YRC Public Data Repository - Protein Structure Prediction

Protein:	UFD4
Organism:	Saccharomyces cerevisiae
Length:	1483 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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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 UFD4.

Description	E-value	Query Range	Subject Range
UFD4 - Ubiquitin-protein ligase (E3) that interacts with Rpt4p and Rpt6p, two subunits of the 19S particle ... UFD4_YEAST - Ubiquitin fusion degradation protein 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=U...	0.0	[1..1483]	[1..1483]
UPL4_ARATH - E3 ubiquitin-protein ligase UPL4 OS=Arabidopsis thaliana GN=UPL4 PE=3 SV=1	0.0	[52..1483]	[26..1502]
gi\|10863903 - ref\|NP_004229.1\| thyroid hormone receptor interactor 12 [Homo sapiens] TRIP12 - thyroid hormone receptor interactor 12	0.0	[641..1483]	[1046..1992]
NEDD4_MOUSE - E3 ubiquitin-protein ligase NEDD4 OS=Mus musculus GN=Nedd4 PE=1 SV=3	0.0	[894..1482]	[437..956]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[894..1482]	[364..886]

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Predicted Domain #1

Region A:
Residues: [1-72]

      1          11         21         31         41         51         
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    1 MSENNSHNLD EHESHSENSD YMMDTQVEDD YDEDGHVQGE YSYYPDEDED EHMLSSVGSF  60
   61 EADDGEDDDN DY

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [73-158]

      1          11         21         31         41         51         
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    1 HHEDDSGLLY GYHRTQNGSD EDRNEEEDGL ERSHDNNEFG SNPLHLPDIL ETFAQRLEQR  60
   61 RQTSEGLGQH PVGRTLPEIL SMIGGR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	2.09691
Match:	1qgkB_
Description:	STRUCTURE OF IMPORTIN BETA BOUND TO THE IBB DOMAIN OF IMPORTIN ALPHA
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	2.86831493830281	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	2.16002474842826	bayes_pls_golite062009
monovalent inorganic cation transmembrane transporter activity	1.81334106667983	bayes_pls_golite062009
protein binding	1.63705839411934	bayes_pls_golite062009
hydrogen ion transmembrane transporter activity	1.4929266246031	bayes_pls_golite062009
inorganic cation transmembrane transporter activity	1.21098157405785	bayes_pls_golite062009
nucleic acid binding	1.13208464017585	bayes_pls_golite062009
ion transmembrane transporter activity	1.1051743850645	bayes_pls_golite062009
cation transmembrane transporter activity	1.03004697855361	bayes_pls_golite062009
protein transporter activity	0.942980596902738	bayes_pls_golite062009
substrate-specific transporter activity	0.820796192007653	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	0.520600504671387	bayes_pls_golite062009
kinase activity	0.49215920455609	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.399777570162093	bayes_pls_golite062009
protein kinase activity	0.304524178731686	bayes_pls_golite062009
transferase activity	0.23030640245878	bayes_pls_golite062009
transcription regulator activity	0.221086931523202	bayes_pls_golite062009
DNA binding	0.171056781378569	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [159-294]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MERSAESSAR NERISKLIEN TGNASEDPYI AMESLKELSE NILMMNQMVV DRIIPMETLI  60
   61 GNIAAILSDK ILREELELQM QACRCMYNLF EVCPESISIA VDEHVIPILQ GKLVEISYID 120
  121 LAEQVLETVE YISRVH

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	113.0
Match:	1ejlI_
Description:	Importin alpha
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [295-343]

      1          11         21         31         41         51         
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    1 GRDILKTGQL SIYVQFFDFL TIHAQRKAIA IVSNACSSIR TDDFKTIVE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	113.0
Match:	1ejlI_
Description:	Importin alpha
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [344-457]

      1          11         21         31         41         51         
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    1 VLPTLKPIFS NATDQPILTR LVNAMYGICG ALHGVDKFET LFSLDLIERI VQLVSIQDTP  60
   61 LENKLKCLDI LTVLAMSSDV LSRELREKTD IVDMATRSFQ HYSKSPNAGL HETL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	113.0
Match:	1ejlI_
Description:	Importin alpha
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
proline-rich region binding	2.77294348104858	bayes_pls_golite062009
ubiquitin-protein ligase activity	2.59532734096591	bayes_pls_golite062009
binding	2.42370909657521	bayes_pls_golite062009
small conjugating protein ligase activity	2.41863405676058	bayes_pls_golite062009
transcription factor binding	1.96854466908038	bayes_pls_golite062009
histone methyltransferase activity	1.90194027965368	bayes_pls_golite062009
acid-amino acid ligase activity	1.6967322982151	bayes_pls_golite062009
protein binding	1.36920369713546	bayes_pls_golite062009
transcription regulator activity	1.32260772865135	bayes_pls_golite062009
lysine N-methyltransferase activity	1.14806422628668	bayes_pls_golite062009
protein-lysine N-methyltransferase activity	1.14806422628668	bayes_pls_golite062009
histone-lysine N-methyltransferase activity	1.14806422628668	bayes_pls_golite062009
protein methyltransferase activity	1.121001087082	bayes_pls_golite062009
transcription activator activity	1.06699689139974	bayes_pls_golite062009
transcription cofactor activity	0.9852373289585	bayes_pls_golite062009
transcription coactivator activity	0.91931537361124	bayes_pls_golite062009
ligase activity, forming carbon-nitrogen bonds	0.568363753662296	bayes_pls_golite062009
transferase activity	0.381275448590978	bayes_pls_golite062009
transcription repressor activity	0.2295693429366	bayes_pls_golite062009
catalytic activity	0.210712504691113	bayes_pls_golite062009
histone methyltransferase activity (H3-K36 specific)	0.173723075520888	bayes_pls_golite062009

Predicted Domain #6

Region A:
Residues: [458-568]

      1          11         21         31         41         51         
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    1 IYVPNSLLIS ISRFIVVLFP PEDERILSAD KYTGNSDRGV ISNQEKFDSL VQCLIPILVE  60
   61 IYTNAADFDV RRYVLIALLR VVSCINNSTA KAINDQLIKL IGSILAQKET A

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	113.0
Match:	1ejlI_
Description:	Importin alpha
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A:
Residues: [569-670]

      1          11         21         31         41         51         
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    1 SNANGTYSSE AGTLLVGGLS LLDLICKKFS ELFFPSIKRE GIFDLVKDLS VDFNNIDLKE  60
   61 DGNENISLSD EEGDLHSSIE ECDEGDEEYD YEFTDMEIPD SV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	113.0
Match:	1ejlI_
Description:	Importin alpha
Matching Structure (courtesy of the PDB):

Predicted Domain #8

Region A:
Residues: [671-973]

      1          11         21         31         41         51         
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    1 KPKKISIHIF RTLSLAYIKN KGVNLVNRVL SQMNVEQEAI TEELHQIEGV VSILENPSTP  60
   61 DKTEEDWKGI WSVLKKCIFH EDFDVSGFEF TSTGLASSIT KRITSSTVSH FILAKSFLEV 120
  121 FEDCIDRFLE ILQSALTRLE NFSIVDCGLH DGGGVSSLAK EIKIKLVYDG DASKDNIGTD 180
  181 LSSTIVSVHC IASFTSLNEF LRHRMVRMRF LNSLIPNLTS SSTEADREEE ENCLDHMRKK 240
  241 NFDFFYDNEK VDMESTVFGV IFNTFVRRNR DLKTLWDDTH TIKFCKSLEG NNRESEAAEE 300
  301 ANE

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #9

Region A:
Residues: [974-1092]

      1          11         21         31         41         51         
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    1 GKKLRDFYKK REFAQVDTGS SADILTLLDF LHSCGVKSDS FINSKLSAKL ARQLDEPLVV  60
   61 ASGALPDWSL FLTRRFPFLF PFDTRMLFLQ CTSFGYGRLI QLWKNKSKGS KDLRNDEAL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	3.09691
Match:	1i5hW_
Description:	Ubiquitin ligase NEDD4 WWIII domain
Matching Structure (courtesy of the PDB):

Predicted Domain #10

Region A:
Residues: [1093-1138]

      1          11         21         31         41         51         
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    1 QQLGRITRRK LRISRKTIFA TGLKILSKYG SSPDVLEIEY QEEAGT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	323.0103
Match:	1c4zA_
Description:	Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap)
Matching Structure (courtesy of the PDB):

Predicted Domain #11

Region A:
Residues: [1139-1263]

      1          11         21         31         41         51         
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    1 GLGPTLEFYS VVSKYFARKS LNMWRCNSYS YRSEMDVDTT DDYITTLLFP EPLNPFSNNE  60
   61 KVIELFGYLG TFVARSLLDN RILDFRFSKV FFELLHRMST PNVTTVPSDV ETCLLMIELV 120
  121 DPLLA

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [1318-1360]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IDQILGKGIE KQLKAFIEGF SKVFSYERML ILFPDELVDI FGR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	323.0103
Match:	1c4zA_
Description:	Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap)
Matching Structure (courtesy of the PDB):

Predicted Domain #12

Region A:
Residues: [1264-1317]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KSLKYIVANK DDNMTLESLS LTFTVPGNDD IELIPGGCNK SLNSSNVEEY IHGV

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [1361-1483]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VEEDWSMATL YTNLNAEHGY TMDSSIIHDF ISIISAFGKH ERRLFLQFLT GSPKLPIGGF  60
   61 KSLNPKFTVV LKHAEDGLTA DEYLPSVMTC ANYLKLPKYT SKDIMRSRLC QAIEEGAGAF 120
  121 LLS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	323.0103
Match:	1c4zA_
Description:	Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap)
Matching Structure (courtesy of the PDB):

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:

Predicted functions: