YRC Public Data Repository - Protein Structure Prediction

Protein:	UPF3_YEAST
Organism:	Saccharomyces cerevisiae S288c
Length:	387 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 UPF3_YEAST.

Description	E-value	Query Range	Subject Range
UPF3_YEAST - Nonsense-mediated mRNA decay protein 3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=U... UPF3 - Component of the nonsense-mediated mRNA decay (NMD) pathway, along with Nam7p and Nmd2p; involved in...	0.0	[1..387]	[1..387]
gi\|25535937, gi\|... - gi\|7242963\|dbj\|BAA92542.1\| KIAA1304 protein [Homo sapiens], pir\|\|G59436 KIAA1304 protein [imported] ...	4.0E-61	[172..335]	[99..245]
gi\|27597098, gi\|... - gi\|27597098\|ref\|NP_536696.2\| brain stress early protein Gbi isoform 1 [Mus musculus], gi\|14028714\|gb...	2.0E-55	[183..335]	[8..144]
srgp-1 - chimaerin like status:Partially_confirmed UniProt:Q19370 protein_id:CAA97790.1	5.0E-35	[193..333]	[161..276]

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Predicted Domain #1

Region A:
Residues: [1-60]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSNVAGELKN SEGKKKGRGN RYHNKNRGKS KNETVDPKKN ENKVNNATNA THNNSKGRRN  60
   61

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.313	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.242	d.58.17	Metal-binding domain
View	Download	0.240	a.4.13	Sigma3 and sigma4 domains of RNA polymerase sigma factors
View	Download	0.307	a.37.1	A DNA-binding domain in eukaryotic transcription factors
View	Download	0.208	a.60.3	C-terminal domain of RNA polymerase alpha subunit

Predicted Domain #2

Region A:
Residues: [61-280]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NKKRNREYYN YKRKARLGKS TENEGFKLVI RLLPPNLTAD EFFAILRDNN NDDGDKQDIQ  60
   61 GKLKYSDWCF FEGHYSSKVF KNSTYSRCNF LFDNLSDLEK CANFIKTCKF IDNKDNITIP 120
  121 DMKLSPYVKK FTQTSKKDAA LVGTIEEDEI FKTFMNSMKQ LNENDEYSFQ DFSVLKSLEK 180
  181 EFSKSIELEN KIAERTERVL TELVGTGDKV KNKNKKKKNK

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	121.070581
Match:	PF03467
Description:	Smg-4/UPF3 family

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted functions:

Term	Confidence	Notes
RNA binding	6.32219487559982	bayes_pls_golite062009
mRNA binding	4.87640532914983	bayes_pls_golite062009
	3.85463717617256	bayes_pls_golite062009
nucleic acid binding	3.74344299117899	bayes_pls_golite062009
binding	2.88749864706998	bayes_pls_golite062009
single-stranded RNA binding	2.55628738360472	bayes_pls_golite062009
poly-pyrimidine tract binding	2.0656412663177	bayes_pls_golite062009
ubiquitin-protein ligase activity	1.79747940153321	bayes_pls_golite062009
structural molecule activity	1.57342338925793	bayes_pls_golite062009
small conjugating protein ligase activity	1.54918359800898	bayes_pls_golite062009
poly(U) RNA binding	1.23190154914055	bayes_pls_golite062009
protein binding	1.19509385638328	bayes_pls_golite062009
transcription regulator activity	1.10029555513317	bayes_pls_golite062009
acid-amino acid ligase activity	1.0920515408093	bayes_pls_golite062009
DNA binding	0.984725930713243	bayes_pls_golite062009
snRNA binding	0.840923669704678	bayes_pls_golite062009
snoRNA binding	0.516511855622792	bayes_pls_golite062009
hydrolase activity	0.418157930682314	bayes_pls_golite062009
transcription factor activity	0.255891228964936	bayes_pls_golite062009
mRNA 3'-UTR binding	0.229644510503376	bayes_pls_golite062009
ligase activity, forming carbon-nitrogen bonds	0.205114038263623	bayes_pls_golite062009
ligase activity	0.115699011007988	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [281-387]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NAKKKFKEEE ASAKIPKKKR NRGKKKRENR EKSTISKTKN SNVVIIEEAG KEVLKQRKKK  60
   61 MLLQEKLKIS NSSQPQSSSA QTQPSFQPKE NLFVPRVKIL HRDDTKK

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.211	b.55.1	PH domain-like

Predicted Domain #4

Region A:
Residues: [303-387]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GKKKRENREK STISKTKNSN VVIIEEAGKE VLKQRKKKML LQEKLKISNS SQPQSSSAQT  60
   61 QPSFQPKENL FVPRVKILHR DDTKK

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.211	b.55.1	PH domain-like

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: