YRC Public Data Repository - Protein Structure Prediction

Protein:	VPS54
Organism:	Saccharomyces cerevisiae
Length:	889 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 VPS54.

Description	E-value	Query Range	Subject Range
gi\|190405000 - gi\|190405000\|gb\|EDV08267.1\| conserved hypothetical protein [Saccharomyces cerevisiae RM11-1a] VPS54 - Component of the GARP (Golgi-associated retrograde protein) complex, Vps51p-Vps52p-Vps53p-Vps54p, wh... VPS54_YEAST - Vacuolar protein sorting-associated protein 54 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S28...	0.0	[1..889]	[1..889]
gi\|32412370, gi\|... - gi\|32412370\|ref\|XP_326665.1\| hypothetical protein [Neurospora crassa], gi\|28923085\|gb\|EAA32302.1\| co... gi\|85103537 - gi\|85103537\|ref\|XP_961538.1\| hypothetical protein NCU01172 [Neurospora crassa OR74A]	0.0	[171..872]	[182..942]
scat-PA - The gene scattered is referred to in FlyBase by the symbol Dmel\scat (CG3766, FBgn0011232). It is a ... gi\|220944740 - gi\|220944740\|gb\|ACL84913.1\| scat-PA [synthetic construct]	0.0	[114..887]	[107..845]
SPAC2F3.10 - GARP complex subunit Vps54 VPS54_SCHPO - Vacuolar protein sorting-associated protein 54 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843...	0.0	[206..872]	[165..833]
VPS54_RAT - Vacuolar protein sorting-associated protein 54 OS=Rattus norvegicus GN=Vps54 PE=2 SV=1	0.0	[120..602]	[47..486]
gi\|7023936 - gi\|7023936\|dbj\|BAA92134.1\| unnamed protein product [Homo sapiens]	1.0E-93	[595..887]	[16..304]
gi\|19353654 - gi\|19353654\|gb\|AAH24789.1\| Vps54 protein [Mus musculus]	4.0E-61	[684..887]	[1..199]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.003	[252..635]	[1845..2259]

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Predicted Domain #1

Region A:
Residues: [1-41]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSISETPHNK SQGLQKAAGR PKIVVPEGSP SRNSDSGSFT I

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [98-245]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 THSGSMDFSP LGNNSIYEIV MNTRRKNWLN YPTVADIPQV SLSKNDLDDH WKTHVIEYVK  60
   61 NIKSDYQIFQ STNNIRNMNQ MEQLKELREG ENMHEESFEA NLRQGDAELI NSIPDFYFSD 120
  121 KFQLDNPRTF HKVLDAIDLF LTKLDMKR

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.08
Match:	3btaA
Description:	Botulinum neurotoxin
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [42-97]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EGDTSLNDDL LSISGSVTPR ARRSSRLSLD SITPRRSFDS RTLSVANSRS FGFENE

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.08
Match:	3btaA
Description:	Botulinum neurotoxin
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	2.3468119246528	bayes_pls_golite062009
cytoskeletal protein binding	2.28760768499625	bayes_pls_golite062009
actin binding	2.06460396235438	bayes_pls_golite062009
protein binding	1.84956862293123	bayes_pls_golite062009
syntaxin binding	1.83513067528946	bayes_pls_golite062009
SNARE binding	1.71642476140333	bayes_pls_golite062009
actin filament binding	1.58451318432641	bayes_pls_golite062009
integrin binding	1.00016212897166	bayes_pls_golite062009
protein complex binding	0.895042950779324	bayes_pls_golite062009
receptor binding	0.497776738275844	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [246-417]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QAERDEAFSE LRDRLNDFLD IVETLLVTEI SKSSHKFFHA LSEVDNIQKR ALDTMSELKE  60
   61 LAQNIKTIDA ENIRKKISHL EMIFKRKNVE KLEQGLLQAK LVLNKTDECK SMYEENKLDN 120
  121 CLELIKSIDY LIKGDDSINE DVQSWTRCWP YKLSNLRTIP ALSATREFLT NM

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	8.47
Match:	1hciA
Description:	alpha-actinin
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [418-556]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KIEIGGKFSL QLSILLIDDL RSFCKSIKPK ETLHRIQTGS NDKKQTIFTD NFSSKITELI  60
   61 VRLNRCEELT SAFDLYREKS ITELKSIIKI YLPTENAHAD NNHDEKHLNN GSTSGSKLSR 120
  121 LIKEQTPAEF QSMLVNIFT

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	8.47
Match:	1hciA
Description:	alpha-actinin
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [557-693]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HALEALRRLY GHQKLLLDIS LNELASVKSP NENQHNMITQ LDIRTGINEI IRIIQLRTGK  60
   61 IIAVRRELNL SLRYDYFLKF YAICVIFIQE CEVLSGEFLT KYLSNVLASQ IKHYANAQSS 120
  121 KNYRNIKKKI DAEEWIP

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	8.47
Match:	1hciA
Description:	alpha-actinin
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [694-889]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YIVDSSIQSD VNDIVSSIDI DPLSWTTILD MVGGSHDCEN GRSEDKEKDE GNETYQGHRK  60
   61 SVVVGDKTFV ASSSLLATIE VIKELMVLSI NLPSIYLSNF EKLCYDALQY YNSSAMASVT 120
  121 QPGNSLLKTG RNLSIMGESL DCLAEFVIIV QRFYQRLSNS NRDFEPFDAS HYTTLLGQFQ 180
  181 ASSNKIYMAN APPPPV

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.226	0.963	Golgi to vacuole transport	c.37.1	P-loop containing nucleoside triphosphate hydrolases

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: