Citrus Sinensis ID: 040033

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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-------16
Protein Sequence
MPTTNQTTCRNSSIPVRGLSRAELQERRAKVCATIATKSFPRDIGERSCFFMEACVKVEDGDVIMEVDENAGVRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFIVNLILQGVYVIVDFNLRELEGYDVVLGTQWLRTLEPILWDFAS
Secondary Structure (PSIPRED)
ccccccccccccccccccccHHHHHHcccccccccccccccccccccccEEccccccccccccEEEcccccccccccccEEEEEEccEEEEEEEccccccccccHHHHHHHcccEEEEEEccEEEEEEEEEEccccccEEEcHHHHHHcccEEEEccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccHHHHHHHHccccEccccccccccccccEEEEccccccccccccEEEEEEEcccccccEEEEEEEEccEEEEEEEEccccccHccHHHHHHcccccEEEEcccEEEEEEEEEEEcccccEEEEHHHHHHcccEEEEccc
Coil and Loop (DISEMBL)
mpttnqttcrnssipvrglsRAELQERRAKVCATIatksfprdigeRSCFFMEACvkvedgdvimevdenagvrasetlringrignispivlvdsgsthnfiSDTFAKKVKNFIVNLILQGVYVIVDfnlrelegydvvlgtqwLRTLEPILWDFAS
Flexible Loop (DISEMBL)
mpttnqttcrnssipvrglsraeLQERRAKVCatiatksfprdigersCFFMEACVKVEDGDVIMEvdenagvrasetlringrigniSPIVLVDSGSTHNFISDTFAKKVKNFIVNLILQGVYVIVDFNLRELEGYDVVLGTQWLRTLEPILWDFAS
Low Complexity Region (SEG)
MPTTNQTTCRNSSIPVRGLSRAELQERRAKVCATIATKSFPRDIGERSCFFMEACVKVEDGDVIMEVDENAGVRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFIVNLILQGVYVIVDFNLRELEGYDVVLGTQWLRTLEPILWDFAS
Disordered region (IsUnstruct)
****************************AKVCATIATKSFPRDIGERSCFFMEACVKVEDGDVIMEVDENAGVRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFIVNLILQGVYVIVDFNLRELEGYDVVLGTQWLRTLEPILWDF**
Disordered Region (DISOPRED)
*******************************CATIATKSFPRDIGERS***********************GVRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFIVNLILQGVYVIVDFNLRELEGYDVVLGTQWLRTLEPILWDFAS
Disordered Region (DISEMBL)
*************IPVRGLSRAELQERRAKVCATIATKSFPRDIGERSCFFMEACVKVEDGDVIMEVDENAGVRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFIVNLILQGVYVIVDFNLRELEGYDVVLGTQWLRTLEPILWDFAS
Disordered Region (DISPRO)
***************VRGLSRAELQERRAKVCATIATKSFPRDIGERSCFFMEACVKVEDGDVIMEVDENAGVRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFIVNLILQGVYVIVDFNLRELEGYDVVLGTQWLRTLEPILWDFAS
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPTTNQTTCRNSSIPVRGLSRAELQERRAKVCATIATKSFPRDIGERSCFFMEACVKVEDGDVIMEVDENAGVRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFIVNLILQGVYVIVDFNLRELEGYDVVLGTQWLRTLEPILWDFAS
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	158
357130210	635	PREDICTED: uncharacterized protein LOC10	0.930	0.231	0.333	9e-15
242085414	1462	hypothetical protein SORBIDRAFT_08g01083	0.892	0.096	0.309	3e-14
218197921	402	hypothetical protein OsI_22431 [Oryza sa	0.886	0.348	0.329	3e-13
147774273	1469	hypothetical protein VITISV_026680 [Viti	0.936	0.100	0.289	4e-12
18425247	848	Putative polyprotein [Oryza sativa] gi|3	0.905	0.168	0.329	5e-12
242065034	1414	hypothetical protein SORBIDRAFT_04g01807	0.886	0.099	0.271	5e-12
147843077	1366	hypothetical protein VITISV_044100 [Viti	0.936	0.108	0.289	7e-12
147789424	2822	hypothetical protein VITISV_017554 [Viti	0.911	0.051	0.295	8e-12
116309032	1448	OSIGBa0114M03.4 [Oryza sativa Indica Gro	0.898	0.098	0.300	9e-11
356529593	572	PREDICTED: uncharacterized protein LOC10	0.905	0.25	0.289	6e-10

>gi|357130210|ref|XP_003566743.1| PREDICTED: uncharacterized protein LOC100838891 [Brachypodium distachyon]

 Score = 85.1 bits (209), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 57/171 (33%), Positives = 84/171 (49%), Gaps = 24/171 (14%)

Query: 10  RNSSIPVRGLSRAELQERRAKVCATIATKSFPRDIGERSCFFMEACVKVEDGDVIMEVDE 69
           R ++   + L+ AE++ER+AK       + F R    +  F++E   K E+ D+ + +  
Sbjct: 128 RGATPVFKKLNAAEMEERQAKGLCFNCDEKFVRGHRCKCLFYIEVADKEEEEDLQISLLA 187

Query: 70  NAGVRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFIVN------LILQGV 123
             GVR S+T+++   +G    + L+DSGSTHNFIS+  A  V             I  G 
Sbjct: 188 ITGVRTSDTMQLVVWVGERELLALIDSGSTHNFISEELAAHVSAPFCTGRRLRVTIANGD 247

Query: 124 YV------------------IVDFNLRELEGYDVVLGTQWLRTLEPILWDF 156
           +V                  +VD     L G+DVVLGT WL+TL PILWDF
Sbjct: 248 HVTCSGLLRHTAIAIGQESFVVDLYAIPLGGFDVVLGTHWLKTLGPILWDF 298

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242085414|ref|XP_002443132.1| hypothetical protein SORBIDRAFT_08g010830 [Sorghum bicolor] gi|241943825|gb|EES16970.1| hypothetical protein SORBIDRAFT_08g010830 [Sorghum bicolor]

 Score = 83.2 bits (204), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 57/184 (30%), Positives = 87/184 (47%), Gaps = 43/184 (23%)

Query: 16  VRGLSRAELQERRAKVCATIATKSFPRDIGERSC---FFMEACVKVEDGDVIMEVDENA- 71
           +R LS+ E+ ERR +       + + R    R C   FF++  V+V+D +   E  + A 
Sbjct: 249 IRRLSKDEMAERRRQGLCFNCNEPYTRG-HNRFCKRLFFVDG-VEVDDVEDAAEAGDQAA 306

Query: 72  -------------GVRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFIVN- 117
                        GVR S+TLR+   +G++S + L DSGS+HNFIS+  A++    +V+ 
Sbjct: 307 GTDAPCYSLHAVAGVRLSDTLRVRVMVGSVSLVALSDSGSSHNFISERAAQRTGLLVVSR 366

Query: 118 -----------------------LILQGVYVIVDFNLRELEGYDVVLGTQWLRTLEPILW 154
                                   ++QG     D  +  L G+DVVLG QWL TL P+ W
Sbjct: 367 PRLSAVVANGERIACPGVLPQAPFVIQGSSFTADLFIMPLAGFDVVLGAQWLGTLGPVTW 426

Query: 155 DFAS 158
           DF +
Sbjct: 427 DFTA 430

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218197921|gb|EEC80348.1| hypothetical protein OsI_22431 [Oryza sativa Indica Group]

 Score = 79.7 bits (195), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 57/173 (32%), Positives = 82/173 (47%), Gaps = 33/173 (19%)

Query: 17  RGLSRAELQERRAKV----CATIATKSFPRDIGERSCFFMEACV-----KVEDGDVIMEV 67
           R LS AE+ E R K     C    +K   R    +  + +E         + D  V + +
Sbjct: 102 RRLSAAEMAECREKGLCFNCPEKFSKDHHRQCSMKGIYLLEMDEGEDDDSINDDTVTISL 161

Query: 68  DENAGVRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKV------KNFIVNLILQ 121
               G+R S+T+R+   IG ++   LVDSGSTH F++   A+++      K+ +  ++  
Sbjct: 162 HALTGIRTSKTMRLAVIIGGVTMSALVDSGSTHTFVATEAARRLGLSPTTKSGLNVMVAN 221

Query: 122 GVYV------------------IVDFNLRELEGYDVVLGTQWLRTLEPILWDF 156
           G  V                  I+D  +  LEGYDVVLG QWLRTL PILWDF
Sbjct: 222 GDQVTSSGICSGIPIKIDSEDFIIDCYVIPLEGYDVVLGVQWLRTLGPILWDF 274

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 76.3 bits (186), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 57/197 (28%), Positives = 91/197 (46%), Gaps = 49/197 (24%)

Query: 10  RNSSIPVRGLSRAELQERRAK-VCATIATKSFPRDIGERSCFFMEACVKVEDGDV----- 63
           + + +PV+ LS ++++ERR K +C     K  P    + +  F+  C +  D +V     
Sbjct: 268 KRAIVPVQRLSPSQMKERRDKGLCYNCDDKWAPGHKCKSARLFIMECDESSDDEVPKSEV 327

Query: 64  -------------IMEVDENAGVRA------SETLRINGRIGNISPIVLVDSGSTHNFI- 103
                        I+E++    + A       +T+R  G I   + ++LVD+GSTHNF+ 
Sbjct: 328 AEGRASKSKEETPIVEIEPGISIHALVGSPNPKTMRFLGHICGRAVVILVDTGSTHNFMD 387

Query: 104 -------------SDTFAKKVKN----------FIVNLILQGVYVIVDFNLRELEGYDVV 140
                        ++  + KV N            V L +QG    +DF +  L G D+V
Sbjct: 388 PSVIQRAHLPSNPTEGLSVKVANGQAVRSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIV 447

Query: 141 LGTQWLRTLEPILWDFA 157
           LG QWL+TL PILWDF+
Sbjct: 448 LGVQWLQTLGPILWDFS 464

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18425247|gb|AAL69425.1|AC098565_7 Putative polyprotein [Oryza sativa] gi|31430198|gb|AAP52144.1| retrotransposon protein, putative, unclassified [Oryza sativa Japonica Group]

 Score = 75.9 bits (185), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 57/173 (32%), Positives = 80/173 (46%), Gaps = 30/173 (17%)

Query: 12  SSIPVRGLSRAELQERRAK-VCATIATKSFPRDIGERSCFFMEACVKVEDGDVIMEVDEN 70
           S++P + LS AE+ +RR++ +C     KS       R      A    E     + +   
Sbjct: 283 SALPRKRLSPAEMAQRRSEGLCYNCDEKSSASQRKLRRTPTAHALTLDEPS---ISLHAL 339

Query: 71  AGVRAS--ETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVK---------------- 112
           AGVR     T+++  RIG    + L+DSGSTHNFISD  A++ +                
Sbjct: 340 AGVRTPTFNTIKVQARIGATDLVALLDSGSTHNFISDVAARRARVPLEPRHGLSVAVANG 399

Query: 113 -------NFIVNLILQGVYV-IVDFNLRELEGYDVVLGTQWLRTLEPILWDFA 157
                   F    +  G +  ++DF    L GYDVVLG QWL +L P LWDFA
Sbjct: 400 DRITSPGCFPSQRVTIGDHTFVIDFYALPLGGYDVVLGAQWLGSLGPTLWDFA 452

Source: Oryza sativa

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242065034|ref|XP_002453806.1| hypothetical protein SORBIDRAFT_04g018075 [Sorghum bicolor] gi|241933637|gb|EES06782.1| hypothetical protein SORBIDRAFT_04g018075 [Sorghum bicolor]

 Score = 75.9 bits (185), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 45/166 (27%), Positives = 79/166 (47%), Gaps = 26/166 (15%)

Query: 19  LSRAELQERRAKVCATIATKSFPRDIG--ERSCFFMEACVKVEDGDVIMEVDENAGVRAS 76
           + R  +Q + +K  + I   +   D      SCF +     ++  + +   D  AGV  +
Sbjct: 234 VQRPRIQHQASKAISFILVPAVVLDTFSIRASCFTLHTSAYMKPAEALFPWDPVAGVPLA 293

Query: 77  ETLRINGRIGNISPIVLVDSGSTHNFISDTFAKK----------VKNFIVN--------- 117
           +T+++   +G  + + L+DSGSTHNFI++  A++          +   + N         
Sbjct: 294 DTMQVRVSVGTATFVALLDSGSTHNFIAEEAARRTGLRVQPRARMTAMVANGEKIPCPGV 353

Query: 118 -----LILQGVYVIVDFNLRELEGYDVVLGTQWLRTLEPILWDFAS 158
                + +      +D  +  L GYD+VLGTQW+ TL PI+WDFA+
Sbjct: 354 IRHAPVTIDNTTFAIDLFVMPLAGYDIVLGTQWMATLGPIVWDFAA 399

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 75.5 bits (184), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 57/197 (28%), Positives = 90/197 (45%), Gaps = 49/197 (24%)

Query: 10  RNSSIPVRGLSRAELQERRAK-VCATIATKSFPRDIGERSCFFMEACVKVEDGDV----- 63
           + + +PV+ LS ++++ERR K +C     K  P    +    F+  C +  D +V     
Sbjct: 235 KRAIVPVQRLSPSQMKERRDKGLCYNCDDKWAPGHKCKSXRLFIMECDESSDDEVPKSEV 294

Query: 64  -------------IMEVDENAGVRA------SETLRINGRIGNISPIVLVDSGSTHNFI- 103
                        I+E++    + A       +T+R  G I   + ++LVD+GSTHNF+ 
Sbjct: 295 AEGRASKSKEETPIVEIEPGISIHALVGSPNPKTMRFLGHICGRAVVILVDTGSTHNFMD 354

Query: 104 -------------SDTFAKKVKN----------FIVNLILQGVYVIVDFNLRELEGYDVV 140
                        ++  + KV N            V L +QG    +DF +  L G D+V
Sbjct: 355 PSVIQRAHLPSNPTEGLSVKVANGQAVRSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIV 414

Query: 141 LGTQWLRTLEPILWDFA 157
           LG QWL+TL PILWDF+
Sbjct: 415 LGVQWLQTLGPILWDFS 431

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 75.1 bits (183), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 57/193 (29%), Positives = 88/193 (45%), Gaps = 49/193 (25%)

Query: 14  IPVRGLSRAELQERRAK-VCATIATKSFPRDIGERSCFFMEACVKVEDGDV--------- 63
           +PV+ LS ++++ERR K +C     K  P    + +  F+  C +  D  V         
Sbjct: 237 VPVQRLSPSQMKERRDKGLCYNCDDKWAPGHKCKSARLFIMECDESSDDKVPKSEVAEGR 296

Query: 64  ---------IMEVDENAGVRA------SETLRINGRIGNISPIVLVDSGSTHNFI----- 103
                    I+E++    + A       +T+R  G I   + ++LVD+GSTHNF+     
Sbjct: 297 ASKSKEETPIVEIEPGISIHALVGSPNPKTMRFLGHICGRAVVILVDTGSTHNFMDPSVI 356

Query: 104 ---------SDTFAKKVKN----------FIVNLILQGVYVIVDFNLRELEGYDVVLGTQ 144
                    ++  + KV N            V L +QG    +DF +  L G D+VLG Q
Sbjct: 357 QRAHLPSNPTEGLSVKVANGQAVCSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIVLGVQ 416

Query: 145 WLRTLEPILWDFA 157
           WL+TL PILWDF+
Sbjct: 417 WLQTLGPILWDFS 429

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 = 71.6 bits (174), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 55/183 (30%), Positives = 84/183 (45%), Gaps = 41/183 (22%)

Query: 16  VRGLSRAELQERRAKVCATIATKSFPRDIGERSC---FFMEACVKVED-------GDV-- 63
           ++ L++AE +ERR K       + + R    R C   F +E   + ED       GD   
Sbjct: 261 IKRLTQAEQEERRRKGLCYNCDEKYTRG-HNRVCQRLFLLEGIEEDEDDGTPEDFGDAGA 319

Query: 64  ----IMEVDENAGVRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKK--------- 110
               +  +   AGV  ++T+++   +G  S + L+DSGSTHNFIS+  A++         
Sbjct: 320 EDAPVFSLQAIAGVSFTDTMQVAVTLGTASLVALLDSGSTHNFISEAAAQRSGLPLQQRP 379

Query: 111 -VKNFIVN--------------LILQGVYVIVDFNLRELEGYDVVLGTQWLRTLEPILWD 155
            +   + N              L + G     D  +  L GYDVVLGT+WL  L PI+WD
Sbjct: 380 RLTAMVANGERVTCIGVIRGAPLTIGGNSFPADLFVMPLAGYDVVLGTRWLGALGPIVWD 439

Query: 156 FAS 158
            A+
Sbjct: 440 LAT 442

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356529593|ref|XP_003533374.1| PREDICTED: uncharacterized protein LOC100812827 [Glycine max]

 Score = 68.9 bits (167), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 55/190 (28%), Positives = 85/190 (44%), Gaps = 47/190 (24%)

Query: 16  VRGLSRAELQERRAK-VCATIATKSFPR-----DIGERSCFFMEACVKVEDGDVIMEVDE 69
           +R +   E +ERRAK +C     K  P      +   R     E     ++G+++   D 
Sbjct: 315 IRSIHNEEFEERRAKGLCFKCGGKYHPTFHKCLERALRVLILGEGETMTKEGEIVSMKDV 374

Query: 70  N-----------------AGVRASETLRINGRIGNISPIVLVDSGSTHNFISD------- 105
                               +  S T+R+ G+I N+  +VL+DSG++HNFIS        
Sbjct: 375 TVESEEEVEVECKLMGVLGSMGESHTMRVEGKIHNVDLLVLIDSGASHNFISPKVTTALG 434

Query: 106 -----TFAKKVK---------NFI---VNLILQGVYVIVDFNLRELEGYDVVLGTQWLRT 148
                T AK +K         N +   VN+ + G+ VIVD  + EL G D+VLG  WLRT
Sbjct: 435 LVITPTVAKSIKLGDGHRLITNGVCKGVNMQMGGIEVIVDALVLELGGMDMVLGVAWLRT 494

Query: 149 LEPILWDFAS 158
           L  ++ D+ +
Sbjct: 495 LGNVIMDWKA 504

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	158
cd00303	92	cd00303, retropepsin_like, Retropepsins; pepsin-li	4e-10
pfam08284	135	pfam08284, RVP_2, Retroviral aspartyl protease	6e-05
pfam13975	72	pfam13975, gag-asp_proteas, gag-polyprotein putati	2e-04

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

 Score = 53.1 bits (128), Expect = 4e-10
 Identities = 29/92 (31%), Positives = 41/92 (44%), Gaps = 25/92 (27%)

Query: 81  INGRIGNISPIVLVDSGSTHNFISDTFAKK-------------VKNF------------I 115
           + G+I  +    LVDSG++ NFIS++ AKK             VK               
Sbjct: 1   LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILP 60

Query: 116 VNLILQGVYVIVDFNLRELEGYDVVLGTQWLR 147
           V + + G    VDF + +L  YDV+LG  WL 
Sbjct: 61  VTIGIGGKTFTVDFYVLDLLSYDVILGRPWLE 92

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

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

 Score = 40.1 bits (94), Expect = 6e-05
 Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 24/86 (27%)

Query: 85  IGNISPIVLVDSGSTHNFISDTFAKK-------VKNFI-----------------VNLIL 120
           + +I   VL DSG++H+FIS  F  +       ++  +                 VN+ +
Sbjct: 28  VNSIPATVLFDSGASHSFISQAFVGRHGLPLEALRTPMLVHSPGGDMTATHRCPSVNIEI 87

Query: 121 QGVYVIVDFNLRELEGYDVVLGTQWL 146
           QGV    +  L + +  DV+LG  WL
Sbjct: 88  QGVDFPANLILLDSKDLDVILGMDWL 113

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

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

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 12/33 (36%), Positives = 21/33 (63%)

Query: 78  TLRINGRIGNISPIVLVDSGSTHNFISDTFAKK 110
            + +   IG +    LVD+G+TH+FIS++ A +
Sbjct: 8   LVTVEVSIGGVEVKALVDTGATHSFISESLAAR 40

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	158
PF08284	135	RVP_2: Retroviral aspartyl protease; InterPro: IPR	99.93
cd05479	124	RP_DDI RP_DDI; retropepsin-like domain of DNA dama	99.86
cd05484	91	retropepsin_like_LTR_2 Retropepsins_like_LTR, peps	99.64
PF09668	124	Asp_protease: Aspartyl protease; InterPro: IPR0191	99.64
TIGR02281	121	clan_AA_DTGA clan AA aspartic protease, TIGR02281	99.52
PF13650	90	Asp_protease_2: Aspartyl protease	99.48
PF00077	100	RVP: Retroviral aspartyl protease The Prosite entr	99.45
cd05480	103	NRIP_C NRIP_C; putative nuclear receptor interacti	99.45
cd05483	96	retropepsin_like_bacteria Bacterial aspartate prot	99.41
PF12384	177	Peptidase_A2B: Ty3 transposon peptidase; InterPro:	99.28
TIGR03698	107	clan_AA_DTGF clan AA aspartic protease, AF_0612 fa	99.28
cd06095	86	RP_RTVL_H_like Retropepsin of the RTVL_H family of	99.24
cd00303	92	retropepsin_like Retropepsins; pepsin-like asparta	99.18
KOG0012	380	consensus DNA damage inducible protein [Replicatio	99.11
PF13975	72	gag-asp_proteas: gag-polyprotein putative aspartyl	99.0
COG3577	215	Predicted aspartyl protease [General function pred	98.88
PF02160	201	Peptidase_A3: Cauliflower mosaic virus peptidase (	98.6
cd05481	93	retropepsin_like_LTR_1 Retropepsins_like_LTR; peps	98.41
cd06094	89	RP_Saci_like RP_Saci_like, retropepsin family. Ret	98.23
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.18
PF05585	164	DUF1758: Putative peptidase (DUF1758); InterPro: I	98.16
COG5550	125	Predicted aspartyl protease [Posttranslational mod	98.1
cd05482	87	HIV_retropepsin_like Retropepsins, pepsin-like asp	97.87
PF13696	32	zf-CCHC_2: Zinc knuckle	96.66
smart00343	26	ZnF_C2HC zinc finger.	95.88
PF13917	42	zf-CCHC_3: Zinc knuckle	95.67
PF12382	137	Peptidase_A2E: Retrotransposon peptidase; InterPro	95.21
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	95.08
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	94.71
PF05618	138	Zn_protease: Putative ATP-dependant zinc protease;	94.21
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	93.89
PF14392	49	zf-CCHC_4: Zinc knuckle	93.23
COG4067	162	Uncharacterized protein conserved in archaea [Post	93.12
PTZ00368	148	universal minicircle sequence binding protein (UMS	91.21
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	90.86
COG5222	427	Uncharacterized conserved protein, contains RING Z	90.13
cd05476	265	pepsin_A_like_plant Chroloplast Nucleoids DNA-bind	89.34
cd05477	318	gastricsin Gastricsins, asparate proteases produce	89.22
PTZ00368	148	universal minicircle sequence binding protein (UMS	88.93
PTZ00013	450	plasmepsin 4 (PM4); Provisional	87.34
cd05470	109	pepsin_retropepsin_like Cellular and retroviral pe	86.83
cd05478	317	pepsin_A Pepsin A, aspartic protease produced in g	86.08
PTZ00147	453	plasmepsin-1; Provisional	85.75
PF15288	40	zf-CCHC_6: Zinc knuckle	85.34
cd06096	326	Plasmepsin_5 Plasmepsins are a class of aspartic p	84.62
cd05474	295	SAP_like SAPs, pepsin-like proteinases secreted fr	84.25
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	81.4

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

Probab=99.93  E-value=1.4e-25  Score=163.35  Aligned_cols=84  Identities=40%  Similarity=0.676  Sum_probs=79.0

Q ss_pred             ccCceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------------------EEEEECCEEEEEEE
Q 040033           74 RASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------------------VNLILQGVYVIVDF  129 (158)
Q Consensus        74 ~~~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------------------A~i~i~g~~~~~~~  129 (158)
                      ..++.|...+.|+++++.+|||||||||||++++|++++++.                        .++.++|++|..+|
T Consensus        17 ~~~~vi~g~~~I~~~~~~vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~~V~~~g~~~~~~~~~~~~~~~i~g~~~~~dl   96 (135)
T PF08284_consen   17 ESPDVITGTFLINSIPASVLIDSGATHSFISSSFAKKLGLPLEPLPRPIVVSAPGGSINCEGVCPDVPLSIQGHEFVVDL   96 (135)
T ss_pred             CCCCeEEEEEEeccEEEEEEEecCCCcEEccHHHHHhcCCEEEEccCeeEEecccccccccceeeeEEEEECCeEEEeee
Confidence            457889999999999999999999999999999999999887                        18899999999999


Q ss_pred             EEecCCCCcEEechhHhhhcCCceeeecC
Q 040033          130 NLRELEGYDVVLGTQWLRTLEPILWDFAS  158 (158)
Q Consensus       130 ~v~~~~~~dvILG~dwL~~~~~i~idw~~  158 (158)
                      .|+++.++|||||||||.+|+| .|||.+
T Consensus        97 ~vl~l~~~DvILGm~WL~~~~~-~IDw~~  124 (135)
T PF08284_consen   97 LVLDLGGYDVILGMDWLKKHNP-VIDWAT  124 (135)
T ss_pred             EEecccceeeEeccchHHhCCC-EEEccC
Confidence            9999999999999999999999 899974

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

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

Probab=99.86  E-value=4.3e-21  Score=137.71  Aligned_cols=82  Identities=21%  Similarity=0.321  Sum_probs=75.6

Q ss_pred             CceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------------------EEEEECCEEEEEEEEE
Q 040033           76 SETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------------------VNLILQGVYVIVDFNL  131 (158)
Q Consensus        76 ~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------------------A~i~i~g~~~~~~~~v  131 (158)
                      ...+.+.+.|||+++.+||||||++|||+.++|+++|++.                        .++.+++.++.++|.|
T Consensus        14 ~~~~~v~~~Ing~~~~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~~~~~V   93 (124)
T cd05479          14 VPMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRIHLAQVKIGNLFLPCSFTV   93 (124)
T ss_pred             eeEEEEEEEECCEEEEEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCCCcEEEeEEEEEEEEECCEEeeeEEEE
Confidence            4578899999999999999999999999999999999853                        1888999999999999


Q ss_pred             ecCCCCcEEechhHhhhcCCceeeecC
Q 040033          132 RELEGYDVVLGTQWLRTLEPILWDFAS  158 (158)
Q Consensus       132 ~~~~~~dvILG~dwL~~~~~i~idw~~  158 (158)
                      +++..+|+|||||||++++. .|||++
T Consensus        94 l~~~~~d~ILG~d~L~~~~~-~ID~~~  119 (124)
T cd05479          94 LEDDDVDFLIGLDMLKRHQC-VIDLKE  119 (124)
T ss_pred             ECCCCcCEEecHHHHHhCCe-EEECCC
Confidence            99999999999999999995 899974

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

>cd05484 retropepsin_like_LTR_2 Retropepsins_like_LTR, pepsin-like aspartate proteases

Probab=99.64  E-value=1.3e-15  Score=103.40  Aligned_cols=67  Identities=19%  Similarity=0.226  Sum_probs=61.1

Q ss_pred             EEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE-----------------------EEEEECCEEEEEEEEEecCCC
Q 040033           80 RINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI-----------------------VNLILQGVYVIVDFNLRELEG  136 (158)
Q Consensus        80 ~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~-----------------------A~i~i~g~~~~~~~~v~~~~~  136 (158)
                      .+.+.|||+++.+||||||++|||+++.+.+++.+.                       ..+++++.++.++|+|++.. 
T Consensus         2 ~~~~~Ing~~i~~lvDTGA~~svis~~~~~~lg~~~~~~~~~~v~~a~G~~~~~~G~~~~~v~~~~~~~~~~~~v~~~~-   80 (91)
T cd05484           2 TVTLLVNGKPLKFQLDTGSAITVISEKTWRKLGSPPLKPTKKRLRTATGTKLSVLGQILVTVKYGGKTKVLTLYVVKNE-   80 (91)
T ss_pred             EEEEEECCEEEEEEEcCCcceEEeCHHHHHHhCCCccccccEEEEecCCCEeeEeEEEEEEEEECCEEEEEEEEEEECC-
Confidence            467899999999999999999999999999999753                       17788999999999999998 


Q ss_pred             CcEEechhHhh
Q 040033          137 YDVVLGTQWLR  147 (158)
Q Consensus       137 ~dvILG~dwL~  147 (158)
                      ++.|||+|||.
T Consensus        81 ~~~lLG~~wl~   91 (91)
T cd05484          81 GLNLLGRDWLD   91 (91)
T ss_pred             CCCccChhhcC
Confidence            99999999984

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

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

Probab=99.64  E-value=2.2e-15  Score=107.97  Aligned_cols=79  Identities=24%  Similarity=0.381  Sum_probs=67.3

Q ss_pred             CceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------------------EEEEECCEEEEEEEEE
Q 040033           76 SETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------------------VNLILQGVYVIVDFNL  131 (158)
Q Consensus        76 ~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------------------A~i~i~g~~~~~~~~v  131 (158)
                      ...+.+.+.|||++++|+|||||.+|.||.++|+++|+..                        +++++++..+.+.|.|
T Consensus        22 v~mLyI~~~ing~~vkA~VDtGAQ~tims~~~a~r~gL~~lid~r~~g~a~GvG~~~i~G~Ih~~~l~ig~~~~~~s~~V  101 (124)
T PF09668_consen   22 VSMLYINCKINGVPVKAFVDTGAQSTIMSKSCAERCGLMRLIDKRFAGVAKGVGTQKILGRIHSVQLKIGGLFFPCSFTV  101 (124)
T ss_dssp             ----EEEEEETTEEEEEEEETT-SS-EEEHHHHHHTTGGGGEEGGG-EE-------EEEEEEEEEEEEETTEEEEEEEEE
T ss_pred             cceEEEEEEECCEEEEEEEeCCCCccccCHHHHHHcCChhhccccccccccCCCcCceeEEEEEEEEEECCEEEEEEEEE
Confidence            4567889999999999999999999999999999999864                        2889999999999999


Q ss_pred             ecCCCCcEEechhHhhhcCCceee
Q 040033          132 RELEGYDVVLGTQWLRTLEPILWD  155 (158)
Q Consensus       132 ~~~~~~dvILG~dwL~~~~~i~id  155 (158)
                      ++-...|+|||.|||++|+. .||
T Consensus       102 le~~~~d~llGld~L~~~~c-~ID  124 (124)
T PF09668_consen  102 LEDQDVDLLLGLDMLKRHKC-CID  124 (124)
T ss_dssp             ETTSSSSEEEEHHHHHHTT--EEE
T ss_pred             eCCCCcceeeeHHHHHHhCc-ccC
Confidence            99889999999999999997 676

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.

>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family

Probab=99.52  E-value=1.4e-13  Score=98.49  Aligned_cols=82  Identities=21%  Similarity=0.239  Sum_probs=72.1

Q ss_pred             cCceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE-----------E------------EEEECCEEEE-EEEE
Q 040033           75 ASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI-----------V------------NLILQGVYVI-VDFN  130 (158)
Q Consensus        75 ~~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~-----------A------------~i~i~g~~~~-~~~~  130 (158)
                      ...++.+++.|||+++.+||||||++++|++++|+++|+..           |            .+.+++..+. +.+.
T Consensus         8 ~~g~~~v~~~InG~~~~flVDTGAs~t~is~~~A~~Lgl~~~~~~~~~~~~ta~G~~~~~~~~l~~l~iG~~~~~nv~~~   87 (121)
T TIGR02281         8 GDGHFYATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIKAARVTLDRVAIGGIVVNDVDAM   87 (121)
T ss_pred             CCCeEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCcccCCceEEEEeCCCcEEEEEEEeCEEEECCEEEeCcEEE
Confidence            35678899999999999999999999999999999999875           1            7888998888 8899


Q ss_pred             EecCC-CCcEEechhHhhhcCCceeee
Q 040033          131 LRELE-GYDVVLGTQWLRTLEPILWDF  156 (158)
Q Consensus       131 v~~~~-~~dvILG~dwL~~~~~i~idw  156 (158)
                      |++.. ..+.+||||||.++..+.+|-
T Consensus        88 v~~~~~~~~~LLGm~fL~~~~~~~~~~  114 (121)
T TIGR02281        88 VAEGGALSESLLGMSFLNRLSRFTVRG  114 (121)
T ss_pred             EeCCCcCCceEcCHHHHhccccEEEEC
Confidence            99886 358999999999998877774

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

>PF13650 Asp_protease_2: Aspartyl protease

Probab=99.48  E-value=2.9e-13  Score=90.28  Aligned_cols=65  Identities=22%  Similarity=0.330  Sum_probs=58.3

Q ss_pred             EEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE-----------------------EEEEECCEEE-EEEEEEec-CC
Q 040033           81 INGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI-----------------------VNLILQGVYV-IVDFNLRE-LE  135 (158)
Q Consensus        81 ~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~-----------------------A~i~i~g~~~-~~~~~v~~-~~  135 (158)
                      ++++|||+++.+||||||+.++|++++++++++..                       ..+++++..+ .+++.+++ ..
T Consensus         1 V~v~vng~~~~~liDTGa~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~~~~i~ig~~~~~~~~~~v~~~~~   80 (90)
T PF13650_consen    1 VPVKVNGKPVRFLIDTGASISVISRSLAKKLGLKPRPKSVPISVSGAGGSVTVYRGRVDSITIGGITLKNVPFLVVDLGD   80 (90)
T ss_pred             CEEEECCEEEEEEEcCCCCcEEECHHHHHHcCCCCcCCceeEEEEeCCCCEEEEEEEEEEEEECCEEEEeEEEEEECCCC
Confidence            46889999999999999999999999999998775                       1888999888 58899999 56


Q ss_pred             CCcEEechhH
Q 040033          136 GYDVVLGTQW  145 (158)
Q Consensus       136 ~~dvILG~dw  145 (158)
                      .+|+|||+||
T Consensus        81 ~~~~iLG~df   90 (90)
T PF13650_consen   81 PIDGILGMDF   90 (90)
T ss_pred             CCEEEeCCcC
Confidence            8999999998

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

Probab=99.45  E-value=6.3e-13  Score=91.18  Aligned_cols=72  Identities=22%  Similarity=0.226  Sum_probs=63.8

Q ss_pred             EEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE--------------------EEEEECCEEEEEEEEEecCCCCc
Q 040033           79 LRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI--------------------VNLILQGVYVIVDFNLRELEGYD  138 (158)
Q Consensus        79 i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~--------------------A~i~i~g~~~~~~~~v~~~~~~d  138 (158)
                      -.+.+.++|+++.+||||||+.|+|+++.++......                    +.+.+++..+...|+|++....|
T Consensus         6 p~i~v~i~g~~i~~LlDTGA~vsiI~~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~v~~~~~~~~~~~~v~~~~~~~   85 (100)
T PF00077_consen    6 PYITVKINGKKIKALLDTGADVSIISEKDWKKLGPPPKTSITVRGAGGSSSILGSTTVEVKIGGKEFNHTFLVVPDLPMN   85 (100)
T ss_dssp             SEEEEEETTEEEEEEEETTBSSEEESSGGSSSTSSEEEEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEESSTCSSE
T ss_pred             ceEEEeECCEEEEEEEecCCCcceecccccccccccccCCceeccCCCcceeeeEEEEEEEEECccceEEEEecCCCCCC
Confidence            3578999999999999999999999999998775532                    18889999999999999987788


Q ss_pred             EEechhHhhhcCC
Q 040033          139 VVLGTQWLRTLEP  151 (158)
Q Consensus       139 vILG~dwL~~~~~  151 (158)
                       |||+|||++++.
T Consensus        86 -ILG~D~L~~~~~   97 (100)
T PF00077_consen   86 -ILGRDFLKKLNA   97 (100)
T ss_dssp             -EEEHHHHTTTTC
T ss_pred             -EeChhHHHHcCC
Confidence             999999999986

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 ....

>cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein

Probab=99.45  E-value=5.3e-13  Score=91.41  Aligned_cols=75  Identities=20%  Similarity=0.184  Sum_probs=68.9

Q ss_pred             EEEECCEeeEEEecCCCceeEECHHHHHHcCCeE--------------------------EEEEECCEEEEEEEEEecCC
Q 040033           82 NGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI--------------------------VNLILQGVYVIVDFNLRELE  135 (158)
Q Consensus        82 ~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~--------------------------A~i~i~g~~~~~~~~v~~~~  135 (158)
                      ..++||++++|+|||||-+|+||..+|+++|+..                          |++++++..+...|.|++-.
T Consensus         2 nCk~nG~~vkAfVDsGaQ~timS~~caercgL~r~v~~~r~~g~A~gvgt~~kiiGrih~~~ikig~~~~~CSftVld~~   81 (103)
T cd05480           2 SCQCAGKELRALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSLPTSVKVIGQIERLVLQLGQLTVECSAQVVDDN   81 (103)
T ss_pred             ceeECCEEEEEEEecCCchhhcCHHHHHHcChHhhhhhccccccccCCCcceeEeeEEEEEEEEeCCEEeeEEEEEEcCC
Confidence            4679999999999999999999999999999863                          28889999999999999988


Q ss_pred             CCcEEechhHhhhcCCceeeec
Q 040033          136 GYDVVLGTQWLRTLEPILWDFA  157 (158)
Q Consensus       136 ~~dvILG~dwL~~~~~i~idw~  157 (158)
                      +.|++||.|-|++|.. .||.+
T Consensus        82 ~~d~llGLdmLkrhqc-~IdL~  102 (103)
T cd05480          82 EKNFSLGLQTLKSLKC-VINLE  102 (103)
T ss_pred             CcceEeeHHHHhhcce-eeecc
Confidence            9999999999999998 79864

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.

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

Probab=99.41  E-value=2.1e-12  Score=87.03  Aligned_cols=70  Identities=21%  Similarity=0.318  Sum_probs=62.0

Q ss_pred             eEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE----------E------------EEEECCEEEE-EEEEEecC
Q 040033           78 TLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI----------V------------NLILQGVYVI-VDFNLREL  134 (158)
Q Consensus        78 ~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~----------A------------~i~i~g~~~~-~~~~v~~~  134 (158)
                      .+.+++.||++++.+||||||++++|+..+++++++..          |            .+++++..+. ..+.+++.
T Consensus         2 ~~~v~v~i~~~~~~~llDTGa~~s~i~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~ig~~~~~~~~~~v~d~   81 (96)
T cd05483           2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAARVRLDSLQIGGITLRNVPAVVLPG   81 (96)
T ss_pred             cEEEEEEECCEEEEEEEECCCCcEEcCHHHHHHcCCCccCCCcEEEEecCCCccceEEEcceEEECCcEEeccEEEEeCC
Confidence            46789999999999999999999999999999988522          1            8889999887 68999999


Q ss_pred             CC--CcEEechhHhh
Q 040033          135 EG--YDVVLGTQWLR  147 (158)
Q Consensus       135 ~~--~dvILG~dwL~  147 (158)
                      ..  .|.|||+|||+
T Consensus        82 ~~~~~~gIlG~d~l~   96 (96)
T cd05483          82 DALGVDGLLGMDFLR   96 (96)
T ss_pred             cccCCceEeChHHhC
Confidence            87  99999999984

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

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

Probab=99.28  E-value=3.4e-11  Score=89.37  Aligned_cols=79  Identities=16%  Similarity=0.216  Sum_probs=72.2

Q ss_pred             cccCceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE---------------------E---EEEECCEEEEEE
Q 040033           73 VRASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI---------------------V---NLILQGVYVIVD  128 (158)
Q Consensus        73 ~~~~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~---------------------A---~i~i~g~~~~~~  128 (158)
                      -.-..+...+..++|.++.+|+||||-.|||+..++.+|+++.                     |   ++.+++..+.+.
T Consensus        29 Pevg~T~~v~l~~~~t~i~vLfDSGSPTSfIr~di~~kL~L~~~~app~~fRG~vs~~~~~tsEAv~ld~~i~n~~i~i~  108 (177)
T PF12384_consen   29 PEVGKTAIVQLNCKGTPIKVLFDSGSPTSFIRSDIVEKLELPTHDAPPFRFRGFVSGESATTSEAVTLDFYIDNKLIDIA  108 (177)
T ss_pred             cccCcEEEEEEeecCcEEEEEEeCCCccceeehhhHHhhCCccccCCCEEEeeeccCCceEEEEeEEEEEEECCeEEEEE
Confidence            3345778889999999999999999999999999999999987                     1   788999999999


Q ss_pred             EEEecCCCCcEEechhHhhhcCC
Q 040033          129 FNLRELEGYDVVLGTQWLRTLEP  151 (158)
Q Consensus       129 ~~v~~~~~~dvILG~dwL~~~~~  151 (158)
                      ++|++..++|+|+|.+.|+++..
T Consensus       109 aYV~d~m~~dlIIGnPiL~ryp~  131 (177)
T PF12384_consen  109 AYVTDNMDHDLIIGNPILDRYPT  131 (177)
T ss_pred             EEEeccCCcceEeccHHHhhhHH
Confidence            99999999999999999999875

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 [].

>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family

Probab=99.28  E-value=3.5e-11  Score=84.30  Aligned_cols=70  Identities=19%  Similarity=0.229  Sum_probs=59.3

Q ss_pred             CEeeEEEecCCCceeE-ECHHHHHHcCCeE--------------------EEEEECCEEEEEEEEEecCCCCcEEechhH
Q 040033           87 NISPIVLVDSGSTHNF-ISDTFAKKVKNFI--------------------VNLILQGVYVIVDFNLRELEGYDVVLGTQW  145 (158)
Q Consensus        87 ~~~v~aLiDSGat~sf-I~~~~a~~~~~~~--------------------A~i~i~g~~~~~~~~v~~~~~~dvILG~dw  145 (158)
                      ..++.+||||||+..+ |++++|+++|+..                    +.+.++|.+....+.+.+..+ +++|||.|
T Consensus        14 ~~~v~~LVDTGat~~~~l~~~~a~~lgl~~~~~~~~~tA~G~~~~~~v~~~~v~igg~~~~~~v~~~~~~~-~~LLG~~~   92 (107)
T TIGR03698        14 FMEVRALVDTGFSGFLLVPPDIVNKLGLPELDQRRVYLADGREVLTDVAKASIIINGLEIDAFVESLGYVD-EPLLGTEL   92 (107)
T ss_pred             ceEEEEEEECCCCeEEecCHHHHHHcCCCcccCcEEEecCCcEEEEEEEEEEEEECCEEEEEEEEecCCCC-ccEecHHH
Confidence            3589999999999998 9999999999886                    178889988866666666656 89999999


Q ss_pred             hhhcCCceeeecC
Q 040033          146 LRTLEPILWDFAS  158 (158)
Q Consensus       146 L~~~~~i~idw~~  158 (158)
                      |.+++. .+||++
T Consensus        93 L~~l~l-~id~~~  104 (107)
T TIGR03698        93 LEGLGI-VIDYRN  104 (107)
T ss_pred             HhhCCE-EEehhh
Confidence            999984 899974

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

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

Probab=99.24  E-value=6.1e-11  Score=79.73  Aligned_cols=65  Identities=25%  Similarity=0.272  Sum_probs=54.6

Q ss_pred             EEEECCEeeEEEecCCCceeEECHHHHHHcCCeE-------E-------------EEEECCEEEEEEEEEecCCCCcEEe
Q 040033           82 NGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI-------V-------------NLILQGVYVIVDFNLRELEGYDVVL  141 (158)
Q Consensus        82 ~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~-------A-------------~i~i~g~~~~~~~~v~~~~~~dvIL  141 (158)
                      .+.|||+++.+|+||||+++.|++..++++....       |             .+.+++++....+.+++-. .+.||
T Consensus         2 ~v~InG~~~~fLvDTGA~~tii~~~~a~~~~~~~~~~~v~gagG~~~~~v~~~~~~v~vg~~~~~~~~~v~~~~-~~~lL   80 (86)
T cd06095           2 TITVEGVPIVFLVDTGATHSVLKSDLGPKQELSTTSVLIRGVSGQSQQPVTTYRTLVDLGGHTVSHSFLVVPNC-PDPLL   80 (86)
T ss_pred             EEEECCEEEEEEEECCCCeEEECHHHhhhccCCCCcEEEEeCCCcccccEEEeeeEEEECCEEEEEEEEEEcCC-CCcEe
Confidence            5789999999999999999999999999852211       0             3788999999999888753 69999


Q ss_pred             chhHhh
Q 040033          142 GTQWLR  147 (158)
Q Consensus       142 G~dwL~  147 (158)
                      |||||.
T Consensus        81 G~dfL~   86 (86)
T cd06095          81 GRDLLS   86 (86)
T ss_pred             chhhcC
Confidence            999984

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

>cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases

Probab=99.18  E-value=1.6e-10  Score=73.92  Aligned_cols=66  Identities=41%  Similarity=0.663  Sum_probs=57.3

Q ss_pred             EEEECCEeeEEEecCCCceeEECHHHHHHcCC-eE------------------------EEEEECCEEEEEEEEEecCCC
Q 040033           82 NGRIGNISPIVLVDSGSTHNFISDTFAKKVKN-FI------------------------VNLILQGVYVIVDFNLRELEG  136 (158)
Q Consensus        82 ~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~-~~------------------------A~i~i~g~~~~~~~~v~~~~~  136 (158)
                      .+.+++.++.+|+|+||++++++..++.+++. ..                        ..+.+++..+...|++++...
T Consensus         2 ~~~~~~~~~~~liDtgs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   81 (92)
T cd00303           2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS   81 (92)
T ss_pred             EEEECCEEEEEEEcCCCcccccCHHHHHHcCCCcccCCCceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcCCC
Confidence            46688999999999999999999999999876 22                        055677888999999999999


Q ss_pred             CcEEechhHhh
Q 040033          137 YDVVLGTQWLR  147 (158)
Q Consensus       137 ~dvILG~dwL~  147 (158)
                      +|+|||+|||.
T Consensus        82 ~~~ilG~~~l~   92 (92)
T cd00303          82 YDVILGRPWLE   92 (92)
T ss_pred             cCEEecccccC
Confidence            99999999984

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

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

Probab=99.11  E-value=1.4e-10  Score=95.07  Aligned_cols=80  Identities=24%  Similarity=0.353  Sum_probs=74.1

Q ss_pred             ceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------------------EEEEECCEEEEEEEEEe
Q 040033           77 ETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------------------VNLILQGVYVIVDFNLR  132 (158)
Q Consensus        77 ~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------------------A~i~i~g~~~~~~~~v~  132 (158)
                      ..+.+.+.|||++|+|+|||||-.|.||.++|+++|+..                        +.++++...+...|.|+
T Consensus       234 ~ML~iN~~ing~~VKAfVDsGaq~timS~~Caer~gL~rlid~r~~g~a~gvg~~ki~g~Ih~~~lki~~~~l~c~ftV~  313 (380)
T KOG0012|consen  234 TMLYINCEINGVPVKAFVDSGAQTTIMSAACAERCGLNRLIDKRFQGEARGVGTEKILGRIHQAQLKIEDLYLPCSFTVL  313 (380)
T ss_pred             eEEEEEEEECCEEEEEEEcccchhhhhhHHHHHHhChHHHhhhhhhccccCCCcccccceeEEEEEEeccEeeccceEEe
Confidence            446778999999999999999999999999999999876                        28899999999999999


Q ss_pred             cCCCCcEEechhHhhhcCCceeeec
Q 040033          133 ELEGYDVVLGTQWLRTLEPILWDFA  157 (158)
Q Consensus       133 ~~~~~dvILG~dwL~~~~~i~idw~  157 (158)
                      +-.+.|+.||.|-|++|+. .||.+
T Consensus       314 d~~~~d~llGLd~Lrr~~c-cIdL~  337 (380)
T KOG0012|consen  314 DRRDMDLLLGLDMLRRHQC-CIDLK  337 (380)
T ss_pred             cCCCcchhhhHHHHHhccc-eeecc
Confidence            9999999999999999998 79975

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

Probab=99.00  E-value=8.5e-10  Score=71.85  Aligned_cols=41  Identities=34%  Similarity=0.539  Sum_probs=38.3

Q ss_pred             cCceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE
Q 040033           75 ASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI  115 (158)
Q Consensus        75 ~~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~  115 (158)
                      ....+++.+.|+++.+.+||||||++|||++++|+++|++.
T Consensus         5 ~~g~~~v~~~I~g~~~~alvDtGat~~fis~~~a~rLgl~~   45 (72)
T PF13975_consen    5 DPGLMYVPVSIGGVQVKALVDTGATHNFISESLAKRLGLPL   45 (72)
T ss_pred             cCCEEEEEEEECCEEEEEEEeCCCcceecCHHHHHHhCCCc
Confidence            45788999999999999999999999999999999999877

>COG3577 Predicted aspartyl protease [General function prediction only]

Probab=98.88  E-value=7.7e-09  Score=79.44  Aligned_cols=82  Identities=23%  Similarity=0.285  Sum_probs=70.0

Q ss_pred             ccCceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------------E-----EEEECCEEEE-EEE
Q 040033           74 RASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------------V-----NLILQGVYVI-VDF  129 (158)
Q Consensus        74 ~~~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------------A-----~i~i~g~~~~-~~~  129 (158)
                      +...++...+.|||+.+.+|||||||.-.+++.-|+++|+..                  |     .++|++..+. ++.
T Consensus       101 ~~~GHF~a~~~VNGk~v~fLVDTGATsVal~~~dA~RlGid~~~l~y~~~v~TANG~~~AA~V~Ld~v~IG~I~~~nV~A  180 (215)
T COG3577         101 SRDGHFEANGRVNGKKVDFLVDTGATSVALNEEDARRLGIDLNSLDYTITVSTANGRARAAPVTLDRVQIGGIRVKNVDA  180 (215)
T ss_pred             cCCCcEEEEEEECCEEEEEEEecCcceeecCHHHHHHhCCCccccCCceEEEccCCccccceEEeeeEEEccEEEcCchh
Confidence            345678889999999999999999999999999999999876                  1     7888988887 788


Q ss_pred             EEecCC-CCcEEechhHhhhcCCceee
Q 040033          130 NLRELE-GYDVVLGTQWLRTLEPILWD  155 (158)
Q Consensus       130 ~v~~~~-~~dvILG~dwL~~~~~i~id  155 (158)
                      +|++-+ --..+|||.||.+++-.+.+
T Consensus       181 ~V~~~g~L~~sLLGMSfL~rL~~fq~~  207 (215)
T COG3577         181 MVAEDGALDESLLGMSFLNRLSGFQVD  207 (215)
T ss_pred             heecCCccchhhhhHHHHhhccceEec
Confidence            999766 67789999999998765443

>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=98.60  E-value=1e-07  Score=73.34  Aligned_cols=69  Identities=23%  Similarity=0.334  Sum_probs=53.3

Q ss_pred             EeeEEEecCCCceeEECHHHH-----HHcCCeE----E--------------EEEECCEEEEEEEEEecCCCCcEEechh
Q 040033           88 ISPIVLVDSGSTHNFISDTFA-----KKVKNFI----V--------------NLILQGVYVIVDFNLRELEGYDVVLGTQ  144 (158)
Q Consensus        88 ~~v~aLiDSGat~sfI~~~~a-----~~~~~~~----A--------------~i~i~g~~~~~~~~v~~~~~~dvILG~d  144 (158)
                      ..+.++|||||+.++++..+.     +++.-+.    |              .+.+.|+.|...+.-.--.+.|+|||++
T Consensus        19 ~~~~~~vDTGAt~C~~~~~iiP~e~we~~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~IP~iYq~~~g~d~IlG~N   98 (201)
T PF02160_consen   19 FNYHCYVDTGATICCASKKIIPEEYWEKSKKPIKVKGANGSIIQINKKAKNGKIQIADKIFRIPTIYQQESGIDIILGNN   98 (201)
T ss_pred             EEEEEEEeCCCceEEecCCcCCHHHHHhCCCcEEEEEecCCceEEEEEecCceEEEccEEEeccEEEEecCCCCEEecch
Confidence            567899999999999887654     4444322    2              7889999999865444336899999999


Q ss_pred             HhhhcCCceeeec
Q 040033          145 WLRTLEPILWDFA  157 (158)
Q Consensus       145 wL~~~~~i~idw~  157 (158)
                      |++.+.| -+.|.
T Consensus        99 F~r~y~P-fiq~~  110 (201)
T PF02160_consen   99 FLRLYEP-FIQTE  110 (201)
T ss_pred             HHHhcCC-cEEEc
Confidence            9999999 47774

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

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

Probab=98.41  E-value=1.7e-06  Score=59.06  Aligned_cols=61  Identities=18%  Similarity=0.172  Sum_probs=50.6

Q ss_pred             EEECC-EeeEEEecCCCceeEECHHHHHHcC---CeE----------E-------------EEEECCEEEEEEEEEecCC
Q 040033           83 GRIGN-ISPIVLVDSGSTHNFISDTFAKKVK---NFI----------V-------------NLILQGVYVIVDFNLRELE  135 (158)
Q Consensus        83 ~~i~~-~~v~aLiDSGat~sfI~~~~a~~~~---~~~----------A-------------~i~i~g~~~~~~~~v~~~~  135 (158)
                      ..|++ +++++++||||+.|+|+.+..++++   .+.          |             .+.+++..+.++|+|++..
T Consensus         3 ~~i~g~~~v~~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~~~G~~~~~v~~~~~~~~~~f~Vvd~~   82 (93)
T cd05481           3 MKINGKQSVKFQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIPVEGGVKLKCRYRNPKYNLTFQVVKEE   82 (93)
T ss_pred             eEeCCceeEEEEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEeeeeEEEEEEEEECCcEEEEEEEEECCC
Confidence            56888 9999999999999999999999987   222          1             7778999999999999975


Q ss_pred             CCcEEechh
Q 040033          136 GYDVVLGTQ  144 (158)
Q Consensus       136 ~~dvILG~d  144 (158)
                       ..-|||.+
T Consensus        83 -~~~lLG~~   90 (93)
T cd05481          83 -GPPLLGAK   90 (93)
T ss_pred             -CCceEccc
Confidence             55667764

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

>cd06094 RP_Saci_like RP_Saci_like, retropepsin family

Probab=98.23  E-value=2.8e-06  Score=57.36  Aligned_cols=61  Identities=21%  Similarity=0.278  Sum_probs=46.8

Q ss_pred             EeeEEEecCCCceeEECHHHHHHc-C-CeE---E--------------EEEECC-EEEEEEEEEecCCCCcEEechhHhh
Q 040033           88 ISPIVLVDSGSTHNFISDTFAKKV-K-NFI---V--------------NLILQG-VYVIVDFNLRELEGYDVVLGTQWLR  147 (158)
Q Consensus        88 ~~v~aLiDSGat~sfI~~~~a~~~-~-~~~---A--------------~i~i~g-~~~~~~~~v~~~~~~dvILG~dwL~  147 (158)
                      -.+..||||||.+|.|.....++. . .+.   |              .+.++. +.|.-.|.|.+..  .-|||.|||+
T Consensus         8 s~~~fLVDTGA~vSviP~~~~~~~~~~~~~~l~AANgt~I~tyG~~~l~ldlGlrr~~~w~FvvAdv~--~pIlGaDfL~   85 (89)
T cd06094           8 SGLRFLVDTGAAVSVLPASSTKKSLKPSPLTLQAANGTPIATYGTRSLTLDLGLRRPFAWNFVVADVP--HPILGADFLQ   85 (89)
T ss_pred             CCcEEEEeCCCceEeeccccccccccCCceEEEeCCCCeEeeeeeEEEEEEcCCCcEEeEEEEEcCCC--cceecHHHHH
Confidence            357899999999999999988863 1 111   1              455564 4888899998875  4799999999


Q ss_pred             hcC
Q 040033          148 TLE  150 (158)
Q Consensus       148 ~~~  150 (158)
                      .|+
T Consensus        86 ~~~   88 (89)
T cd06094          86 HYG   88 (89)
T ss_pred             HcC
Confidence            886

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

>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=98.18  E-value=6.1e-07  Score=43.09  Aligned_cols=17  Identities=6%  Similarity=0.001  Sum_probs=15.9

Q ss_pred             ceeecCCCCCCCccCCc
Q 040033           31 VCATIATKSFPRDIGER   47 (158)
Q Consensus        31 ~Cf~Cg~~gH~~~~C~~   47 (158)
                      .||+|++.||++++||+
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            59999999999999985

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 ....

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

Probab=98.16  E-value=4e-06  Score=62.51  Aligned_cols=28  Identities=32%  Similarity=0.485  Sum_probs=26.1

Q ss_pred             EeeEEEecCCCceeEECHHHHHHcCCeE
Q 040033           88 ISPIVLVDSGSTHNFISDTFAKKVKNFI  115 (158)
Q Consensus        88 ~~v~aLiDSGat~sfI~~~~a~~~~~~~  115 (158)
                      .++.+|+||||..|||++++|++++++.
T Consensus        11 ~~~~~LlDsGSq~SfIt~~la~~L~L~~   38 (164)
T PF05585_consen   11 VEARALLDSGSQRSFITESLANKLNLPG   38 (164)
T ss_pred             EEEEEEEecCCchhHHhHHHHHHhCCCC
Confidence            5788999999999999999999999975

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

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

Probab=98.10  E-value=2.7e-05  Score=55.45  Aligned_cols=70  Identities=17%  Similarity=0.155  Sum_probs=58.5

Q ss_pred             CCEeeEEEecCCCc-eeEECHHHHHHcCCeE--------------------EEEEECCEEEEEEEEEecCCCCcEEechh
Q 040033           86 GNISPIVLVDSGST-HNFISDTFAKKVKNFI--------------------VNLILQGVYVIVDFNLRELEGYDVVLGTQ  144 (158)
Q Consensus        86 ~~~~v~aLiDSGat-~sfI~~~~a~~~~~~~--------------------A~i~i~g~~~~~~~~v~~~~~~dvILG~d  144 (158)
                      +++....|||||.+ --.+++++|.+++++.                    |.++++|.+...-..+.+....+ ++|++
T Consensus        23 Gd~~~~~LiDTGFtg~lvlp~~vaek~~~~~~~~~~~~~a~~~~v~t~V~~~~iki~g~e~~~~Vl~s~~~~~~-liG~~  101 (125)
T COG5550          23 GDFVYDELIDTGFTGYLVLPPQVAEKLGLPLFSTIRIVLADGGVVKTSVALATIKIDGVEKVAFVLASDNLPEP-LIGVN  101 (125)
T ss_pred             CcEEeeeEEecCCceeEEeCHHHHHhcCCCccCChhhhhhcCCEEEEEEEEEEEEECCEEEEEEEEccCCCccc-chhhh
Confidence            34455569999999 8899999999999887                    38899999888888888888888 99999


Q ss_pred             HhhhcCCceeeec
Q 040033          145 WLRTLEPILWDFA  157 (158)
Q Consensus       145 wL~~~~~i~idw~  157 (158)
                      ||+.++- .+|..
T Consensus       102 ~lk~l~~-~vn~~  113 (125)
T COG5550         102 LLKLLGL-VVNPK  113 (125)
T ss_pred             hhhhccE-EEcCC
Confidence            9998885 67654

>cd05482 HIV_retropepsin_like Retropepsins, pepsin-like aspartate proteases

Probab=97.87  E-value=6.5e-05  Score=50.68  Aligned_cols=66  Identities=17%  Similarity=-0.018  Sum_probs=49.4

Q ss_pred             EEEECCEeeEEEecCCCceeEECHHHHHHcC----CeE----------------EEEEECCEEEEEEEEEecCCCCcEEe
Q 040033           82 NGRIGNISPIVLVDSGSTHNFISDTFAKKVK----NFI----------------VNLILQGVYVIVDFNLRELEGYDVVL  141 (158)
Q Consensus        82 ~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~----~~~----------------A~i~i~g~~~~~~~~v~~~~~~dvIL  141 (158)
                      ...|+|+.+.+|+||||..++|++.-..+.-    -+.                -.+++.++.....+.|.+.....-||
T Consensus         2 ~~~i~g~~~~~llDTGAd~Tvi~~~~~p~~w~~~~~~~~i~GIGG~~~~~~~~~v~i~i~~~~~~g~vlv~~~~~P~nll   81 (87)
T cd05482           2 TLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVLSLPVNLW   81 (87)
T ss_pred             EEEECCEEEEEEEccCCCCeEEcccccCCCCccCCCCeEEEeccceEEEEEEeeEEEEEcCCeEEEEEEEccCCCcccEE
Confidence            4678999999999999999999986554321    111                16777888888888888864445689


Q ss_pred             chhHhh
Q 040033          142 GTQWLR  147 (158)
Q Consensus       142 G~dwL~  147 (158)
                      |+|.|.
T Consensus        82 GRd~L~   87 (87)
T cd05482          82 GRDILS   87 (87)
T ss_pred             ccccCC
Confidence            999874

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

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=96.66  E-value=0.00073  Score=36.98  Aligned_cols=19  Identities=16%  Similarity=0.048  Sum_probs=17.5

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      .+|+.|+++||+..+||.+
T Consensus         9 Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    9 YVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CEeecCCCCCccHhHCCCC
Confidence            6899999999999999974

>smart00343 ZnF_C2HC zinc finger

Probab=95.88  E-value=0.0036  Score=32.39  Aligned_cols=18  Identities=6%  Similarity=0.051  Sum_probs=16.0

Q ss_pred             ceeecCCCCCCCccCCcc
Q 040033           31 VCATIATKSFPRDIGERS   48 (158)
Q Consensus        31 ~Cf~Cg~~gH~~~~C~~~   48 (158)
                      .||+|++.||.+.+||..
T Consensus         1 ~C~~CG~~GH~~~~C~~~   18 (26)
T smart00343        1 KCYNCGKEGHIARDCPKX   18 (26)
T ss_pred             CCccCCCCCcchhhCCcc
Confidence            499999999999999853

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=95.67  E-value=0.0045  Score=36.05  Aligned_cols=18  Identities=11%  Similarity=-0.040  Sum_probs=16.9

Q ss_pred             cceeecCCCCCCCccCCc
Q 040033           30 KVCATIATKSFPRDIGER   47 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~   47 (158)
                      ..|.+|++.||...+|++
T Consensus         5 ~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    5 VRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CcCcccCCCCcchhhCCC
Confidence            689999999999999994

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

Probab=95.21  E-value=0.051  Score=37.62  Aligned_cols=65  Identities=17%  Similarity=0.254  Sum_probs=48.3

Q ss_pred             EEEEEEECCE--eeEEEecCCCceeEECHHHHHHcCCeE---------E--------------EEEECCEEEEEEEEEec
Q 040033           79 LRINGRIGNI--SPIVLVDSGSTHNFISDTFAKKVKNFI---------V--------------NLILQGVYVIVDFNLRE  133 (158)
Q Consensus        79 i~~~~~i~~~--~v~aLiDSGat~sfI~~~~a~~~~~~~---------A--------------~i~i~g~~~~~~~~v~~  133 (158)
                      |.+++.+...  .+.-|||+||..|.|.+..++...++.         +              .+.++|......|+|+.
T Consensus        35 mvlqa~lp~fkcsipclidtgaq~niiteetvrahklptrpw~~sviyggvyp~kinrkt~kl~i~lngisikteflvvk  114 (137)
T PF12382_consen   35 MVLQAKLPDFKCSIPCLIDTGAQVNIITEETVRAHKLPTRPWSQSVIYGGVYPNKINRKTIKLNINLNGISIKTEFLVVK  114 (137)
T ss_pred             hhhhhhCCCccccceeEEccCceeeeeehhhhhhccCCCCcchhheEeccccccccccceEEEEEEecceEEEEEEEEEE
Confidence            3344444333  346799999999999999999888876         0              67789999999999998


Q ss_pred             CCCCcEEech
Q 040033          134 LEGYDVVLGT  143 (158)
Q Consensus       134 ~~~~dvILG~  143 (158)
                      .-.++.-+.+
T Consensus       115 kfshpaaisf  124 (137)
T PF12382_consen  115 KFSHPAAISF  124 (137)
T ss_pred             eccCcceEEE
Confidence            6655554443

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.

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

Probab=95.08  E-value=0.0074  Score=33.74  Aligned_cols=19  Identities=5%  Similarity=-0.027  Sum_probs=12.4

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ++|++|++..|.+.+|..+
T Consensus         3 ~~CprC~kg~Hwa~~C~sk   21 (36)
T PF14787_consen    3 GLCPRCGKGFHWASECRSK   21 (36)
T ss_dssp             -C-TTTSSSCS-TTT---T
T ss_pred             ccCcccCCCcchhhhhhhh
Confidence            7899999999999999875

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

Probab=94.71  E-value=0.012  Score=44.95  Aligned_cols=21  Identities=19%  Similarity=0.180  Sum_probs=17.9

Q ss_pred             hhcc-cceeecCCCCCCCccCC
Q 040033           26 ERRA-KVCATIATKSFPRDIGE   46 (158)
Q Consensus        26 ~rR~-~~Cf~Cg~~gH~~~~C~   46 (158)
                      .+++ ..||+||+.||.+++||
T Consensus        56 ~~~~~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          56 IREENPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             ccccccccchhcccCcccccCC
Confidence            3344 88999999999999999

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

Probab=94.21  E-value=0.14  Score=37.36  Aligned_cols=33  Identities=30%  Similarity=0.526  Sum_probs=25.2

Q ss_pred             EEEECCEEEEEEEEEecCC--CCcEEec-hhHhhhc
Q 040033          117 NLILQGVYVIVDFNLRELE--GYDVVLG-TQWLRTL  149 (158)
Q Consensus       117 ~i~i~g~~~~~~~~v~~~~--~~dvILG-~dwL~~~  149 (158)
                      .+.++|..+.+.|.+.+=+  .|+|+|| ..||...
T Consensus        89 ~~~lg~~~~~~e~tL~dR~~m~yp~LlGrR~~l~~~  124 (138)
T PF05618_consen   89 TLCLGGKTWKIEFTLTDRSNMKYPMLLGRRNFLRGR  124 (138)
T ss_dssp             EEEETTEEEEEEEEEE-S--SS-SEEE-HHHHHHTT
T ss_pred             EEEECCEEEEEEEEEcCCCcCcCCEEEEehHHhcCC
Confidence            7788999999999998754  7999999 9999653

; PDB: 2PMA_B.

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

Probab=93.89  E-value=0.024  Score=43.41  Aligned_cols=19  Identities=11%  Similarity=0.034  Sum_probs=16.9

Q ss_pred             cceeecCCCCCCCccC-Ccc
Q 040033           30 KVCATIATKSFPRDIG-ERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C-~~~   48 (158)
                      ..||+||+.||++++| |++
T Consensus        98 ~~C~~Cg~~GH~~~dC~P~~  117 (190)
T COG5082          98 KKCYNCGETGHLSRDCNPSK  117 (190)
T ss_pred             cccccccccCccccccCccc
Confidence            5799999999999999 655

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=93.23  E-value=0.028  Score=33.63  Aligned_cols=22  Identities=9%  Similarity=0.129  Sum_probs=18.7

Q ss_pred             hhcc-cceeecCCCCCCCccCCc
Q 040033           26 ERRA-KVCATIATKSFPRDIGER   47 (158)
Q Consensus        26 ~rR~-~~Cf~Cg~~gH~~~~C~~   47 (158)
                      +-|- ..||+||..||....||+
T Consensus        27 YE~lp~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   27 YERLPRFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             ECCcChhhcCCCCcCcCHhHcCC
Confidence            3355 789999999999999985

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

Probab=93.12  E-value=0.26  Score=36.62  Aligned_cols=38  Identities=32%  Similarity=0.533  Sum_probs=31.1

Q ss_pred             EEEECCEEEEEEEEEecCC--CCcEEechhHhhhcCCceee
Q 040033          117 NLILQGVYVIVDFNLRELE--GYDVVLGTQWLRTLEPILWD  155 (158)
Q Consensus       117 ~i~i~g~~~~~~~~v~~~~--~~dvILG~dwL~~~~~i~id  155 (158)
                      .+.++|....+.|.+.+=.  .|+|+||.-+|..... .+|
T Consensus       113 ~l~lG~~~~~~E~tLtDR~~m~Yp~LlGrk~l~~~~~-~VD  152 (162)
T COG4067         113 TLCLGGRILPIEFTLTDRSNMRYPVLLGRKALRHFGA-VVD  152 (162)
T ss_pred             EEeeCCeeeeEEEEeecccccccceEecHHHHhhCCe-EEC
Confidence            6778999999999988754  7999999999998654 444

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

Probab=91.21  E-value=0.089  Score=38.43  Aligned_cols=17  Identities=12%  Similarity=0.077  Sum_probs=14.2

Q ss_pred             ceeecCCCCCCCccCCc
Q 040033           31 VCATIATKSFPRDIGER   47 (158)
Q Consensus        31 ~Cf~Cg~~gH~~~~C~~   47 (158)
                      +||+|++.||++++||.
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=90.86  E-value=0.092  Score=41.99  Aligned_cols=18  Identities=11%  Similarity=0.110  Sum_probs=16.2

Q ss_pred             cceeecCCCCCCCccCCc
Q 040033           30 KVCATIATKSFPRDIGER   47 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~   47 (158)
                      ..||.||+.||+.++||.
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~  161 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPE  161 (261)
T ss_pred             CccCCCCcCCcchhhCCC
Confidence            349999999999999994

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

Probab=90.13  E-value=0.21  Score=41.07  Aligned_cols=19  Identities=16%  Similarity=0.041  Sum_probs=17.5

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+||++||....||.+
T Consensus       177 Y~CyRCGqkgHwIqnCpTN  195 (427)
T COG5222         177 YVCYRCGQKGHWIQNCPTN  195 (427)
T ss_pred             eeEEecCCCCchhhcCCCC
Confidence            6799999999999999966

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

Probab=89.34  E-value=1.4  Score=34.86  Aligned_cols=62  Identities=18%  Similarity=0.272  Sum_probs=38.4

Q ss_pred             eEEEecCCCceeEECHHHHHHcCCeEEEEEEC-CEEEEEE--------------EEEecC-CCCcEEechhHhhhcCCce
Q 040033           90 PIVLVDSGSTHNFISDTFAKKVKNFIVNLILQ-GVYVIVD--------------FNLREL-EGYDVVLGTQWLRTLEPIL  153 (158)
Q Consensus        90 v~aLiDSGat~sfI~~~~a~~~~~~~A~i~i~-g~~~~~~--------------~~v~~~-~~~dvILG~dwL~~~~~i~  153 (158)
                      ..++||||++..++.+.+.-.+     .+.++ +..+.+.              +.++.. ..--.|||-.||+.+-- .
T Consensus       177 ~~ai~DTGTs~~~lp~~~~P~i-----~~~f~~~~~~~i~~~~y~~~~~~~~~C~~~~~~~~~~~~ilG~~fl~~~~~-v  250 (265)
T cd05476         177 GGTIIDSGTTLTYLPDPAYPDL-----TLHFDGGADLELPPENYFVDVGEGVVCLAILSSSSGGVSILGNIQQQNFLV-E  250 (265)
T ss_pred             CcEEEeCCCcceEcCccccCCE-----EEEECCCCEEEeCcccEEEECCCCCEEEEEecCCCCCcEEEChhhcccEEE-E
Confidence            3489999999999998876222     23333 3322211              122222 34568999999998764 4


Q ss_pred             eeec
Q 040033          154 WDFA  157 (158)
Q Consensus       154 idw~  157 (158)
                      .|+.
T Consensus       251 FD~~  254 (265)
T cd05476         251 YDLE  254 (265)
T ss_pred             EECC
Confidence            5654

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

>cd05477 gastricsin Gastricsins, asparate proteases produced in gastric mucosa

Probab=89.22  E-value=1.8  Score=35.14  Aligned_cols=67  Identities=15%  Similarity=0.207  Sum_probs=43.8

Q ss_pred             eEEEecCCCceeEECHHHHHHcC----CeE-----------E-------EEEECCEEEEEE-------------EEEecC
Q 040033           90 PIVLVDSGSTHNFISDTFAKKVK----NFI-----------V-------NLILQGVYVIVD-------------FNLREL  134 (158)
Q Consensus        90 v~aLiDSGat~sfI~~~~a~~~~----~~~-----------A-------~i~i~g~~~~~~-------------~~v~~~  134 (158)
                      ..++||||++..++...+++.+-    ...           .       .+.++|.++.+.             +.+.+.
T Consensus       202 ~~~iiDSGtt~~~lP~~~~~~l~~~~~~~~~~~~~~~~~C~~~~~~p~l~~~f~g~~~~v~~~~y~~~~~~~C~~~i~~~  281 (318)
T cd05477         202 CQAIVDTGTSLLTAPQQVMSTLMQSIGAQQDQYGQYVVNCNNIQNLPTLTFTINGVSFPLPPSAYILQNNGYCTVGIEPT  281 (318)
T ss_pred             ceeeECCCCccEECCHHHHHHHHHHhCCccccCCCEEEeCCccccCCcEEEEECCEEEEECHHHeEecCCCeEEEEEEec
Confidence            36899999999999998877642    111           0       456677766642             122211


Q ss_pred             ------CCCcEEechhHhhhcCCceeeec
Q 040033          135 ------EGYDVVLGTQWLRTLEPILWDFA  157 (158)
Q Consensus       135 ------~~~dvILG~dwL~~~~~i~idw~  157 (158)
                            +....|||..||+.+-- ..|+.
T Consensus       282 ~~~~~~~~~~~ilG~~fl~~~y~-vfD~~  309 (318)
T cd05477         282 YLPSQNGQPLWILGDVFLRQYYS-VYDLG  309 (318)
T ss_pred             ccCCCCCCceEEEcHHHhhheEE-EEeCC
Confidence                  12358999999998775 46764

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

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

Probab=88.93  E-value=0.17  Score=36.90  Aligned_cols=18  Identities=6%  Similarity=0.064  Sum_probs=11.0

Q ss_pred             cceeecCCCCCCCccCCc
Q 040033           30 KVCATIATKSFPRDIGER   47 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~   47 (158)
                      ..||+|++.||++++||+
T Consensus       104 ~~C~~Cg~~gH~~~~C~~  121 (148)
T PTZ00368        104 RACYNCGGEGHISRDCPN  121 (148)
T ss_pred             hhhcccCcCCcchhcCCC
Confidence            356666666666666665

>PTZ00013 plasmepsin 4 (PM4); Provisional

Probab=87.34  E-value=2  Score=37.29  Aligned_cols=26  Identities=19%  Similarity=0.480  Sum_probs=21.1

Q ss_pred             EEEEEC--CEeeEEEecCCCceeEECHH
Q 040033           81 INGRIG--NISPIVLVDSGSTHNFISDT  106 (158)
Q Consensus        81 ~~~~i~--~~~v~aLiDSGat~sfI~~~  106 (158)
                      .++.|+  .+++.+++||||+..+|...
T Consensus       141 ~~i~IGTP~Q~f~vi~DTGSsdlWV~s~  168 (450)
T PTZ00013        141 GEGEVGDNHQKFMLIFDTGSANLWVPSK  168 (450)
T ss_pred             EEEEECCCCeEEEEEEeCCCCceEEecc
Confidence            355665  79999999999999999643

>cd05470 pepsin_retropepsin_like Cellular and retroviral pepsin-like aspartate proteases

Probab=86.83  E-value=0.79  Score=30.93  Aligned_cols=25  Identities=28%  Similarity=0.414  Sum_probs=20.1

Q ss_pred             EEEECC--EeeEEEecCCCceeEECHH
Q 040033           82 NGRIGN--ISPIVLVDSGSTHNFISDT  106 (158)
Q Consensus        82 ~~~i~~--~~v~aLiDSGat~sfI~~~  106 (158)
                      ++.|+.  +++.++|||||+..++...
T Consensus         2 ~i~vGtP~q~~~~~~DTGSs~~Wv~~~   28 (109)
T cd05470           2 EIGIGTPPQTFNVLLDTGSSNLWVPSV   28 (109)
T ss_pred             EEEeCCCCceEEEEEeCCCCCEEEeCC
Confidence            355654  8999999999999888765

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

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

Probab=86.08  E-value=2.8  Score=34.03  Aligned_cols=74  Identities=16%  Similarity=0.183  Sum_probs=48.3

Q ss_pred             EEECCEee------EEEecCCCceeEECHHHHHHc----CCeE-------------E-----EEEECCEEEEEE------
Q 040033           83 GRIGNISP------IVLVDSGSTHNFISDTFAKKV----KNFI-------------V-----NLILQGVYVIVD------  128 (158)
Q Consensus        83 ~~i~~~~v------~aLiDSGat~sfI~~~~a~~~----~~~~-------------A-----~i~i~g~~~~~~------  128 (158)
                      +.|+++.+      .++||||++..++......++    +...             .     .+.++|..|.+.      
T Consensus       194 v~v~g~~~~~~~~~~~iiDTGts~~~lp~~~~~~l~~~~~~~~~~~~~~~~~C~~~~~~P~~~f~f~g~~~~i~~~~y~~  273 (317)
T cd05478         194 VTINGQVVACSGGCQAIVDTGTSLLVGPSSDIANIQSDIGASQNQNGEMVVNCSSISSMPDVVFTINGVQYPLPPSAYIL  273 (317)
T ss_pred             EEECCEEEccCCCCEEEECCCchhhhCCHHHHHHHHHHhCCccccCCcEEeCCcCcccCCcEEEEECCEEEEECHHHhee
Confidence            46777654      689999999999998877653    2211             0     455677766642      


Q ss_pred             -------EEEecCC-CCcEEechhHhhhcCCceeeec
Q 040033          129 -------FNLRELE-GYDVVLGTQWLRTLEPILWDFA  157 (158)
Q Consensus       129 -------~~v~~~~-~~dvILG~dwL~~~~~i~idw~  157 (158)
                             +.+.+.. ....|||-.||+.+-. ..|+.
T Consensus       274 ~~~~~C~~~~~~~~~~~~~IlG~~fl~~~y~-vfD~~  309 (317)
T cd05478         274 QDQGSCTSGFQSMGLGELWILGDVFIRQYYS-VFDRA  309 (317)
T ss_pred             cCCCEEeEEEEeCCCCCeEEechHHhcceEE-EEeCC
Confidence                   1122222 2458999999998775 46664

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

>PTZ00147 plasmepsin-1; Provisional

Probab=85.75  E-value=3.1  Score=36.11  Aligned_cols=26  Identities=15%  Similarity=0.304  Sum_probs=21.6

Q ss_pred             EEEEEEC--CEeeEEEecCCCceeEECH
Q 040033           80 RINGRIG--NISPIVLVDSGSTHNFISD  105 (158)
Q Consensus        80 ~~~~~i~--~~~v~aLiDSGat~sfI~~  105 (158)
                      ...+.|+  .+++.++|||||+..+|..
T Consensus       141 ~~~I~IGTP~Q~f~Vi~DTGSsdlWVps  168 (453)
T PTZ00147        141 YGEAKLGDNGQKFNFIFDTGSANLWVPS  168 (453)
T ss_pred             EEEEEECCCCeEEEEEEeCCCCcEEEee
Confidence            4466776  7999999999999999964

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=85.34  E-value=0.45  Score=27.34  Aligned_cols=18  Identities=11%  Similarity=0.025  Sum_probs=15.6

Q ss_pred             ceeecCCCCCCC--ccCCcc
Q 040033           31 VCATIATKSFPR--DIGERS   48 (158)
Q Consensus        31 ~Cf~Cg~~gH~~--~~C~~~   48 (158)
                      .|-.||..||.+  +.||-+
T Consensus         3 kC~~CG~~GH~~t~k~CP~~   22 (40)
T PF15288_consen    3 KCKNCGAFGHMRTNKRCPMY   22 (40)
T ss_pred             cccccccccccccCccCCCC
Confidence            499999999998  789865

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

Probab=84.62  E-value=2.2  Score=34.86  Aligned_cols=68  Identities=19%  Similarity=0.312  Sum_probs=42.7

Q ss_pred             eeEEEecCCCceeEECHHHHHHcCC--eEEEEEEC-CEEEEEE-------------EEEecCCCCcEEechhHhhhcCCc
Q 040033           89 SPIVLVDSGSTHNFISDTFAKKVKN--FIVNLILQ-GVYVIVD-------------FNLRELEGYDVVLGTQWLRTLEPI  152 (158)
Q Consensus        89 ~v~aLiDSGat~sfI~~~~a~~~~~--~~A~i~i~-g~~~~~~-------------~~v~~~~~~dvILG~dwL~~~~~i  152 (158)
                      ...++||||++..++...+.+++.-  +.-.+.++ |..+.+.             +..+....--.|||-.||+.+-- 
T Consensus       231 ~~~aivDSGTs~~~lp~~~~~~l~~~~P~i~~~f~~g~~~~i~p~~y~~~~~~~~c~~~~~~~~~~~ILG~~flr~~y~-  309 (326)
T cd06096         231 GLGMLVDSGSTLSHFPEDLYNKINNFFPTITIIFENNLKIDWKPSSYLYKKESFWCKGGEKSVSNKPILGASFFKNKQI-  309 (326)
T ss_pred             CCCEEEeCCCCcccCCHHHHHHHHhhcCcEEEEEcCCcEEEECHHHhccccCCceEEEEEecCCCceEEChHHhcCcEE-
Confidence            3458999999999999999887542  11134444 4433320             11122223357999999998774 


Q ss_pred             eeeec
Q 040033          153 LWDFA  157 (158)
Q Consensus       153 ~idw~  157 (158)
                      ..|+.
T Consensus       310 vFD~~  314 (326)
T cd06096         310 IFDLD  314 (326)
T ss_pred             EEECc
Confidence            56764

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

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

Probab=84.25  E-value=4.1  Score=32.31  Aligned_cols=64  Identities=22%  Similarity=0.299  Sum_probs=40.5

Q ss_pred             EEEEECC--EeeEEEecCCCceeEECHHHHHHcCC--eE------EEEEECCEEEE-EEEEEecC-CCCcEEechhH
Q 040033           81 INGRIGN--ISPIVLVDSGSTHNFISDTFAKKVKN--FI------VNLILQGVYVI-VDFNLREL-EGYDVVLGTQW  145 (158)
Q Consensus        81 ~~~~i~~--~~v~aLiDSGat~sfI~~~~a~~~~~--~~------A~i~i~g~~~~-~~~~v~~~-~~~dvILG~dw  145 (158)
                      +++.|+.  +++.+++||||+..+|.. +-..++-  ..      ..+.+++.... ..|.++.. ...|-|||..+
T Consensus         5 ~~i~iGtp~q~~~v~~DTgS~~~wv~~-~~~~Y~~g~~~~G~~~~D~v~~g~~~~~~~~fg~~~~~~~~~GilGLg~   80 (295)
T cd05474           5 AELSVGTPPQKVTVLLDTGSSDLWVPD-FSISYGDGTSASGTWGTDTVSIGGATVKNLQFAVANSTSSDVGVLGIGL   80 (295)
T ss_pred             EEEEECCCCcEEEEEEeCCCCcceeee-eEEEeccCCcEEEEEEEEEEEECCeEecceEEEEEecCCCCcceeeECC
Confidence            4566665  899999999999998881 1111111  11      17777776553 45655543 46888988764

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

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

Probab=81.40  E-value=0.76  Score=37.67  Aligned_cols=17  Identities=6%  Similarity=-0.023  Sum_probs=16.3

Q ss_pred             eeecCCCCCCCccCCcc
Q 040033           32 CATIATKSFPRDIGERS   48 (158)
Q Consensus        32 Cf~Cg~~gH~~~~C~~~   48 (158)
                      ||.||+.||.+.+||..
T Consensus       163 cyrcGkeghwskEcP~~  179 (346)
T KOG0109|consen  163 CYRCGKEGHWSKECPVD  179 (346)
T ss_pred             heeccccccccccCCcc
Confidence            99999999999999976

---

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	158
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	9e-06

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

 Score = 42.0 bits (98), Expect = 9e-06
 Identities = 17/99 (17%), Positives = 37/99 (37%), Gaps = 24/99 (24%)

Query: 79  LRINGRIGNISPIVLVDSGSTHNFISDTFAKKV-------KNFI---------------- 115
           L IN ++        VDSG+    +S   A++        + +                 
Sbjct: 25  LYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIIGRVH 84

Query: 116 -VNLILQGVYVIVDFNLRELEGYDVVLGTQWLRTLEPIL 153
              + ++G ++   F++ E +  D++LG   LR  +  +
Sbjct: 85  LAQIQIEGDFLQCSFSILEDQPMDMLLGLDMLRRHQCSI 123

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	158
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	99.81
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	99.72
3slz_A	132	GAG-Pro-POL polyprotein; beta sheet and dimer, pro	98.75
1fmb_A	104	EIAV protease; hydrolase (acid proteinase), RNA-di	98.7
3ec0_A	99	Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1	98.45
2hs1_A	99	HIV-1 protease; ultra-high resolution active site	98.39
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	98.15
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.02
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.95
2hah_A	116	Protease, retropepsin; retroviral, aspartyl, hydro	97.95
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	97.94
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.73
3ka2_A	203	[L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro	97.53
3sqf_A	114	Protease; folded monomer, retropepsin, D-type retr	97.22
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.2
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.02
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.0
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	96.94
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	96.92
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	96.87
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	96.86
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	96.74
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	96.74
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	96.68
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	96.64
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	96.64
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	96.63
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	96.61
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	96.51
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	96.5
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	96.39
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	96.09
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	95.43
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	95.27
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	94.97
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	94.92
2rsp_A	124	RSV protease; hydrolase(aspartyl proteinase); 2.00	94.14
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	93.86
3liy_A	116	Protease; hydrolase, hydrolase-hydrolase inhibitor	93.14
2pma_A	146	Uncharacterized protein; APC86035.2, protein LPG00	92.89
2jys_A	107	Protease/reverse transcriptase; retroviral proteas	91.36
1lya_A	97	Cathepsin D; lysosomal aspartic protease; HET: NAG	89.21

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

Probab=99.81  E-value=1.8e-19  Score=132.02  Aligned_cols=82  Identities=22%  Similarity=0.344  Sum_probs=75.7

Q ss_pred             CceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------------------EEEEECCEEEEEEEEE
Q 040033           76 SETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------------------VNLILQGVYVIVDFNL  131 (158)
Q Consensus        76 ~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------------------A~i~i~g~~~~~~~~v  131 (158)
                      ...+.+.+.|||+++++||||||+++||+.++|+++|+..                        +++++++..+.++|.|
T Consensus        22 ~~~l~v~~~Ing~~v~~LVDTGAs~s~Is~~~A~rlGL~~~~~~~~~~~a~g~G~~~~~g~v~~~~I~Ig~~~~~~~~~V  101 (148)
T 3s8i_A           22 VTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIIGRVHLAQIQIEGDFLQCSFSI  101 (148)
T ss_dssp             CCCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHTTCGGGEEGGGCEECCC---CEEEEEEEEEEEEETTEEEEEEEEE
T ss_pred             cCEEEEEEEECCEEEEEEEeCCCCcEeeCHHHHHHcCCccccCcceeEEEEcCCccEEEEEEEEEEEEECCEEEEEEEEE
Confidence            5678899999999999999999999999999999999852                        2789999999999999


Q ss_pred             ecCCCCcEEechhHhhhcCCceeeecC
Q 040033          132 RELEGYDVVLGTQWLRTLEPILWDFAS  158 (158)
Q Consensus       132 ~~~~~~dvILG~dwL~~~~~i~idw~~  158 (158)
                      ++...+|+|||||||++++. .|||++
T Consensus       102 le~~~~d~LLGmD~L~~~~~-~ID~~~  127 (148)
T 3s8i_A          102 LEDQPMDMLLGLDMLRRHQC-SIDLKK  127 (148)
T ss_dssp             ETTCSSSEEECHHHHHHTTC-EEETTT
T ss_pred             eCCCCcCeeccHHHHHhCCE-EEEcCC
Confidence            99999999999999999997 899974

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

Probab=99.72  E-value=3.3e-17  Score=119.18  Aligned_cols=82  Identities=23%  Similarity=0.314  Sum_probs=73.4

Q ss_pred             cCceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------------------EEEEECCEEEEEEEE
Q 040033           75 ASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------------------VNLILQGVYVIVDFN  130 (158)
Q Consensus        75 ~~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------------------A~i~i~g~~~~~~~~  130 (158)
                      ....+.+.+.|||+++.+||||||++++|+.++|+++|+..                        +.+.+++..+.++|.
T Consensus        23 ~~~~~~v~v~InG~~~~~LvDTGAs~s~is~~~a~~lgl~~~~~~~~~~~a~g~g~~~~~~~~~~~~i~ig~~~~~~~~~  102 (148)
T 2i1a_A           23 QVPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGKIIGRIHQAQVKIETQYIPCSFT  102 (148)
T ss_dssp             CCCCCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHHTGGGGCBCCCC-----------CEEEEEEEEEETTEEEEEEEE
T ss_pred             ccceEEEEEEECCEEEEEEEECCCCccccCHHHHHHcCCCccCCcceEEEEecCCCcccccEEEEEEEEECCEEeceeEE
Confidence            35678899999999999999999999999999999998642                        178899999999999


Q ss_pred             EecCCCCcEEechhHhhhcCCceeeecC
Q 040033          131 LRELEGYDVVLGTQWLRTLEPILWDFAS  158 (158)
Q Consensus       131 v~~~~~~dvILG~dwL~~~~~i~idw~~  158 (158)
                      |++ .++|+|||||||++++. .|||.+
T Consensus       103 vl~-~~~d~iLG~d~L~~~~~-~ID~~~  128 (148)
T 2i1a_A          103 VLD-TDIDVLIGLDMLKRHLA-CVDLKE  128 (148)
T ss_dssp             EEC-SSCSEEECHHHHHHTTC-EEETTT
T ss_pred             Eec-CCCCeEecHHHHhhCCE-EEECCC
Confidence            999 77999999999999987 899863

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

Probab=98.75  E-value=2.3e-08  Score=71.46  Aligned_cols=80  Identities=20%  Similarity=0.214  Sum_probs=60.3

Q ss_pred             ccCceEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE-----E------------EEEECCEEEEEEEEEecCCC
Q 040033           74 RASETLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI-----V------------NLILQGVYVIVDFNLRELEG  136 (158)
Q Consensus        74 ~~~~~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~-----A------------~i~i~g~~~~~~~~v~~~~~  136 (158)
                      ++.....+.++|+|+++.+|+||||+.+.+++.-+. ...+.     |            .+++.++.....+.|++-. 
T Consensus        18 d~~~RP~v~i~I~G~~~~~LlDTGAd~tVl~~~~~p-~~~~p~~I~GiGG~i~vr~~~~i~IeI~g~~~~~~~lV~~~t-   95 (132)
T 3slz_A           18 EPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGP-LSDKSAWVQGATGGKRYRWTTDRKVHLATGKVTHSFLHVPDC-   95 (132)
T ss_dssp             CCCCSSEEEEEETTEEEEEEECTTCSSCEECSCCCS-EEEEEEEEECSSCEEEEEEECCEEEEETTEEEEECCEECTTS-
T ss_pred             CccCCCEEEEEECCEEEEEEEeCCCCeEEEccccCC-CCCCceEEEccCCEEEEEEEeeeEEEECCeeecceEEEECCC-
Confidence            344455678999999999999999999999986554 22211     0            5788888888777664333 


Q ss_pred             CcEEechhHhhhcCCceeee
Q 040033          137 YDVVLGTQWLRTLEPILWDF  156 (158)
Q Consensus       137 ~dvILG~dwL~~~~~i~idw  156 (158)
                      ...|||+|||.+++. .+++
T Consensus        96 PvnLLGrd~Ltqlg~-tL~f  114 (132)
T 3slz_A           96 PYPLLGRDLLTKLKA-QIHF  114 (132)
T ss_dssp             SSCEECHHHHHHHTC-EEEE
T ss_pred             CccEECHhhHhhCCc-EEEC
Confidence            357899999999997 7876

>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=98.70  E-value=1.9e-07  Score=64.08  Aligned_cols=76  Identities=16%  Similarity=0.176  Sum_probs=60.8

Q ss_pred             eEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE---------------------EEEEECCEEEEEEEEEecCCC
Q 040033           78 TLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI---------------------VNLILQGVYVIVDFNLRELEG  136 (158)
Q Consensus        78 ~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~---------------------A~i~i~g~~~~~~~~v~~~~~  136 (158)
                      ...+.++|+|+...+|+||||..++|+.+.+.+++++.                     ..+++.|+.....++|-+.  
T Consensus         8 RP~v~v~I~Gq~~e~LLDTGAD~TVl~~~~w~~i~lp~~~w~p~~i~GiGG~i~v~~~~i~i~i~g~~~~gtvlv~~t--   85 (104)
T 1fmb_A            8 RPTTIVLINDTPLNVLLDTGADTSVLTTAHYNRLKYRGRKYQGTGIGGVGGNVETFSTPVTIKKKGRHIKTRMLVADI--   85 (104)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHCSSCCCCEECCCEEETTEEECCEEEEEEEEETTEEEEEEEEEESC--
T ss_pred             CCEEEEEECCEEEEEEeccCCCcEEEccccCcccCCCCccCCccEEEeCCCeEEeeEeeeEEEECCeEEEEEEEECCC--
Confidence            34567999999999999999999999998887655332                     1677888888888888663  


Q ss_pred             CcEEechhHhhhcCCceeee
Q 040033          137 YDVVLGTQWLRTLEPILWDF  156 (158)
Q Consensus       137 ~dvILG~dwL~~~~~i~idw  156 (158)
                      ..=|+|+|||.+.+. .+||
T Consensus        86 p~niiGRd~L~qlg~-tLnf  104 (104)
T 1fmb_A           86 PVTILGRDILQDLGA-KLVL  104 (104)
T ss_dssp             SSCEECHHHHHHTTC-CCCC
T ss_pred             CCCEecHhHHhhcCc-EEeC
Confidence            346899999999997 6664

>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=98.45  E-value=1.9e-06  Score=58.46  Aligned_cols=69  Identities=13%  Similarity=0.133  Sum_probs=54.5

Q ss_pred             EEEEEECCEeeEEEecCCCceeEECHHHHHHcCCe----E----E-------------EEEECCEEEEEEEEEecCCCCc
Q 040033           80 RINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNF----I----V-------------NLILQGVYVIVDFNLRELEGYD  138 (158)
Q Consensus        80 ~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~----~----A-------------~i~i~g~~~~~~~~v~~~~~~d  138 (158)
                      .+.++|+|+.+.+|+||||.++.|++     ..++    .    +             ++++.|+.....++|-+. +. 
T Consensus        10 ~vti~I~Gq~~e~LLDTGAD~TVl~~-----~~~Pg~w~pk~igGiGG~i~v~qy~~i~iei~g~~~~gtvlV~~t-Pv-   82 (99)
T 3ec0_A           10 VVTAYIEGQPVEVLLDTGADDSIVAG-----IELGNNYSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTGDT-PI-   82 (99)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEESS-----CCCCSCCEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEECC-SS-
T ss_pred             eEEEEECCEEEEEEEecCCCceEEcC-----cccCCCCCceEEEecCCcEeeeEEeeEEEEECCeEEEEEEEeCCC-Cc-
Confidence            46789999999999999999999974     3333    1    1             778899988888888553 23 


Q ss_pred             EEechhHhhhcCCceeee
Q 040033          139 VVLGTQWLRTLEPILWDF  156 (158)
Q Consensus       139 vILG~dwL~~~~~i~idw  156 (158)
                      =|+|+|+|.+.+. +++|
T Consensus        83 niiGRnlLtqlG~-tLnf   99 (99)
T 3ec0_A           83 NIFGRNILTALGM-SLNL   99 (99)
T ss_dssp             CEECHHHHHHHTC-EEEC
T ss_pred             CeeehhhHhhcCc-EEeC
Confidence            5799999999997 7765

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

Probab=98.39  E-value=2e-06  Score=58.46  Aligned_cols=73  Identities=15%  Similarity=0.193  Sum_probs=55.4

Q ss_pred             EEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE-----------------EEEEECCEEEEEEEEEecCCCCcEEec
Q 040033           80 RINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI-----------------VNLILQGVYVIVDFNLRELEGYDVVLG  142 (158)
Q Consensus        80 ~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~-----------------A~i~i~g~~~~~~~~v~~~~~~dvILG  142 (158)
                      .+.++|+|+...||+||||..++|++.-... ..+.                 -++++.|+.....++|-+. .. =|+|
T Consensus        10 ~vtvkI~Gq~~eaLLDTGAD~TVl~~~~~p~-~wkpk~igGiGG~i~v~qy~qi~iei~g~~~~gtvlV~~t-Pv-niiG   86 (99)
T 2hs1_A           10 LVTIKIGGQLKEALLDTGADDTIIEEMSLPG-RWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPT-PV-NIIG   86 (99)
T ss_dssp             EEEEEETTEEEEEEECTTCSSEEESCCSSCC-CCEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEESCC-SS-CEEC
T ss_pred             EEEEEECCEEEEEEeccCCCcEEEecccCCC-CCCCcEEEeCCCcEeeeEeccEEEEEeCCEEEEEEEeCCC-cc-Cchh
Confidence            4678999999999999999999999632211 1111                 1778899998888888553 23 4899


Q ss_pred             hhHhhhcCCceeee
Q 040033          143 TQWLRTLEPILWDF  156 (158)
Q Consensus       143 ~dwL~~~~~i~idw  156 (158)
                      +|||.+.+. +++|
T Consensus        87 Rd~Ltqlg~-tLnf   99 (99)
T 2hs1_A           87 RNLLTQIGA-TLNF   99 (99)
T ss_dssp             HHHHTTTTC-EEEC
T ss_pred             HhHHHHcCC-EEeC
Confidence            999999997 6765

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

Probab=98.15  E-value=1.7e-05  Score=60.35  Aligned_cols=71  Identities=17%  Similarity=0.240  Sum_probs=56.8

Q ss_pred             EEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE---------------------EEEEECCEEEEEEEEEecCCCC
Q 040033           79 LRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI---------------------VNLILQGVYVIVDFNLRELEGY  137 (158)
Q Consensus        79 i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~---------------------A~i~i~g~~~~~~~~v~~~~~~  137 (158)
                      ..+.++|+|+.+.+|+||||.++.+.+     .+++-                     .++++.|+.....++|-+. ..
T Consensus         9 P~vtv~I~Gq~~e~LLDTGAD~TVl~~-----~~lpg~w~pk~igGIGG~i~vrqy~~i~iei~g~~~~gtvlVg~t-Pv   82 (203)
T 3ka2_A            9 PLVTIRIGGQLKEALLDTGADDTVIEE-----LNLPGXWKPKLIGGIAGFIKVRQYDQIPVEIXGHKAIGTVLVGPT-PV   82 (203)
T ss_dssp             CEEEEEETTEEEEEEECTTCSSCEECS-----CCCSSCEEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEESCC-SS
T ss_pred             CeEEEEECCEEEEEEEecCCCceEEec-----ccCCCCCCceEEEEccCcEEEEEEcceeEEEcCeEEEEEEeeCCC-Cc
Confidence            356799999999999999999999984     33332                     1778899998888888553 34


Q ss_pred             cEEechhHhhhcCCceeeec
Q 040033          138 DVVLGTQWLRTLEPILWDFA  157 (158)
Q Consensus       138 dvILG~dwL~~~~~i~idw~  157 (158)
                      + |+|+|.|.+++. .++|.
T Consensus        83 n-IiGRd~LtqlG~-tLnf~  100 (203)
T 3ka2_A           83 N-IIGRNLLTQIGX-TLNFX  100 (203)
T ss_dssp             C-EECHHHHTTTTC-EEEGG
T ss_pred             C-ccchhhhhhcCc-eEEec
Confidence            4 899999999997 78874

>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=98.02  E-value=8.7e-07  Score=46.92  Aligned_cols=20  Identities=5%  Similarity=0.023  Sum_probs=18.0

Q ss_pred             ccceeecCCCCCCCccCCcc
Q 040033           29 AKVCATIATKSFPRDIGERS   48 (158)
Q Consensus        29 ~~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ...||+||+.||++++|+.+
T Consensus         6 ~~~C~nCgk~GH~ar~C~~p   25 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSS
T ss_pred             CCEEEECCccccCHhHCccc
Confidence            37799999999999999875

>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=97.95  E-value=2.2e-06  Score=48.76  Aligned_cols=19  Identities=16%  Similarity=0.078  Sum_probs=18.1

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+||+.||.+++||++
T Consensus        11 ~~C~~Cgk~GH~ardCP~~   29 (40)
T 1a6b_B           11 DQCAYCKEKGHWAKDCPKK   29 (40)
T ss_dssp             SSCSSSCCTTCCTTSCSSS
T ss_pred             CeeeECCCCCcchhhCcCC
Confidence            7899999999999999986

>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=97.95  E-value=3.3e-05  Score=53.81  Aligned_cols=69  Identities=13%  Similarity=0.107  Sum_probs=49.7

Q ss_pred             EEECCEeeEEEecCCCceeEECHHHHHHcCCe------E--------------EEEEECCEE-----EEEEEEEec-CCC
Q 040033           83 GRIGNISPIVLVDSGSTHNFISDTFAKKVKNF------I--------------VNLILQGVY-----VIVDFNLRE-LEG  136 (158)
Q Consensus        83 ~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~------~--------------A~i~i~g~~-----~~~~~~v~~-~~~  136 (158)
                      ++|+|+.+.+|+||||..++|++.-.......      +              -.+++.++.     ....++|.+ ...
T Consensus        18 ikI~Gq~~eaLLDTGAD~TVi~~~~~~~~p~~wkpk~~igGiGG~i~v~qy~qv~iei~g~~~~~~~~~gtvlV~p~tP~   97 (116)
T 2hah_A           18 IFVNGYPIKFLLDTGADITVLNRRDFQVKNSIENGRQMIGGIGGFIRGTNYINVHLEIRDENYKTQCIFGNVCVLEDNST   97 (116)
T ss_dssp             EEETTEEEEEEECTTCSSCEEEGGGCCCTTCEEEEEEEEEETTEEEEEEEEEEEEEEECCTTSCCEEEEEEEEEETTCCC
T ss_pred             EEECCEEEEEEecCCCCcEEEcccccccCCCCCCCceEEecCCCceeeeEEccEEEEEeCCCCCcceeEEEEEECCCCCc
Confidence            99999999999999999999997433100111      1              055677765     667778877 431


Q ss_pred             CcEEechhHhhhcCC
Q 040033          137 YDVVLGTQWLRTLEP  151 (158)
Q Consensus       137 ~dvILG~dwL~~~~~  151 (158)
                      .-=|+|+|+|.+.+.
T Consensus        98 ~vniiGRd~Ltqlg~  112 (116)
T 2hah_A           98 PVNILGRDNMIKFNI  112 (116)
T ss_dssp             SSEEECHHHHTTTTC
T ss_pred             cccEecHHHHhHcCC
Confidence            235899999999986

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1

Probab=97.94  E-value=2e-06  Score=44.33  Aligned_cols=19  Identities=11%  Similarity=0.163  Sum_probs=17.4

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+||+.||++++||++
T Consensus         3 ~~Cf~CG~~GH~ardC~~~   21 (26)
T 1dsq_A            3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CeeEeCCCCCcccccCCCc
Confidence            5699999999999999975

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

Probab=97.73  E-value=6.9e-06  Score=50.03  Aligned_cols=19  Identities=16%  Similarity=0.078  Sum_probs=18.1

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+||+.||++++||++
T Consensus        24 ~~C~~Cge~GH~ardCp~~   42 (56)
T 1u6p_A           24 DQCAYCKEKGHWAKDCPKK   42 (56)
T ss_dssp             TBCSSSCCBSSCGGGCTTC
T ss_pred             CcceeCCCCCcccccCcCC
Confidence            7799999999999999986

>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=97.53  E-value=0.0008  Score=51.07  Aligned_cols=70  Identities=17%  Similarity=0.210  Sum_probs=55.4

Q ss_pred             EEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE---------------------EEEEECCEEEEEEEEEecCCCC
Q 040033           79 LRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI---------------------VNLILQGVYVIVDFNLRELEGY  137 (158)
Q Consensus        79 i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~---------------------A~i~i~g~~~~~~~~v~~~~~~  137 (158)
                      -.+.++|+|+.+.+|+||||.++.|.+     ..++-                     .++++.|+.....++|-+.  .
T Consensus       113 P~~~iki~Gq~~e~LlDTGAD~TVl~~-----~~lpg~w~pk~igGiGg~i~v~qy~~i~iei~g~~~~~tvlVgpt--P  185 (203)
T 3ka2_A          113 PLVTIRIGGQLKEALLDTGADDTVIEE-----LNLPGXWKPKLIGGIGGFIKVRQYDQIPVEIXGHKAIGTVLVGPT--P  185 (203)
T ss_dssp             CEEEEEETTEEEEEEECTTCSSCEECS-----CCCCSCCEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEESCC--S
T ss_pred             CcEEEEECCEEEeeeecccCCceeeec-----ccCCCCCCceEEeeccceEEEEEeccEEEEECCeEEEEEEEECCC--C
Confidence            456799999999999999999999974     33321                     1778899988888888774  3


Q ss_pred             cEEechhHhhhcCCceeee
Q 040033          138 DVVLGTQWLRTLEPILWDF  156 (158)
Q Consensus       138 dvILG~dwL~~~~~i~idw  156 (158)
                      -=|+|+|.|.+++. +++|
T Consensus       186 vniiGRn~LtqlG~-tl~f  203 (203)
T 3ka2_A          186 VNIIGRNLLTQIGX-TLNF  203 (203)
T ss_dssp             SCEECHHHHGGGTC-EEEC
T ss_pred             cCeechhhHHHhCC-eeeC
Confidence            44789999999997 6664

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

Probab=97.22  E-value=0.00089  Score=46.32  Aligned_cols=74  Identities=8%  Similarity=-0.062  Sum_probs=48.2

Q ss_pred             EEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE---------------E------E-EE-ECCEEEEEEEEEecCCC
Q 040033           80 RINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI---------------V------N-LI-LQGVYVIVDFNLRELEG  136 (158)
Q Consensus        80 ~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~---------------A------~-i~-i~g~~~~~~~~v~~~~~  136 (158)
                      .+.++|+|+.+.+|+||||..+.|...-.-. +.+.               +      . ++ +.|+.-....+|.+-.+
T Consensus        11 ~vti~I~Gq~~eaLLDTGADdTVi~~~~lpg-~W~p~~~~k~igGIGG~i~v~qy~~~~~~~~i~g~k~i~tvlV~~ptP   89 (114)
T 3sqf_A           11 SLTLWLDDKMFTGLINTGADVTIIKLEDWPP-NWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPNLP   89 (114)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEEEGGGSCT-TSCEEECCCCCTTCCGGGCCEEESSCEEEECTTCCEEEECCEEETTCS
T ss_pred             eEEEEECCEEEEEEEccCCCceEEecccCCC-CcccCcCceEEEeccceEEEEEeccceEEEecCCCEEEEEEEECCCCc
Confidence            3568999999999999999999998633211 1111               0      2 22 56777666666663233


Q ss_pred             CcEEechhHhhhcCCceeee
Q 040033          137 YDVVLGTQWLRTLEPILWDF  156 (158)
Q Consensus       137 ~dvILG~dwL~~~~~i~idw  156 (158)
                      .+ |+|+|.|.+.+. .++|
T Consensus        90 vN-IiGRn~LtqlG~-tLnf  107 (114)
T 3sqf_A           90 VN-LWGRDLLSQMKI-MMAS  107 (114)
T ss_dssp             SC-EECHHHHTTSCC-----
T ss_pred             cc-EEchhhHhhcCc-EEEC
Confidence            44 599999999996 6665

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

Probab=97.20  E-value=8e-05  Score=45.10  Aligned_cols=19  Identities=5%  Similarity=-0.059  Sum_probs=17.3

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+||++||..++||..
T Consensus         8 ~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            8 YTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             CCCTTTCCTTSCGGGCSGG
T ss_pred             CccccCCCcCcccccCCCC
Confidence            6799999999999999954

>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=97.02  E-value=0.00017  Score=42.48  Aligned_cols=19  Identities=5%  Similarity=0.022  Sum_probs=15.6

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+|++.||.+++||.+
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            6788888888888888764

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

Probab=97.00  E-value=0.00022  Score=39.45  Aligned_cols=18  Identities=6%  Similarity=0.063  Sum_probs=16.3

Q ss_pred             ceeecCCCCCCCccCCcc
Q 040033           31 VCATIATKSFPRDIGERS   48 (158)
Q Consensus        31 ~Cf~Cg~~gH~~~~C~~~   48 (158)
                      .||+|++.||.+++||.+
T Consensus         2 ~C~~Cg~~GH~~~~C~~~   19 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAP   19 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCB
T ss_pred             cccccCCCCcchhhCcCc
Confidence            599999999999999975

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

Probab=96.94  E-value=0.0002  Score=40.07  Aligned_cols=18  Identities=6%  Similarity=0.204  Sum_probs=16.1

Q ss_pred             ceeecCCCCCCCccCCcc
Q 040033           31 VCATIATKSFPRDIGERS   48 (158)
Q Consensus        31 ~Cf~Cg~~gH~~~~C~~~   48 (158)
                      .||+|++.||.+++||++
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            599999999999999864

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

Probab=96.92  E-value=0.00024  Score=39.73  Aligned_cols=18  Identities=11%  Similarity=0.084  Sum_probs=16.8

Q ss_pred             cceeecCCCCCCCccCCc
Q 040033           30 KVCATIATKSFPRDIGER   47 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~   47 (158)
                      ..||+|++.||.+++||+
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            679999999999999985

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

Probab=96.87  E-value=0.00027  Score=43.50  Aligned_cols=19  Identities=11%  Similarity=0.170  Sum_probs=15.2

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+|++.||++++||.+
T Consensus         5 ~~C~~Cg~~GH~a~~C~~~   23 (61)
T 2ihx_A            5 GLCYTCGSPGHYQAQCPKK   23 (61)
T ss_dssp             TBCSSSCCBTCCGGGCTTT
T ss_pred             CcccccCCCCeehhhCcCC
Confidence            6688888888888888764

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

Probab=96.86  E-value=0.00023  Score=39.32  Aligned_cols=18  Identities=17%  Similarity=0.130  Sum_probs=16.6

Q ss_pred             cceeecCCCCCCCccCCc
Q 040033           30 KVCATIATKSFPRDIGER   47 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~   47 (158)
                      ..||+|++.||++++||+
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            679999999999999984

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

Probab=96.74  E-value=0.0004  Score=40.82  Aligned_cols=19  Identities=5%  Similarity=-0.034  Sum_probs=17.5

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+||+.||++++||.+
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            6799999999999999975

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

Probab=96.74  E-value=0.00042  Score=42.36  Aligned_cols=19  Identities=5%  Similarity=0.046  Sum_probs=17.6

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+|++.||++++|+.+
T Consensus        31 ~~C~~Cg~~GH~ar~C~~~   49 (60)
T 1cl4_A           31 GLCPRCKRGKHWANECKSK   49 (60)
T ss_dssp             CSCSSCSSCSSCSTTCCCT
T ss_pred             cceeECCCCCCccCcCCCc
Confidence            7899999999999999975

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

Probab=96.68  E-value=0.00043  Score=41.56  Aligned_cols=19  Identities=5%  Similarity=0.003  Sum_probs=16.7

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+|++.||.+++||.+
T Consensus        13 ~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           13 VKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             CBCTTTCCBSSCGGGCSSC
T ss_pred             cceeeeCCCCcChhhcCCC
Confidence            7799999999999999864

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

Probab=96.64  E-value=0.00043  Score=42.54  Aligned_cols=19  Identities=5%  Similarity=0.066  Sum_probs=17.7

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+|++.||++++||++
T Consensus        31 ~~C~~Cg~~GH~ar~C~~~   49 (61)
T 2ihx_A           31 ERCQLCNGMGHNAKQCRKR   49 (61)
T ss_dssp             SBCTTTCCBSSCGGGCCCC
T ss_pred             CeeCCCCCCCCCcCCCcCC
Confidence            6799999999999999975

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

Probab=96.64  E-value=0.0003  Score=43.04  Aligned_cols=19  Identities=11%  Similarity=0.039  Sum_probs=0.0

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      +.||+|++.||++++||..
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~~   20 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHEH   20 (60)
T ss_dssp             -------------------
T ss_pred             CccccCCCCCcCHhhCcCC
Confidence            3599999999999999975

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

Probab=96.63  E-value=0.00044  Score=45.26  Aligned_cols=19  Identities=16%  Similarity=0.076  Sum_probs=17.8

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+||+.||++++||.+
T Consensus        47 ~~CYnCG~~GH~~rdC~~~   65 (83)
T 3nyb_B           47 IYCYNCGGKGHFGDDCKEK   65 (83)
T ss_dssp             CBCSSSSCBSSCGGGCSSC
T ss_pred             CeecccCCCCcCcccCCcc
Confidence            6799999999999999986

>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=96.61  E-value=0.00065  Score=42.04  Aligned_cols=18  Identities=6%  Similarity=-0.034  Sum_probs=13.0

Q ss_pred             cceeecCCCCCCCccCCc
Q 040033           30 KVCATIATKSFPRDIGER   47 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~   47 (158)
                      ..||+|++.||.+++|+.
T Consensus         8 ~~C~~Cg~~GH~a~~C~~   25 (63)
T 2cqf_A            8 DRCYNCGGLDHHAKECKL   25 (63)
T ss_dssp             CCCSSSCCSSSCTTTCCS
T ss_pred             CcccccCCCCcChhhCCC
Confidence            457777777777777774

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

Probab=96.51  E-value=0.0006  Score=40.89  Aligned_cols=19  Identities=11%  Similarity=0.034  Sum_probs=17.6

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+|++.||++++||.+
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            6799999999999999974

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

Probab=96.50  E-value=0.00046  Score=44.22  Aligned_cols=18  Identities=6%  Similarity=-0.034  Sum_probs=16.5

Q ss_pred             cceeecCCCCCCCccCCc
Q 040033           30 KVCATIATKSFPRDIGER   47 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~   47 (158)
                      ..||+|++.||.+++|+.
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            789999999999999985

>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=96.39  E-value=0.00092  Score=41.35  Aligned_cols=19  Identities=16%  Similarity=-0.013  Sum_probs=17.8

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+|++.||++++||.+
T Consensus        30 ~~C~~Cg~~GH~ar~Cp~~   48 (63)
T 2cqf_A           30 KKCHFCQSISHMVASCPLK   48 (63)
T ss_dssp             SCCTTTCCSSSCTTTCTGG
T ss_pred             CccCCcCCcCCccCcCCCc
Confidence            7799999999999999976

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

Probab=96.09  E-value=0.0014  Score=41.85  Aligned_cols=19  Identities=16%  Similarity=-0.013  Sum_probs=17.9

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+|++.||++++||.+
T Consensus        47 ~~C~~Cg~~GH~ar~Cp~~   65 (74)
T 2li8_A           47 KKCHFCQSISHMVASCPLK   65 (74)
T ss_dssp             CCCTTTCCTTSCGGGCTTG
T ss_pred             CccCCcCCcCCccCcCcCC
Confidence            7899999999999999976

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

Probab=95.43  E-value=0.0035  Score=43.57  Aligned_cols=19  Identities=16%  Similarity=0.076  Sum_probs=17.6

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+|++.||++++||+.
T Consensus       106 ~~Cy~Cg~~GH~a~dCp~~  124 (124)
T 2lli_A          106 IYCYNCGGKGHFGDDCKEK  124 (124)
T ss_dssp             CCTTTTSSSCTTTTTSCCC
T ss_pred             CCcCCCCCCCcCcccCcCC
Confidence            7899999999999999973

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

Probab=95.27  E-value=0.0043  Score=44.70  Aligned_cols=18  Identities=6%  Similarity=-0.034  Sum_probs=15.7

Q ss_pred             cceeecCCCCCCCccCCc
Q 040033           30 KVCATIATKSFPRDIGER   47 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~   47 (158)
                      ..||+|++.||.+++|+.
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            469999999999999987

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

Probab=94.97  E-value=0.0059  Score=43.97  Aligned_cols=17  Identities=6%  Similarity=-0.070  Sum_probs=16.4

Q ss_pred             eeecCCCCCCCccCCcc
Q 040033           32 CATIATKSFPRDIGERS   48 (158)
Q Consensus        32 Cf~Cg~~gH~~~~C~~~   48 (158)
                      ||+|++.||++++||++
T Consensus       122 C~~Cg~~GH~~r~Cp~~  138 (148)
T 3ts2_A          122 CHFCQSINHMVASCPLK  138 (148)
T ss_dssp             CTTTCCSSCCGGGCTTT
T ss_pred             ccccCCcCCEeccCcCC
Confidence            99999999999999986

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

Probab=94.92  E-value=0.0066  Score=39.60  Aligned_cols=19  Identities=11%  Similarity=0.172  Sum_probs=16.9

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+|+++||.+++||..
T Consensus         6 ~~C~~Cg~~GH~~~~Cp~~   24 (83)
T 3nyb_B            6 VQCTLCKSKKHSKERCPSI   24 (83)
T ss_dssp             -CCSSSCCSSSCGGGCGGG
T ss_pred             CCCCCCCCCCCccccCCCc
Confidence            5699999999999999975

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

Probab=94.14  E-value=0.028  Score=39.35  Aligned_cols=70  Identities=20%  Similarity=0.056  Sum_probs=42.0

Q ss_pred             ECCEeeEEEecCCCceeEECHHHH-HHcC-C-----eE---------E------EEEECCE--EEEEEEEEecCC--CCc
Q 040033           85 IGNISPIVLVDSGSTHNFISDTFA-KKVK-N-----FI---------V------NLILQGV--YVIVDFNLRELE--GYD  138 (158)
Q Consensus        85 i~~~~v~aLiDSGat~sfI~~~~a-~~~~-~-----~~---------A------~i~i~g~--~~~~~~~v~~~~--~~d  138 (158)
                      |+|+...+|+||||..++|.+.-. .+-. .     .+         .      .+++-|+  .....+.|.|..  ..-
T Consensus        27 i~gq~~eaLLDTGAD~TVl~~~~lP~~W~k~~~~~~~igGIGG~i~v~qy~~~i~iei~g~~g~~~~tvlV~P~~~~tPv  106 (124)
T 2rsp_A           27 QRSVYITALLDSGADITIISEEDWPTDWPVMEAANPQIHGIGGGIPMRKSRDMIELGVINRDGSLERPLLLFPAVAMVRG  106 (124)
T ss_dssp             CSEEEEEEEECTTCSSCEEETTTSCTTSCEEECC---------CCCEEEESSCEEEEEECTTSCBCCCEEECCEEESCSS
T ss_pred             CCCEEEEEEecCCCCcEEEecccCCCcceeeccccceeeecCceEeeEEeCCceEEEEeCCCCcEEEEEEECcCCCCCce
Confidence            899999999999999999986432 1100 0     01         0      2333332  222334554520  123


Q ss_pred             EEechhHhhhcCCcee
Q 040033          139 VVLGTQWLRTLEPILW  154 (158)
Q Consensus       139 vILG~dwL~~~~~i~i  154 (158)
                      =|+|+|.|.+.+....
T Consensus       107 nIiGRdlLtqlG~tL~  122 (124)
T 2rsp_A          107 SILGRDCLQGLGLRLT  122 (124)
T ss_dssp             EEECHHHHHHTTCEEE
T ss_pred             eEECHhHHhhCCcEEe
Confidence            4899999999997443

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

Probab=93.86  E-value=0.019  Score=39.78  Aligned_cols=17  Identities=6%  Similarity=0.173  Sum_probs=7.9

Q ss_pred             ceeecCCC-CCCCccCCc
Q 040033           31 VCATIATK-SFPRDIGER   47 (158)
Q Consensus        31 ~Cf~Cg~~-gH~~~~C~~   47 (158)
                      .||+|++. ||.++.||+
T Consensus        24 ~C~~Cg~~~gH~~~~C~~   41 (124)
T 2lli_A           24 ICSYCGATDDHYSRHCPK   41 (124)
T ss_dssp             CCTTTCCTTTCCTTTGGG
T ss_pred             cCcCCCCcCCccCcccCC
Confidence            34444444 444444444

>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=93.14  E-value=0.069  Score=36.78  Aligned_cols=28  Identities=18%  Similarity=0.281  Sum_probs=24.0

Q ss_pred             EEEEEEC-----CEeeEEEecCCCceeEECHHH
Q 040033           80 RINGRIG-----NISPIVLVDSGSTHNFISDTF  107 (158)
Q Consensus        80 ~~~~~i~-----~~~v~aLiDSGat~sfI~~~~  107 (158)
                      .+.++|+     |+.+.||+||||..+.|.+.-
T Consensus        12 lvtikI~~~~~~Gq~~eaLLDTGADdTVl~~~~   44 (116)
T 3liy_A           12 VIKAQVDTQTSHPKTIEALLDTGADMTVIPIAL   44 (116)
T ss_dssp             EEEEEEECSSSCCEEEEEEECTTBSSCEEEGGG
T ss_pred             eEEEEEccccCCCeEeEEEeccCCCccEEeccc
Confidence            3577888     999999999999999998643

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

Probab=92.89  E-value=0.25  Score=35.40  Aligned_cols=38  Identities=21%  Similarity=0.265  Sum_probs=31.8

Q ss_pred             EEEECCEEEEEEEEEecCC--CCcEEechhHhhhcCCceee
Q 040033          117 NLILQGVYVIVDFNLRELE--GYDVVLGTQWLRTLEPILWD  155 (158)
Q Consensus       117 ~i~i~g~~~~~~~~v~~~~--~~dvILG~dwL~~~~~i~id  155 (158)
                      .+.+++..+.+.|.+.+=+  .|.|+||..||+..+. .+|
T Consensus        97 ~i~lG~~~~~ie~tLtdRs~m~ypmLLGR~~L~~~~~-lVD  136 (146)
T 2pma_A           97 NIKLGDKVRTIKVNLTNRKRFLYPLLLGRDAIIDFNG-AVD  136 (146)
T ss_dssp             EEEETTEEEEEEEEEECCCCCSCSEEECHHHHHHTTE-EEE
T ss_pred             EEEECCEEEEEEEEEcCCCcCCCCEEechhHHhhCCE-EEC
Confidence            7788999999999999854  7999999999987653 454

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

Probab=91.36  E-value=1.4  Score=29.28  Aligned_cols=67  Identities=21%  Similarity=0.282  Sum_probs=48.1

Q ss_pred             EEEEECCEeeEEEecCCCceeEECHHHHHHcC-CeE-------------E---EEEECCEEEEEEEEEecCCCCcEEe--
Q 040033           81 INGRIGNISPIVLVDSGSTHNFISDTFAKKVK-NFI-------------V---NLILQGVYVIVDFNLRELEGYDVVL--  141 (158)
Q Consensus        81 ~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~-~~~-------------A---~i~i~g~~~~~~~~v~~~~~~dvIL--  141 (158)
                      +++.|.|..+++--||||+.+.|.+.|...-. +..             +   .++++|+.....++--++   |.||  
T Consensus        10 L~vEiKg~kLkg~WDsGA~ITCiP~~fL~~E~PI~~~~I~TIHG~k~q~vYYl~fKv~GRKveaEVi~sp~---dYvli~   86 (107)
T 2jys_A           10 LEAEIKGTKLKAHWDSGATITCVPEAFLEDERPIQTMLIKTIHGEKQQDVYYLTFKVQGRKVEAEVLASPY---DYILLN   86 (107)
T ss_dssp             EEEEETTEEEEEEECTTCSSEEEEGGGTTTCCCSEEEEEECSSCEEEEEEEEEEEEESSCEEEEEEEEESS---SSEEEC
T ss_pred             eeEEEeCcEEEEEecCCCeEEEcchHHhcccccccceEEEEecCceeceEEEEEEEEcCeEEEEEEecCcc---cEEEEc
Confidence            67889999999999999999999999876422 111             1   788899877776665553   3332  


Q ss_pred             --chhHhhhcC
Q 040033          142 --GTQWLRTLE  150 (158)
Q Consensus       142 --G~dwL~~~~  150 (158)
                        -.+|+.+..
T Consensus        87 P~DiPW~~~~p   97 (107)
T 2jys_A           87 PSDVPWLMKKP   97 (107)
T ss_dssp             TTTCHHHHSCC
T ss_pred             CcCccccccCc
Confidence              248887644

>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=89.21  E-value=0.58  Score=30.72  Aligned_cols=28  Identities=21%  Similarity=0.242  Sum_probs=23.1

Q ss_pred             eEEEEEEEC--CEeeEEEecCCCceeEECH
Q 040033           78 TLRINGRIG--NISPIVLVDSGSTHNFISD  105 (158)
Q Consensus        78 ~i~~~~~i~--~~~v~aLiDSGat~sfI~~  105 (158)
                      ...+.+.|+  .+++.++|||||+..+|..
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            345677887  8999999999999998853

---

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	158
d2fmba_	104	EIAV protease {Equine infectious anemia virus [Tax	98.82
d4fiva_	113	Feline immunodeficiency virus (FIV) protease {Feli	98.1
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.96
d2nmza1	99	Human immunodeficiency virus type 1 protease {Huma	97.72
d1nsoa_	107	Mason-Pfizer monkey virus protease {Simian retrovi	97.72
d1hvca_	203	Human immunodeficiency virus type 1 protease {Huma	97.66
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	97.33
d3ecga1	99	Human immunodeficiency virus type 2 (HIV-2) protea	97.31
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.04
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	96.93
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	96.74
d2pmaa1	141	Uncharacterized protein LPG0085 {Legionella pneumo	96.65
d1hvca_	203	Human immunodeficiency virus type 1 protease {Huma	95.81
d2rspa_	124	Rous sarcoma virus protease {Rous sarcoma virus, s	93.29
d1izea_	323	Acid protease {Fungus (Aspergillus oryzae) [TaxId:	91.34
d1wkra_	340	Acid protease {Irpex lacteus (Polyporus tulipifera	91.14
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	91.03
d1bxoa_	323	Acid protease {Fungus (Penicillium janthinellum),	90.31
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	89.8
d3cmsa_	323	Chymosin (synonym: renin) {Cow (Bos taurus) [TaxId	86.45
d2bjua1	329	Plasmepsin (a hemoglobin-degrading enzyme) {Plasmo	85.78
d1miqa_	373	Plasmepsin (a hemoglobin-degrading enzyme) {Plasmo	83.67
d1am5a_	324	Pepsin(ogen) {Atlantic cod (Gadus morhua) [TaxId:	83.3
d1bxoa_	323	Acid protease {Fungus (Penicillium janthinellum),	81.36

>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=98.82  E-value=2.1e-08  Score=67.28  Aligned_cols=72  Identities=17%  Similarity=0.218  Sum_probs=57.1

Q ss_pred             eEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE---------------------EEEEECCEEEEEEEEEecCCC
Q 040033           78 TLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI---------------------VNLILQGVYVIVDFNLRELEG  136 (158)
Q Consensus        78 ~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~---------------------A~i~i~g~~~~~~~~v~~~~~  136 (158)
                      .-.+.+.|+|+++.+|+||||.++.|+..-..+.....                     -.+.+.|+.....++|.|. +
T Consensus         8 RP~~~i~I~Gq~v~~LLDTGAD~TVI~~~~~p~~~~~~~~~~~~~igg~g~~~~~~~~~v~i~~~g~~~~~~~lV~p~-P   86 (104)
T d2fmba_           8 RPTTIVLINDTPLNVLLDTGADTSVLTTAHYNRLKYRGRKYQGTGIGGVGGNVETFSTPVTIKKKGRHIKTRMLVADI-P   86 (104)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEEHHHHHHCSSCCCCEECCCEEETTEEECCEEEEEEEEETTEEEEEEEEEESC-S
T ss_pred             CeEEEEEECCEEEEEEEeCCCCeEEEcccccCccCCCCCCcceeEEEEecceEEEEEEEEEEEECCeEEEEEEEECCC-C
Confidence            34578899999999999999999999998766432111                     0667789898889999884 3


Q ss_pred             CcEEechhHhhhcCC
Q 040033          137 YDVVLGTQWLRTLEP  151 (158)
Q Consensus       137 ~dvILG~dwL~~~~~  151 (158)
                      .+ |||+|.|++.+.
T Consensus        87 vn-LlGRdlL~qlG~  100 (104)
T d2fmba_          87 VT-ILGRDILQDLGA  100 (104)
T ss_dssp             SC-EECHHHHHHHTC
T ss_pred             cc-eecHHHHHHhCC
Confidence            33 999999999885

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

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

Probab=98.10  E-value=1.6e-06  Score=58.66  Aligned_cols=73  Identities=11%  Similarity=0.012  Sum_probs=47.6

Q ss_pred             EEEEEEECCEeeEEEecCCCceeEECHHHHHHcC-CeEE-------------------EEEECCEE-----EEEEEEEec
Q 040033           79 LRINGRIGNISPIVLVDSGSTHNFISDTFAKKVK-NFIV-------------------NLILQGVY-----VIVDFNLRE  133 (158)
Q Consensus        79 i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~-~~~A-------------------~i~i~g~~-----~~~~~~v~~  133 (158)
                      -.+.+.|+|+++.+|+||||.++.|+..=..... .+..                   .+++.++.     ....+-|++
T Consensus        11 P~v~v~I~Gq~v~~LLDTGAD~TVi~~~d~p~~~~~~~~~~~~~GIGG~~~v~~~~~v~i~~~~~~~~gtvl~g~~pvlp   90 (113)
T d4fiva_          11 PEILIFVNGYPIKFLLDTGADITILNRRDFQVKNSIENGRQNMIGVGGGKRGTNYINVHLEIRDENYKTQCIFGNVCVLE   90 (113)
T ss_dssp             CEEEEEETTEEEEEEECTTCSSCEEEGGGCCCTTCEEEEEEEEECSSCEEEEEEEEEEEEEECCTTSCCCEEEEEEEEET
T ss_pred             CeEEEEECCEEEEEEEcCCCCcEEEeccccCCCCCCCCCCCeEEecCeEEeeeEEceEEEEEcCCeEeEEEEEccccccC
Confidence            3568899999999999999999999885433221 1110                   34443332     223444444


Q ss_pred             CCCCc-EEechhHhhhcCC
Q 040033          134 LEGYD-VVLGTQWLRTLEP  151 (158)
Q Consensus       134 ~~~~d-vILG~dwL~~~~~  151 (158)
                      ..+.+ =|||+|.|++++.
T Consensus        91 ~~~~p~nllGRd~LtqlG~  109 (113)
T d4fiva_          91 DNSLIQPLLGRDNMIKFNI  109 (113)
T ss_dssp             TCCCSSCEECHHHHHHTTC
T ss_pred             CCCCcCCEEChhhhHHhCC
Confidence            43332 3999999999986

>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=97.96  E-value=8.2e-07  Score=44.55  Aligned_cols=19  Identities=5%  Similarity=0.022  Sum_probs=17.5

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+||+.||.+++|..+
T Consensus         7 ikCfNCGkeGH~ar~CrAP   25 (29)
T d1nc8a_           7 IRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CBCTTTSCBSSCGGGCCSS
T ss_pred             eEeecCCccchhhhhccCc
Confidence            7799999999999999865

>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=97.72  E-value=0.00019  Score=46.52  Aligned_cols=69  Identities=16%  Similarity=0.233  Sum_probs=56.0

Q ss_pred             EEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE---------------------EEEEECCEEEEEEEEEecCCCCc
Q 040033           80 RINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI---------------------VNLILQGVYVIVDFNLRELEGYD  138 (158)
Q Consensus        80 ~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~---------------------A~i~i~g~~~~~~~~v~~~~~~d  138 (158)
                      .+.++|+|+...||+||||..+.+.+     ++++-                     -++++.|+....+++|-|- +.+
T Consensus        10 ~vtvkIgGq~~eaLLDTGADdTVlee-----i~lpg~WkPk~IgGIGGfikVrqYd~i~iei~g~k~~gtVLVgpT-PvN   83 (99)
T d2nmza1          10 LVTIKIGGQLKEALLDTGADDTVIEE-----MSLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPT-PAN   83 (99)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEEES-----CCCCSCCEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEESC-SSC
T ss_pred             eEEEEECCEEEEEeeccCCCceEEec-----ccCCCCCCceEEEeccceEEEEEeCceEEEECCcEEEEEEEECCC-Ccc
Confidence            46889999999999999999999964     34332                     1788899999999999883 333


Q ss_pred             EEechhHhhhcCCceeee
Q 040033          139 VVLGTQWLRTLEPILWDF  156 (158)
Q Consensus       139 vILG~dwL~~~~~i~idw  156 (158)
                       |+|++.|.+.+. +++|
T Consensus        84 -IiGRN~Ltq~Gc-tLnf   99 (99)
T d2nmza1          84 -IIGRNLLTQIGA-TLNF   99 (99)
T ss_dssp             -EECHHHHTTTTC-EEEC
T ss_pred             -EEcccchhhcCc-eecC
Confidence             789999999997 7765

>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=97.72  E-value=1e-05  Score=54.05  Aligned_cols=69  Identities=9%  Similarity=-0.048  Sum_probs=45.6

Q ss_pred             EEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE------------E----------EEEE-CCEEEEEEEEEecCCCC
Q 040033           81 INGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI------------V----------NLIL-QGVYVIVDFNLRELEGY  137 (158)
Q Consensus        81 ~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~------------A----------~i~i-~g~~~~~~~~v~~~~~~  137 (158)
                      +.+.|+|+++.+|+||||.++.|+..-... +.+.            +          .+.. ++..-.+..++++-.+.
T Consensus        12 ~~v~I~G~~v~~LLDTGAD~TVI~~~~~p~-~wp~~~~~~~~~GiGg~~~~~~~~~~l~~~~~~~~~~~~~p~vv~~~Pv   90 (107)
T d1nsoa_          12 LTLWLDDKMFTGLINTGADVTIIKLEDWPP-NWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPNLPV   90 (107)
T ss_dssp             EEEEETTEEEEECCCSSCSSCBCCGGGSCT-TSCCCCCEEEECSSSEEEECCCBCCCEEEEETTTEEEEECCBBCTTCCC
T ss_pred             EEEEECCEEEEeeecCCCCcEEEeccccCC-CCCcCcCccEEEEecCeeeEEEeeeeEEEEeCCCceEEEcceECCCCCc
Confidence            567899999999999999999998864332 1111            1          1111 23333333345554455


Q ss_pred             cEEechhHhhhcCC
Q 040033          138 DVVLGTQWLRTLEP  151 (158)
Q Consensus       138 dvILG~dwL~~~~~  151 (158)
                      + |||+|.|.+++-
T Consensus        91 n-llGRd~L~qlg~  103 (107)
T d1nsoa_          91 N-LWGRDLLSQMKI  103 (107)
T ss_dssp             C-BCCHHHHHHHHT
T ss_pred             C-cccHHHHHHhCC
Confidence            5 999999999875

>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=97.66  E-value=0.00012  Score=53.07  Aligned_cols=69  Identities=16%  Similarity=0.202  Sum_probs=56.3

Q ss_pred             EEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE---------------------EEEEECCEEEEEEEEEecCCCCc
Q 040033           80 RINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI---------------------VNLILQGVYVIVDFNLRELEGYD  138 (158)
Q Consensus        80 ~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~---------------------A~i~i~g~~~~~~~~v~~~~~~d  138 (158)
                      .+.++|+|+.+.||+||||.++.+..     .+++-                     -++++.|+....+++|.| .+. 
T Consensus        10 ~VtVkIgGQ~~eaLLDTGADDTVLe~-----inLpG~WkPkiIGGIGGfIkVrqY~~V~IeI~gkk~~gTVLVgP-TPv-   82 (203)
T d1hvca_          10 LVTIRIGGQLKEALLDTGADDTVLEE-----MNLPGKWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGP-TPV-   82 (203)
T ss_dssp             EEEEESSSCEEEEEECTTCSSEEEEC-----CCCSSCEEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEES-CSS-
T ss_pred             eEEEEECCEEEEEEecCCCCceEEec-----ccCCCCCcccEEEecCceEEEEEeCCEEEEECCcEEEEEEEECC-CCc-
Confidence            46889999999999999999999954     33322                     178889999999999998 333 


Q ss_pred             EEechhHhhhcCCceeee
Q 040033          139 VVLGTQWLRTLEPILWDF  156 (158)
Q Consensus       139 vILG~dwL~~~~~i~idw  156 (158)
                      =|||++.|.+.+. +++|
T Consensus        83 NIIGRNlLtqlG~-tLnF   99 (203)
T d1hvca_          83 NIIGRNLLTQIGC-TLNF   99 (203)
T ss_dssp             CEECHHHHGGGTC-EEEC
T ss_pred             cccchhhhhhhhh-eeec
Confidence            4789999999997 7776

>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=97.33  E-value=2.5e-05  Score=37.45  Aligned_cols=19  Identities=11%  Similarity=0.163  Sum_probs=16.8

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      -+||.||+.||..++|...
T Consensus         3 pvcfscgktghikkdck~e   21 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CEEEecCCcccchhhhhhh
Confidence            4799999999999999753

>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=97.31  E-value=0.0016  Score=41.93  Aligned_cols=68  Identities=15%  Similarity=0.134  Sum_probs=53.3

Q ss_pred             EEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE---------------------EEEEECCEEEEEEEEEecCCCCc
Q 040033           80 RINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI---------------------VNLILQGVYVIVDFNLRELEGYD  138 (158)
Q Consensus        80 ~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~---------------------A~i~i~g~~~~~~~~v~~~~~~d  138 (158)
                      .+.++|+|+...||+||||..+.+..     ++++-                     -++++-|+....+++|-|.  .=
T Consensus        10 ~vtvkIgGq~~eaLLDTGADdTVle~-----i~lpg~WkPk~iGGIGGfikVrqYd~i~Ieicg~k~~gtVLvgpT--Pv   82 (99)
T d3ecga1          10 VVTAYIEGQPVEVLLDTGADDSIVAG-----IELGNNYSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTGDT--PI   82 (99)
T ss_dssp             EEEEEETTEEEEEEECTTCSSCEECS-----CCCCSCCEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEECC--SS
T ss_pred             eEEEEECCEEeeeecccCCCceeeec-----cCCCCCCcceEEEEeeeeEEEEEeCcEEEEECCcEEEEEEEeCCC--Cc
Confidence            46789999999999999999999953     33332                     1778889988888888663  23


Q ss_pred             EEechhHhhhcCCceee
Q 040033          139 VVLGTQWLRTLEPILWD  155 (158)
Q Consensus       139 vILG~dwL~~~~~i~id  155 (158)
                      =|+|++.|.+.+. +++
T Consensus        83 NIiGRNlLtqlGc-tLn   98 (99)
T d3ecga1          83 NIFGRNILTALGM-SLN   98 (99)
T ss_dssp             CEECHHHHHHTTC-EEE
T ss_pred             eEEccchhhhhCc-ccC
Confidence            3789999999997 554

>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=97.04  E-value=7e-05  Score=41.48  Aligned_cols=18  Identities=6%  Similarity=0.069  Sum_probs=16.6

Q ss_pred             ceeecCCCCCCCccCCcc
Q 040033           31 VCATIATKSFPRDIGERS   48 (158)
Q Consensus        31 ~Cf~Cg~~gH~~~~C~~~   48 (158)
                      .||+|++.||.+.+||++
T Consensus         3 ~C~~Cg~~GH~~~~Cp~~   20 (42)
T d2exfa1           3 KCFNCGKEGHTARNCRAP   20 (42)
T ss_dssp             CCTTTCCSSSCTTTCSSC
T ss_pred             ccccCCCcCcCcccCcCC
Confidence            599999999999999985

>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=96.93  E-value=0.00011  Score=40.59  Aligned_cols=19  Identities=11%  Similarity=0.034  Sum_probs=17.3

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..||+||+.||.+.+||++
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            4699999999999999974

>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=96.74  E-value=0.00019  Score=38.31  Aligned_cols=19  Identities=16%  Similarity=0.078  Sum_probs=17.7

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ..|-||.|+||.+++||++
T Consensus        11 DQCAyCke~GHW~~dCPkk   29 (40)
T d1a6bb_          11 DQCAYCKEKGHWAKDCPKK   29 (40)
T ss_dssp             SSCSSSCCTTCCTTSCSSS
T ss_pred             hhhHHHhhcCchhhhCccC
Confidence            5699999999999999986

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

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

Probab=96.65  E-value=0.002  Score=44.36  Aligned_cols=38  Identities=21%  Similarity=0.265  Sum_probs=31.9

Q ss_pred             EEEECCEEEEEEEEEecCC--CCcEEechhHhhhcCCceee
Q 040033          117 NLILQGVYVIVDFNLRELE--GYDVVLGTQWLRTLEPILWD  155 (158)
Q Consensus       117 ~i~i~g~~~~~~~~v~~~~--~~dvILG~dwL~~~~~i~id  155 (158)
                      .+.++|..+.+.|.+.+=+  .|+|+||..||...+- .+|
T Consensus        94 ~i~ig~~~~~ie~tL~dR~~m~yp~LiGR~~L~~~~~-~VD  133 (141)
T d2pmaa1          94 NIKLGDKVRTIKVNLTNRKRFLYPLLLGRDAIIDFNG-AVD  133 (141)
T ss_dssp             EEEETTEEEEEEEEEECCCCCSCSEEECHHHHHHTTE-EEE
T ss_pred             EEEECCEEEEEEEEECCCCCCCCCEEECHHHHhcCCE-EEC
Confidence            6788999999999999864  7999999999988663 455

>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=95.81  E-value=0.04  Score=39.48  Aligned_cols=71  Identities=14%  Similarity=0.151  Sum_probs=56.2

Q ss_pred             eEEEEEEECCEeeEEEecCCCceeEECHHHHHHcCCeE---------------------EEEEECCEEEEEEEEEecCCC
Q 040033           78 TLRINGRIGNISPIVLVDSGSTHNFISDTFAKKVKNFI---------------------VNLILQGVYVIVDFNLRELEG  136 (158)
Q Consensus        78 ~i~~~~~i~~~~v~aLiDSGat~sfI~~~~a~~~~~~~---------------------A~i~i~g~~~~~~~~v~~~~~  136 (158)
                      .-.+.++|+++...||+||||..+.+.+     ++++-                     -++++-|+...-+++|-|-  
T Consensus       112 rp~vt~ki~gq~~ealldtgaddtv~e~-----~~lpgrwkpk~iggiggfikvrqy~~v~iei~g~k~~gtvlvgpt--  184 (203)
T d1hvca_         112 RPLVTIKIGGQLKEALLDTGADDTVLEE-----MSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT--  184 (203)
T ss_dssp             CCEEEEEETTEEEEEEECTTCSSCEEES-----CCCSSCCEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEECC--
T ss_pred             cceEEEecchhHHHHHhcccCCceEEec-----ccCCCCCcceEEEEeccccceeeEccEEEEECCCEEEEEEEECCC--
Confidence            4457899999999999999999999843     44432                     1788889988888888873  


Q ss_pred             CcEEechhHhhhcCCceeee
Q 040033          137 YDVVLGTQWLRTLEPILWDF  156 (158)
Q Consensus       137 ~dvILG~dwL~~~~~i~idw  156 (158)
                      .==|+|++.|.+.+. +.+|
T Consensus       185 p~niigrn~ltq~g~-tlnf  203 (203)
T d1hvca_         185 PVNIIGRNLLTQIGC-TLNF  203 (203)
T ss_dssp             SSCEECHHHHTTTTC-EEEC
T ss_pred             CceEEcccchhhcCc-cccC
Confidence            233789999999997 7765

>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=93.29  E-value=0.0087  Score=40.23  Aligned_cols=25  Identities=24%  Similarity=0.262  Sum_probs=21.3

Q ss_pred             EEECCEeeEEEecCCCceeEECHHH
Q 040033           83 GRIGNISPIVLVDSGSTHNFISDTF  107 (158)
Q Consensus        83 ~~i~~~~v~aLiDSGat~sfI~~~~  107 (158)
                      ++++|+.+.+|+||||..+.|++.-
T Consensus        25 ~k~~g~~i~~LLDTGAD~TVI~~~d   49 (124)
T d2rspa_          25 VKQRSVYITALLDSGADITIISEED   49 (124)
T ss_dssp             CSCSEEEEEEEECTTCSSCEEETTT
T ss_pred             EeeCCEEEEEEEcCCCCeEEEcCCc
Confidence            3456789999999999999999854

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

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

Probab=91.34  E-value=0.16  Score=37.58  Aligned_cols=68  Identities=15%  Similarity=0.238  Sum_probs=44.3

Q ss_pred             eeEEEecCCCceeEECHHHHHHcCCeE----------------------EEEEECCEEEEE-------------EE--EE
Q 040033           89 SPIVLVDSGSTHNFISDTFAKKVKNFI----------------------VNLILQGVYVIV-------------DF--NL  131 (158)
Q Consensus        89 ~v~aLiDSGat~sfI~~~~a~~~~~~~----------------------A~i~i~g~~~~~-------------~~--~v  131 (158)
                      ...++||||++..++...+++.+--..                      -.+.++|..+.+             .+  .+
T Consensus       208 ~~~~ivDSGts~~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~i~f~f~g~~~~ip~~~~~~~~~~~~~C~~~i  287 (323)
T d1izea_         208 SITGIADTGTTLLLLDDSIVDAYYEQVNGASYDSSQGGYVFPSSASLPDFSVTIGDYTATVPGEYISFADVGNGQTFGGI  287 (323)
T ss_dssp             CEEEEECTTCCSEEECHHHHHHHHTTSTTCEEETTTTEEEEETTCCCCCEEEEETTEEEEECHHHHEEEECSTTEEEESE
T ss_pred             CceEEeccCCccccCCHHHHHHHHHHcCCccccCCCCcEEeecccCCceEEEEECCEEEEcChHHEEEEeCCCCEEEEEE
Confidence            457899999999999999877653221                      055666665543             11  12


Q ss_pred             ecCCC-CcEEechhHhhhcCCceeeec
Q 040033          132 RELEG-YDVVLGTQWLRTLEPILWDFA  157 (158)
Q Consensus       132 ~~~~~-~dvILG~dwL~~~~~i~idw~  157 (158)
                      .+..+ -..|||..||+.+-- ..|+.
T Consensus       288 ~~~~~~~~~iLG~~flr~~y~-vfD~~  313 (323)
T d1izea_         288 QSNSGIGFSIFGDVFLKSQYV-VFDAS  313 (323)
T ss_dssp             EECTTTSSEEECHHHHTTEEE-EEETT
T ss_pred             ECCCCCCCEEECHHHhCCEEE-EEECC
Confidence            22222 336999999998764 56664

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

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

Probab=91.14  E-value=0.26  Score=36.87  Aligned_cols=67  Identities=19%  Similarity=0.288  Sum_probs=43.1

Q ss_pred             eEEEecCCCceeEECHHHHHHc----CCeE-------------------EEEEECCEEEEEEE--EE-------------
Q 040033           90 PIVLVDSGSTHNFISDTFAKKV----KNFI-------------------VNLILQGVYVIVDF--NL-------------  131 (158)
Q Consensus        90 v~aLiDSGat~sfI~~~~a~~~----~~~~-------------------A~i~i~g~~~~~~~--~v-------------  131 (158)
                      ..|+||||++..++...++.++    +...                   -.+.++|.++.+..  ++             
T Consensus       207 ~~aiiDSGtt~~~lP~~~~~~l~~~~~~~~~~~~~~~~~~c~~~~~~P~i~f~f~g~~~~i~~~~yi~~~~~~~~~~~~~  286 (340)
T d1wkra_         207 TAGIVDTGTTLTLIASDAFAKYKKATGAVADNNTGLLRLTTAQYANLQSLFFTIGGQTFELTANAQIWPRNLNTAIGGSA  286 (340)
T ss_dssp             EEEEECTTBCSEEECHHHHHHHHHHHTCEECTTTSSEEECHHHHHTCCCEEEEETTEEEEECTGGGBCCGGGGGGGTCCS
T ss_pred             cceEEecCCccEeccHHHHHHHHHHhCccccCCceEEEEeccccCCCCceEEEECCEEEEEChHHeEeeccCceeecCcc
Confidence            4589999999999998776654    3222                   16677887766431  11             


Q ss_pred             ---------ecC---CCCcEEechhHhhhcCCceeeec
Q 040033          132 ---------REL---EGYDVVLGTQWLRTLEPILWDFA  157 (158)
Q Consensus       132 ---------~~~---~~~dvILG~dwL~~~~~i~idw~  157 (158)
                               +..   ....+|||..||+.+-- ..|..
T Consensus       287 ~~~~~~~~~~~~~~~~~~~~ILG~~fl~~~yv-vfD~~  323 (340)
T d1wkra_         287 SSVYLIVGDLGSDSGEGLDFINGLTFLERFYS-VYDTT  323 (340)
T ss_dssp             SCEEBCEEECSSCTTSSCCEEECHHHHTSEEE-EEETT
T ss_pred             ceEEEEEecccCCCCCCCCEEechHHhCCEEE-EEECC
Confidence                     111   13457999999988653 35543

>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=91.03  E-value=0.039  Score=27.83  Aligned_cols=19  Identities=5%  Similarity=0.046  Sum_probs=17.8

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ++|-+|++-.|.+++|..+
T Consensus         3 ~lCPrC~kG~HWa~~Crsk   21 (32)
T d1cl4a_           3 GLCPRCKRGKHWANECKSK   21 (32)
T ss_dssp             CSCSSCSSCSSCSTTCCCT
T ss_pred             ccCccccCcchHHHHhhhh
Confidence            7899999999999999876

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

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

Probab=90.31  E-value=0.3  Score=36.01  Aligned_cols=68  Identities=15%  Similarity=0.257  Sum_probs=46.1

Q ss_pred             eeEEEecCCCceeEECHHHHHHcCCeE----------------------EEEEECCEEEEEE----------------EE
Q 040033           89 SPIVLVDSGSTHNFISDTFAKKVKNFI----------------------VNLILQGVYVIVD----------------FN  130 (158)
Q Consensus        89 ~v~aLiDSGat~sfI~~~~a~~~~~~~----------------------A~i~i~g~~~~~~----------------~~  130 (158)
                      ...++||||++..++...++.++--..                      -.+.++|.++.+.                +.
T Consensus       207 ~~~aiiDSGTs~~~lp~~~~~~l~~~i~~~~~~~~~~~~~~~c~~~~p~itf~f~g~~~~i~~~~~~~~~~~~~~~C~~~  286 (323)
T d1bxoa_         207 GFSGIADTGTTLLLLDDSVVSQYYSQVSGAQQDSNAGGYVFDCSTNLPDFSVSISGYTATVPGSLINYGPSGDGSTCLGG  286 (323)
T ss_dssp             EEEEEECTTCSSEEECHHHHHHHHTTSTTCEEETTTTEEEECTTCCCCCEEEEETTEEEEECHHHHEEEECSSSSCEEES
T ss_pred             CcceEEecccccccCCHHHHHHHHHHhCCccccCCCCcEEEeccCCCCcEEEEECCEEEEEChHHeEEEEcCCCCEEEEE
Confidence            467999999999999999988873211                      0566777766541                11


Q ss_pred             EecCCCCc-EEechhHhhhcCCceeeec
Q 040033          131 LRELEGYD-VVLGTQWLRTLEPILWDFA  157 (158)
Q Consensus       131 v~~~~~~d-vILG~dwL~~~~~i~idw~  157 (158)
                      +.+....+ .|||..||+.+-- ..|+.
T Consensus       287 i~~~~~~~~~ILG~~flr~~y~-vfD~~  313 (323)
T d1bxoa_         287 IQSNSGIGFSIFGDIFLKSQYV-VFDSD  313 (323)
T ss_dssp             EEECTTCSSEEECHHHHTTEEE-EEETT
T ss_pred             EECCCCCCcEEECHHHhCCEEE-EEECC
Confidence            22233334 6999999998775 46764

>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=89.80  E-value=0.05  Score=27.27  Aligned_cols=19  Identities=5%  Similarity=0.045  Sum_probs=17.7

Q ss_pred             cceeecCCCCCCCccCCcc
Q 040033           30 KVCATIATKSFPRDIGERS   48 (158)
Q Consensus        30 ~~Cf~Cg~~gH~~~~C~~~   48 (158)
                      ++|-+|++-.|.+++|..+
T Consensus         3 ~lCPrC~kG~HWa~~Crsk   21 (31)
T d1dsva_           3 GLCPRCKKGYHWKSECKSK   21 (31)
T ss_dssp             CBCTTTCSSBSCTTTCCCS
T ss_pred             ccCccccCcchHHHHhhhh
Confidence            6899999999999999876

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

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

Probab=86.45  E-value=0.51  Score=34.38  Aligned_cols=68  Identities=15%  Similarity=0.213  Sum_probs=44.4

Q ss_pred             eeEEEecCCCceeEECHHHHHHcCCeE----------------------EEEEECCEEEEEE-------------EEEec
Q 040033           89 SPIVLVDSGSTHNFISDTFAKKVKNFI----------------------VNLILQGVYVIVD-------------FNLRE  133 (158)
Q Consensus        89 ~v~aLiDSGat~sfI~~~~a~~~~~~~----------------------A~i~i~g~~~~~~-------------~~v~~  133 (158)
                      ...++||||++..++...++.++--..                      -.+.++|..+.+.             +.+.+
T Consensus       210 ~~~~iiDSGtt~~~lp~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~i~f~f~g~~~~l~~~~y~~~~~~~c~~~i~~  289 (323)
T d3cmsa_         210 GCQAILDTGTSKLVGPSSDILNIQQAIGATQNQYGEFDIDCDNLSYMPTVVFEINGKMYPLTPSAYTSQDQGFCTSGFQS  289 (323)
T ss_dssp             CEEEEECTTCCSEEECHHHHHHHHHHHTCEEETTTEEEECTTCTTTSCCEEEEETTEEEEECHHHHEEEETTEEEESEEE
T ss_pred             CeeEEEecCcceEEecHHHHHHHHHHhCceeccCCceeEeccccCCCCeEEEEECCEEEEECHHHeEEcCCCEEEEEEEe
Confidence            457999999999999999887652111                      1556677665431             22223


Q ss_pred             CCC-CcEEechhHhhhcCCceeeec
Q 040033          134 LEG-YDVVLGTQWLRTLEPILWDFA  157 (158)
Q Consensus       134 ~~~-~dvILG~dwL~~~~~i~idw~  157 (158)
                      ... ...|||..||+.+-- ..|+.
T Consensus       290 ~~~~~~~iLG~~~l~~~yv-vfD~~  313 (323)
T d3cmsa_         290 ENHSQKWILGDVFIREYYS-VFDRA  313 (323)
T ss_dssp             C---CCEEECHHHHTTEEE-EEETT
T ss_pred             CCCCCCEEEcHHhhCcEEE-EEECC
Confidence            332 347999999998764 56664

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

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

Probab=85.78  E-value=1.1  Score=32.62  Aligned_cols=69  Identities=14%  Similarity=0.241  Sum_probs=45.2

Q ss_pred             EeeEEEecCCCceeEECHHHHHHcCCeE------------E----------EEEECCEEEEE------------------
Q 040033           88 ISPIVLVDSGSTHNFISDTFAKKVKNFI------------V----------NLILQGVYVIV------------------  127 (158)
Q Consensus        88 ~~v~aLiDSGat~sfI~~~~a~~~~~~~------------A----------~i~i~g~~~~~------------------  127 (158)
                      ....++||||++..++...++.++--..            .          .+.++|..+.+                  
T Consensus       207 ~~~~~~iDSGt~~~~lp~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~f~~~g~~~~i~p~~y~~~~~~~~~~~C~  286 (329)
T d2bjua1         207 EKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCM  286 (329)
T ss_dssp             EEEEEEECTTCCSEEECHHHHHHHTTTSSCEECTTSSCEEEETTCTTCCCEEEECSSCEEEECHHHHEEECTTTSTTEEE
T ss_pred             cCCcccccccccceeCCHHHHHHHHHHhCCeecCCCCeeEeecccCCCCceeEEeCCEEEEECHHHhEEEeecCCCCEEE
Confidence            3568999999999999999988874332            0          34445544432                  


Q ss_pred             -EEEEecCCCCcEEechhHhhhcCCceeeec
Q 040033          128 -DFNLRELEGYDVVLGTQWLRTLEPILWDFA  157 (158)
Q Consensus       128 -~~~v~~~~~~dvILG~dwL~~~~~i~idw~  157 (158)
                       -|...+......|||..||+.+-- ..|+.
T Consensus       287 ~~i~~~~~~~~~~IlG~~fl~~~y~-vfD~~  316 (329)
T d2bjua1         287 LNIIGLDFPVPTFILGDPFMRKYFT-VFDYD  316 (329)
T ss_dssp             ECEEECCCSSCEEEECHHHHHHEEE-EEETT
T ss_pred             EEEEECCCCCCCEEEchHhhCcEEE-EEECC
Confidence             111122233456999999998764 46664

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

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

Probab=83.67  E-value=1.4  Score=32.97  Aligned_cols=78  Identities=17%  Similarity=0.351  Sum_probs=48.2

Q ss_pred             EEEEEEECC---EeeEEEecCCCceeEECHHHHHHc----CCeE------------------EEEEECCEEEEEE-----
Q 040033           79 LRINGRIGN---ISPIVLVDSGSTHNFISDTFAKKV----KNFI------------------VNLILQGVYVIVD-----  128 (158)
Q Consensus        79 i~~~~~i~~---~~v~aLiDSGat~sfI~~~~a~~~----~~~~------------------A~i~i~g~~~~~~-----  128 (158)
                      +.+.+.+++   ....++||||++..++....++++    +...                  -.+.++|..+.+.     
T Consensus       241 i~l~~~~~~~~~~~~~~iiDTGTs~~~lP~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~P~itf~f~g~~~~l~p~~y~  320 (373)
T d1miqa_         241 IDLDVHFGKQTMEKANVIVDSGTTTITAPSEFLNKFFANLNVIKVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYM  320 (373)
T ss_dssp             EEEEEEETTEEEEEEEEEECTTBSSEEECHHHHHHHHHHHTCEECTTSSCEEEETTCTTCCCEEEECSSCEEEECGGGSE
T ss_pred             EEEEEEECcEecCCcceEeccCCceeccCHHHHHHHHHHhCCeeccCCCeeEeccccCCCceEEEEECCEEEEECHHHee
Confidence            444555554   346799999999999999877664    2222                  0555566655431     


Q ss_pred             ------------EEEe--cCCCCcEEechhHhhhcCCceeeec
Q 040033          129 ------------FNLR--ELEGYDVVLGTQWLRTLEPILWDFA  157 (158)
Q Consensus       129 ------------~~v~--~~~~~dvILG~dwL~~~~~i~idw~  157 (158)
                                  +.+.  +....-.|||..||+.+-- ..|+.
T Consensus       321 ~~~~~~~~~~C~~~~~~~~~~~~~~ILG~~fl~~~y~-vfD~~  362 (373)
T d1miqa_         321 NPILEVDDTLCMITMLPVDIDSNTFILGDPFMRKYFT-VFDYD  362 (373)
T ss_dssp             EESSSSSCSEEEESEEECCSSSSEEEECHHHHHHEEE-EEETT
T ss_pred             EEEEeCCCCEEEEEEEECCCCCCCEEEcHHhhCcEEE-EEECC
Confidence                        1112  2223346999999998764 45653

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

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

Probab=83.30  E-value=0.86  Score=33.31  Aligned_cols=69  Identities=13%  Similarity=0.195  Sum_probs=44.3

Q ss_pred             EeeEEEecCCCceeEECHHHHHHc----CCeE-----------------EEEEECCEEEEEE---------------EEE
Q 040033           88 ISPIVLVDSGSTHNFISDTFAKKV----KNFI-----------------VNLILQGVYVIVD---------------FNL  131 (158)
Q Consensus        88 ~~v~aLiDSGat~sfI~~~~a~~~----~~~~-----------------A~i~i~g~~~~~~---------------~~v  131 (158)
                      ....++||||++..++...+..++    +...                 -.+.++|..+.+.               +..
T Consensus       207 ~~~~~iiDsGts~~~lp~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~P~i~f~f~g~~~~l~~~~y~~~~~~~c~~~i~~  286 (324)
T d1am5a_         207 EGCQAIVDTGTSKIVAPVSALANIMKDIGASENQGEMMGNCASVQSLPDITFTINGVKQPLPPSAYIEGDQAFCTSGLGS  286 (324)
T ss_dssp             CCEEEEECTTCSSEEECTTTHHHHHHHHTCEECCCCEECCTTSSSSSCCEEEEETTEEEEECHHHHEEESSSCEEECEEE
T ss_pred             CCcceeeccCcccccCCHHHHHHHHHHhCCcccCCcccccccccccCCceEEEECCEEEEECHHHhEecCCCeEEEEEEe
Confidence            456799999999999999876653    3322                 1666677666431               122


Q ss_pred             ecC--C-CCcEEechhHhhhcCCceeeec
Q 040033          132 REL--E-GYDVVLGTQWLRTLEPILWDFA  157 (158)
Q Consensus       132 ~~~--~-~~dvILG~dwL~~~~~i~idw~  157 (158)
                      +++  . ..-.|||..||+.+-- ..|+.
T Consensus       287 ~~~~~~~~~~~ILG~~fl~~~y~-vfD~~  314 (324)
T d1am5a_         287 SGVPSNTSELWIFGDVFLRNYYT-IYDRT  314 (324)
T ss_dssp             CCSCCSSSCEEEECHHHHHHEEE-EEETT
T ss_pred             cCcCCCCCCCEEECHHhhcCEEE-EEECC
Confidence            222  1 2335899999998764 45653

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

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

Probab=81.36  E-value=0.83  Score=33.38  Aligned_cols=28  Identities=18%  Similarity=0.188  Sum_probs=23.6

Q ss_pred             eEEEEEEECCEeeEEEecCCCceeEECH
Q 040033           78 TLRINGRIGNISPIVLVDSGSTHNFISD  105 (158)
Q Consensus        78 ~i~~~~~i~~~~v~aLiDSGat~sfI~~  105 (158)
                      -..+++.|++++..++|||||+...|..
T Consensus        16 ~Y~~~i~vG~~~~~v~~DTGSs~~Wv~~   43 (323)
T d1bxoa_          16 EYITPVTIGGTTLNLNFDTGSADLWVFS   43 (323)
T ss_dssp             CEEEEEEETTEEEEEEEETTCCCEEECB
T ss_pred             EEEEEEEECCccEEEEEECCCcceEEEC
Confidence            3566889999999999999999887754