Citrus Sinensis ID: 044180

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130
Protein Sequence
MAAEMQICRAQGLRFNCDEPFNPAIEKIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKLVGAQNIRPKPTQSIHLQSRIFDSP
Secondary Structure (PSIPRED)
cHHHHHHHHHcccEEccccccccccccccEEEEEEEcccEEEEcEEEccEEEEEccEEEEEEEEEEccccccEEEEHHHHHHHccEEEEcccEEEEEEEccEEEEEEEccccccccccHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHcccEEcccccccccccccccEEEEEEcccEEEcccEEccEEEEEEcEEEEEEEEEEEccccHEHHHHHHHHHcccEEEEccEEEEEEEEcccEEEEEccccccccHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MAAEMQICRAqglrfncdepfnPAIEKIMSFLVDVsngeqirseghcskvkfemqgvefeadfhildffGANAVLAVQWLEKLGKIVTDHKALtmeftyrgqpiklvgaqnirpkptqsihlqsrifdsp
Flexible Loop (DISEMBL)
MAAEMQICRAQGLRFNCDEPFNPAIEKIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKlvgaqnirpkptqsihlqsrifdsp
Low Complexity Region (SEG)
MAAEMQICRAQGLRFNCDEPFNPAIEKIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKLVGAQNIRPKPTQSIHLQSRIFDSP
Disordered region (IsUnstruct)
******ICRAQGLRFNCDEPFNPAIEKIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKLVGAQ********************
Disordered Region (DISOPRED)
********RAQGLRFNCDEPFNPAIEKIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKLVG***************SRI****
Disordered Region (DISEMBL)
MAAEMQICRAQGLRFNCDEPFNPAIEKIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKLVGAQNIRPKPTQSIHLQSRIFDSP
Disordered Region (DISPRO)
MAAEMQICRAQGLRFNCDEPFNPAIEKIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKLVGAQNIRPKPTQSIHLQSRIFD**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAAEMQICRAQGLRFNCDEPFNPAIEKIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKLVGAQNIRPKPTQSIHLQSRIFDSP
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	130
147843077	1366	hypothetical protein VITISV_044100 [Viti	0.584	0.055	0.473	8e-12
147774273	1469	hypothetical protein VITISV_026680 [Viti	0.584	0.051	0.473	1e-11
147772855	1308	hypothetical protein VITISV_003711 [Viti	0.776	0.077	0.394	3e-11
170660047	953	polyprotein [Ananas comosus]	0.792	0.108	0.368	4e-11
147773289	1575	hypothetical protein VITISV_003835 [Viti	0.607	0.050	0.430	1e-10
89887334	1359	polyprotein [Primula vulgaris]	0.607	0.058	0.443	1e-10
147789424	2822	hypothetical protein VITISV_017554 [Viti	0.653	0.030	0.426	1e-10
225016150	1261	retrotransposon protein [Glycine max] gi	0.607	0.062	0.430	1e-10
359479937	787	PREDICTED: uncharacterized protein LOC10	0.7	0.115	0.397	3e-10
147842329	522	hypothetical protein VITISV_041623 [Viti	0.692	0.172	0.380	8e-10

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

 Score = 75.1 bits (183), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 47/76 (61%)

Query: 33  VDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKA 92
           V V+NG+ +RSEG C+ V   MQG  +  DF+IL   G + VL VQWL+ LG I+ D   
Sbjct: 373 VKVANGQAVRSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIVLGVQWLQTLGPILWDFSR 432

Query: 93  LTMEFTYRGQPIKLVG 108
           L MEF+   +P KL G
Sbjct: 433 LQMEFSVWDKPRKLQG 448

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 47/76 (61%)

Query: 33  VDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKA 92
           V V+NG+ +RSEG C+ V   MQG  +  DF+IL   G + VL VQWL+ LG I+ D   
Sbjct: 406 VKVANGQAVRSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIVLGVQWLQTLGPILWDFSR 465

Query: 93  LTMEFTYRGQPIKLVG 108
           L MEF+   +P KL G
Sbjct: 466 LQMEFSVWDKPRKLQG 481

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147772855|emb|CAN73669.1| hypothetical protein VITISV_003711 [Vitis vinifera]

 Score = 73.2 bits (178), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 41/104 (39%), Positives = 55/104 (52%), Gaps = 3/104 (2%)

Query: 25  IEKIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLG 84
           ++    F V V+NGE++  +G   K+   +QG EF  DF  +   G + VL +QWLE LG
Sbjct: 262 VKPTTPFTVRVANGERLSCKGKYEKLTVNLQGNEFHLDFFSVPLNGLDMVLGIQWLETLG 321

Query: 85  KIVTDHKALTMEFTYRGQPIKLVGAQNIRPKPTQSIHLQSRIFD 128
            +V D K  TM+F +  QP KL   Q I   P Q   LQ  I D
Sbjct: 322 SVVCDWKKRTMDFIWEQQPKKL---QGIEIPPIQDTTLQGFIKD 362

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|170660047|gb|ACB28472.1| polyprotein [Ananas comosus]

 Score = 72.8 bits (177), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 38/103 (36%), Positives = 59/103 (57%)

Query: 26  EKIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGK 85
           E I +  V V++G ++ S   C   K++MQG+EF+A+  +L   G + VL VQWL++LG 
Sbjct: 49  ENIPAVNVTVADGNKLISSSTCRAFKWKMQGLEFKANLLLLPLRGCDMVLGVQWLKQLGP 108

Query: 86  IVTDHKALTMEFTYRGQPIKLVGAQNIRPKPTQSIHLQSRIFD 128
           I+ D   L MEF ++GQ I L G+     K  +   L+  + D
Sbjct: 109 ILWDFSKLRMEFQFQGQKIVLRGSSGPSLKIIEGKQLKKMVLD 151

Source: Ananas comosus

Species: Ananas comosus

Genus: Ananas

Family: Bromeliaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147773289|emb|CAN64782.1| hypothetical protein VITISV_003835 [Vitis vinifera]

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 47/79 (59%)

Query: 30  SFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTD 89
           SF+V V+NGE +R +G   +V+  +QG  F    + L   G + VL +QWLE LG +  D
Sbjct: 674 SFMVRVANGENLRCQGRFEEVQINLQGTIFSLTLYSLPLTGLDIVLGIQWLELLGSVGCD 733

Query: 90  HKALTMEFTYRGQPIKLVG 108
            + LTMEF +  Q  KLVG
Sbjct: 734 WRELTMEFMWENQTKKLVG 752

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 48/79 (60%)

Query: 33  VDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKA 92
           V ++NG++I+S G C KVK  +Q  +FE DF +L   G + VL V WL +LG I  D K 
Sbjct: 335 VKIANGDKIKSSGTCEKVKLLIQENQFEVDFLLLPLVGYDLVLGVHWLSQLGVINCDFKN 394

Query: 93  LTMEFTYRGQPIKLVGAQN 111
           LTM FT+  + + L G  N
Sbjct: 395 LTMTFTHGNKKVCLKGLNN 413

Source: Primula vulgaris

Species: Primula vulgaris

Genus: Primula

Family: Primulaceae

Order: Ericales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 71.2 bits (173), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 38/89 (42%), Positives = 49/89 (55%), Gaps = 4/89 (4%)

Query: 20  PFNPAIEKIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQW 79
           P NP         V V+NG+ + SEG C+ V   MQG  +  DF+IL   G + VL VQW
Sbjct: 362 PSNPT----EGLSVKVANGQAVCSEGSCAAVPLHMQGNLYTIDFYILTLGGCDIVLGVQW 417

Query: 80  LEKLGKIVTDHKALTMEFTYRGQPIKLVG 108
           L+ LG I+ D   L MEF+   +P KL G
Sbjct: 418 LQTLGPILWDFSRLQMEFSVWDKPQKLQG 446

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225016150|gb|ACN78974.1| retrotransposon protein [Glycine max] gi|225016158|gb|ACN78981.1| retrotransposon protein [Glycine max]

 Score = 71.2 bits (173), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 34/79 (43%), Positives = 49/79 (62%)

Query: 33  VDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKA 92
           V V NGE+++    C +V   +Q   F  DFHIL   GA+ VL VQWL+ LG ++TD+  
Sbjct: 458 VTVGNGEELQCNQVCPEVAVHIQAHTFLVDFHILPICGADVVLGVQWLKSLGPVLTDYAT 517

Query: 93  LTMEFTYRGQPIKLVGAQN 111
           LTM+F Y  + I+L G ++
Sbjct: 518 LTMKFIYNDKLIELKGDRD 536

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 69.7 bits (169), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 37/93 (39%), Positives = 54/93 (58%), Gaps = 2/93 (2%)

Query: 30  SFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTD 89
           +F V V+NGE+++ +G   KV+ E+QG EF      L   G + VL VQWLE LG +V +
Sbjct: 373 TFPVWVANGERLKCQGRYDKVRVELQGTEFYLTLFSLPLSGLDLVLGVQWLEMLGSVVCN 432

Query: 90  HKALTMEFTYRGQPIKLVG--AQNIRPKPTQSI 120
            K LTM+F +  Q  +L G   Q I+   ++ I
Sbjct: 433 WKQLTMDFIWENQDRRLQGVDVQTIQSASSEEI 465

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147842329|emb|CAN76208.1| hypothetical protein VITISV_041623 [Vitis vinifera]

 Score = 68.6 bits (166), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 35/92 (38%), Positives = 54/92 (58%), Gaps = 2/92 (2%)

Query: 31  FLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDH 90
           F V V+NG+ ++ +G    +   +QG+ F   F+ L   G + VL VQWLE+LG +V D 
Sbjct: 362 FHVRVANGQPLKCQGRFDNIHILLQGIPFSITFYSLPLNGLDLVLGVQWLEQLGSVVCDW 421

Query: 91  KALTMEFTYRGQPIKLVG--AQNIRPKPTQSI 120
           K +TMEF +  +P  L G  AQN++    ++I
Sbjct: 422 KQMTMEFQWANKPRLLQGSRAQNLQQASLEAI 453

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00029562001 SubName- Full=Chromosome chr9 scaffold_49, whole genome shotgun sequence; (219 aa) (Vitis vinifera)

Predicted Functional Partners:

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

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	130
cd00303	92	cd00303, retropepsin_like, Retropepsins; pepsin-li	4e-07

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

 Score = 44.6 bits (106), Expect = 4e-07
 Identities = 14/45 (31%), Positives = 22/45 (48%)

Query: 37 NGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLE 81
          NG  +++ G    V   + G  F  DF++LD    + +L   WLE
Sbjct: 48 NGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDVILGRPWLE 92

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	130
PF08284	135	RVP_2: Retroviral aspartyl protease; InterPro: IPR	99.83
cd05479	124	RP_DDI RP_DDI; retropepsin-like domain of DNA dama	99.53
cd05484	91	retropepsin_like_LTR_2 Retropepsins_like_LTR, peps	98.93
PF02160	201	Peptidase_A3: Cauliflower mosaic virus peptidase (	98.2
cd00303	92	retropepsin_like Retropepsins; pepsin-like asparta	98.16
TIGR03698	107	clan_AA_DTGF clan AA aspartic protease, AF_0612 fa	97.84
PF09668	124	Asp_protease: Aspartyl protease; InterPro: IPR0191	97.59
PF00077	100	RVP: Retroviral aspartyl protease The Prosite entr	97.4
cd05483	96	retropepsin_like_bacteria Bacterial aspartate prot	97.29
PF13650	90	Asp_protease_2: Aspartyl protease	97.28
TIGR02281	121	clan_AA_DTGA clan AA aspartic protease, TIGR02281	96.97
cd05480	103	NRIP_C NRIP_C; putative nuclear receptor interacti	96.32
cd06094	89	RP_Saci_like RP_Saci_like, retropepsin family. Ret	96.03
cd06095	86	RP_RTVL_H_like Retropepsin of the RTVL_H family of	95.43
COG5550	125	Predicted aspartyl protease [Posttranslational mod	94.51
cd05481	93	retropepsin_like_LTR_1 Retropepsins_like_LTR; peps	91.9
KOG0012	380	consensus DNA damage inducible protein [Replicatio	91.13
PF12384	177	Peptidase_A2B: Ty3 transposon peptidase; InterPro:	89.07

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

Probab=99.83  E-value=5.9e-21  Score=139.86  Aligned_cols=70  Identities=33%  Similarity=0.593  Sum_probs=64.2

Q ss_pred             CceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEEEEEeC
Q 044180           29 MSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYR  100 (130)
Q Consensus        29 ~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~~  100 (130)
                      .++.|. ++|+.+.|.+.|++++|.+||++|..||++|++++||||||||||++|+| .|||.+++++|+..
T Consensus        63 ~~~~V~-~~g~~~~~~~~~~~~~~~i~g~~~~~dl~vl~l~~~DvILGm~WL~~~~~-~IDw~~k~v~f~~p  132 (135)
T PF08284_consen   63 RPIVVS-APGGSINCEGVCPDVPLSIQGHEFVVDLLVLDLGGYDVILGMDWLKKHNP-VIDWATKTVTFNSP  132 (135)
T ss_pred             CeeEEe-cccccccccceeeeEEEEECCeEEEeeeEEecccceeeEeccchHHhCCC-EEEccCCEEEEeCC
Confidence            345555 67888999999999999999999999999999999999999999999999 89999999999843

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=99.53  E-value=2.1e-14  Score=103.15  Aligned_cols=68  Identities=12%  Similarity=0.133  Sum_probs=61.9

Q ss_pred             CceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEEEE
Q 044180           29 MSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEF   97 (130)
Q Consensus        29 ~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f   97 (130)
                      .++.+++++++...+.+.|..++++++|.+|..+|.++|+.++|+|||||||++++ +.|||++++|+|
T Consensus        57 ~~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~~~~~Vl~~~~~d~ILG~d~L~~~~-~~ID~~~~~i~~  124 (124)
T cd05479          57 KRFQGIAKGVGTQKILGRIHLAQVKIGNLFLPCSFTVLEDDDVDFLIGLDMLKRHQ-CVIDLKENVLRI  124 (124)
T ss_pred             cceEEEEecCCCcEEEeEEEEEEEEECCEEeeeEEEEECCCCcCEEecHHHHHhCC-eEEECCCCEEEC
Confidence            35677888766688899999999999999999999999999999999999999999 599999999975

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=98.93  E-value=2.4e-09  Score=72.42  Aligned_cols=53  Identities=15%  Similarity=0.207  Sum_probs=49.5

Q ss_pred             ccCceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchh
Q 044180           27 KIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLE   81 (130)
Q Consensus        27 ~~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~   81 (130)
                      +....+|..|||+.+.+.+.| .+++.++|.+|..+++|++.. +|.|||+|||+
T Consensus        39 ~~~~~~v~~a~G~~~~~~G~~-~~~v~~~~~~~~~~~~v~~~~-~~~lLG~~wl~   91 (91)
T cd05484          39 KPTKKRLRTATGTKLSVLGQI-LVTVKYGGKTKVLTLYVVKNE-GLNLLGRDWLD   91 (91)
T ss_pred             ccccEEEEecCCCEeeEeEEE-EEEEEECCEEEEEEEEEEECC-CCCccChhhcC
Confidence            345689999999999999999 899999999999999999999 99999999985

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

>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=98.20  E-value=1e-05  Score=63.36  Aligned_cols=76  Identities=16%  Similarity=0.240  Sum_probs=65.5

Q ss_pred             ccCceeEEeeCCCeEeecceeeccEEeecCEEEEceeE-EeecCCcceeecccchhccCceEEeccccEEEEEeCC-eEE
Q 044180           27 KIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFH-ILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRG-QPI  104 (130)
Q Consensus        27 ~~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~-vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~~g-~~I  104 (130)
                      ...++.|+.|||+......+|++..++|.|+.|...++ ..+ .|.|+|||+.+|+.+.|. +.|.. +++|+..+ ..+
T Consensus        47 ~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~IP~iYq~~-~g~d~IlG~NF~r~y~Pf-iq~~~-~I~f~~~~~~~~  123 (201)
T PF02160_consen   47 SKKPIKVKGANGSIIQINKKAKNGKIQIADKIFRIPTIYQQE-SGIDIILGNNFLRLYEPF-IQTED-RIQFHKKGLQKV  123 (201)
T ss_pred             CCCcEEEEEecCCceEEEEEecCceEEEccEEEeccEEEEec-CCCCEEecchHHHhcCCc-EEEcc-EEEEEeCCccee
Confidence            34468999999999999999999999999999998776 566 689999999999999994 88864 79999877 444


Q ss_pred             E
Q 044180          105 K  105 (130)
Q Consensus       105 ~  105 (130)
                      .
T Consensus       124 ~  124 (201)
T PF02160_consen  124 E  124 (201)
T ss_pred             e
Confidence            3

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

>cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases

Probab=98.16  E-value=8.2e-06  Score=50.33  Aligned_cols=54  Identities=28%  Similarity=0.525  Sum_probs=47.5

Q ss_pred             cCceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchh
Q 044180           28 IMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLE   81 (130)
Q Consensus        28 ~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~   81 (130)
                      ..+..+..++|......+.+..+.+.+++..+...+++.+..++|+|||++||.
T Consensus        39 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~ilG~~~l~   92 (92)
T cd00303          39 PTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDVILGRPWLE   92 (92)
T ss_pred             CCceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcCCCcCEEecccccC
Confidence            345677888888888888888999999999999999999999999999999984

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

>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family

Probab=97.84  E-value=4.4e-05  Score=53.65  Aligned_cols=63  Identities=24%  Similarity=0.388  Sum_probs=47.8

Q ss_pred             CceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEE
Q 044180           29 MSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTM   95 (130)
Q Consensus        29 ~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl   95 (130)
                      ...+|..|||.......  .-..+.++|.+....+.+.+... ++.|||.||++++ +.+||++..|
T Consensus        45 ~~~~~~tA~G~~~~~~v--~~~~v~igg~~~~~~v~~~~~~~-~~LLG~~~L~~l~-l~id~~~~~~  107 (107)
T TIGR03698        45 DQRRVYLADGREVLTDV--AKASIIINGLEIDAFVESLGYVD-EPLLGTELLEGLG-IVIDYRNQGL  107 (107)
T ss_pred             cCcEEEecCCcEEEEEE--EEEEEEECCEEEEEEEEecCCCC-ccEecHHHHhhCC-EEEehhhCcC
Confidence            35689999998766553  46677889998855544445545 8999999999997 5899998754

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.

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

Probab=97.59  E-value=0.00014  Score=52.96  Aligned_cols=50  Identities=18%  Similarity=0.320  Sum_probs=42.5

Q ss_pred             CeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEe
Q 044180           39 EQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTD   89 (130)
Q Consensus        39 ~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD   89 (130)
                      +.-...|....+++++++..|+..|.|+|-...|++||.|||.+|.. .||
T Consensus        75 G~~~i~G~Ih~~~l~ig~~~~~~s~~Vle~~~~d~llGld~L~~~~c-~ID  124 (124)
T PF09668_consen   75 GTQKILGRIHSVQLKIGGLFFPCSFTVLEDQDVDLLLGLDMLKRHKC-CID  124 (124)
T ss_dssp             ---EEEEEEEEEEEEETTEEEEEEEEEETTSSSSEEEEHHHHHHTT--EEE
T ss_pred             CcCceeEEEEEEEEEECCEEEEEEEEEeCCCCcceeeeHHHHHHhCc-ccC
Confidence            55567778999999999999999999999889999999999999976 565

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

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

Probab=97.40  E-value=0.00028  Score=47.76  Aligned_cols=55  Identities=25%  Similarity=0.392  Sum_probs=45.3

Q ss_pred             cCceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCc
Q 044180           28 IMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGK   85 (130)
Q Consensus        28 ~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~   85 (130)
                      .....|.-++|.. ...+. ..+.+.+.+..|...+++.+-..+| |||.|||.+++.
T Consensus        43 ~~~~~v~~~~g~~-~~~~~-~~~~v~~~~~~~~~~~~v~~~~~~~-ILG~D~L~~~~~   97 (100)
T PF00077_consen   43 KTSITVRGAGGSS-SILGS-TTVEVKIGGKEFNHTFLVVPDLPMN-ILGRDFLKKLNA   97 (100)
T ss_dssp             EEEEEEEETTEEE-EEEEE-EEEEEEETTEEEEEEEEESSTCSSE-EEEHHHHTTTTC
T ss_pred             cCCceeccCCCcc-eeeeE-EEEEEEEECccceEEEEecCCCCCC-EeChhHHHHcCC
Confidence            3445666677776 66665 5889999999999999999988888 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 ....

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

Probab=97.29  E-value=0.00059  Score=44.83  Aligned_cols=53  Identities=13%  Similarity=0.150  Sum_probs=43.5

Q ss_pred             ccCceeEEeeCCCeEeecceeeccEEeecCEEEE-ceeEEeecCC--cceeecccchh
Q 044180           27 KIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFE-ADFHILDFFG--ANAVLAVQWLE   81 (130)
Q Consensus        27 ~~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~-~dl~vL~l~g--~DvILGmdWL~   81 (130)
                      .....++..++|........  -.++++++..|. ..+.++|...  .|.|||+|||.
T Consensus        41 ~~~~~~~~~~~G~~~~~~~~--~~~i~ig~~~~~~~~~~v~d~~~~~~~gIlG~d~l~   96 (96)
T cd05483          41 LGGKVTVQTANGRVRAARVR--LDSLQIGGITLRNVPAVVLPGDALGVDGLLGMDFLR   96 (96)
T ss_pred             CCCcEEEEecCCCccceEEE--cceEEECCcEEeccEEEEeCCcccCCceEeChHHhC
Confidence            34567888899998877666  446789999998 5899999997  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.

>PF13650 Asp_protease_2: Aspartyl protease

Probab=97.28  E-value=0.0011  Score=43.11  Aligned_cols=48  Identities=15%  Similarity=0.305  Sum_probs=38.5

Q ss_pred             ceeEEeeCCCeEeecceeeccEEeecCEEE-EceeEEee-cCCcceeecccc
Q 044180           30 SFLVDVSNGEQIRSEGHCSKVKFEMQGVEF-EADFHILD-FFGANAVLAVQW   79 (130)
Q Consensus        30 ~~~V~vanG~~l~~~~~c~~~~~~iqg~~f-~~dl~vL~-l~g~DvILGmdW   79 (130)
                      +..+..++|.........+  ++++++..+ ..++.+.+ -..+|.||||||
T Consensus        41 ~~~~~~~~g~~~~~~~~~~--~i~ig~~~~~~~~~~v~~~~~~~~~iLG~df   90 (90)
T PF13650_consen   41 PISVSGAGGSVTVYRGRVD--SITIGGITLKNVPFLVVDLGDPIDGILGMDF   90 (90)
T ss_pred             eEEEEeCCCCEEEEEEEEE--EEEECCEEEEeEEEEEECCCCCCEEEeCCcC
Confidence            4778889998555444544  788999998 67888999 678999999998

>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family

Probab=96.97  E-value=0.0035  Score=44.84  Aligned_cols=64  Identities=14%  Similarity=0.280  Sum_probs=48.3

Q ss_pred             ceeEEeeCCCeEeecceeeccEEeecCEEEE-ceeEEeecCC-cceeecccchhccCceEEeccccEE
Q 044180           30 SFLVDVSNGEQIRSEGHCSKVKFEMQGVEFE-ADFHILDFFG-ANAVLAVQWLEKLGKIVTDHKALTM   95 (130)
Q Consensus        30 ~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~-~dl~vL~l~g-~DvILGmdWL~~~g~i~iD~~~~tl   95 (130)
                      +..+..|||.....  ...--++++.+..+. .++.++|.+. .|.+||||+|.++.++.+|-.+.+|
T Consensus        54 ~~~~~ta~G~~~~~--~~~l~~l~iG~~~~~nv~~~v~~~~~~~~~LLGm~fL~~~~~~~~~~~~l~l  119 (121)
T TIGR02281        54 TVTVSTANGQIKAA--RVTLDRVAIGGIVVNDVDAMVAEGGALSESLLGMSFLNRLSRFTVRGGKLIL  119 (121)
T ss_pred             eEEEEeCCCcEEEE--EEEeCEEEECCEEEeCcEEEEeCCCcCCceEcCHHHHhccccEEEECCEEEE
Confidence            56788899976432  335556789999988 7888999874 5899999999999877777655444

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

>cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein

Probab=96.32  E-value=0.0098  Score=42.11  Aligned_cols=54  Identities=17%  Similarity=0.225  Sum_probs=47.4

Q ss_pred             CCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccc
Q 044180           38 GEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKA   92 (130)
Q Consensus        38 G~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~   92 (130)
                      |....-.|....++++|++..++-.|.|||-...|++||.|=|.+|.. .||.++
T Consensus        50 gt~~kiiGrih~~~ikig~~~~~CSftVld~~~~d~llGLdmLkrhqc-~IdL~k  103 (103)
T cd05480          50 PTSVKVIGQIERLVLQLGQLTVECSAQVVDDNEKNFSLGLQTLKSLKC-VINLEK  103 (103)
T ss_pred             CcceeEeeEEEEEEEEeCCEEeeEEEEEEcCCCcceEeeHHHHhhcce-eeeccC
Confidence            444567788899999999999999999999999999999999999977 788653

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.

>cd06094 RP_Saci_like RP_Saci_like, retropepsin family

Probab=96.03  E-value=0.017  Score=39.93  Aligned_cols=55  Identities=20%  Similarity=0.391  Sum_probs=47.6

Q ss_pred             ccCceeEEeeCCCeEeecceeeccEEeecCE-EEEceeEEeecCCcceeecccchhccC
Q 044180           27 KIMSFLVDVSNGEQIRSEGHCSKVKFEMQGV-EFEADFHILDFFGANAVLAVQWLEKLG   84 (130)
Q Consensus        27 ~~~~~~V~vanG~~l~~~~~c~~~~~~iqg~-~f~~dl~vL~l~g~DvILGmdWL~~~g   84 (130)
                      +..++.++.|||..|..-|. ..+.+.++.. .|.-+|.|=|+.  .-|||+|.|..|+
T Consensus        33 ~~~~~~l~AANgt~I~tyG~-~~l~ldlGlrr~~~w~FvvAdv~--~pIlGaDfL~~~~   88 (89)
T cd06094          33 KPSPLTLQAANGTPIATYGT-RSLTLDLGLRRPFAWNFVVADVP--HPILGADFLQHYG   88 (89)
T ss_pred             cCCceEEEeCCCCeEeeeee-EEEEEEcCCCcEEeEEEEEcCCC--cceecHHHHHHcC
Confidence            45678999999999999995 8888888875 999999998886  4799999999886

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

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

Probab=95.43  E-value=0.043  Score=36.57  Aligned_cols=52  Identities=13%  Similarity=0.206  Sum_probs=36.5

Q ss_pred             cCceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchh
Q 044180           28 IMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLE   81 (130)
Q Consensus        28 ~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~   81 (130)
                      ..+..|.-++|..-.......+ .+.+.+.++..++.+.+- ..|.|||||+|.
T Consensus        35 ~~~~~v~gagG~~~~~v~~~~~-~v~vg~~~~~~~~~v~~~-~~~~lLG~dfL~   86 (86)
T cd06095          35 TTSVLIRGVSGQSQQPVTTYRT-LVDLGGHTVSHSFLVVPN-CPDPLLGRDLLS   86 (86)
T ss_pred             CCcEEEEeCCCcccccEEEeee-EEEECCEEEEEEEEEEcC-CCCcEechhhcC
Confidence            3467788888886111111222 688999999998888773 469999999984

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

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

Probab=94.51  E-value=0.077  Score=38.79  Aligned_cols=63  Identities=21%  Similarity=0.295  Sum_probs=49.9

Q ss_pred             ceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEEE
Q 044180           30 SFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTME   96 (130)
Q Consensus        30 ~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~   96 (130)
                      ..++..++|+.+.+.  .....++++|.+..+-....+....+ ++|++||+.+|- .+|.+.-.++
T Consensus        56 ~~~~~~a~~~~v~t~--V~~~~iki~g~e~~~~Vl~s~~~~~~-liG~~~lk~l~~-~vn~~~g~LE  118 (125)
T COG5550          56 TIRIVLADGGVVKTS--VALATIKIDGVEKVAFVLASDNLPEP-LIGVNLLKLLGL-VVNPKTGKLE  118 (125)
T ss_pred             ChhhhhhcCCEEEEE--EEEEEEEECCEEEEEEEEccCCCccc-chhhhhhhhccE-EEcCCcceEe
Confidence            456778888876654  34667789999998888888888888 999999999976 8998665554

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

Probab=91.90  E-value=0.6  Score=31.78  Aligned_cols=49  Identities=18%  Similarity=0.314  Sum_probs=41.6

Q ss_pred             ccCceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecc
Q 044180           27 KIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAV   77 (130)
Q Consensus        27 ~~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGm   77 (130)
                      +.+++.++.+||..+...|. ..+++.+++..+..+|+|+|..+-. |||.
T Consensus        41 ~~t~~~L~~~~g~~~~~~G~-~~~~v~~~~~~~~~~f~Vvd~~~~~-lLG~   89 (93)
T cd05481          41 RPSPVRLTAYGGSTIPVEGG-VKLKCRYRNPKYNLTFQVVKEEGPP-LLGA   89 (93)
T ss_pred             ccCCeEEEeeCCCEeeeeEE-EEEEEEECCcEEEEEEEEECCCCCc-eEcc
Confidence            45678999999999999999 6899999999999999999986544 4454

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

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

Probab=91.13  E-value=0.29  Score=41.69  Aligned_cols=62  Identities=13%  Similarity=0.212  Sum_probs=56.3

Q ss_pred             eEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEEEEEeCCe
Q 044180           40 QIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQ  102 (130)
Q Consensus        40 ~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~~g~  102 (130)
                      ...-.|.+..++++|+...++-.|-|++-...|+-||.|=|.+|+. -||.++..|.|...+.
T Consensus       287 ~~ki~g~Ih~~~lki~~~~l~c~ftV~d~~~~d~llGLd~Lrr~~c-cIdL~~~~L~ig~~~t  348 (380)
T KOG0012|consen  287 TEKILGRIHQAQLKIEDLYLPCSFTVLDRRDMDLLLGLDMLRRHQC-CIDLKTNVLRIGNTET  348 (380)
T ss_pred             cccccceeEEEEEEeccEeeccceEEecCCCcchhhhHHHHHhccc-eeecccCeEEecCCCc
Confidence            4555778899999999999999999999999999999999999998 7999999999876655

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

Probab=89.07  E-value=1.2  Score=34.37  Aligned_cols=58  Identities=10%  Similarity=0.129  Sum_probs=45.5

Q ss_pred             ccCceeEEeeC-CCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCc
Q 044180           27 KIMSFLVDVSN-GEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGK   85 (130)
Q Consensus        27 ~~~~~~V~van-G~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~   85 (130)
                      .+++++++-+- ++...|... ..+++.+++..|...++|+|--++|+|+|..-|.++..
T Consensus        73 ~app~~fRG~vs~~~~~tsEA-v~ld~~i~n~~i~i~aYV~d~m~~dlIIGnPiL~ryp~  131 (177)
T PF12384_consen   73 DAPPFRFRGFVSGESATTSEA-VTLDFYIDNKLIDIAAYVTDNMDHDLIIGNPILDRYPT  131 (177)
T ss_pred             cCCCEEEeeeccCCceEEEEe-EEEEEEECCeEEEEEEEEeccCCcceEeccHHHhhhHH
Confidence            46777777333 333444443 67899999999999999999999999999999988763

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 [].

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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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	130
3s8i_A	148	Protein DDI1 homolog 1; protease, structural genom	99.34
2i1a_A	148	DNA damage-inducible protein DDI1; acid protease f	98.93
3slz_A	132	GAG-Pro-POL polyprotein; beta sheet and dimer, pro	95.15
1fmb_A	104	EIAV protease; hydrolase (acid proteinase), RNA-di	91.89
3ec0_A	99	Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1	90.98
2hs1_A	99	HIV-1 protease; ultra-high resolution active site	89.58

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

Probab=99.34  E-value=8.9e-13  Score=96.80  Aligned_cols=80  Identities=14%  Similarity=0.138  Sum_probs=65.9

Q ss_pred             eEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEEEEEeCCeEEEEEeccC
Q 044180           32 LVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKLVGAQN  111 (130)
Q Consensus        32 ~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~~g~~I~l~G~~~  111 (130)
                      .+.++..+...+.+.++.++++|++..|..++.|+|...+|+|||||||.+++. .|||++++|+|...++.|.+-+..+
T Consensus        68 ~~~a~g~G~~~~~g~v~~~~I~Ig~~~~~~~~~Vle~~~~d~LLGmD~L~~~~~-~ID~~~~~L~l~~~~~~~pfl~~~~  146 (148)
T 3s8i_A           68 AGVAKGVGTQRIIGRVHLAQIQIEGDFLQCSFSILEDQPMDMLLGLDMLRRHQC-SIDLKKNVLVIGTTGTQTYFLPEGE  146 (148)
T ss_dssp             CEECCC---CEEEEEEEEEEEEETTEEEEEEEEEETTCSSSEEECHHHHHHTTC-EEETTTTEEECTTTCCEEECCCGGG
T ss_pred             eEEEEcCCccEEEEEEEEEEEEECCEEEEEEEEEeCCCCcCeeccHHHHHhCCE-EEEcCCCEEEEccCCeEEeecCccc
Confidence            344444345567778999999999999999999999999999999999999986 9999999999987778888766544


Q ss_pred             C
Q 044180          112 I  112 (130)
Q Consensus       112 ~  112 (130)
                      +
T Consensus       147 ~  147 (148)
T 3s8i_A          147 L  147 (148)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=98.93  E-value=1.6e-09  Score=77.82  Aligned_cols=63  Identities=11%  Similarity=0.226  Sum_probs=54.0

Q ss_pred             cceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEEEEEeCCeEEEEEecc
Q 044180           44 EGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKLVGAQ  110 (130)
Q Consensus        44 ~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~~g~~I~l~G~~  110 (130)
                      .+.+...++++++..|..++.++| .++|+|||||||++++. .+||++++|+|.  ++.+.+....
T Consensus        82 ~~~~~~~~i~ig~~~~~~~~~vl~-~~~d~iLG~d~L~~~~~-~ID~~~~~l~l~--~~~~~f~~~~  144 (148)
T 2i1a_A           82 IGRIHQAQVKIETQYIPCSFTVLD-TDIDVLIGLDMLKRHLA-CVDLKENVLRIA--EVETSFLSEA  144 (148)
T ss_dssp             CEEEEEEEEEETTEEEEEEEEEEC-SSCSEEECHHHHHHTTC-EEETTTTEEEET--TEEEECCCTT
T ss_pred             ccEEEEEEEEECCEEeceeEEEec-CCCCeEecHHHHhhCCE-EEECCCCEEEEc--cEEEecCChh
Confidence            556677799999999999999999 78999999999999976 999999999986  4666665443

>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=95.15  E-value=0.017  Score=41.34  Aligned_cols=58  Identities=17%  Similarity=0.107  Sum_probs=38.7

Q ss_pred             ceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEecc
Q 044180           30 SFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHK   91 (130)
Q Consensus        30 ~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~   91 (130)
                      +..|.-++|. +. ......+++++.|..+...+.+++- ...-|||+|||.++|. ++|+.
T Consensus        58 p~~I~GiGG~-i~-vr~~~~i~IeI~g~~~~~~~lV~~~-tPvnLLGrd~Ltqlg~-tL~fp  115 (132)
T 3slz_A           58 SAWVQGATGG-KR-YRWTTDRKVHLATGKVTHSFLHVPD-CPYPLLGRDLLTKLKA-QIHFE  115 (132)
T ss_dssp             EEEEECSSCE-EE-EEEECCEEEEETTEEEEECCEECTT-SSSCEECHHHHHHHTC-EEEEE
T ss_pred             ceEEEccCCE-EE-EEEEeeeEEEECCeeecceEEEECC-CCccEECHhhHhhCCc-EEECC
Confidence            3445445554 44 3333567899999998887765422 2357899999999988 55543

>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=91.89  E-value=0.15  Score=34.82  Aligned_cols=54  Identities=15%  Similarity=0.173  Sum_probs=43.8

Q ss_pred             eEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEec
Q 044180           32 LVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDH   90 (130)
Q Consensus        32 ~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~   90 (130)
                      ....+.|+.+...  ..++++++.|+.....+++-|.  ..=|+|-|||.++|. ++||
T Consensus        51 ~~i~GiGG~i~v~--~~~i~i~i~g~~~~gtvlv~~t--p~niiGRd~L~qlg~-tLnf  104 (104)
T 1fmb_A           51 TGIGGVGGNVETF--STPVTIKKKGRHIKTRMLVADI--PVTILGRDILQDLGA-KLVL  104 (104)
T ss_dssp             CCEEETTEEECCE--EEEEEEEETTEEEEEEEEEESC--SSCEECHHHHHHTTC-CCCC
T ss_pred             cEEEeCCCeEEee--EeeeEEEECCeEEEEEEEECCC--CCCEecHhHHhhcCc-EEeC
Confidence            5567889998888  6999999999999888877553  356899999999987 4543

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

Probab=90.98  E-value=0.63  Score=31.65  Aligned_cols=55  Identities=16%  Similarity=0.111  Sum_probs=44.0

Q ss_pred             eEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEec
Q 044180           32 LVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDH   90 (130)
Q Consensus        32 ~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~   90 (130)
                      .+..+.|+.+...+. .+++|++.|+.....++|=|.. . =|+|-|+|.++|. +++|
T Consensus        45 k~igGiGG~i~v~qy-~~i~iei~g~~~~gtvlV~~tP-v-niiGRnlLtqlG~-tLnf   99 (99)
T 3ec0_A           45 KIVGGIGGFINTKEY-KNVEIEVLNKKVRATIMTGDTP-I-NIFGRNILTALGM-SLNL   99 (99)
T ss_dssp             EEEEETTEEEEEEEE-EEEEEEETTEEEEEEEEEECCS-S-CEECHHHHHHHTC-EEEC
T ss_pred             eEEEecCCcEeeeEE-eeEEEEECCeEEEEEEEeCCCC-c-CeeehhhHhhcCc-EEeC
Confidence            367888999998884 8899999999988888774432 2 4789999999987 5654

>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=89.58  E-value=0.98  Score=30.60  Aligned_cols=55  Identities=11%  Similarity=0.105  Sum_probs=43.7

Q ss_pred             eEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEec
Q 044180           32 LVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDH   90 (130)
Q Consensus        32 ~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~   90 (130)
                      .+..+.|+.+...+. .++++++.|+.....++|-|.. . =|+|-|||.++|. ++||
T Consensus        45 k~igGiGG~i~v~qy-~qi~iei~g~~~~gtvlV~~tP-v-niiGRd~Ltqlg~-tLnf   99 (99)
T 2hs1_A           45 KMIGGIGGFIKVRQY-DQIIIEIAGHKAIGTVLVGPTP-V-NIIGRNLLTQIGA-TLNF   99 (99)
T ss_dssp             EEEEETTEEEEEEEE-EEEEEEETTEEEEEEEEESCCS-S-CEECHHHHTTTTC-EEEC
T ss_pred             cEEEeCCCcEeeeEe-ccEEEEEeCCEEEEEEEeCCCc-c-CchhHhHHHHcCC-EEeC
Confidence            466778888887754 7999999999999999885543 3 3789999999987 5654

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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

No hit with probability above 80.00