NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q8N7C4 UniProt NPD GO	CF128_HUMAN	Protein C6orf128	0.23	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				229
Q9Y530 UniProt NPD GO	CF130_HUMAN	Protein C6orf130	0.23	-	cyt	0					152
Q99KU6 UniProt NPD GO	CF089_MOUSE	Protein C6orf89 homolog	0.23	-	mit	1	Membrane; single-pass membrane protein (Potential)				348
Q91YV9 UniProt NPD GO	CI125_MOUSE	Protein C9orf125 homolog	0.23	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				403
Q5EB73 UniProt NPD GO	CI125_RAT	Protein C9orf125 homolog	0.23	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				403
Q567E6 UniProt NPD GO	CQ10A_BRARE	Protein COQ10 A, mitochondrial precursor	0.23	-	mit	0	Mitochondrion (Potential)				238
P33309 UniProt NPD GO	DOM34_YEAST	Protein DOM34	0.23	-	cyt	0	Nucleus (Potential)	cytoplasm [IDA]			311
Q5SQY2 UniProt NPD GO	FA44B_MOUSE	Protein FAM44B	0.23	-	nuc	0					173
Q9NUQ9 UniProt NPD GO	FA49B_HUMAN	Protein FAM49B (L1)	0.23	-	cyt	0					324
Q9D650 UniProt NPD GO	FA84A_MOUSE	Protein FAM84A	0.23	-	cyt	0					292
Q03768 UniProt NPD GO	GIR2_YEAST	Protein GIR2	0.23	-	cyt	0		cytoplasm [IDA]			265
Q5RBY7 UniProt NPD GO	LMBRL_PONPY	Protein LMBR1L	0.23	-	end	9 *	Cell membrane; multi-pass membrane protein (By similarity)				490
Q66KM2 UniProt NPD GO	NDRG2_XENTR	Protein NDRG2	0.23	-	cyt	0	Cytoplasm (By similarity)				360
Q9QYF9 UniProt NPD GO	NDRG3_MOUSE	Protein NDRG3 (Protein Ndr3)	0.23	-	cyt	0		cytoplasm [ISS]			375
P25560 UniProt NPD GO	RER1_YEAST	Protein RER1 (Retention of ER proteins 1)	0.23	-	end	2	Golgi apparatus; Golgi membrane; multi-pass membrane protein	COPI-coated vesicle [IDA] ER to Golgi transport vesicle [IDA]			188
P40395 UniProt NPD GO	RIC1_YEAST	Protein RIC1	0.23	-	cyt	0		Golgi membrane [IDA] guanyl-nucleotide exchange factor complex [IDA]			1056
Q99287 UniProt NPD GO	SEY1_YEAST	Protein SEY1 (Synthetic enhancer of YOP1 protein)	0.23	-	end	2	Intracytoplasmic membrane; multi-pass membrane protein. Cytoplasmic, punctate pattern	cytoplasm [IDA]			776
Q2QLB6 UniProt NPD GO	WNT2_CALMO	Protein Wnt-2 precursor	0.23	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
Q5JUW0 UniProt NPD GO	ZN673_HUMAN	Protein ZNF673	0.23	-	cyt	0			300585		171
Q4R5M3 UniProt NPD GO	ANM5_MACFA	Protein arginine N-methyltransferase 5 (EC 2.1.1.-) (Shk1 kinase-binding protein 1 homolog) (SKB1 ho ...	0.23	-	cyt	0	Cytoplasm (By similarity)				636
O14744 UniProt NPD GO	ANM5_HUMAN	Protein arginine N-methyltransferase 5 (EC 2.1.1.-) (Shk1 kinase-binding protein 1 homolog) (SKB1Hs) ...	0.23	-	cyt	0	Cytoplasm		604045		636
P38657 UniProt NPD GO	PDIA3_BOVIN	Protein disulfide-isomerase A3 precursor (EC 5.3.4.1) (Disulfide isomerase ER-60) (ERP60) (58 kDa mi ...	0.23	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				505
Q5R4K9 UniProt NPD GO	KPCI_PONPY	Protein kinase C iota type (EC 2.7.11.13) (nPKC-iota)	0.23	-	cyt	0	Endosome (By similarity)				587
Q09794 UniProt NPD GO	PYR1_SCHPO	Protein ura1 [Includes: Glutamine-dependent carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate car ...	0.23	-	cyt	0					2244
Q9ULC6 UniProt NPD GO	PADI1_HUMAN	Protein-arginine deiminase type-1 (EC 3.5.3.15) (Protein-arginine deiminase type I) (Peptidylarginin ...	0.23	-	cyt	0	Cytoplasm		607934		663
P00735 UniProt NPD GO	THRB_BOVIN	Prothrombin precursor (EC 3.4.21.5) (Coagulation factor II) [Contains: Activation peptide fragment 1 ...	0.23	-	gol	0	Secreted protein; extracellular space			2SPT	625
Q5DRB3 UniProt NPD GO	PCDG7_PANTR	Protocadherin gamma A7 precursor (PCDH-gamma-A7)	0.23	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				932
Q01688 UniProt NPD GO	YS4L_PNECA	Putative 40S ribosomal protein S4-like (Fragment)	0.23	-	cyt	0	Mitochondrion (Potential)				169
P03010 UniProt NPD GO	TRAC9_MAIZE	Putative AC9 transposase	0.23	-	vac	2					839
Q16740 UniProt NPD GO	CLPP_HUMAN	Putative ATP-dependent Clp protease proteolytic subunit, mitochondrial precursor (EC 3.4.21.92) (End ...	0.23	-	mit	0	Mitochondrion		601119	1TG6	277
Q9BZ01 UniProt NPD GO	FRGL_HUMAN	Putative FRG1-like protein C20orf80	0.23	-	nuc	0					182
P81833 UniProt NPD GO	TL29_SPIOL	Putative L-ascorbate peroxidase, chloroplast (EC 1.11.1.11) (Thylakoid lumenal 29 kDa protein) (TL29 ...	0.23	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				30
Q09376 UniProt NPD GO	TBX35_CAEEL	Putative T-box protein 35	0.23	-	cyt	0	Nucleus (Potential)				181
Q09448 UniProt NPD GO	PPAV_CAEEL	Putative acid phosphatase C05C10.1 (EC 3.1.3.2)	0.23	-	nuc	0					471
Q04458 UniProt NPD GO	YM00_YEAST	Putative aldehyde dehydrogenase-like protein YMR110C (EC 1.2.1.-)	0.23	-	mit	1		endosome [IDA] integral to mitochondrial outer membrane [IDA] lipid particle [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			532
O88788 UniProt NPD GO	AG10B_RAT	Putative alpha-1,2-glucosyltransferase ALG10-B (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10-B) (A ...	0.23	-	end	11 *	Cell membrane; multi-pass membrane protein				474
Q20605 UniProt NPD GO	AMT2_CAEEL	Putative ammonium transporter 2	0.23	+	end	8 *	Membrane; multi-pass membrane protein (Probable)				554
O64806 UniProt NPD GO	ACA7_ARATH	Putative calcium-transporting ATPase 7, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 7)	0.23	-	end	8	Membrane; multi-pass membrane protein				1015
Q8IQ72 UniProt NPD GO	GR65A_DROME	Putative chemosensory receptor 65a	0.23	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			408
Q10318 UniProt NPD GO	ILV3_SCHPO	Putative dihydroxy-acid dehydratase, mitochondrial precursor (EC 4.2.1.9) (DAD) (2,3-dihydroxy acid ...	0.23	-	mit	0	Mitochondrion (Potential)				598
Q09509 UniProt NPD GO	FOLC_CAEEL	Putative folylpolyglutamate synthase (EC 6.3.2.17) (Folylpoly-gamma-glutamate synthetase) (FPGS) (Te ...	0.23	-	mit	0					510
Q8INM9 UniProt NPD GO	GR85A_DROME	Putative gustatory receptor 85a	0.23	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			397
Q9VEU0 UniProt NPD GO	GR89A_DROME	Putative gustatory receptor 89a	0.23	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			362
Q9VB26 UniProt NPD GO	GR98B_DROME	Putative gustatory receptor 98b	0.23	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			403
Q9LZ45 UniProt NPD GO	H2B9_ARATH	Putative histone H2B.9 (HTB10)	0.23	-	nuc	0	Nucleus (By similarity)				131
O82243 UniProt NPD GO	GH39_ARATH	Putative indole-3-acetic acid-amido synthetase GH3.9 (EC 6.3.2.-) (Auxin-responsive GH3-like protein ...	0.23	-	cyt	0					585
Q4I2X5 UniProt NPD GO	NNT1_GIBZE	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.23	-	nuc	0	Cytoplasm (By similarity)				594
Q9LTZ0 UniProt NPD GO	PEL11_ARATH	Putative pectate lyase 11 precursor (EC 4.2.2.2)	0.23	-	nuc	0					409
P49537 UniProt NPD GO	YCF42_ODOSI	Putative peroxiredoxin ycf42 (EC 1.11.1.15) (Thioredoxin reductase)	0.23	-	cyt	1 *	Plastid; chloroplast				204
Q9LK71 UniProt NPD GO	DGP11_ARATH	Putative protease Do-like 11, mitochondrial precursor (EC 3.4.21.-)	0.23	-	nuc	0	Mitochondrion; mitochondrial membrane (Potential)				565

You are viewing entries 47801 to 47850 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.