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
Q14896 UniProt NPD GO	MYPC3_HUMAN	Myosin-binding protein C, cardiac-type (Cardiac MyBP-C) (C-protein, cardiac muscle isoform)	0.35	-	cyt	0			115197	1PD6	1274
Q9Z2C5 UniProt NPD GO	MTM1_MOUSE	Myotubularin (EC 3.1.3.48)	0.35	-	nuc	0					603
Q31849 UniProt NPD GO	NU5C_AMBTR	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.35	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				743
Q33113 UniProt NPD GO	NU5C_SESIN	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.35	-	end	12 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				684
P56756 UniProt NPD GO	NUKC_ARATH	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.35	-	nuc	0	Plastid; chloroplast				225
P56755 UniProt NPD GO	NUIC_ARATH	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.35	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				172
Q332S3 UniProt NPD GO	NUIC_LACSA	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.35	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				166
P42029 UniProt NPD GO	NDUA8_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.35	-	nuc	0	Mitochondrion				171
P53164 UniProt NPD GO	NPY1_YEAST	NADH pyrophosphatase (EC 3.6.1.22)	0.35	-	mit	0		cytoplasm [IDA] peroxisome [IDA]			384
P03908 UniProt NPD GO	NU4M_PONPY	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.35	-	end	12 *					459
O00221 UniProt NPD GO	IKBE_HUMAN	NF-kappa-B inhibitor epsilon (NF-kappa-BIE) (I-kappa-B-epsilon) (IkappaBepsilon) (IKB-epsilon) (IKBE ...	0.35	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [TAS]	604548		361
Q8WX92 UniProt NPD GO	NELFB_HUMAN	Negative elongation factor B (NELF-B) (Cofactor of BRCA1)	0.35	-	cyt	0	Nucleus				580
P58417 UniProt NPD GO	NXPH1_HUMAN	Neurexophilin-1 precursor	0.35	-	nuc	0	Secreted protein (Potential)		604639		271
Q63366 UniProt NPD GO	NXPH1_RAT	Neurexophilin-1 precursor (Neurophilin)	0.35	-	nuc	0	Secreted protein (Potential)				271
Q8BYM5 UniProt NPD GO	NLGN3_MOUSE	Neuroligin-3 precursor (Gliotactin homolog)	0.35	-	end	1	Membrane; single-pass type I membrane protein (Potential)				825
Q6W5P4 UniProt NPD GO	NPSR1_HUMAN	Neuropeptide S receptor (G-protein coupled receptor 154) (G-protein coupled receptor for asthma susc ...	0.35	-	end	6	Isoform 1, isoform 3, isoform 4: Cell membrane; multi-pass membrane protein. Isoform 2, isoform 5, i ...		608595		371
Q9XSW6 UniProt NPD GO	NEUY_MACMU	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.35	-	exc	1 *	Secreted protein			1R9N	97
P30989 UniProt NPD GO	NTR1_HUMAN	Neurotensin receptor type 1 (NT-R-1) (High-affinity levocabastine-insensitive neurotensin receptor) ...	0.35	-	end	6	Membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] Golgi apparatus [TAS] integral to plasma membrane [TAS]	162651		418
P82319 UniProt NPD GO	DEF4_MACMU	Neutrophil defensin 4 precursor (RMAD-4) [Contains: Neutrophil defensin 5 (RMAD-5)]	0.35	-	exc	0	Secreted protein				94
Q9D7C9 UniProt NPD GO	NRK2_MOUSE	Nicotinamide riboside kinase 2 (EC 2.7.1.-) (Integrin beta-1-binding protein 3) (Muscle integrin-bin ...	0.35	-	cyt	0		intracellular [IPI]			195
P79386 UniProt NPD GO	DAX1_PIG	Nuclear receptor 0B1 (Nuclear receptor DAX-1)	0.35	-	pox	0	Nucleus (By similarity)				471
Q9NSY0 UniProt NPD GO	NRBP2_HUMAN	Nuclear receptor-binding protein 2 (Transformation-related protein 16)	0.35	-	cyt	0					258
P19338 UniProt NPD GO	NUCL_HUMAN	Nucleolin (Protein C23)	0.35	+	nuc	0	Nucleus; nucleolus	nucleolus [TAS]	164035		709
P06748 UniProt NPD GO	NPM_HUMAN	Nucleophosmin (NPM) (Nucleolar phosphoprotein B23) (Numatrin) (Nucleolar protein NO38)	0.35	-	nuc	0	Nucleus; nucleolus. Generally nucleolar, but is translocated to the nucleoplasm in case of serum sta ...	centrosome [IDA] cytoplasm [IDA] nucleolus [IDA] nucleus [IDA]	164040		294
Q6P0U9 UniProt NPD GO	NUPL2_BRARE	Nucleoporin-like 2	0.35	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side (By similarity)				414
O88425 UniProt NPD GO	NDK6_MOUSE	Nucleoside diphosphate kinase 6 (EC 2.7.4.6) (NDK 6) (NDP kinase 6) (nm23-M6)	0.35	-	mit	0					189
Q21815 UniProt NPD GO	MIG23_CAEEL	Nucleoside-diphosphatase mig-23 (EC 3.6.1.-) (NDPase) (Abnormal cell migration protein 23)	0.35	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				552
P28656 UniProt NPD GO	NP1L1_MOUSE	Nucleosome assembly protein 1-like 1 (NAP-1-related protein) (Brain protein DN38)	0.35	+	cyt	0	Nucleus				391
Q5U2Z3 UniProt NPD GO	NP1L4_RAT	Nucleosome assembly protein 1-like 4	0.35	+	cyt	0	Nucleus (By similarity)				386
P16405 UniProt NPD GO	ORA_PLAFN	Octapeptide-repeat antigen (ORA) (Fragment)	0.35	-	nuc	0	Probably in the parasitophorous vacuole				701
P58917 UniProt NPD GO	CXO6A_CONCT	Omega-conotoxin CVIA precursor	0.35	-	exc	1 *	Secreted protein				71
P18743 UniProt NPD GO	ZO2_XENLA	Oocyte zinc finger protein XLCOF2 (Fragment)	0.35	-	nuc	0	Nucleus (Potential)				157
P83861 UniProt NPD GO	QRFPR_MOUSE	Orexigenic neuropeptide QRFP receptor (G-protein coupled receptor 103) (SP9155) (AQ27)	0.35	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]			433
O43612 UniProt NPD GO	OREX_HUMAN	Orexin precursor (Hypocretin) (Hcrt) [Contains: Orexin-A (Hypocretin-1) (Hcrt1); Orexin-B (Hypocreti ...	0.35	-	exc	1 *	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Associated with perikaryal rough ...	synaptic vesicle [TAS]	161400	1WSO	131
P29145 UniProt NPD GO	NECB_HYDAT	PC3-like endoprotease variant B precursor (EC 3.4.21.-) (SPC3)	0.35	-	mit	1 *					710
Q43111 UniProt NPD GO	PME3_PHAVU	Pectinesterase-3 precursor (EC 3.1.1.11) (Pectin methylesterase 3) (PE 3)	0.35	-	mit	1 *					581
Q6DC93 UniProt NPD GO	PEF1_BRARE	Peflin (PEF protein with a long N-terminal hydrophobic domain) (Penta-EF hand domain-containing prot ...	0.35	-	nuc	0	Cytoplasm (By similarity)				270
P07547 UniProt NPD GO	ARO1_EMENI	Pentafunctional AROM polypeptide [Includes: 3-dehydroquinate synthase (EC 4.2.3.4); 3-dehydroquinate ...	0.35	-	nuc	0	Cytoplasm			1SG6	1586
Q2U5W8 UniProt NPD GO	PPIL2_ASPOR	Peptidyl-prolyl cis-trans isomerase-like 2 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-60) (Cyclop ...	0.35	-	nuc	0	Nucleus (By similarity)				570
Q43729 UniProt NPD GO	PER57_ARATH	Peroxidase 57 precursor (EC 1.11.1.7) (Atperox P57) (PRXR10) (ATP13a)	0.35	-	exc	1 *	Secreted protein (By similarity)				313
Q92968 UniProt NPD GO	PEX13_HUMAN	Peroxisomal membrane protein PEX13 (Peroxin-13)	0.35	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein	integral to peroxisomal membrane [TAS] membrane fraction [TAS]	601789		403
Q8HXW8 UniProt NPD GO	PEX10_MACFA	Peroxisome assembly protein 10 (Peroxin-10) (Peroxisome biogenesis factor 10)	0.35	-	nuc	1	Peroxisome; peroxisomal membrane; peripheral membrane protein (Potential)				326
P18408 UniProt NPD GO	MET16_YEAST	Phosphoadenosine phosphosulfate reductase (EC 1.8.4.8) (PAPS reductase, thioredoxin dependent) (PAdo ...	0.35	-	cyt	0		cytoplasm [TAS] intracellular [TAS]			261
P84740 UniProt NPD GO	PBL9F_EUGGR	Photoactivated adenylate cyclase subunit beta-like protein 1224-5/9F	0.35	-	mit	0	Flagellum. Paraxonemal body. And paraxonemal bodies (PABs)				855
P93527 UniProt NPD GO	PHYB_SORBI	Phytochrome B	0.35	-	mit	0					1178
Q9JKL9 UniProt NPD GO	PRLPK_RAT	Placental prolactin-like protein K precursor (PRL-like protein K) (PLP-K)	0.35	-	mit	0	Secreted protein (By similarity)				228
P07359 UniProt NPD GO	GP1BA_HUMAN	Platelet glycoprotein Ib alpha chain precursor (Glycoprotein Ibalpha) (GP-Ib alpha) (GPIbA) (GPIb-al ...	0.35	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] membrane fraction [IDA] plasma membrane [IDA]	153670	2BP3	626
O24367 UniProt NPD GO	TUR2_SPIPO	Pleiotropic drug resistance protein TUR2 (Protein Turion 2)	0.35	-	end	13	Cell membrane; multi-pass membrane protein				1441
Q9P215 UniProt NPD GO	POGK_HUMAN	Pogo transposable element with KRAB domain (LST003/SLTP003)	0.35	-	cyt	0	Nucleus (Probable)				609
Q6BVZ3 UniProt NPD GO	PFS2_DEBHA	Polyadenylation factor subunit 2	0.35	-	nuc	0	Nucleus (By similarity)				504

You are viewing entries 36051 to 36100 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.