YRC Public Data Repository - Protein Structure Prediction

Protein:	NMD2
Organism:	Saccharomyces cerevisiae
Length:	1089 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 NMD2.

Description	E-value	Query Range	Subject Range
NMD2 - Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p; ... NMD2_YEAST - Nonsense-mediated mRNA decay protein 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=N...	0.0	[1..1089]	[1..1089]
upf2 - nonsense-mediated decay protein Upf2 NMD2_SCHPO - Nonsense-mediated mRNA decay protein 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=upf...	0.0	[10..974]	[17..1046]
gi\|7243197 - gi\|7243197\|dbj\|BAA92646.1\| KIAA1408 protein [Homo sapiens]	0.0	[6..810]	[167..1032]
smg-3 - status:Confirmed UniProt:Q95XD2 protein_id:AAK68590.2	0.0	[30..1022]	[44..1112]
gi\|16117302 - gi\|16117302\|dbj\|BAB16725.2\| hypothetical protein [Macaca fascicularis]	3.0E-96	[397..810]	[1..418]
Upf2-PA - The gene Upf2 is referred to in FlyBase by the symbol Dmel\Upf2 (CG2253, FBgn0029992). It is a prote...	3.0E-95	[6..392]	[79..450]

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Predicted Domain #1

Region A:
Residues: [1-272]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDDGRKKELH DLNTRAWNGE EVFPLKSKKL DSSIKRNTGF IKKLKKGFVK GSESSLLKDL  60
   61 SEASLEKYLS EIIVTVTECL LNVLNKNDDV IAAVEIISGL HQRFNGRFTS PLLGAFLQAF 120
  121 ENPSVDIESE RDELQRITRV KGNLRVFTEL YLVGVFRTLD DIESKDAIPN FLQKKTGRKD 180
  181 PLLFSILREI LNYKFKLGFT TTIATAFIKK FAPLFRDDDN SWDDLIYDSK LKGALQSLFK 240
  241 NFIDATFARA TELHKKVNKL QREHQKCQIR TG

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	28.070581
Match:	PF02854
Description:	MIF4G domain

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 Domain #2

Region A:
Residues: [273-336]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KLRDEYVEEY DKLLPIFIRF KTSAITLGEF FKLEIPELEG ASNDDLKETA SPMITNQILP  60
   61 PNQR

[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	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.689	0.025	mRNA catabolic process	a.4.1	Homeodomain-like
View	Download	0.681	0.025	mRNA catabolic process	a.60.1	SAM/Pointed domain
View	Download	0.871	0.025	mRNA catabolic process	a.60.3	C-terminal domain of RNA polymerase alpha subunit
View	Download	0.674	0.025	mRNA catabolic process	a.60.1	SAM/Pointed domain
View	Download	0.648	0.025	mRNA catabolic process	d.45.1	ClpS-like
View	Download	0.608	0.025	mRNA catabolic process	a.60.2	RuvA domain 2-like
View	Download	0.592	0.025	mRNA catabolic process	d.58.17	Metal-binding domain
View	Download	0.592	0.025	mRNA catabolic process	d.52.1	Alpha-lytic protease prodomain
View	Download	0.561	0.025	mRNA catabolic process	a.60.2	RuvA domain 2-like
View	Download	0.537	0.025	mRNA catabolic process	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.501	0.025	mRNA catabolic process	d.58.17	Metal-binding domain
View	Download	0.489	0.025	mRNA catabolic process	d.58.40	D-ribose-5-phosphate isomerase (RpiA), lid domain
View	Download	0.481	0.025	mRNA catabolic process	d.58.3	Protease propeptides/inhibitors
View	Download	0.478	0.025	mRNA catabolic process	b.84.2	Rudiment single hybrid motif
View	Download	0.476	0.025	mRNA catabolic process	d.58.12	eEF-1beta-like
View	Download	0.460	0.025	mRNA catabolic process	d.67.2	Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain
View	Download	0.453	0.025	mRNA catabolic process	a.3.1	Cytochrome c
View	Download	0.449	0.025	mRNA catabolic process	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.447	0.025	mRNA catabolic process	d.58.5	GlnB-like
View	Download	0.446	0.025	mRNA catabolic process	a.39.1	EF-hand
View	Download	0.445	0.025	mRNA catabolic process	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.426	0.025	mRNA catabolic process	d.58.44	Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
View	Download	0.421	0.025	mRNA catabolic process	a.159.1	Protein serine/threonine phosphatase 2C, C-terminal domain
View	Download	0.413	0.025	mRNA catabolic process	d.48.1	RecA protein, C-terminal domain
View	Download	0.409	0.025	mRNA catabolic process	b.107.1	Urease metallochaperone UreE, N-terminal domain
View	Download	0.404	0.025	mRNA catabolic process	d.74.1	Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH)
View	Download	0.399	0.025	mRNA catabolic process	d.58.24	CheY-binding domain of CheA
View	Download	0.385	0.025	mRNA catabolic process	d.52.5	Probable GTPase Der, C-terminal domain
View	Download	0.377	0.025	mRNA catabolic process	d.58.18	Regulatory domain in the aminoacid metabolism
View	Download	0.370	0.025	mRNA catabolic process	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.365	0.025	mRNA catabolic process	d.58.12	eEF-1beta-like
View	Download	0.364	0.025	mRNA catabolic process	a.4.1	Homeodomain-like
View	Download	0.359	0.025	mRNA catabolic process	a.4.7	Ribosomal protein L11, C-terminal domain
View	Download	0.357	0.025	mRNA catabolic process	a.60.5	Barrier-to-autointegration factor, BAF
View	Download	0.355	0.025	mRNA catabolic process	a.3.1	Cytochrome c
View	Download	0.348	0.025	mRNA catabolic process	a.164.1	C-terminal domain of DFF45/ICAD (DFF-C domain)
View	Download	0.342	0.025	mRNA catabolic process	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.334	0.025	mRNA catabolic process	d.141.1	Ribosomal protein L6
View	Download	0.324	0.025	mRNA catabolic process	a.60.12	DNA polymerase beta-like, second domain
View	Download	0.323	0.025	mRNA catabolic process	d.50.3	PI-Pfui intein middle domain
View	Download	0.315	0.025	mRNA catabolic process	d.50.1	dsRNA-binding domain-like
View	Download	0.309	0.025	mRNA catabolic process	g.60.1	TSP-1 type 1 repeat
View	Download	0.303	0.025	mRNA catabolic process	a.36.1	Signal peptide-binding domain
View	Download	0.301	0.025	mRNA catabolic process	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.295	0.025	mRNA catabolic process	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.294	0.025	mRNA catabolic process	d.58.3	Protease propeptides/inhibitors
View	Download	0.293	0.025	mRNA catabolic process	d.49.1	Signal recognition particle alu RNA binding heterodimer, SRP9/14
View	Download	0.293	0.025	mRNA catabolic process	d.52.4	YhbC-like, N-terminal domain
View	Download	0.287	0.025	mRNA catabolic process	d.201.1	SRP19
View	Download	0.285	0.025	mRNA catabolic process	a.60.11	Hypothetical protein YjbJ
View	Download	0.280	0.025	mRNA catabolic process	b.84.2	Rudiment single hybrid motif
View	Download	0.279	0.025	mRNA catabolic process	d.51.1	Eukaryotic type KH-domain (KH-domain type I)
View	Download	0.274	0.025	mRNA catabolic process	a.77.1	DEATH domain
View	Download	0.265	0.025	mRNA catabolic process	d.58.49	YajQ-like
View	Download	0.259	0.025	mRNA catabolic process	d.94.1	HPr-like
View	Download	0.248	0.025	mRNA catabolic process	d.58.11	EF-G/eEF-2 domains III and V
View	Download	0.245	0.025	mRNA catabolic process	d.58.11	EF-G/eEF-2 domains III and V
View	Download	0.241	0.025	mRNA catabolic process	d.10.1	DNA-binding domain
View	Download	0.240	0.025	mRNA catabolic process	d.51.1	Eukaryotic type KH-domain (KH-domain type I)
View	Download	0.227	0.025	mRNA catabolic process	a.4.1	Homeodomain-like
View	Download	0.226	0.025	mRNA catabolic process	d.58.8	Viral DNA-binding domain
View	Download	0.215	0.025	mRNA catabolic process	a.6.1	Putative DNA-binding domain
View	Download	0.215	0.025	mRNA catabolic process	g.57.1	Serine proteinase inhibitor lekti
View	Download	0.214	0.025	mRNA catabolic process	d.58.18	Regulatory domain in the aminoacid metabolism
View	Download	0.209	0.025	mRNA catabolic process	d.56.1	GroEL-intermediate domain like
View	Download	0.208	0.025	mRNA catabolic process	d.50.2	Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain
View	Download	0.204	0.025	mRNA catabolic process	a.163.1	Crustacean CHH/MIH/GIH neurohormone

