YRC Public Data Repository - Protein Structure Prediction

Protein:	ubp13
Organism:	Schizosaccharomyces pombe
Length:	1115 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for ubp13.

Description	E-value	Query Range	Subject Range
PAN2_RAT - PAB-dependent poly(A)-specific ribonuclease subunit PAN2 OS=Rattus norvegicus GN=Pan2 PE=2 SV=1	529.0	[0..20]	[1108..75]
gi\|51259008 - gi\|51259008\|gb\|AAH79841.1\| Usp52 protein [Mus musculus]	527.0	[0..20]	[1097..75]
gi\|73968387 - gi\|73968387\|ref\|XP_857120.1\| PREDICTED: similar to ubiquitin specific protease 52 isoform 6 [Canis f...	524.0	[0..20]	[1097..75]
gi\|119892450, gi... - gi\|76618633\|ref\|XP_870733.1\| PREDICTED: similar to ubiquitin specific protease 52 isoform 3 [Bos tau...	522.0	[0..20]	[1097..75]
PAN2_EMENI - PAB-dependent poly(A)-specific ribonuclease subunit pan2 OS=Emericella nidulans GN=pan2 PE=3 SV=1 PAN2_EMENI - PAB-dependent poly(A)-specific ribonuclease subunit pan2 OS=Emericella nidulans (strain FGSC A4 / AT...	520.0	[0..2]	[1114..3]
gi\|38453757, gi\|... - gi\|38453757\|dbj\|BAD02263.1\| PABP1-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2 [Homo sapiens...	517.0	[0..20]	[1097..75]

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Predicted Domain #1

Region A:
Residues: [1-184]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDAWKEITKT TENDGVSTCS LSSIAFDPYS ELVWTGHKNG QIKSSFGPSL TSYTQFIGHE  60
   61 GPVHQVLPQE RGVFSLSSKS LRLSNRKGTI RWRYHSVPCV QRSMIILYSC FLCSKHAVLI 120
  121 SRDSDCIDYR AMFYQSRNNP EVVIGGYHQK LTVVNAERGI SIHKDKNVSD IFIMRRNRLL 180
  181 CCGS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	72.69897
Match:	1vyhC
Description:	PAF-AH Holoenzyme: Lis1/Alfa2
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [185-376]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TNGEIILRDP NSFQPVNKVV AHTGTISDID TSGNLLLSCG YSLRHGTYML DPFVKVWDLR  60
   61 NLSSLVPIPF PAGPTIIRMH PKLSTTAVVC SCSGQFHIVD TGNPLDAKLM QIPLTSYLTG 120
  121 MDIASTGDAM VFTDVEDNIH LWSPLENPSF SDLKLPIQLP NTSTETVQLE NNDPLNSIGL 180
  181 PYYKDELLSS WS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	4.522879
Match:	1z68A
Description:	Crystal Structure Of Human Fibroblast Activation Protein alpha
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [377-884]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KYLIFDVGKP ILDSNLLIAK QISENSHPVP QEIKSFHRNQ IIEVPWLNRK LISEGATPKF  60
   61 HSERQKDIMS GNDIEGSASY FEEIEDTISG PDSIPKFYQR PVIKYSKFGI EDFDFGFYNK 120
  121 TKYAGLETDI TNSYCNSVLQ LLSYVPSFSK AAISHSLGPC DLMECLLCEL GFLFAMLKES 180
  181 TGRNCQATNF LRAFSNSSFA QSLGIVFDDY SDGTFPDSFV IQKFTKFMLT EISRIADYED 240
  241 KKDGTSFPVS FLLKSFCIPE MQTYRCGICG ITSQKIKSSL YIIDLHYPSQ QLESILSFEW 300
  301 LFKMSLDRRV DLPPGWCEYC LAHQPFLLRS FIRSLPDCLF INTQVKHHEH WKLWARKNWL 360
  361 PKKLHLRRVN DTMQCVSQKI SNLDKDQQSL SVYVLRGIIY EIRQNGEEPH FVSTIRVSDN 420
  421 TSSDNPDDNR WYIFNDFLVK EVTEEEALTV HGPWKIPIIV YYEKLDTKIP QWDEVSDYTL 480
  481 LYQPYSLNKN PPINKIQPLT TDEMLYPK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	60.0
Match:	2f1zA
Description:	Crystal structure of HAUSP
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [885-1115]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLVGIDSEFV ALQQEETEVR SDGTKSTIKP SKLSLARVSV LRGEGPNKGL PFIDDYVATD  60
   61 DKVTDYLTEY SGIHPGDLDP DRSPYNVVPL KVAYKKLRLL VNAGCIFVGH GLQKDFRIIN 120
  121 LLVPPEQVVD TVDLFFLSSR QRKLSLKFLA WYLLDEEIQL TEHDSIEDAL TALKLYDCYD 180
  181 KLKSQGKLEE TLDNIYEVGR RFKFRPPSVA SMSLEDRNSY GDESVISNQT N

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	39.69897
Match:	1j53A
Description:	N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
ribonuclease activity	4.62036729045506	bayes_pls_golite062009
poly(A)-specific ribonuclease activity	4.26301879074656	bayes_pls_golite062009
exoribonuclease activity	3.12138921263133	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	2.99795146290131	bayes_pls_golite062009
exonuclease activity	2.86892175148145	bayes_pls_golite062009
nuclease activity	2.84202779131927	bayes_pls_golite062009
hydrolase activity	2.78602644579272	bayes_pls_golite062009
endoribonuclease activity	2.59247838057313	bayes_pls_golite062009
endonuclease activity	2.57451891632839	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	2.43032491532703	bayes_pls_golite062009
	2.34629145895727	bayes_pls_golite062009
ribonuclease H activity	2.21066093729724	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	1.94077739152313	bayes_pls_golite062009
deoxyribonuclease activity	1.87431870698721	bayes_pls_golite062009
DNA polymerase activity	1.64519652804477	bayes_pls_golite062009
DNA-directed DNA polymerase activity	1.54576601235316	bayes_pls_golite062009
3'-5'-exoribonuclease activity	1.46367653485697	bayes_pls_golite062009
RNA binding	1.43166314878142	bayes_pls_golite062009
catalytic activity	1.25233849524628	bayes_pls_golite062009
nucleic acid binding	0.867535868813106	bayes_pls_golite062009
endoribonuclease activity, producing 5'-phosphomonoesters	0.830848153280868	bayes_pls_golite062009
exodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.782108781904855	bayes_pls_golite062009
exodeoxyribonuclease activity	0.77421125364834	bayes_pls_golite062009
transcription regulator activity	0.763906045630221	bayes_pls_golite062009
binding	0.715089866064182	bayes_pls_golite062009
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.681014317532767	bayes_pls_golite062009
3'-5' exonuclease activity	0.64268174969672	bayes_pls_golite062009
DNA binding	0.573012783711078	bayes_pls_golite062009
endodeoxyribonuclease activity	0.48776342704945	bayes_pls_golite062009
protein binding	0.035326007863533	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: