.+...||+||+.||+++|||
T Consensus        56 ~~~~~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          56 IREENPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             ccccccccchhcccCcccccCC
Confidence            3345567999999999999999

>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=95.77  E-value=0.035  Score=40.71  Aligned_cols=71  Identities=17%  Similarity=0.244  Sum_probs=53.2

Q ss_pred             HHHhhcccc--cccHhhHHHHHHHHHHHh--CCC-C-----HHHHHHHHHhhcchhHHhHccccCCCCHHHHHHHHHHHH
Q 036272          122 FGDLCKLKQ--TGTVSDYQPQFERLLARA--GSL-T-----DKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYE  191 (383)
Q Consensus       122 ~~~l~~~~q--~~sv~~Y~~~f~~l~~~~--~~~-~-----e~~~~~~f~~gL~~~l~~~l~~~~~~~l~~~~~~a~~~e  191 (383)
                      ..+|+..+.  +++..+++.++..|+..=  +.. +     |-.++..|+..||++++..+..+.|.+..++..+|..+.
T Consensus         6 r~~FR~~~~~~~~~p~e~~~rL~~l~~~WL~pe~~tkeqi~ellvlEQFL~~lP~e~~~wV~e~~p~s~~ea~~Lae~~~   85 (95)
T PF02023_consen    6 RQRFRSFQYQEGEGPREFLSRLRELCDRWLQPEVHTKEQILELLVLEQFLNILPPEVQTWVRERKPESAEEAVALAEDYQ   85 (95)
T ss_dssp             HHHHHT--CCTTTSHHHHHHHHHHHHHHHH-TTTS-HHHHHHHHHHHHHHHHS-HHHHHHHHTCS-SSHHHHHHHHHHHH
T ss_pred             HHHHhCCCCCCCCCHHHHHHHHHHHHHHhCccccCcHHHHHHHHHHHHHHHHCCHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence            345555554  788899999999887654  222 2     346788999999999999999999999999999998876


Q ss_pred             H
Q 036272          192 L  192 (383)
Q Consensus       192 ~  192 (383)
                      .
T Consensus        86 ~   86 (95)
T PF02023_consen   86 R   86 (95)
T ss_dssp             C
T ss_pred             H
Confidence            3

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.

>PF14244 UBN2_3: gag-polypeptide of LTR copia-type

Probab=95.67  E-value=0.081  Score=42.74  Aligned_cols=107  Identities=16%  Similarity=0.170  Sum_probs=69.0

Q ss_pred             CCCCCCCccCCCChHHHHHHHHHHHHHhCC----------chhhHHHHhh-hhcccchhhHHHHhhhc------CCCCCH
Q 036272           40 AKLDFPCYDGSEDPTLWICRAEQFFEFQGT----------SLENQVKLAA-YHLENDAQLWFQQRKNQ------GHLVTW  102 (383)
Q Consensus        40 ~~~~~p~F~G~~d~~~w~~~~e~~~~~~~~----------~d~~k~~~~~-~~L~g~A~~w~~~~~~~------~~~~~w  102 (383)
                      ..+.+++++|+ |+..|...++.++...+.          |+.....|.. ..-...+..|+......      ....+=
T Consensus         6 ~~i~~~kL~g~-NY~~W~~~~~~~L~~~~l~~~i~g~~~~P~~~~~~~~~W~~~d~~v~swl~~sis~~i~~~i~~~~ta   84 (152)
T PF14244_consen    6 QPITSIKLNGS-NYLSWSQQMEMALRGKGLWGFIDGTIPKPPETDPAYEKWERKDQLVLSWLLNSISPDILSTIIFCETA   84 (152)
T ss_pred             CcccccCCCCc-cHHHHHHHHHHHHHhCCCcccccCccccccccchhhhhHHHhhhHHHHHHHHhhcHHHHhhhHhhhhH
Confidence            34556788995 999999999999987542          1111111111 12233355566442110      012344


Q ss_pred             HHHHHHHHhhhcCcc-cc---cHHHHhhcccc-cccHhhHHHHHHHHHHH
Q 036272          103 DGLKAGLLAKFAATE-YE---DSFGDLCKLKQ-TGTVSDYQPQFERLLAR  147 (383)
Q Consensus       103 ~~~~~~l~~~F~~~~-~~---~~~~~l~~~~q-~~sv~~Y~~~f~~l~~~  147 (383)
                      .++.+.|..+|.... ..   +...+|..++| +.++.+|+.+|..|...
T Consensus        85 k~~W~~L~~~f~~~~~~~r~~~L~~~l~~~kq~~~sv~ey~~~lk~l~~~  134 (152)
T PF14244_consen   85 KEIWDALKERFSQKSNASRVFQLRNELHSLKQGDKSVTEYFNKLKSLWQE  134 (152)
T ss_pred             HHHHHHHHHHhhcccHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHhHH
Confidence            467788888898777 32   46688999999 99999999999999843

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

Probab=95.37  E-value=0.0055  Score=50.05  Aligned_cols=19  Identities=26%  Similarity=0.753  Sum_probs=16.8

Q ss_pred             ccccccCCCccccccc-cee
Q 036272          251 ELCYSCDENYTVGHKC-KKL  269 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~C-p~~  269 (383)
                      .+||+||+.||++++| |++
T Consensus        98 ~~C~~Cg~~GH~~~dC~P~~  117 (190)
T COG5082          98 KKCYNCGETGHLSRDCNPSK  117 (190)
T ss_pred             cccccccccCccccccCccc
Confidence            5799999999999999 554

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=95.31  E-value=0.0059  Score=38.68  Aligned_cols=19  Identities=21%  Similarity=0.676  Sum_probs=17.0

Q ss_pred             CccccccCCCcccccccce
Q 036272          250 QELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       250 ~~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ...||+||..||...+||+
T Consensus        31 p~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   31 PRFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             ChhhcCCCCcCcCHhHcCC
Confidence            3579999999999999984

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=94.59  E-value=0.016  Score=34.26  Aligned_cols=20  Identities=15%  Similarity=0.386  Sum_probs=16.3

Q ss_pred             ccccccCCCcccc--cccceeE
Q 036272          251 ELCYSCDENYTVG--HKCKKLF  270 (383)
Q Consensus       251 ~~Cf~C~~~GH~a--~~Cp~~~  270 (383)
                      .+|.+||..||++  +.||...
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~   23 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYC   23 (40)
T ss_pred             ccccccccccccccCccCCCCC
Confidence            4699999999998  5698643

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

Probab=94.13  E-value=0.021  Score=45.94  Aligned_cols=17  Identities=24%  Similarity=0.837  Sum_probs=10.9

Q ss_pred             cccccCCCcccccccce
Q 036272          252 LCYSCDENYTVGHKCKK  268 (383)
Q Consensus       252 ~Cf~C~~~GH~a~~Cp~  268 (383)
                      .||+|++.||++++||.
T Consensus       105 ~C~~Cg~~gH~~~~C~~  121 (148)
T PTZ00368        105 ACYNCGGEGHISRDCPN  121 (148)
T ss_pred             hhcccCcCCcchhcCCC
Confidence            56666666666666655

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

Probab=94.11  E-value=0.16  Score=38.53  Aligned_cols=56  Identities=20%  Similarity=0.178  Sum_probs=42.4

Q ss_pred             EEEEEeeCCCc-chhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCee
Q 036272          317 PLTILIDSGST-HNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVP  376 (383)
Q Consensus       317 ~v~~LiDsGAt-~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~  376 (383)
                      ....|||||.+ -..|+.+.+++++++...  ...+..++|+...+.=  ....+.|+|+.
T Consensus        26 ~~~~LiDTGFtg~lvlp~~vaek~~~~~~~--~~~~~~a~~~~v~t~V--~~~~iki~g~e   82 (125)
T COG5550          26 VYDELIDTGFTGYLVLPPQVAEKLGLPLFS--TIRIVLADGGVVKTSV--ALATIKIDGVE   82 (125)
T ss_pred             EeeeEEecCCceeEEeCHHHHHhcCCCccC--ChhhhhhcCCEEEEEE--EEEEEEECCEE
Confidence            33459999999 899999999999986654  4677888888776633  24677788754

>PF02093 Gag_p30: Gag P30 core shell protein; InterPro: IPR003036 P30 is essential for viral assembly []

Probab=93.81  E-value=0.26  Score=41.15  Aligned_cols=70  Identities=13%  Similarity=0.186  Sum_probs=20.4

Q ss_pred             HHHhhcccc--cccHhhHHHHHHHHHHHhCCCCHH------HHHHHHHhhcchhHHhHccccC---CCCHHHHHHHHHHH
Q 036272          122 FGDLCKLKQ--TGTVSDYQPQFERLLARAGSLTDK------QEAACFISGLKDGLRADVRAQN---PQNLSAAIGLARNY  190 (383)
Q Consensus       122 ~~~l~~~~q--~~sv~~Y~~~f~~l~~~~~~~~e~------~~~~~f~~gL~~~l~~~l~~~~---~~~l~~~~~~a~~~  190 (383)
                      +.++..+.|  +|+...|+.++++..+.--.++++      .+...|+.---++|++++....   -.++.++++.|..+
T Consensus       126 lsKv~~v~Qg~~EsPs~FLeRL~ea~r~yTp~dP~~~~~~~~v~~~Fi~QsapDIrkKLq~~eg~~~~~l~~Ll~~A~kV  205 (211)
T PF02093_consen  126 LSKVREVTQGPNESPSAFLERLREAYRKYTPFDPESPEGQASVAMSFITQSAPDIRKKLQKLEGLQGKTLSELLKEAEKV  205 (211)
T ss_dssp             --S--TTTTTGGGHHHHHHHHHHHHHHHTS--------------------------------------------------
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHHHHhcCCCCCCCCccchhHHHHHHHhccHHHHHHHHhhcCcccCCHHHHHHHHHHH
Confidence            344556677  899999999999998877434322      5777899999999999998654   57889999988765


Q ss_pred             H
Q 036272          191 E  191 (383)
Q Consensus       191 e  191 (383)
                      -
T Consensus       206 f  206 (211)
T PF02093_consen  206 F  206 (211)
T ss_dssp             -
T ss_pred             H
Confidence            4

Cleavage of P70 in vitro can be accompanied by a shift from a concentrically coiled internal strand ("immature") to a collapsed ("mature") form of the virus core [].; GO: 0019068 virion assembly; PDB: 3BP9_U 1U7K_D 2Y4Z_A 1BM4_A.

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

Probab=93.24  E-value=0.13  Score=44.72  Aligned_cols=18  Identities=22%  Similarity=0.628  Sum_probs=16.6

Q ss_pred             ccccccCCCcccccccce
Q 036272          251 ELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ..||+||++||+...||.
T Consensus       177 Y~CyRCGqkgHwIqnCpT  194 (427)
T COG5222         177 YVCYRCGQKGHWIQNCPT  194 (427)
T ss_pred             eeEEecCCCCchhhcCCC
Confidence            579999999999999985

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

Probab=91.80  E-value=0.07  Score=42.87  Aligned_cols=17  Identities=24%  Similarity=0.737  Sum_probs=14.5

Q ss_pred             cccccCCCcccccccce
Q 036272          252 LCYSCDENYTVGHKCKK  268 (383)
Q Consensus       252 ~Cf~C~~~GH~a~~Cp~  268 (383)
                      +||+|++.||++++||.
T Consensus         2 ~C~~C~~~GH~~~~c~~   18 (148)
T PTZ00368          2 VCYRCGGVGHQSRECPN   18 (148)
T ss_pred             cCCCCCCCCcCcccCcC
Confidence            58888888888888886

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

Probab=89.65  E-value=0.19  Score=44.60  Aligned_cols=18  Identities=33%  Similarity=0.879  Sum_probs=16.2

Q ss_pred             ccccccCCCcccccccce
Q 036272          251 ELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ..||+||+.||+.++||.
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~  161 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPE  161 (261)
T ss_pred             CccCCCCcCCcchhhCCC
Confidence            569999999999999994

>cd07936 SCAN SCAN oligomerization domain

Probab=89.56  E-value=1.5  Score=31.32  Aligned_cols=68  Identities=16%  Similarity=0.125  Sum_probs=51.7

Q ss_pred             HHhhcccc--cccHhhHHHHHHHHHHHh--CC-CC-----HHHHHHHHHhhcchhHHhHccccCCCCHHHHHHHHHHH
Q 036272          123 GDLCKLKQ--TGTVSDYQPQFERLLARA--GS-LT-----DKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNY  190 (383)
Q Consensus       123 ~~l~~~~q--~~sv~~Y~~~f~~l~~~~--~~-~~-----e~~~~~~f~~gL~~~l~~~l~~~~~~~l~~~~~~a~~~  190 (383)
                      .+++.+..  ..+..+++.++++|+..=  +. -+     +-..+..|+.-|+++++..+..+.|.+-.++..++..+
T Consensus         6 ~~FR~f~~~~~~~p~eal~~L~eLc~~WLrpe~~tkeqilelLVlEQfl~~lp~e~q~~v~~~~p~s~eea~~l~e~~   83 (85)
T cd07936           6 QRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLAEDL   83 (85)
T ss_pred             HHHhccccCCCCChHHHHHHHHHHHHHHcchhhcCHHHHHHHHHHHHHhhhCCHHHHHHHHhcCCCCHHHHHHHHHHh
Confidence            34455443  778889999998887764  11 12     23577889999999999999999999999999988654

The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.

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

Probab=89.46  E-value=0.14  Score=44.63  Aligned_cols=21  Identities=19%  Similarity=0.377  Sum_probs=18.3

Q ss_pred             ccccccCCCcccccccceeEE
Q 036272          251 ELCYSCDENYTVGHKCKKLFF  271 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~~~~  271 (383)
                      ..||.||+.||.+++||..+.
T Consensus       161 ~~cyrcGkeghwskEcP~~~~  181 (346)
T KOG0109|consen  161 SGCYRCGKEGHWSKECPVDRT  181 (346)
T ss_pred             HHheeccccccccccCCccCC
Confidence            459999999999999997654

>smart00431 SCAN leucine rich region

Probab=83.80  E-value=4.6  Score=30.49  Aligned_cols=69  Identities=20%  Similarity=0.228  Sum_probs=52.5

Q ss_pred             HHhhcccc--cccHhhHHHHHHHHHHHh--CCC-C-----HHHHHHHHHhhcchhHHhHccccCCCCHHHHHHHHHHHH
Q 036272          123 GDLCKLKQ--TGTVSDYQPQFERLLARA--GSL-T-----DKQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYE  191 (383)
Q Consensus       123 ~~l~~~~q--~~sv~~Y~~~f~~l~~~~--~~~-~-----e~~~~~~f~~gL~~~l~~~l~~~~~~~l~~~~~~a~~~e  191 (383)
                      .+++++..  ..+..+++.++++|+..=  +.. +     +-..+.+|+.-|+.+++..+..+.|.+-++++.++....
T Consensus         6 ~~FR~f~y~e~~gp~eaL~~L~eLc~~WLrPe~~tKeqilElLVlEQFL~ilP~e~q~wv~~~~p~sgeeav~l~E~l~   84 (113)
T smart00431        6 QRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLLEDLE   84 (113)
T ss_pred             HHhhccccCCCCChHHHHHHHHHHHHhhcChhhhhHHHHHHHHHHHHHhccCcHHHHHHHHhcCCCCHHHHHHHHHHhc
Confidence            34555544  678889999998887764  111 2     224678899999999999999999999999999987664

---

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	383
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-10
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	5e-06

>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 = 61.4 bits (148), Expect = 2e-10
 Identities = 73/431 (16%), Positives = 134/431 (31%), Gaps = 137/431 (31%)

Query: 23  QGQGGAGYAGGLVAPK--LAK---LDFPCYDGSEDPTLWI----CRAEQFFEFQGTSLEN 73
            G  G+G        K  +A    L +      +    W+    C + +      T LE 
Sbjct: 156 DGVLGSG--------KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPE------TVLEM 201

Query: 74  QVKLAAYHLENDAQLWFQQRKNQGHLVTWDGLKAGLLAKFAATEYEDS------------ 121
             KL  Y ++ +         N    +    ++A L     +  YE+             
Sbjct: 202 LQKLL-YQIDPNWTSRSDHSSNIKLRIHS--IQAELRRLLKSKPYENCLLVLLNVQNAKA 258

Query: 122 ---FGDLCKLKQTGTVSDYQPQFERLLARAGSLTDKQEAAC----FISGLKDGLRADVRA 174
              F   CK+  T T             R   +TD   AA      +      L  D   
Sbjct: 259 WNAFNLSCKILLT-T-------------RFKQVTDFLSAATTTHISLDHHSMTLTPD--- 301

Query: 175 QNPQNLSAAIGLARNYELKAQEIRR---SVNP----TFSSSVRNSSNQWNSSLTPSGSKT 227
              +  S    L +  + + Q++ R   + NP      + S+R+    W++    +  K 
Sbjct: 302 ---EVKSL---LLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKL 355

Query: 228 IN-LEMIFPIRNLTPIELQRRREQ--------------------ELCYSCDENYTVGHKC 266
              +E    +  L P E ++  ++                    ++  S      V +K 
Sbjct: 356 TTIIESS--LNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMV--VVNKL 411

Query: 267 KKLFFIEIDEEGEEATGEMYTEETPVISLHALA---GIQTPHTMRVHSQIS---KIP--- 317
            K   +E     +E+T          IS+ ++     ++  +   +H  I     IP   
Sbjct: 412 HKYSLVEKQ--PKEST----------ISIPSIYLELKVKLENEYALHRSIVDHYNIPKTF 459

Query: 318 ----LTILIDSGSTHNYL-HHRFAKITRIKPERSCLFSVVVAN----GERL---SSPGRC 365
               L         ++++ HH    I     ER  LF +V  +     +++   S+    
Sbjct: 460 DSDDLIPPYLDQYFYSHIGHH-LKNIEHP--ERMTLFRMVFLDFRFLEQKIRHDSTAWNA 516

Query: 366 KGVRL-TLQDV 375
            G  L TLQ +
Sbjct: 517 SGSILNTLQQL 527

>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 = 45.1 bits (106), Expect = 5e-06
 Identities = 10/77 (12%), Positives = 28/77 (36%)

Query: 303 TPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSP 362
               + ++ +++  PL   +DSG+    +    A+   I       ++ V          
Sbjct: 21  QVTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRII 80

Query: 363 GRCKGVRLTLQDVPIEN 379
           GR    ++ ++   ++ 
Sbjct: 81  GRVHLAQIQIEGDFLQC 97

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	383
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	98.98
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	98.74
1fmb_A	104	EIAV protease; hydrolase (acid proteinase), RNA-di	98.51
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.43
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.37
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.33
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	98.14
3ec0_A	99	Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1	97.98
2hs1_A	99	HIV-1 protease; ultra-high resolution active site	97.88
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.75
3slz_A	132	GAG-Pro-POL polyprotein; beta sheet and dimer, pro	97.68
2hah_A	116	Protease, retropepsin; retroviral, aspartyl, hydro	97.51
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.5
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.47
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.46
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.46
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.44
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	97.42
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.28
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.25
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.21
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	97.2
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.16
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.13
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.11
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.08
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.0
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	96.94
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	96.86
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	96.83
3liy_A	116	Protease; hydrolase, hydrolase-hydrolase inhibitor	96.71
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	96.7
2rsp_A	124	RSV protease; hydrolase(aspartyl proteinase); 2.00	96.62
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.49
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	96.46
3sqf_A	114	Protease; folded monomer, retropepsin, D-type retr	96.37
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.19
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	96.12
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	94.57
3lhr_A	93	Zinc finger protein 24; SCAN domain, protein struc	91.57
2jys_A	107	Protease/reverse transcriptase; retroviral proteas	89.27
2fi2_A	94	Zinc finger protein 42; SCAN domain, ZNF-42, MZF-1	85.18
1y7q_A	98	AW-1, zinc finger protein 174; SCAN domain, retrov	84.79
4e6s_A	93	Zinc finger and SCAN domain-containing protein 10;	84.54
2jyl_A	105	Capsid protein P24 (Ca); HIV-1, carboxy-terminal,	80.98
1eoq_A	96	GAG polyprotein capsid protein P27; virus/viral pr	80.92
1lya_A	97	Cathepsin D; lysosomal aspartic protease; HET: NAG	80.5

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

Probab=98.98  E-value=9.1e-10  Score=87.15  Aligned_cols=75  Identities=13%  Similarity=0.176  Sum_probs=56.8

Q ss_pred             CcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          304 PHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       304 ~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      ...+++.+.|||.++++||||||++|||+.++|+++|+.....................|.+..++|.|+++.+.
T Consensus        22 ~~~l~v~~~Ing~~v~~LVDTGAs~s~Is~~~A~rlGL~~~~~~~~~~~a~g~G~~~~~g~v~~~~I~Ig~~~~~   96 (148)
T 3s8i_A           22 VTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIIGRVHLAQIQIEGDFLQ   96 (148)
T ss_dssp             CCCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHTTCGGGEEGGGCEECCC---CEEEEEEEEEEEEETTEEEE
T ss_pred             cCEEEEEEEECCEEEEEEEeCCCCcEeeCHHHHHHcCCccccCcceeEEEEcCCccEEEEEEEEEEEEECCEEEE
Confidence            467899999999999999999999999999999999997542222222222223456677778899999998764

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

Probab=98.74  E-value=2.1e-08  Score=79.93  Aligned_cols=74  Identities=18%  Similarity=0.266  Sum_probs=52.8

Q ss_pred             CcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceE-EEEeCCCeEecCceeeceEEEecCeeee
Q 036272          304 PHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFS-VVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       304 ~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~-v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      ...+.+.+.|||.++.+||||||++++|+.++|+++|+......... ...+.|.. ...+.+....|.|+++.+.
T Consensus        24 ~~~~~v~v~InG~~~~~LvDTGAs~s~is~~~a~~lgl~~~~~~~~~~~a~g~g~~-~~~~~~~~~~i~ig~~~~~   98 (148)
T 2i1a_A           24 VPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTG-KIIGRIHQAQVKIETQYIP   98 (148)
T ss_dssp             CCCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHHTGGGGCBCCCC------------CEEEEEEEEEETTEEEE
T ss_pred             cceEEEEEEECCEEEEEEEECCCCccccCHHHHHHcCCCccCCcceEEEEecCCCc-ccccEEEEEEEEECCEEec
Confidence            45788999999999999999999999999999999999765433332 22333333 2356666678999998764

>1fmb_A EIAV protease; hydrolase (acid proteinase), RNA-directed DNA polymerase, AS protease, endonuclease, polyprotein; HET: HYB; 1.80A {Equine infectious anemia virus} SCOP: b.50.1.1 PDB: 2fmb_A*

Probab=98.51  E-value=3.3e-07  Score=67.13  Aligned_cols=71  Identities=14%  Similarity=0.170  Sum_probs=59.1

Q ss_pred             cceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          305 HTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       305 ~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      ..+.+.+.|+|..+.+|+||||+.++|++..+..++++..+.. .....+.|..+...  ..++++++.|+.+.
T Consensus         7 ~RP~v~v~I~Gq~~e~LLDTGAD~TVl~~~~w~~i~lp~~~w~-p~~i~GiGG~i~v~--~~~i~i~i~g~~~~   77 (104)
T 1fmb_A            7 KRPTTIVLINDTPLNVLLDTGADTSVLTTAHYNRLKYRGRKYQ-GTGIGGVGGNVETF--STPVTIKKKGRHIK   77 (104)
T ss_dssp             SCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHCSSCCCCEE-CCCEEETTEEECCE--EEEEEEEETTEEEE
T ss_pred             CCCEEEEEECCEEEEEEeccCCCcEEEccccCcccCCCCccCC-ccEEEeCCCeEEee--EeeeEEEECCeEEE
Confidence            3466889999999999999999999999999999999876222 36677889988887  67899999987653

>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=98.37  E-value=8.6e-08  Score=52.68  Aligned_cols=22  Identities=14%  Similarity=0.465  Sum_probs=18.6

Q ss_pred             cCccccccCCCcccccccceeE
Q 036272          249 EQELCYSCDENYTVGHKCKKLF  270 (383)
Q Consensus       249 ~~~~Cf~C~~~GH~a~~Cp~~~  270 (383)
                      +...||+|++.||++++|+.+.
T Consensus         5 ~~~~C~nCgk~GH~ar~C~~pr   26 (29)
T 1nc8_A            5 KVIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSSS
T ss_pred             CCCEEEECCccccCHhHCcccc
Confidence            3467999999999999998653

>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=98.33  E-value=1.2e-07  Score=55.80  Aligned_cols=22  Identities=23%  Similarity=0.397  Sum_probs=19.1

Q ss_pred             CccccccCCCcccccccceeEE
Q 036272          250 QELCYSCDENYTVGHKCKKLFF  271 (383)
Q Consensus       250 ~~~Cf~C~~~GH~a~~Cp~~~~  271 (383)
                      ...||+|++.||++++||++..
T Consensus        10 ~~~C~~Cgk~GH~ardCP~~~~   31 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPKKPR   31 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSCC
T ss_pred             CCeeeECCCCCcchhhCcCCcc
Confidence            4679999999999999998553

>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=98.14  E-value=5.4e-07  Score=57.39  Aligned_cols=22  Identities=23%  Similarity=0.397  Sum_probs=19.0

Q ss_pred             CccccccCCCcccccccceeEE
Q 036272          250 QELCYSCDENYTVGHKCKKLFF  271 (383)
Q Consensus       250 ~~~Cf~C~~~GH~a~~Cp~~~~  271 (383)
                      ...||+||+.||++++||++..
T Consensus        23 ~~~C~~Cge~GH~ardCp~~~~   44 (56)
T 1u6p_A           23 RDQCAYCKEKGHWAKDCPKKPR   44 (56)
T ss_dssp             TTBCSSSCCBSSCGGGCTTCCC
T ss_pred             CCcceeCCCCCcccccCcCCcc
Confidence            4679999999999999998544

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

Probab=97.98  E-value=1.8e-05  Score=56.86  Aligned_cols=65  Identities=17%  Similarity=0.257  Sum_probs=50.9

Q ss_pred             ceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       306 ~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      ...+.+.|+|..+.+|+||||++++|++     ..++....  ...+.+.|..+..... ..++++|.|+...
T Consensus         8 RP~vti~I~Gq~~e~LLDTGAD~TVl~~-----~~~Pg~w~--pk~igGiGG~i~v~qy-~~i~iei~g~~~~   72 (99)
T 3ec0_A            8 RPVVTAYIEGQPVEVLLDTGADDSIVAG-----IELGNNYS--PKIVGGIGGFINTKEY-KNVEIEVLNKKVR   72 (99)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEESS-----CCCCSCCE--EEEEEETTEEEEEEEE-EEEEEEETTEEEE
T ss_pred             CCeEEEEECCEEEEEEEecCCCceEEcC-----cccCCCCC--ceEEEecCCcEeeeEE-eeEEEEECCeEEE
Confidence            4567889999999999999999999963     44544332  4578889999988874 6799999887643

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

Probab=97.88  E-value=4.7e-05  Score=54.88  Aligned_cols=64  Identities=9%  Similarity=0.073  Sum_probs=50.3

Q ss_pred             ceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeee
Q 036272          306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPI  377 (383)
Q Consensus       306 ~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~  377 (383)
                      ...+.+.|+|..+.+|+||||+.++|++     ..++...  ......+.|..+...+. .+++++|.|...
T Consensus         8 rP~vtvkI~Gq~~eaLLDTGAD~TVl~~-----~~~p~~w--kpk~igGiGG~i~v~qy-~qi~iei~g~~~   71 (99)
T 2hs1_A            8 RPLVTIKIGGQLKEALLDTGADDTIIEE-----MSLPGRW--KPKMIGGIGGFIKVRQY-DQIIIEIAGHKA   71 (99)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSEEESC-----CSSCCCC--EEEEEEETTEEEEEEEE-EEEEEEETTEEE
T ss_pred             CCEEEEEECCEEEEEEeccCCCcEEEec-----ccCCCCC--CCcEEEeCCCcEeeeEe-ccEEEEEeCCEE
Confidence            3567889999999999999999999995     3454433  24678888988888754 579999998654

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

Probab=97.75  E-value=8.6e-06  Score=51.61  Aligned_cols=18  Identities=17%  Similarity=0.497  Sum_probs=16.6

Q ss_pred             ccccccCCCcccccccce
Q 036272          251 ELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ..||+||+.||++++||.
T Consensus         8 ~~C~kCGk~GH~~k~Cp~   25 (55)
T 2ysa_A            8 YTCFRCGKPGHYIKNCPT   25 (55)
T ss_dssp             CCCTTTCCTTSCGGGCSG
T ss_pred             CccccCCCcCcccccCCC
Confidence            579999999999999984

>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=97.68  E-value=3.4e-05  Score=58.79  Aligned_cols=68  Identities=19%  Similarity=0.217  Sum_probs=47.0

Q ss_pred             CCcceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          303 TPHTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       303 ~~~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      ....+.+.+.|||..+.+||||||+.++|++..+.     . +..+..+..++| .+. ......++|+|.+..+.
T Consensus        19 ~~~RP~v~i~I~G~~~~~LlDTGAd~tVl~~~~~p-----~-~~~p~~I~GiGG-~i~-vr~~~~i~IeI~g~~~~   86 (132)
T 3slz_A           19 PPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGP-----L-SDKSAWVQGATG-GKR-YRWTTDRKVHLATGKVT   86 (132)
T ss_dssp             CCCSSEEEEEETTEEEEEEECTTCSSCEECSCCCS-----E-EEEEEEEECSSC-EEE-EEEECCEEEEETTEEEE
T ss_pred             ccCCCEEEEEECCEEEEEEEeCCCCeEEEccccCC-----C-CCCceEEEccCC-EEE-EEEEeeeEEEECCeeec
Confidence            34567788999999999999999999999975333     2 222344444455 444 44445678888887654

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

Probab=97.51  E-value=0.00011  Score=54.57  Aligned_cols=65  Identities=15%  Similarity=0.195  Sum_probs=46.5

Q ss_pred             ceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEE-EEeCCCeEecCceeeceEEEecCee
Q 036272          306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSV-VVANGERLSSPGRCKGVRLTLQDVP  376 (383)
Q Consensus       306 ~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v-~~~~g~~~~~~~~~~~~~v~i~~~~  376 (383)
                      ...+ +.|+|..+.+|+||||+.++|++.-+...  +...  .... ..+.|..+.... ..+++++|.|..
T Consensus        14 rP~v-ikI~Gq~~eaLLDTGAD~TVi~~~~~~~~--p~~w--kpk~~igGiGG~i~v~q-y~qv~iei~g~~   79 (116)
T 2hah_A           14 PEIL-IFVNGYPIKFLLDTGADITVLNRRDFQVK--NSIE--NGRQMIGGIGGFIRGTN-YINVHLEIRDEN   79 (116)
T ss_dssp             CEEE-EEETTEEEEEEECTTCSSCEEEGGGCCCT--TCEE--EEEEEEEETTEEEEEEE-EEEEEEEECCTT
T ss_pred             CCEE-EEECCEEEEEEecCCCCcEEEcccccccC--CCCC--CCceEEecCCCceeeeE-EccEEEEEeCCC
Confidence            4556 89999999999999999999996422111  3322  2344 778888888864 457888888753

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

Probab=97.50  E-value=3.1e-05  Score=45.76  Aligned_cols=18  Identities=28%  Similarity=0.610  Sum_probs=15.7

Q ss_pred             ccccccCCCcccccccce
Q 036272          251 ELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ..||+|++.||++++||+
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            579999999999999984

>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=97.47  E-value=2.2e-05  Score=48.96  Aligned_cols=19  Identities=16%  Similarity=0.599  Sum_probs=13.7

Q ss_pred             ccccccCCCccccccccee
Q 036272          251 ELCYSCDENYTVGHKCKKL  269 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~~  269 (383)
                      ..||+|++.||++++||.+
T Consensus         7 ~~C~~Cg~~GH~a~~C~~~   25 (49)
T 2ec7_A            7 IRCWNCGKEGHSARQCRAP   25 (49)
T ss_dssp             CBCTTTCCBTCCTTTCCCS
T ss_pred             CeeeecCCCCcChhhCcCC
Confidence            4577777777777777764

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

Probab=97.46  E-value=3.7e-05  Score=44.81  Aligned_cols=16  Identities=25%  Similarity=0.939  Sum_probs=8.2

Q ss_pred             ccccCCCcccccccce
Q 036272          253 CYSCDENYTVGHKCKK  268 (383)
Q Consensus       253 Cf~C~~~GH~a~~Cp~  268 (383)
                      ||+|++.||++++||.
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            5555555555555543

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

Probab=97.46  E-value=2.9e-05  Score=45.89  Aligned_cols=18  Identities=17%  Similarity=0.683  Sum_probs=16.8

Q ss_pred             cccccCCCccccccccee
Q 036272          252 LCYSCDENYTVGHKCKKL  269 (383)
Q Consensus       252 ~Cf~C~~~GH~a~~Cp~~  269 (383)
                      .||+|++.||++++||.+
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            599999999999999975

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

Probab=97.44  E-value=3.7e-05  Score=44.80  Aligned_cols=18  Identities=17%  Similarity=0.835  Sum_probs=16.5

Q ss_pred             ccccccCCCcccccccce
Q 036272          251 ELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ..||+|++.||++++||+
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            579999999999999984

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

Probab=97.42  E-value=4.1e-05  Score=53.39  Aligned_cols=23  Identities=26%  Similarity=0.589  Sum_probs=19.8

Q ss_pred             cCccccccCCCcccccccceeEE
Q 036272          249 EQELCYSCDENYTVGHKCKKLFF  271 (383)
Q Consensus       249 ~~~~Cf~C~~~GH~a~~Cp~~~~  271 (383)
                      ....||+||+.||++++||.++.
T Consensus        45 ~~~~CYnCG~~GH~~rdC~~~r~   67 (83)
T 3nyb_B           45 HTIYCYNCGGKGHFGDDCKEKRS   67 (83)
T ss_dssp             CCCBCSSSSCBSSCGGGCSSCCS
T ss_pred             CCCeecccCCCCcCcccCCcccc
Confidence            34689999999999999998664

>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=97.28  E-value=9.4e-05  Score=47.45  Aligned_cols=21  Identities=14%  Similarity=0.645  Sum_probs=15.8

Q ss_pred             cCccccccCCCccccccccee
Q 036272          249 EQELCYSCDENYTVGHKCKKL  269 (383)
Q Consensus       249 ~~~~Cf~C~~~GH~a~~Cp~~  269 (383)
                      +...||+|++.||++++||.+
T Consensus        11 ~~~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           11 KTVKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             GTCBCTTTCCBSSCGGGCSSC
T ss_pred             CCcceeeeCCCCcChhhcCCC
Confidence            345688888888888888764

>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=97.25  E-value=8.7e-05  Score=46.25  Aligned_cols=19  Identities=26%  Similarity=0.600  Sum_probs=17.2

Q ss_pred             ccccccCCCccccccccee
Q 036272          251 ELCYSCDENYTVGHKCKKL  269 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~~  269 (383)
                      ..||+|++.||++++||..
T Consensus        28 ~~C~~Cg~~GH~~~~C~~~   46 (49)
T 2ec7_A           28 QGCWKCGKTGHVMAKCPER   46 (49)
T ss_dssp             CSCSSSCCSSCCGGGCCSS
T ss_pred             CeeCcCCCcCCccCCCcCC
Confidence            5799999999999999964

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

Probab=97.21  E-value=8.7e-05  Score=48.66  Aligned_cols=18  Identities=33%  Similarity=0.802  Sum_probs=11.9

Q ss_pred             ccccccCCCcccccccce
Q 036272          251 ELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ..||+|++.||++++||.
T Consensus         5 ~~C~~Cg~~GH~a~~C~~   22 (61)
T 2ihx_A            5 GLCYTCGSPGHYQAQCPK   22 (61)
T ss_dssp             TBCSSSCCBTCCGGGCTT
T ss_pred             CcccccCCCCeehhhCcC
Confidence            456666666666666665

>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=97.20  E-value=0.00084  Score=54.94  Aligned_cols=65  Identities=8%  Similarity=0.013  Sum_probs=50.0

Q ss_pred             ceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       306 ~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      .+.+.+.|+|..+.+|+||||+.|+|.     .++++...  ....+.+.|..+..... ..++++|.|+...
T Consensus         8 RP~vtv~I~Gq~~e~LLDTGAD~TVl~-----~~~lpg~w--~pk~igGIGG~i~vrqy-~~i~iei~g~~~~   72 (203)
T 3ka2_A            8 RPLVTIRIGGQLKEALLDTGADDTVIE-----ELNLPGXW--KPKLIGGIAGFIKVRQY-DQIPVEIXGHKAI   72 (203)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEC-----SCCCSSCE--EEEEEEETTEEEEEEEE-EEEEEEETTEEEE
T ss_pred             CCeEEEEECCEEEEEEEecCCCceEEe-----cccCCCCC--CceEEEEccCcEEEEEE-cceeEEEcCeEEE
Confidence            456788999999999999999999998     36665532  24567788887777655 4689999887643

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

Probab=97.16  E-value=0.00011  Score=48.24  Aligned_cols=21  Identities=24%  Similarity=0.341  Sum_probs=18.1

Q ss_pred             ccccccCCCcccccccceeEE
Q 036272          251 ELCYSCDENYTVGHKCKKLFF  271 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~~~~  271 (383)
                      ..||+|++.||++++||....
T Consensus        31 ~~C~~Cg~~GH~ar~C~~~~~   51 (61)
T 2ihx_A           31 ERCQLCNGMGHNAKQCRKRDG   51 (61)
T ss_dssp             SBCTTTCCBSSCGGGCCCCC-
T ss_pred             CeeCCCCCCCCCcCCCcCCCc
Confidence            679999999999999997543

>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=97.13  E-value=0.00013  Score=47.70  Aligned_cols=20  Identities=25%  Similarity=0.577  Sum_probs=17.8

Q ss_pred             CccccccCCCccccccccee
Q 036272          250 QELCYSCDENYTVGHKCKKL  269 (383)
Q Consensus       250 ~~~Cf~C~~~GH~a~~Cp~~  269 (383)
                      ...||+|++.||++++||..
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~   49 (60)
T 1cl4_A           30 PGLCPRCKRGKHWANECKSK   49 (60)
T ss_dssp             CCSCSSCSSCSSCSTTCCCT
T ss_pred             CcceeECCCCCCccCcCCCc
Confidence            46799999999999999864

>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=97.11  E-value=0.00013  Score=46.71  Aligned_cols=19  Identities=16%  Similarity=0.503  Sum_probs=17.3

Q ss_pred             ccccccCCCccccccccee
Q 036272          251 ELCYSCDENYTVGHKCKKL  269 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~~  269 (383)
                      ..||+|++.||++++||..
T Consensus        34 ~~C~~Cg~~GH~~~~C~~~   52 (55)
T 1a1t_A           34 KGCWKCGKEGHQMKDCTER   52 (55)
T ss_dssp             CBCTTTCCBSSCGGGCSSS
T ss_pred             CEeCCCCCcCCccCCCcCc
Confidence            5799999999999999964

>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=97.08  E-value=8.1e-05  Score=48.72  Aligned_cols=20  Identities=15%  Similarity=0.571  Sum_probs=0.0

Q ss_pred             ccccccCCCcccccccceeE
Q 036272          251 ELCYSCDENYTVGHKCKKLF  270 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~~~  270 (383)
                      ..||+|++.||++++||...
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~~~   21 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHEHA   21 (60)
T ss_dssp             --------------------
T ss_pred             CccccCCCCCcCHhhCcCCC
Confidence            35999999999999999753

>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=97.00  E-value=0.00021  Score=47.15  Aligned_cols=20  Identities=15%  Similarity=0.290  Sum_probs=16.5

Q ss_pred             CccccccCCCccccccccee
Q 036272          250 QELCYSCDENYTVGHKCKKL  269 (383)
Q Consensus       250 ~~~Cf~C~~~GH~a~~Cp~~  269 (383)
                      ...||+|++.||++++||..
T Consensus        29 ~~~C~~Cg~~GH~ar~Cp~~   48 (63)
T 2cqf_A           29 PKKCHFCQSISHMVASCPLK   48 (63)
T ss_dssp             SSCCTTTCCSSSCTTTCTGG
T ss_pred             CCccCCcCCcCCccCcCCCc
Confidence            35799999999999999864

>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=96.94  E-value=0.00025  Score=46.78  Aligned_cols=19  Identities=26%  Similarity=0.632  Sum_probs=17.1

Q ss_pred             ccccccCCCccccccccee
Q 036272          251 ELCYSCDENYTVGHKCKKL  269 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~~  269 (383)
                      ..||+|++.||++++||.+
T Consensus         8 ~~C~~Cg~~GH~a~~C~~~   26 (63)
T 2cqf_A            8 DRCYNCGGLDHHAKECKLP   26 (63)
T ss_dssp             CCCSSSCCSSSCTTTCCSC
T ss_pred             CcccccCCCCcChhhCCCC
Confidence            5699999999999999964

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

Probab=96.86  E-value=0.00029  Score=47.98  Aligned_cols=18  Identities=28%  Similarity=0.709  Sum_probs=14.2

Q ss_pred             ccccccCCCcccccccce
Q 036272          251 ELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ..||+|++.||++++|+.
T Consensus        25 ~~C~~Cg~~GH~a~~C~~   42 (74)
T 2li8_A           25 DRCYNCGGLDHHAKECKL   42 (74)
T ss_dssp             SCCTTTCCSSSCTTTCSS
T ss_pred             CcccccCCcCcCcccCCC
Confidence            468888888888888874

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

Probab=96.83  E-value=0.00035  Score=47.51  Aligned_cols=20  Identities=15%  Similarity=0.290  Sum_probs=17.8

Q ss_pred             CccccccCCCccccccccee
Q 036272          250 QELCYSCDENYTVGHKCKKL  269 (383)
Q Consensus       250 ~~~Cf~C~~~GH~a~~Cp~~  269 (383)
                      ...||+|++.||++++||..
T Consensus        46 ~~~C~~Cg~~GH~ar~Cp~~   65 (74)
T 2li8_A           46 PKKCHFCQSISHMVASCPLK   65 (74)
T ss_dssp             CCCCTTTCCTTSCGGGCTTG
T ss_pred             CCccCCcCCcCCccCcCcCC
Confidence            46799999999999999864

>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=96.71  E-value=0.004  Score=45.41  Aligned_cols=63  Identities=13%  Similarity=0.162  Sum_probs=41.5

Q ss_pred             ceEEEEEEc-----CeEEEEEeeCCCcchhccHHHHHHhCCccccCC-ceEEEEeCCCeEecCceeeceEEEecC
Q 036272          306 TMRVHSQIS-----KIPLTILIDSGSTHNYLHHRFAKITRIKPERSC-LFSVVVANGERLSSPGRCKGVRLTLQD  374 (383)
Q Consensus       306 ~~~~~~~i~-----~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~-~~~v~~~~g~~~~~~~~~~~~~v~i~~  374 (383)
                      ...+.+.|+     |..+.||+||||+.++|.+     ..++..... ...++.+-|..+.. -....++|.+-.
T Consensus        10 RPlvtikI~~~~~~Gq~~eaLLDTGADdTVl~~-----~~lPg~Wkp~~tkiiGGiGg~~~~-~qs~~~pv~i~l   78 (116)
T 3liy_A           10 RPVIKAQVDTQTSHPKTIEALLDTGADMTVIPI-----ALFSSNTPLKNTSVLGAGGQTQDH-FKLTSLPVLIRL   78 (116)
T ss_dssp             CCEEEEEEECSSSCCEEEEEEECTTBSSCEEEG-----GGSCTTCCEEECCEEETTEEESSS-EEEESSCEEEEC
T ss_pred             CCeEEEEEccccCCCeEeEEEeccCCCccEEec-----ccCCCCCcccccceEeecccceee-eEecCCCeEEEe
Confidence            456788899     9999999999999999984     445544322 11345555544433 344567777665

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

Probab=96.70  E-value=0.0058  Score=49.99  Aligned_cols=64  Identities=9%  Similarity=0.070  Sum_probs=49.2

Q ss_pred             ceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeee
Q 036272          306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPI  377 (383)
Q Consensus       306 ~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~  377 (383)
                      ...+.+.++|..+.+|+||||++|+|.     .++++....  +....+-|..+..... ..+++++.|+..
T Consensus       112 rP~~~iki~Gq~~e~LlDTGAD~TVl~-----~~~lpg~w~--pk~igGiGg~i~v~qy-~~i~iei~g~~~  175 (203)
T 3ka2_A          112 RPLVTIRIGGQLKEALLDTGADDTVIE-----ELNLPGXWK--PKLIGGIGGFIKVRQY-DQIPVEIXGHKA  175 (203)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEC-----SCCCCSCCE--EEEEEETTEEEEEEEE-EEEEEEETTEEE
T ss_pred             CCcEEEEECCEEEeeeecccCCceeee-----cccCCCCCC--ceEEeeccceEEEEEe-ccEEEEECCeEE
Confidence            456788999999999999999999995     355554432  3567788888888766 568888888754

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

Probab=96.62  E-value=0.0019  Score=48.41  Aligned_cols=58  Identities=12%  Similarity=0.161  Sum_probs=34.1

Q ss_pred             EcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCc--eE-EEEeCCCeEecCceeeceEEEecCe
Q 036272          313 ISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCL--FS-VVVANGERLSSPGRCKGVRLTLQDV  375 (383)
Q Consensus       313 i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~--~~-v~~~~g~~~~~~~~~~~~~v~i~~~  375 (383)
                      ++|+.+.+|+||||+.++|.+     ..++.....-  .. .+.+.|..+.....-..+++++-|.
T Consensus        27 i~gq~~eaLLDTGAD~TVl~~-----~~lP~~W~k~~~~~~~igGIGG~i~v~qy~~~i~iei~g~   87 (124)
T 2rsp_A           27 QRSVYITALLDSGADITIISE-----EDWPTDWPVMEAANPQIHGIGGGIPMRKSRDMIELGVINR   87 (124)
T ss_dssp             CSEEEEEEEECTTCSSCEEET-----TTSCTTSCEEECC---------CCCEEEESSCEEEEEECT
T ss_pred             CCCEEEEEEecCCCCcEEEec-----ccCCCcceeeccccceeeecCceEeeEEeCCceEEEEeCC
Confidence            789999999999999999985     4444433210  00 1455566666655433777777664

>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=96.49  E-value=0.0008  Score=52.76  Aligned_cols=18  Identities=28%  Similarity=0.709  Sum_probs=15.3

Q ss_pred             ccccccCCCcccccccce
Q 036272          251 ELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ..||+|++.||++++||.
T Consensus        98 ~~C~~Cg~~GH~a~~C~~  115 (148)
T 3ts2_A           98 DRCYNCGGLDHHAKECKL  115 (148)
T ss_dssp             CCCTTTCCSSCCGGGCCS
T ss_pred             CcccEeCCccchhhhCCC
Confidence            469999999999999986

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

Probab=96.46  E-value=0.00084  Score=46.70  Aligned_cols=20  Identities=15%  Similarity=0.516  Sum_probs=16.8

Q ss_pred             CccccccCCCccccccccee
Q 036272          250 QELCYSCDENYTVGHKCKKL  269 (383)
Q Consensus       250 ~~~Cf~C~~~GH~a~~Cp~~  269 (383)
                      ...||+|++.||++++||..
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            45799999999999999975

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

Probab=96.37  E-value=0.0024  Score=46.98  Aligned_cols=53  Identities=11%  Similarity=0.115  Sum_probs=35.8

Q ss_pred             ceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCC--ceEEEEeCCCeEecCc
Q 036272          306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSC--LFSVVVANGERLSSPG  363 (383)
Q Consensus       306 ~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~--~~~v~~~~g~~~~~~~  363 (383)
                      ...+.+.|+|..+.+|+||||+.++|..     ..++....+  ....+.+-|..+....
T Consensus         9 RP~vti~I~Gq~~eaLLDTGADdTVi~~-----~~lpg~W~p~~~~k~igGIGG~i~v~q   63 (114)
T 3sqf_A            9 KPSLTLWLDDKMFTGLINTGADVTIIKL-----EDWPPNWPITDTLTNLRGIGQSNNPKQ   63 (114)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEEG-----GGSCTTSCEEECCCCCTTCCGGGCCEE
T ss_pred             CCeEEEEECCEEEEEEEccCCCceEEec-----ccCCCCcccCcCceEEEeccceEEEEE
Confidence            4567789999999999999999999985     344443222  1234445555555544

>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=96.19  E-value=0.0014  Score=51.37  Aligned_cols=20  Identities=15%  Similarity=0.298  Sum_probs=17.8

Q ss_pred             CccccccCCCccccccccee
Q 036272          250 QELCYSCDENYTVGHKCKKL  269 (383)
Q Consensus       250 ~~~Cf~C~~~GH~a~~Cp~~  269 (383)
                      ...||+|++.||++++||..
T Consensus       119 ~~~C~~Cg~~GH~~r~Cp~~  138 (148)
T 3ts2_A          119 PKKCHFCQSINHMVASCPLK  138 (148)
T ss_dssp             CCCCTTTCCSSCCGGGCTTT
T ss_pred             CCcccccCCcCCEeccCcCC
Confidence            46799999999999999964

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

Probab=96.12  E-value=0.0015  Score=49.69  Aligned_cols=20  Identities=30%  Similarity=0.811  Sum_probs=17.9

Q ss_pred             cCccccccCCCcccccccce
Q 036272          249 EQELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       249 ~~~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ....||+|++.||+++|||+
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            34789999999999999996

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

Probab=94.57  E-value=0.01  Score=44.99  Aligned_cols=18  Identities=22%  Similarity=0.582  Sum_probs=9.5

Q ss_pred             ccccccCCC-cccccccce
Q 036272          251 ELCYSCDEN-YTVGHKCKK  268 (383)
Q Consensus       251 ~~Cf~C~~~-GH~a~~Cp~  268 (383)
                      ..||+|++. ||++++||.
T Consensus        23 ~~C~~Cg~~~gH~~~~C~~   41 (124)
T 2lli_A           23 IICSYCGATDDHYSRHCPK   41 (124)
T ss_dssp             CCCTTTCCTTTCCTTTGGG
T ss_pred             CcCcCCCCcCCccCcccCC
Confidence            345555555 555555554

>3lhr_A Zinc finger protein 24; SCAN domain, protein structure initiative, center for eukary structural genomics, PSI-2, CESG, nucleus, phosphoprotein; 1.90A {Homo sapiens} SCOP: a.28.3.0

Probab=91.57  E-value=2.1  Score=30.09  Aligned_cols=72  Identities=17%  Similarity=0.134  Sum_probs=54.9

Q ss_pred             HHHhhcccc--cccHhhHHHHHHHHHHHh--CCC-CHH-----HHHHHHHhhcchhHHhHccccCCCCHHHHHHHHHHHH
Q 036272          122 FGDLCKLKQ--TGTVSDYQPQFERLLARA--GSL-TDK-----QEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYE  191 (383)
Q Consensus       122 ~~~l~~~~q--~~sv~~Y~~~f~~l~~~~--~~~-~e~-----~~~~~f~~gL~~~l~~~l~~~~~~~l~~~~~~a~~~e  191 (383)
                      ..+|+....  ..+..+.+.++.+|+..=  +.+ +.+     .++..|+.-||.+++..+..+.|.+-.+++.++..+.
T Consensus         9 rq~FR~f~y~e~~gp~eal~~L~eLc~~WLrPe~htKEQileLLVLEQFL~ilP~e~q~wv~~~~p~s~~eav~l~E~l~   88 (93)
T 3lhr_A            9 RQRFRQFGYQDSPGPREAVSQLRELCRLWLRPETHTKEQILELVVLEQFVAILPKELQTWVRDHHPENGEEAVTVLEDLE   88 (93)
T ss_dssp             HHHHHHCCGGGSSSHHHHHHHHHHHHHHHHCTTTSCHHHHHHHHHHHHHHHTSCHHHHHHHHHTCCSSHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCCHHHHHHHHHHHHHHhcCcccCCHHHHHHHHHHHHHHHhCCHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            344444443  678888888988887765  222 333     3678899999999999999999999999999988766


Q ss_pred             HH
Q 036272          192 LK  193 (383)
Q Consensus       192 ~~  193 (383)
                      ..
T Consensus        89 ~~   90 (93)
T 3lhr_A           89 SE   90 (93)
T ss_dssp             HH
T ss_pred             hh
Confidence            43

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

Probab=89.27  E-value=0.83  Score=31.64  Aligned_cols=62  Identities=16%  Similarity=0.168  Sum_probs=45.5

Q ss_pred             EEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeee
Q 036272          309 VHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPI  377 (383)
Q Consensus       309 ~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~  377 (383)
                      +.+.+.|..+.+--||||+++.|.+.+...    -.|.....+....|+..-..-   .+.+.|+|+-+
T Consensus        10 L~vEiKg~kLkg~WDsGA~ITCiP~~fL~~----E~PI~~~~I~TIHG~k~q~vY---Yl~fKv~GRKv   71 (107)
T 2jys_A           10 LEAEIKGTKLKAHWDSGATITCVPEAFLED----ERPIQTMLIKTIHGEKQQDVY---YLTFKVQGRKV   71 (107)
T ss_dssp             EEEEETTEEEEEEECTTCSSEEEEGGGTTT----CCCSEEEEEECSSCEEEEEEE---EEEEEESSCEE
T ss_pred             eeEEEeCcEEEEEecCCCeEEEcchHHhcc----cccccceEEEEecCceeceEE---EEEEEEcCeEE
Confidence            566788999999999999999999987543    234445667777777654433   47777777654

>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=85.18  E-value=1.9  Score=30.12  Aligned_cols=61  Identities=16%  Similarity=0.206  Sum_probs=46.8

Q ss_pred             cccHhhHHHHHHHHHHHh--CCC-CHH-----HHHHHHHhhcchhHHhHccccCCCCHHHHHHHHHHHH
Q 036272          131 TGTVSDYQPQFERLLARA--GSL-TDK-----QEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYE  191 (383)
Q Consensus       131 ~~sv~~Y~~~f~~l~~~~--~~~-~e~-----~~~~~f~~gL~~~l~~~l~~~~~~~l~~~~~~a~~~e  191 (383)
                      .....+-+.++++|+..=  +.+ +.+     ..+..|+.-||.+++..+..+.|.+-++++.++..+.
T Consensus        21 ~~gPreaL~rLreLc~qWLrPe~hTKEQIlElLVLEQFL~iLP~eiq~wV~~~~P~s~eeav~lvEdl~   89 (94)
T 2fi2_A           21 ATGPQEALAQLRELCRQWLRPEVRSKEQMLELLVLEQFLGALPPEIQARVQGQRPGSPEEAAALVDGLR   89 (94)
T ss_dssp             TTCHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHHHSCHHHHHHHHHHCCCSHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHHCCcccccHHHHHHHHHHHHHHHhCcHHHHHHHHhcCCCcHHHHHHHHHHHH
Confidence            455666677777776654  222 333     4678899999999999999999999999999987654

>1y7q_A AW-1, zinc finger protein 174; SCAN domain, retroviral capsid C-terminal domain, dimer, C2H2 zinc finger associated, transcription; NMR {Homo sapiens} SCOP: a.28.3.2

Probab=84.79  E-value=2.7  Score=29.63  Aligned_cols=69  Identities=14%  Similarity=0.184  Sum_probs=50.7

Q ss_pred             HHhhcccc--cccHhhHHHHHHHHHHHh--CCC-CHH-----HHHHHHHhhcchhHHhHccccCCCCHHHHHHHHHHHH
Q 036272          123 GDLCKLKQ--TGTVSDYQPQFERLLARA--GSL-TDK-----QEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYE  191 (383)
Q Consensus       123 ~~l~~~~q--~~sv~~Y~~~f~~l~~~~--~~~-~e~-----~~~~~f~~gL~~~l~~~l~~~~~~~l~~~~~~a~~~e  191 (383)
                      ..|+...-  .....+-+.++++|+..=  +.+ +.+     ..+..|+.-||.+++..+..+.|.+-++++.++..+.
T Consensus        13 q~FR~f~y~e~~gPreaL~rLreLC~qWLrPe~hTKEQIlElLVLEQFL~iLP~eiq~wV~~~~P~s~eeav~lvEdl~   91 (98)
T 1y7q_A           13 QSFRRFCYQEVSGPQEALSQLRQLCRQWLQPELHTKEQILELLVMEQFLTILPEEIQARVRHRCLMSSKEIVTLVEDFH   91 (98)
T ss_dssp             HHHHTCCSCSCCSSHHHHHHHHHHHHHHHCCSSCCHHHHHHHHHHHHHHHHSCTHHHHHHHTSCCCCHHHHHHHHHHHH
T ss_pred             HHhccCCCCCCCCHHHHHHHHHHHHHHHCCcccccHHHHHHHHHHHHHHHhCCHHHHHHHhccCCCcHHHHHHHHHHHH
Confidence            33444433  455667777777777665  322 333     4678899999999999999999999999999987765

>4e6s_A Zinc finger and SCAN domain-containing protein 10; protein interaction, other scans, N-terminal PA finger transcription factor, transcription; 1.85A {Mus musculus}

Probab=84.54  E-value=4.6  Score=28.33  Aligned_cols=69  Identities=10%  Similarity=-0.029  Sum_probs=50.6

Q ss_pred             HHHhhcccc--cccHhhHHHHHHHHHHHh--CCC-CHH-----HHHHHHHhhcchhHHhHccccCCCCHHHHHHHHHHHH
Q 036272          122 FGDLCKLKQ--TGTVSDYQPQFERLLARA--GSL-TDK-----QEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNYE  191 (383)
Q Consensus       122 ~~~l~~~~q--~~sv~~Y~~~f~~l~~~~--~~~-~e~-----~~~~~f~~gL~~~l~~~l~~~~~~~l~~~~~~a~~~e  191 (383)
                      ..+|+....  ..+..+.+.++.+|+..=  +.. +.+     .++..|+.-||.+++..+..+.|.+-.+++. +..+.
T Consensus         9 rq~Fr~f~y~e~~gPreal~~L~eLc~~WLrPe~htKEQIleLLVLEQFL~ilP~e~q~wv~~~~p~s~eeav~-~E~l~   87 (93)
T 4e6s_A            9 HQLFRCFQYQEDMGPRASLGRLRELCNHWLRPALHTKKQILELLVLEQFLSVLPPHVLSRLHGAPLRDGEEVAQ-LEGVP   87 (93)
T ss_dssp             HHHHHTCCCCTTTCHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHHTSCHHHHGGGTTCCCSCHHHHHH-TTC--
T ss_pred             HHHHhccCCCCCCCHHHHHHHHHHHHHHHcCcccCCHHHHHHHHHHHHHHHhCCHHHHHHHHHhCCCcHHHHHH-HHHHh
Confidence            344555443  677888888888887765  222 333     3568899999999999999999999999988 65443

>2jyl_A Capsid protein P24 (Ca); HIV-1, carboxy-terminal, dimerization domain, CTD, 3D- NMR, capsid protein (Ca), double mutant; NMR {Human immunodeficiency virus 1} PDB: 2k1c_A* 2l6e_A*

Probab=80.98  E-value=4.1  Score=29.33  Aligned_cols=64  Identities=13%  Similarity=0.274  Sum_probs=45.1

Q ss_pred             Hhhcccc--cccHhhHHHHHHHHHHHhC---CCCHHHHHHHHHhhcchhHHhHccccCC-CCHHHHHHHH
Q 036272          124 DLCKLKQ--TGTVSDYQPQFERLLARAG---SLTDKQEAACFISGLKDGLRADVRAQNP-QNLSAAIGLA  187 (383)
Q Consensus       124 ~l~~~~q--~~sv~~Y~~~f~~l~~~~~---~~~e~~~~~~f~~gL~~~l~~~l~~~~~-~~l~~~~~~a  187 (383)
                      .+..++|  .|++++|+.+|........   ....-.....++.+-+++.+..+....+ .+|++.+..+
T Consensus        23 si~~IkQGpKEPf~dyVdR~~k~l~ae~~~~~vK~~mt~tL~~qNANpdCk~ilk~lg~~~tlee~~~ac   92 (105)
T 2jyl_A           23 SILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTAC   92 (105)
T ss_dssp             CGGGCCCCSSSCHHHHHHHHHHHHHHHCCCTTTTTSCHHHHHHHTSCHHHHHHHHHHCTTCCHHHHHHHH
T ss_pred             chhhhhcCCCCcHHHHHHHHHHHHHHhhcchhhHHHhhhhhhHhhcCcchhhHHHccCCCCCHHHHHHHc
Confidence            3567888  8999999999998877653   1122244555677889998888876554 4777766543

>1eoq_A GAG polyprotein capsid protein P27; virus/viral protein; NMR {Rous sarcoma virus - prague C} SCOP: a.28.3.1

Probab=80.92  E-value=8  Score=26.96  Aligned_cols=64  Identities=11%  Similarity=0.212  Sum_probs=47.6

Q ss_pred             cccc--cccHhhHHHHHHHHHHHhCCCCH----HHHHHHHHhhcchhHHhHcccc-CC-CCHHHHHHHHHHHH
Q 036272          127 KLKQ--TGTVSDYQPQFERLLARAGSLTD----KQEAACFISGLKDGLRADVRAQ-NP-QNLSAAIGLARNYE  191 (383)
Q Consensus       127 ~~~q--~~sv~~Y~~~f~~l~~~~~~~~e----~~~~~~f~~gL~~~l~~~l~~~-~~-~~l~~~~~~a~~~e  191 (383)
                      .++|  .|++++|+.||-.-.+..+ .+.    -.....++.+-+++-+..++.. .+ .++.|.+...+...
T Consensus         2 dIkQGPkEPFrDyVdRf~kalraeq-a~~~vK~wmt~tLlvQNANPdCk~iLkal~g~~~tl~em~~yi~~~~   73 (96)
T 1eoq_A            2 DIMQGPSESFVDFANRLIKAVEGSD-LPPSARAPVIIDCFRQKSQPDIQQLIRTAPSTLTTPGEIIKYVLDRQ   73 (96)
T ss_dssp             CCCCCTTCCHHHHHHHHHHHHHTTT-CCHHHHHHHHHHHHHHHSCHHHHHHHHHCCSCCCSHHHHHHHHHHHS
T ss_pred             CcccCCCCcHHHHHHHHHHHHHHhh-ccHhHhhhhHHHHHHHhcCHHHHHHHHccCCCCCCHHHHHHHHHHHH
Confidence            4678  8999999999998877643 222    2455777888899999888865 44 68888888765544

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

Probab=80.50  E-value=1.6  Score=31.11  Aligned_cols=28  Identities=18%  Similarity=0.249  Sum_probs=22.7

Q ss_pred             ceEEEEEEc--CeEEEEEeeCCCcchhccH
Q 036272          306 TMRVHSQIS--KIPLTILIDSGSTHNYLHH  333 (383)
Q Consensus       306 ~~~~~~~i~--~~~v~~LiDsGAt~s~Is~  333 (383)
                      ...+.+.|+  .+++.++|||||+...|..
T Consensus        14 ~Y~~~i~iGTP~Q~~~v~~DTGSs~lWv~~   43 (97)
T 1lya_A           14 QYYGEIGIGTPPQCFTVVFDTGSSNLWVPS   43 (97)
T ss_dssp             EEEEEEEETTTTEEEEEEEETTCCCEEEEB
T ss_pred             eEEEEEEECCCCeEEEEEEeCCCCceEEeE
Confidence            355667787  6899999999999998764

---

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	383
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.64
d2fmba_	104	EIAV protease {Equine infectious anemia virus [Tax	98.15
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	97.88
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.69
d2nmza1	99	Human immunodeficiency virus type 1 protease {Huma	97.63
d4fiva_	113	Feline immunodeficiency virus (FIV) protease {Feli	97.55
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.54
d3ecga1	99	Human immunodeficiency virus type 2 (HIV-2) protea	97.5
d1nsoa_	107	Mason-Pfizer monkey virus protease {Simian retrovi	97.37
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	97.22
d1hvca_	203	Human immunodeficiency virus type 1 protease {Huma	97.02
d2fi2a1	92	Zinc finger protein 42 {Human (Homo sapiens) [TaxI	96.04
d1hvca_	203	Human immunodeficiency virus type 1 protease {Huma	95.91
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	95.83
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	95.71
d1y7qa1	96	Zinc finger protein 174 {Human (Homo sapiens) [Tax	95.3
d2rspa_	124	Rous sarcoma virus protease {Rous sarcoma virus, s	95.04
d1qrjb1	84	HTLV-I capsid protein {Human T-cell leukemia virus	92.64
d2eiaa1	75	EIAV capsid protein p26 {Equine infectious anemia	89.05
d1d1da1	80	RSV capsid protein {Rous sarcoma virus [TaxId: 118	87.57
d1a8oa_	70	HIV capsid protein, dimerisation domain {Human imm	85.7

>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=98.64  E-value=1.8e-09  Score=54.49  Aligned_cols=23  Identities=17%  Similarity=0.512  Sum_probs=19.2

Q ss_pred             hcCccccccCCCcccccccceeE
Q 036272          248 REQELCYSCDENYTVGHKCKKLF  270 (383)
Q Consensus       248 ~~~~~Cf~C~~~GH~a~~Cp~~~  270 (383)
                      ++...|||||+.||++++|..|+
T Consensus         4 r~~ikCfNCGkeGH~ar~CrAPR   26 (29)
T d1nc8a_           4 RKVIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCCCBCTTTSCBSSCGGGCCSSS
T ss_pred             cceeEeecCCccchhhhhccCcc
Confidence            34568999999999999997654

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

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

Probab=98.15  E-value=3.3e-06  Score=60.19  Aligned_cols=71  Identities=14%  Similarity=0.174  Sum_probs=50.7

Q ss_pred             cceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeeee
Q 036272          305 HTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPIE  378 (383)
Q Consensus       305 ~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~~  378 (383)
                      ..+.+.+.|+|+++.+|+||||++|+|++.-+........+. ......+.|..+...  ...+.+.+.|..+.
T Consensus         7 ~RP~~~i~I~Gq~v~~LLDTGAD~TVI~~~~~p~~~~~~~~~-~~~~igg~g~~~~~~--~~~v~i~~~g~~~~   77 (104)
T d2fmba_           7 KRPTTIVLINDTPLNVLLDTGADTSVLTTAHYNRLKYRGRKY-QGTGIGGVGGNVETF--STPVTIKKKGRHIK   77 (104)
T ss_dssp             SCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHCSSCCCCE-ECCCEEETTEEECCE--EEEEEEEETTEEEE
T ss_pred             cCeEEEEEECCEEEEEEEeCCCCeEEEcccccCccCCCCCCc-ceeEEEEecceEEEE--EEEEEEEECCeEEE
Confidence            346788899999999999999999999999988765443332 234455566655543  34577777776654

>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=97.88  E-value=1.8e-06  Score=41.30  Aligned_cols=18  Identities=28%  Similarity=0.890  Sum_probs=16.3

Q ss_pred             ccccccCCCcccccccce
Q 036272          251 ELCYSCDENYTVGHKCKK  268 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~  268 (383)
                      ..||.||+.||+.+||..
T Consensus         3 pvcfscgktghikkdck~   20 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKE   20 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTC
T ss_pred             CEEEecCCcccchhhhhh
Confidence            479999999999999974

>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=97.69  E-value=5e-06  Score=48.34  Aligned_cols=20  Identities=15%  Similarity=0.552  Sum_probs=15.8

Q ss_pred             ccccccCCCcccccccceeE
Q 036272          251 ELCYSCDENYTVGHKCKKLF  270 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~~~  270 (383)
                      ..||+|++.||++++||.+.
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~   21 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPR   21 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCC
T ss_pred             CccccCCCcCcCcccCcCCC
Confidence            46888888888888888753

>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=97.63  E-value=0.00012  Score=49.55  Aligned_cols=64  Identities=9%  Similarity=0.082  Sum_probs=51.7

Q ss_pred             ceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeee
Q 036272          306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPI  377 (383)
Q Consensus       306 ~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~  377 (383)
                      ...+.+.|+|..+.||+||||+.+++.+     ++|+....  +++..+-|..+.+... .+++++|-|...
T Consensus         8 RP~vtvkIgGq~~eaLLDTGADdTVlee-----i~lpg~Wk--Pk~IgGIGGfikVrqY-d~i~iei~g~k~   71 (99)
T d2nmza1           8 RPLVTIKIGGQLKEALLDTGADDTVIEE-----MSLPGRWK--PKMIGGIGGFIKVRQY-DQIIIEIAGHKA   71 (99)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEES-----CCCCSCCE--EEEEEETTEEEEEEEE-EEEEEEETTEEE
T ss_pred             CCeEEEEECCEEEEEeeccCCCceEEec-----ccCCCCCC--ceEEEeccceEEEEEe-CceEEEECCcEE
Confidence            4567889999999999999999999954     77766553  5668888999888764 579999988754

>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=97.55  E-value=0.0001  Score=52.84  Aligned_cols=67  Identities=15%  Similarity=0.197  Sum_probs=45.2

Q ss_pred             cceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCe
Q 036272          305 HTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDV  375 (383)
Q Consensus       305 ~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~  375 (383)
                      ....+.+.|+|+.+++|+||||++|+|++.-+....-  .+ .....+.+-|..+...... .+.+.+.+.
T Consensus         9 ~RP~v~v~I~Gq~v~~LLDTGAD~TVi~~~d~p~~~~--~~-~~~~~~~GIGG~~~v~~~~-~v~i~~~~~   75 (113)
T d4fiva_           9 KRPEILIFVNGYPIKFLLDTGADITILNRRDFQVKNS--IE-NGRQNMIGVGGGKRGTNYI-NVHLEIRDE   75 (113)
T ss_dssp             SCCEEEEEETTEEEEEEECTTCSSCEEEGGGCCCTTC--EE-EEEEEEECSSCEEEEEEEE-EEEEEECCT
T ss_pred             cCCeEEEEECCEEEEEEEcCCCCcEEEeccccCCCCC--CC-CCCCeEEecCeEEeeeEEc-eEEEEEcCC
Confidence            4567888899999999999999999999874332211  11 1123334667777776653 577777654

>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=97.54  E-value=1.1e-05  Score=46.80  Aligned_cols=19  Identities=16%  Similarity=0.503  Sum_probs=17.0

Q ss_pred             ccccccCCCccccccccee
Q 036272          251 ELCYSCDENYTVGHKCKKL  269 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~~  269 (383)
                      ..||+||+.||++++||++
T Consensus        23 ~~C~~Cg~~GH~~~~Cp~r   41 (42)
T d2exfa1          23 KGCWKCGKEGHQMKDCTER   41 (42)
T ss_dssp             SSCSSSCCSSSCTTTCCSS
T ss_pred             CccccCCCCCeecccCCCC
Confidence            4699999999999999964

>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=97.50  E-value=0.00019  Score=48.50  Aligned_cols=64  Identities=16%  Similarity=0.220  Sum_probs=51.5

Q ss_pred             ceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeee
Q 036272          306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPI  377 (383)
Q Consensus       306 ~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~  377 (383)
                      ...+.+.++|..+.||+||||+.+++.     .++|+...  .+.+..+-|..+.+... .+++++|-|+..
T Consensus         8 RP~vtvkIgGq~~eaLLDTGADdTVle-----~i~lpg~W--kPk~iGGIGGfikVrqY-d~i~Ieicg~k~   71 (99)
T d3ecga1           8 RPVVTAYIEGQPVEVLLDTGADDSIVA-----GIELGNNY--SPKIVGGIGGFINTKEY-KNVEIEVLNKKV   71 (99)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEC-----SCCCCSCC--EEEEEEETTEEEEEEEE-EEEEEEETTEEE
T ss_pred             CCeEEEEECCEEeeeecccCCCceeee-----ccCCCCCC--cceEEEEeeeeEEEEEe-CcEEEEECCcEE
Confidence            456788999999999999999999984     47776655  34677888888888774 679999988754

>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=97.37  E-value=0.00023  Score=50.56  Aligned_cols=57  Identities=9%  Similarity=-0.028  Sum_probs=37.6

Q ss_pred             ceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCcee
Q 036272          306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRC  365 (383)
Q Consensus       306 ~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~  365 (383)
                      .+.+.+.|+|+.+.+|+||||++|+|++.-+..   ............+-|..+......
T Consensus         9 RP~~~v~I~G~~v~~LLDTGAD~TVI~~~~~p~---~wp~~~~~~~~~GiGg~~~~~~~~   65 (107)
T d1nsoa_           9 KPSLTLWLDDKMFTGLINTGADVTIIKLEDWPP---NWPITDTLTNLRGIGQSNNPKQSS   65 (107)
T ss_dssp             SSCEEEEETTEEEEECCCSSCSSCBCCGGGSCT---TSCCCCCEEEECSSSEEEECCCBC
T ss_pred             CcEEEEEECCEEEEeeecCCCCcEEEeccccCC---CCCcCcCccEEEEecCeeeEEEee
Confidence            455678899999999999999999998874321   111122344455556655555443

>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=97.22  E-value=4.7e-05  Score=41.31  Aligned_cols=21  Identities=24%  Similarity=0.392  Sum_probs=18.2

Q ss_pred             ccccccCCCcccccccceeEE
Q 036272          251 ELCYSCDENYTVGHKCKKLFF  271 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~~~~  271 (383)
                      ..|-+|.+.||.+++||++..
T Consensus        11 DQCAyCke~GHW~~dCPkkpr   31 (40)
T d1a6bb_          11 DQCAYCKEKGHWAKDCPKKPR   31 (40)
T ss_dssp             SSCSSSCCTTCCTTSCSSSCC
T ss_pred             hhhHHHhhcCchhhhCccCCC
Confidence            469999999999999997543

>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=97.02  E-value=0.00065  Score=52.09  Aligned_cols=64  Identities=11%  Similarity=0.085  Sum_probs=50.8

Q ss_pred             ceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeee
Q 036272          306 TMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPI  377 (383)
Q Consensus       306 ~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~  377 (383)
                      ...+.+.|+|..+.||+||||+.+++.+     ++++..+.  ..+..+-|..+..... ..++++|.|...
T Consensus         8 RP~VtVkIgGQ~~eaLLDTGADDTVLe~-----inLpG~Wk--PkiIGGIGGfIkVrqY-~~V~IeI~gkk~   71 (203)
T d1hvca_           8 RPLVTIRIGGQLKEALLDTGADDTVLEE-----MNLPGKWK--PKMIGGIGGFIKVRQY-DQILIEICGHKA   71 (203)
T ss_dssp             CCEEEEESSSCEEEEEECTTCSSEEEEC-----CCCSSCEE--EEEEEETTEEEEEEEE-EEEEEEETTEEE
T ss_pred             CCeEEEEECCEEEEEEecCCCCceEEec-----ccCCCCCc--ccEEEecCceEEEEEe-CCEEEEECCcEE
Confidence            4568889999999999999999999953     66765543  4667788888888766 678999988764

>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=96.04  E-value=0.006  Score=41.39  Aligned_cols=70  Identities=14%  Similarity=0.101  Sum_probs=55.5

Q ss_pred             HHHHhhcccc--cccHhhHHHHHHHHHHHh--CC-CCH-----HHHHHHHHhhcchhHHhHccccCCCCHHHHHHHHHHH
Q 036272          121 SFGDLCKLKQ--TGTVSDYQPQFERLLARA--GS-LTD-----KQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNY  190 (383)
Q Consensus       121 ~~~~l~~~~q--~~sv~~Y~~~f~~l~~~~--~~-~~e-----~~~~~~f~~gL~~~l~~~l~~~~~~~l~~~~~~a~~~  190 (383)
                      ...+|+...-  .++..+++.++++|+..=  +. -+-     -.++..|+..||++++..+..+.|.+..+++.+|..+
T Consensus         7 ~rq~FR~f~y~e~~~p~e~l~rL~eLc~~WL~pe~~tkeqilelLVLEQFl~~lP~e~~~~V~e~~p~s~~eav~L~Edl   86 (92)
T d2fi2a1           7 ARLRFRCFHYEEATGPQEALAQLRELCRQWLRPEVRSKEQMLELLVLEQFLGALPPEIQARVQGQRPGSPEEAAALVDGL   86 (92)
T ss_dssp             HHHHHHSCCCCTTTCHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHHHSCHHHHHHHHHHCCCSHHHHHHHHHHH
T ss_pred             HHHHHhcCCCcccCCHHHHHHHHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHCCHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            3445565554  889999999999987775  22 232     3577899999999999999999999999999998754

>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=95.91  E-value=0.011  Score=45.10  Aligned_cols=65  Identities=11%  Similarity=0.067  Sum_probs=52.2

Q ss_pred             cceEEEEEEcCeEEEEEeeCCCcchhccHHHHHHhCCccccCCceEEEEeCCCeEecCceeeceEEEecCeee
Q 036272          305 HTMRVHSQISKIPLTILIDSGSTHNYLHHRFAKITRIKPERSCLFSVVVANGERLSSPGRCKGVRLTLQDVPI  377 (383)
Q Consensus       305 ~~~~~~~~i~~~~v~~LiDsGAt~s~Is~~~~~~l~l~~~~~~~~~v~~~~g~~~~~~~~~~~~~v~i~~~~~  377 (383)
                      ....+.+.++|....||+||||+.+++.     .++|+...+  +.+.-+-|..+++... .+|+++|-|+..
T Consensus       111 qrp~vt~ki~gq~~ealldtgaddtv~e-----~~~lpgrwk--pk~iggiggfikvrqy-~~v~iei~g~k~  175 (203)
T d1hvca_         111 QRPLVTIKIGGQLKEALLDTGADDTVLE-----EMSLPGRWK--PKMIGGIGGFIKVRQY-DQILIEICGHKA  175 (203)
T ss_dssp             SCCEEEEEETTEEEEEEECTTCSSCEEE-----SCCCSSCCE--EEEEEETTEEEEEEEE-EEEEEEETTEEE
T ss_pred             ccceEEEecchhHHHHHhcccCCceEEe-----cccCCCCCc--ceEEEEeccccceeeE-ccEEEEECCCEE
Confidence            3467889999999999999999999883     477876553  5777888988888665 679999988754

>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=95.83  E-value=0.0017  Score=33.42  Aligned_cols=21  Identities=33%  Similarity=0.714  Sum_probs=18.8

Q ss_pred             ccccccCCCcccccccceeEE
Q 036272          251 ELCYSCDENYTVGHKCKKLFF  271 (383)
Q Consensus       251 ~~Cf~C~~~GH~a~~Cp~~~~  271 (383)
                      ++|.+|++.-|.+++|.++..
T Consensus         3 ~lCPrC~kG~HWa~~Crsk~~   23 (31)
T d1dsva_           3 GLCPRCKKGYHWKSECKSKFD   23 (31)
T ss_dssp             CBCTTTCSSBSCTTTCCCSEE
T ss_pred             ccCccccCcchHHHHhhhhhc
Confidence            689999999999999987654

>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=95.71  E-value=0.0016  Score=33.71  Aligned_cols=21  Identities=24%  Similarity=0.515  Sum_probs=18.3

Q ss_pred             CccccccCCCcccccccceeE
Q 036272          250 QELCYSCDENYTVGHKCKKLF  270 (383)
Q Consensus       250 ~~~Cf~C~~~GH~a~~Cp~~~  270 (383)
                      .++|.+|++.-|.+++|.++.
T Consensus         2 P~lCPrC~kG~HWa~~Crsk~   22 (32)
T d1cl4a_           2 PGLCPRCKRGKHWANECKSKT   22 (32)
T ss_dssp             CCSCSSCSSCSSCSTTCCCTT
T ss_pred             CccCccccCcchHHHHhhhhh
Confidence            368999999999999998644

>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=95.30  E-value=0.02  Score=38.90  Aligned_cols=71  Identities=14%  Similarity=0.148  Sum_probs=55.9

Q ss_pred             HHHHhhcccc--cccHhhHHHHHHHHHHHh--CCC-CH-----HHHHHHHHhhcchhHHhHccccCCCCHHHHHHHHHHH
Q 036272          121 SFGDLCKLKQ--TGTVSDYQPQFERLLARA--GSL-TD-----KQEAACFISGLKDGLRADVRAQNPQNLSAAIGLARNY  190 (383)
Q Consensus       121 ~~~~l~~~~q--~~sv~~Y~~~f~~l~~~~--~~~-~e-----~~~~~~f~~gL~~~l~~~l~~~~~~~l~~~~~~a~~~  190 (383)
                      ....|+..+-  +++..+++.++++|+..=  +.. +-     -.++..|+..|+.+++..+..+.|.+..+++.++..+
T Consensus         9 ~rqrFR~f~~~e~~~P~eal~rL~eLc~~WLrPe~~tKEqilelLVLEQFl~~lP~e~q~wV~e~~p~s~eeav~L~Edl   88 (96)
T d1y7qa1           9 CRQSFRRFCYQEVSGPQEALSQLRQLCRQWLQPELHTKEQILELLVMEQFLTILPEEIQARVRHRCLMSSKEIVTLVEDF   88 (96)
T ss_dssp             HHHHHHTCCSCSCCSSHHHHHHHHHHHHHHHCCSSCCHHHHHHHHHHHHHHHHSCTHHHHHHHTSCCCCHHHHHHHHHHH
T ss_pred             HHHHhcCCCcccCCCHHHHHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHCCHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            3445665554  778889999999987765  222 32     2577899999999999999999999999999999876


Q ss_pred             H
Q 036272          191 E  191 (383)
Q Consensus       191 e  191 (383)
                      .
T Consensus        89 ~   89 (96)
T d1y7qa1          89 H   89 (96)
T ss_dssp             H
T ss_pred             H
Confidence            5

>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=95.04  E-value=0.0021  Score=46.40  Aligned_cols=23  Identities=22%  Similarity=0.297  Sum_probs=19.9

Q ss_pred             EcCeEEEEEeeCCCcchhccHHH
Q 036272          313 ISKIPLTILIDSGSTHNYLHHRF  335 (383)
Q Consensus       313 i~~~~v~~LiDsGAt~s~Is~~~  335 (383)
                      ++|+.+.+|+||||++|+|++.-
T Consensus        27 ~~g~~i~~LLDTGAD~TVI~~~d   49 (124)
T d2rspa_          27 QRSVYITALLDSGADITIISEED   49 (124)
T ss_dssp             CSEEEEEEEECTTCSSCEEETTT
T ss_pred             eCCEEEEEEEcCCCCeEEEcCCc
Confidence            35678999999999999998874

>d1qrjb1 a.28.3.1 (B:131-214) HTLV-I capsid protein {Human T-cell leukemia virus type 1 [TaxId: 11908]}

class: All alpha proteins
fold: Acyl carrier protein-like
superfamily: Retrovirus capsid dimerization domain-like
family: Retrovirus capsid protein C-terminal domain
domain: HTLV-I capsid protein
species: Human T-cell leukemia virus type 1 [TaxId: 11908]

Probab=92.64  E-value=0.24  Score=32.58  Aligned_cols=63  Identities=10%  Similarity=0.043  Sum_probs=49.3

Q ss_pred             hhcccc--cccHhhHHHHHHHHHHHhC---CCCHHHHHHHHHhhcchhHHhHccccC--CCCHHHHHHHH
Q 036272          125 LCKLKQ--TGTVSDYQPQFERLLARAG---SLTDKQEAACFISGLKDGLRADVRAQN--PQNLSAAIGLA  187 (383)
Q Consensus       125 l~~~~q--~~sv~~Y~~~f~~l~~~~~---~~~e~~~~~~f~~gL~~~l~~~l~~~~--~~~l~~~~~~a  187 (383)
                      +.+++|  .|++.+|+.||.+......   ...........+.+=+++-+..++...  ..+|+|.+..+
T Consensus         3 ~~~IkQGpkEpf~dfVdRl~~a~~~~~~~~~~k~~l~~~L~~qNANpdCk~~lr~l~~~~~tlee~~~aC   72 (84)
T d1qrjb1           3 WASILQGLEEPYHAFVERLNIALDNGLPEGTPKDPILRSLAYSNANKECQKLLQARGHTNSPLGDMLRAC   72 (84)
T ss_dssp             GGGCCBCTTSCHHHHHHHHHHHHHTTCCTTSCCHHHHHHHHTTTBCHHHHHHHHHTTCSSSCHHHHHHHH
T ss_pred             cccCccCCCCcHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHcccHHHHHHHHhcCCCCCCHHHHHHHh
Confidence            567899  9999999999999887763   345667788888888999998887443  45788887654

>d2eiaa1 a.28.3.1 (A:148-222) EIAV capsid protein p26 {Equine infectious anemia virus [TaxId: 11665]}

class: All alpha proteins
fold: Acyl carrier protein-like
superfamily: Retrovirus capsid dimerization domain-like
family: Retrovirus capsid protein C-terminal domain
domain: EIAV capsid protein p26
species: Equine infectious anemia virus [TaxId: 11665]

Probab=89.05  E-value=0.47  Score=30.36  Aligned_cols=63  Identities=10%  Similarity=0.129  Sum_probs=46.4

Q ss_pred             hhcccc--cccHhhHHHHHHHHHHHhCCC---CHHHHHHHHHhhcchhHHhHccccC-CCCHHHHHHHH
Q 036272          125 LCKLKQ--TGTVSDYQPQFERLLARAGSL---TDKQEAACFISGLKDGLRADVRAQN-PQNLSAAIGLA  187 (383)
Q Consensus       125 l~~~~q--~~sv~~Y~~~f~~l~~~~~~~---~e~~~~~~f~~gL~~~l~~~l~~~~-~~~l~~~~~~a  187 (383)
                      +..++|  .|++++|+.+|..-.......   .........+.+-+++-+..++... -.+|+|.+..+
T Consensus         3 ~~dIkQGpkEpf~dfVdRl~~a~~~~~~~~~~k~~~~~~L~~qNANpdCk~iLr~l~~~~tLeemm~aC   71 (75)
T d2eiaa1           3 AQNIRQGAKEPYPEFVDRLLSQIKSEGHPQEISKFLTDTLTIQNANEECRNAMRHLRPEDTLEEKMYAC   71 (75)
T ss_dssp             STTCCCCTTCCHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTSCTTTTTTTTTCCTTSCHHHHHHHT
T ss_pred             ccccccCCCCCHHHHHHHHHHHHHhhcCcHhHHHHHHHHHhHhcCCHHHHHHHHhcCCCCCHHHHHHHh
Confidence            356889  899999999999888876422   2234556677777899888887654 46798887653

>d1d1da1 a.28.3.1 (A:151-230) RSV capsid protein {Rous sarcoma virus [TaxId: 11886]}

class: All alpha proteins
fold: Acyl carrier protein-like
superfamily: Retrovirus capsid dimerization domain-like
family: Retrovirus capsid protein C-terminal domain
domain: RSV capsid protein
species: Rous sarcoma virus [TaxId: 11886]

Probab=87.57  E-value=0.75  Score=29.73  Aligned_cols=67  Identities=12%  Similarity=0.188  Sum_probs=50.2

Q ss_pred             hhcccc--cccHhhHHHHHHHHHHHhC---CCCHHHHHHHHHhhcchhHHhHccccCC-CC-HHHHHHHHHHHH
Q 036272          125 LCKLKQ--TGTVSDYQPQFERLLARAG---SLTDKQEAACFISGLKDGLRADVRAQNP-QN-LSAAIGLARNYE  191 (383)
Q Consensus       125 l~~~~q--~~sv~~Y~~~f~~l~~~~~---~~~e~~~~~~f~~gL~~~l~~~l~~~~~-~~-l~~~~~~a~~~e  191 (383)
                      +..++|  .|++.+|+.||......-.   ..-........+.+-+++.+..++.... .+ +.+.++.....+
T Consensus         3 ~t~IkQGpkEpf~dfVdRl~~al~~~~~~~~~k~~~~~~L~~qNANpdCk~iLral~~~~tl~~emi~~~~~~~   76 (80)
T d1d1da1           3 WADITQGPSESFVDFANRLIKAVEGSDLPPSARAPVIIDCFRQKSQPDIQQLIRAAPSTLTTPGEIIKYVLDRQ   76 (80)
T ss_dssp             TTSCCCCSSSCHHHHHHHHHHHHHTSSCCTTTTTHHHHHHHTTSSCHHHHHHHHTSCTTCCSTTHHHHHHHHHH
T ss_pred             ccccccCCCccHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCHHHHHHHHhCCCCCCcHHHHHHHHHHHh
Confidence            346889  8999999999998877752   3345577888888999999999986543 34 477887765544

>d1a8oa_ a.28.3.1 (A:) HIV capsid protein, dimerisation domain {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: All alpha proteins
fold: Acyl carrier protein-like
superfamily: Retrovirus capsid dimerization domain-like
family: Retrovirus capsid protein C-terminal domain
domain: HIV capsid protein, dimerisation domain
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=85.70  E-value=1  Score=28.32  Aligned_cols=59  Identities=14%  Similarity=0.284  Sum_probs=44.2

Q ss_pred             cccc--cccHhhHHHHHHHHHHHhCCCCHH----HHHHHHHhhcchhHHhHccccCC-CCHHHHHHH
Q 036272          127 KLKQ--TGTVSDYQPQFERLLARAGSLTDK----QEAACFISGLKDGLRADVRAQNP-QNLSAAIGL  186 (383)
Q Consensus       127 ~~~q--~~sv~~Y~~~f~~l~~~~~~~~e~----~~~~~f~~gL~~~l~~~l~~~~~-~~l~~~~~~  186 (383)
                      .++|  .|++++|+.+|......... +.+    ......+.+-+++.+..+....+ .+|++.+..
T Consensus         2 dIkQgpkEpf~dfV~Rl~~~~~~~~~-~~~~k~~~~~~l~~~nANpdCk~ilr~l~~~~tLeemm~a   67 (70)
T d1a8oa_           2 DIRQGPKEPFRDYVDRFYKTLRAEQA-SQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTA   67 (70)
T ss_dssp             CCCCCTTSCHHHHHHHHHHHHHTTTC-CHHHHHHHHHTHHHHTSCHHHHHHHHTTCTTCCHHHHHHH
T ss_pred             CCccCCCCCHHHHHHHHHHHHHhhcC-CHHHHHHHHHHHHHhhCCHHHHHHHHccCCCCCHHHHHHh
Confidence            4788  89999999999988887642 333    44556777788999988886655 478887764