Predicted Domain #3

Region A:
Residues: [337-589]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LWENEDTRKF YEILPDISKT VEESQSSKTE KDSNVNSKNI NLFFTDLEMA DCKDIIDDLS  60
   61 NRYWSSYLDN KATRNRILKF FMETQDWSKL PVYSRFIATN SKYMPEIVSE FINYLDNGFR 120
  121 SQLHSNKINV KNIIFFSEMI KFQLIPSFMI FHKIRTLIMY MQVPNNVEIL TVLLEHSGKF 180
  181 LLNKPEYKEL MEKMVQLIKD KKNDRQLNMN MKSALENIIT LLYPPSVKSL NVTVKTITPE 240
  241 QQFYRILIRS ELS

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	13.8
Match:	1h2vC
Description:	CBP80, 80KDa nuclear cap-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	4.05046860305563	bayes_pls_golite062009
mRNA binding	2.35042158577052	bayes_pls_golite062009
binding	1.72811847650743	bayes_pls_golite062009
protein binding	1.3800948965226	bayes_pls_golite062009
nucleic acid binding	0.916304573557693	bayes_pls_golite062009
structural molecule activity	0.867897004862886	bayes_pls_golite062009
RNA cap binding	0.357520253345298	bayes_pls_golite062009
hydrolase activity	0.33256091835104	bayes_pls_golite062009
transcription regulator activity	0.0462205765670426	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [590-944]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SLDFKHIVKL VRKAHWDDVA IQKVLFSLFS KPHKISYQNI PLLTKVLGGL YSYRRDFVIR  60
   61 CIDQVLENIE RGLEINDYGQ NMHRISNVRY LTEIFNFEMI KSDVLLDTIY HIIRFGHINN 120
  121 QPNPFYLNYS DPPDNYFRIQ LVTTILLNIN RTPAAFTKKC KLLLRFFEYY TFIKEQPLPK 180
  181 ETEFRVSSTF KKYENIFGNT KFERSENLVE SASRLESLLK SLNAIKSKDD RVKGSSASIH 240
  241 NGKESAVPIE SITEDDEDED DENDDGVDLL GEDEDAEIST PNTESAPGKH QAKQDESEDE 300
  301 DDEDDDEDDD DDDDDDDDDG EEGDEDDDED DDDEDDDDEE EEDSDSDLEY GGDLD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	48.522879
Match:	1i84S_
Description:	Heavy meromyosin subfragment
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	4.20683443264388	bayes_pls_golite062009
mRNA binding	2.49094746544717	bayes_pls_golite062009
binding	1.83406697369076	bayes_pls_golite062009
protein binding	1.50566694420704	bayes_pls_golite062009
nucleic acid binding	0.967597910409065	bayes_pls_golite062009
structural molecule activity	0.868289396026548	bayes_pls_golite062009
RNA cap binding	0.66277586901495	bayes_pls_golite062009
hydrolase activity	0.29428275639657	bayes_pls_golite062009
transcription regulator activity	0.022274123463527	bayes_pls_golite062009

Predicted Domain #5

Region A:
Residues: [945-1089]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ADRDIEMKRM YEEYERKLKD EEERKAEEEL ERQFQKMMQE SIDARKSEKV VASKIPVISK  60
   61 PVSVQKPLLL KKSEEPSSSK ETYEELSKPK KIAFTFLTKS GKKTQSRILQ LPTDVKFVSD 120
  121 VLEEEEKLKT ERNKIKKIVL KRSFD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	17.221849
Match:	2tmaA_
Description:	Tropomyosin
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: