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
Q2KI78 UniProt NPD GO	NDP_BOVIN	Norrin precursor	0.42	-	exc	0	Secreted protein (Potential)				133
P48744 UniProt NPD GO	NDP_MOUSE	Norrin precursor (Norrie disease protein homolog)	0.42	-	nuc	0	Secreted protein (Potential)				131
Q08920 UniProt NPD GO	NCBP2_YEAST	Nuclear cap-binding protein subunit 2	0.42	-	nuc	0	Nucleus	commitment complex [IDA] snRNA cap binding complex [IDA]			208
O16360 UniProt NPD GO	NHR18_CAEEL	Nuclear hormone receptor family member nhr-18	0.42	-	nuc	0	Nucleus (Potential)				394
O17025 UniProt NPD GO	NHR90_CAEEL	Nuclear hormone receptor family member nhr-90	0.42	-	mit	0	Nucleus (Potential)				393
Q62881 UniProt NPD GO	NOL3_RAT	Nucleolar protein 3	0.42	-	nuc	0	Nucleus (By similarity)				221
Q8R332 UniProt NPD GO	NUPL1_MOUSE	Nucleoporin p58/p45 (Nucleoporin-like 1)	0.42	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Biased toward ...				587
P70581 UniProt NPD GO	NUPL1_RAT	Nucleoporin p58/p45 (Nucleoporin-like 1)	0.42	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Biased toward ...	nuclear pore [IDA]			585
Q8CE23 UniProt NPD GO	OX26_MOUSE	Orexigenic neuropeptide QRFP precursor (P518) [Contains: QRF-amide (Pyroglutamylated arginine-phenyl ...	0.42	-	exc	0	Secreted protein				124
P84010 UniProt NPD GO	OTC_SHEEP	Ornithine carbamoyltransferase, mitochondrial (EC 2.1.3.3) (OTCase) (Ornithine transcarbamylase)	0.42	-	cyt	0	Mitochondrion; mitochondrial matrix			1FB5	320
O18638 UniProt NPD GO	OAF_DROVI	Out at first protein	0.42	-	mit	0					305
Q5B8X6 UniProt NPD GO	OXR1_EMENI	Oxidation resistance protein 1	0.42	-	nuc	0	Mitochondrion (By similarity)				393
Q14242 UniProt NPD GO	SELPL_HUMAN	P-selectin glycoprotein ligand 1 precursor (PSGL-1) (Selectin P ligand) (CD162 antigen)	0.42	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	600738	1G1S	412
P36102 UniProt NPD GO	PAN3_YEAST	PAB-dependent poly(A)-specific ribonuclease subunit PAN3 (EC 3.1.13.4) (PAB1P-dependent poly(A)-nucl ...	0.42	-	nuc	0		cytoplasm [IDA] PAN complex [IDA]			679
Q96JY6 UniProt NPD GO	PDLI2_HUMAN	PDZ and LIM domain protein 2 (PDZ-LIM protein mystique) (PDZ-LIM protein)	0.42	-	nuc	0	Cytoplasm. Isoform 1, isoform 2: Cytoskeleton. Isoform 3: Nucleus. May be partially nuclear. Isoform ...	cell surface [IEP]	609722		352
P32115 UniProt NPD GO	PAX4_MOUSE	Paired box protein Pax-4	0.42	+	nuc	0	Nucleus	transcription factor complex [TAS]			349
Q2YFS3 UniProt NPD GO	PILRA_MOUSE	Paired immunoglobulin-like type 2 receptor alpha precursor (Inhibitory receptor PILR-alpha) (Cell su ...	0.42	-	end	1	Membrane; single-pass type I membrane protein (Potential)				302
Q4IA62 UniProt NPD GO	PFA3_GIBZE	Palmitoyltransferase PFA3 (EC 2.3.1.-) (Protein fatty acyltransferase 3)	0.42	-	mit	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				550
Q9NUE0 UniProt NPD GO	ZDH18_HUMAN	Palmitoyltransferase ZDHHC18 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 18) (DHHC-18)	0.42	+	end	4	Membrane; multi-pass membrane protein (Potential)				388
Q9UL42 UniProt NPD GO	PNMA2_HUMAN	Paraneoplastic antigen Ma2 (Onconeuronal antigen MA2) (Paraneoplastic neuronal antigen MM2) (40 kDa ...	0.42	-	cyt	0	Nucleus; nucleolus		603970		364
Q9BYG4 UniProt NPD GO	PAR6G_HUMAN	Partitioning defective 6 homolog gamma (PAR-6 gamma) (PAR6D)	0.42	-	mit	0	Cytoplasm (Probable)		608976		376
P10820 UniProt NPD GO	PERF_MOUSE	Perforin-1 precursor (P1) (Lymphocyte pore-forming protein) (Cytolysin)	0.42	-	nuc	0	Integral membrane protein. Cytoplasmic granules of cytolytic T-lymphocytes	cytoplasmic membrane-bound vesicle [IDA]			554
Q9XS39 UniProt NPD GO	PHOS_HORSE	Phosducin (PHD)	0.42	-	nuc	0	Outer and inner segments of the rod cells				245
P20942 UniProt NPD GO	PHOS_RAT	Phosducin (PHD) (33 kDa phototransducing protein) (MEKA protein) (Rod photoreceptor 1) (RPR-1)	0.42	-	nuc	0	Outer and inner segments of the rod cells			2TRC	246
Q63789 UniProt NPD GO	P55G_RAT	Phosphatidylinositol 3-kinase regulatory subunit gamma (PI3-kinase p85-subunit gamma) (PtdIns-3-kina ...	0.42	-	nuc	0					461
Q6XPS3 UniProt NPD GO	TPTE2_HUMAN	Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TPTE2 (EC 3.1.3.67) (TPTE and PTEN homologous ...	0.42	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Isoform 4: Cytop ...		606791		522
Q9SMM0 UniProt NPD GO	PGMP_BRANA	Phosphoglucomutase, chloroplast precursor (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.42	-	mit	0	Plastid; chloroplast				629
Q9Z239 UniProt NPD GO	PLM_MOUSE	Phospholemman precursor (FXYD domain-containing ion transport regulator 1)	0.42	-	exc	1 *	Membrane; single-pass type I membrane protein				92
O94680 UniProt NPD GO	PDAT_SCHPO	Phospholipid:diacylglycerol acyltransferase (EC 2.3.1.158) (PDAT) (Pombe LRO1 homolog 1)	0.42	-	gol	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				623
Q3U1F9 UniProt NPD GO	PAG1_MOUSE	Phosphoprotein associated with glycosphingolipid-enriched microdomains 1 (Csk-binding protein) (Tran ...	0.42	-	exc	1 *	Cell membrane; single-pass type III membrane protein. Present in lipid rafts				429
Q9NWQ8 UniProt NPD GO	PAG1_HUMAN	Phosphoprotein associated with glycosphingolipid-enriched microdomains 1 (Transmembrane adapter prot ...	0.42	-	exc	1 *	Cell membrane; single-pass type III membrane protein. Present in lipid rafts		605767		432
O78678 UniProt NPD GO	RR4_OROMI	Plastid 30S ribosomal protein S4	0.42	-	mit	0	Plastid				203
Q8CCS6 UniProt NPD GO	PABP2_MOUSE	Polyadenylate-binding protein 2 (Poly(A)-binding protein 2) (Poly(A)-binding protein II) (PABII) (Po ...	0.42	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between the nucleus and the cytoplasm b ...				301
Q9H361 UniProt NPD GO	PABP3_HUMAN	Polyadenylate-binding protein 3 (Poly(A)-binding protein 3) (PABP 3) (Testis-specific poly(A)-bindin ...	0.42	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [NAS]	604680		631
Q8VZY7 UniProt NPD GO	FIE1_MAIZE	Polycomb group protein FIE1 (FERTILIZATION-INDEPENDENT ENDOSPERM 1)	0.42	+	mit	0					461
P15083 UniProt NPD GO	PIGR_RAT	Polymeric-immunoglobulin receptor precursor (Poly-Ig receptor) (PIGR) [Contains: Secretory component ...	0.42	-	exc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein				769
Q9WTW3 UniProt NPD GO	KCNE4_MOUSE	Potassium voltage-gated channel subfamily E member 4 (Minimum potassium ion channel-related peptide ...	0.42	-	nuc	1 *	Membrane; single-pass type I membrane protein				170
O54853 UniProt NPD GO	KCNH6_RAT	Potassium voltage-gated channel subfamily H member 6 (Voltage-gated potassium channel subunit Kv11.2 ...	0.42	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			950
Q6Q899 UniProt NPD GO	DDX58_MOUSE	Probable ATP-dependent RNA helicase DDX58 (EC 3.6.1.-) (DEAD-box protein 58) (Retinoic acid-inducibl ...	0.42	-	nuc	0	Cytoplasm (By similarity)				926
Q08234 UniProt NPD GO	YO075_YEAST	Probable ATP-dependent transporter YOL075C/YOL074C	0.42	-	end	13	Membrane; multi-pass membrane protein (Potential)				1294
Q5XIQ4 UniProt NPD GO	MGRN1_RAT	Probable E3 ubiquitin-protein ligase MGRN1 (EC 6.3.2.-) (Mahogunin ring finger protein 1)	0.42	-	nuc	0					533
Q8IZF5 UniProt NPD GO	GP113_HUMAN	Probable G-protein coupled receptor 113 precursor (G-protein coupled receptor PGR23)	0.42	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]			1079
Q8IZF2 UniProt NPD GO	GP116_HUMAN	Probable G-protein coupled receptor 116 precursor	0.42	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [TAS]			1346
Q8BM96 UniProt NPD GO	GP128_MOUSE	Probable G-protein coupled receptor 128 precursor	0.42	-	end	8 *	Membrane; multi-pass membrane protein				785
Q8BZA7 UniProt NPD GO	GPR26_MOUSE	Probable G-protein coupled receptor 26	0.42	-	end	6 *	Membrane; multi-pass membrane protein				337
Q9QXI3 UniProt NPD GO	GPR26_RAT	Probable G-protein coupled receptor 26	0.42	-	end	6 *	Membrane; multi-pass membrane protein				337
Q6EQG2 UniProt NPD GO	NADHK_ORYSA	Probable NADH kinase (EC 2.7.1.86)	0.42	-	nuc	0	Cytoplasm (By similarity)				325
P43607 UniProt NPD GO	YFK2_YEAST	Probable RNA-binding protein YFR032C	0.42	-	nuc	0					289
Q96261 UniProt NPD GO	DHLEA_ARATH	Probable dehydrin LEA	0.42	-	nuc	0					185
Q8W3J8 UniProt NPD GO	DRL10_ARATH	Probable disease resistance protein RDL5/RF45	0.42	-	cyt	0					855

You are viewing entries 30551 to 30600 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.