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
Q965W2 UniProt NPD GO	NHR86_CAEEL	Nuclear hormone receptor family member nhr-86	0.32	-	cyt	0	Nucleus (Potential)				407
Q9JJR9 UniProt NPD GO	NRIP3_MOUSE	Nuclear receptor-interacting protein 3	0.32	-	nuc	0					240
P25209 UniProt NPD GO	NFYB_MAIZE	Nuclear transcription factor Y subunit B (NF-YB) (CAAT-box DNA-binding protein subunit B)	0.32	-	nuc	0	Nucleus				179
Q4VBT2 UniProt NPD GO	NOC4L_BRARE	Nucleolar complex protein 4 homolog (NOC4 protein homolog) (NOC4-like protein) (Nucleolar complex-as ...	0.32	-	nuc	0	Nucleus; nuclear membrane; multi-pass membrane protein (By similarity). Nucleus; nucleolus (By simil ...				525
Q5I0I8 UniProt NPD GO	NOC4L_RAT	Nucleolar complex protein 4 homolog (NOC4 protein homolog) (NOC4-like protein) (Nucleolar complex-as ...	0.32	-	nuc	0	Nucleus; nuclear membrane; multi-pass membrane protein (By similarity). Nucleus; nucleolus (By simil ...				516
Q6INI5 UniProt NPD GO	NOL11_XENLA	Nucleolar protein 11	0.32	-	nuc	0	Nucleus; nucleolus (By similarity)				720
P70563 UniProt NPD GO	NUDT6_RAT	Nucleoside diphosphate-linked moiety X motif 6 (Nudix motif 6) (Protein GFG)	0.32	-	cyt	0					313
O95221 UniProt NPD GO	OR5F1_HUMAN	Olfactory receptor 5F1 (Olfactory receptor 11-10) (OR11-10)	0.32	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	608492		314
P54964 UniProt NPD GO	ORN_YEAST	Oligoribonuclease, mitochondrial precursor (EC 3.1.-.-)	0.32	-	mit	0	Mitochondrion	mitochondrion [IDA]			269
P46596 UniProt NPD GO	OPS4_CANAL	Opaque-phase-specific protein OP4 precursor	0.32	-	exc	0					402
Q6VZZ7 UniProt NPD GO	OPN5_MOUSE	Opsin-5 (Neuropsin) (G-protein coupled receptor 136) (G-protein coupled receptor PGR12)	0.32	+	end	7 *	Membrane; multi-pass membrane protein				377
P40310 UniProt NPD GO	TOK1_YEAST	Outward-rectifier potassium channel TOK1 (Two-domain outward rectifier K(+) channel YORK)	0.32	-	end	10	Membrane; multi-pass membrane protein	plasma membrane [IDA]			691
Q9TZQ3 UniProt NPD GO	PGL1_CAEEL	P granule abnormality protein 1	0.32	+	nuc	0	Cytoplasm	P granule [IDA]			730
Q15004 UniProt NPD GO	PAF_HUMAN	PCNA-associated factor (p15PAF) (Overexpressed in anaplastic thyroid carcinoma 1) (OEATC-1) (HCV NS5 ...	0.32	-	mit	0	Nucleus. Mitochondrion				111
Q9PW72 UniProt NPD GO	PDLI4_CHICK	PDZ and LIM domain protein 4 (LIM protein RIL) (Reversion-induced LIM protein)	0.32	-	nuc	0					330
Q3TJD7 UniProt NPD GO	PDLI7_MOUSE	PDZ and LIM domain protein 7 (LIM mineralization protein) (LMP) (Protein enigma)	0.32	-	nuc	0	Cytoplasm (By similarity). Colocalizes with RET to the cell periphery and in some cytoskeletal compo ...	cytoplasm [IDA] ruffle [IDA] stress fiber [IDA]			457
Q9QZP2 UniProt NPD GO	PRDM4_RAT	PR domain zinc finger protein 4 (PR domain-containing protein 4)	0.32	-	nuc	0	Nucleus (Potential)				798
Q5ADN9 UniProt NPD GO	PFA3_CANAL	Palmitoyltransferase PFA3 (EC 2.3.1.-) (Protein fatty acyltransferase 3)	0.32	+	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				386
Q8VHZ4 UniProt NPD GO	PNMA1_RAT	Paraneoplastic antigen Ma1 homolog	0.32	+	cyt	0	Nucleus; nucleolus (By similarity)				353
Q9JK84 UniProt NPD GO	PAR6G_MOUSE	Partitioning defective 6 homolog gamma (PAR-6 gamma) (PAR6A)	0.32	-	nuc	0	Cytoplasm (Probable)				382
Q9SL42 UniProt NPD GO	PIN1_ARATH	Peptidyl-prolyl cis-trans isomerase 1 (EC 5.2.1.8) (Rotamase Pin1) (PPIase Pin1) (PIN1At)	0.32	-	nuc	0				1J6Y	119
Q6FNU6 UniProt NPD GO	PPID_CANGA	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.32	-	cyt	0	Cytoplasm (By similarity)				371
Q4IBK5 UniProt NPD GO	PPIL2_GIBZE	Peptidyl-prolyl cis-trans isomerase-like 2 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-60) (Cyclop ...	0.32	-	cyt	0	Nucleus (By similarity)				588
P53112 UniProt NPD GO	PEX14_YEAST	Peroxisomal membrane protein PEX14 (Peroxin-14)	0.32	-	nuc	0	Peroxisome; peroxisomal membrane; peripheral membrane protein; cytoplasmic side	peroxisomal membrane [IDA]		1N5Z	341
P40155 UniProt NPD GO	PEX17_YEAST	Peroxisomal membrane protein PEX17 (Peroxin-17)	0.32	-	nuc	1 *	Peroxisome; peroxisomal membrane; peripheral membrane protein; cytoplasmic side	peroxisomal membrane [IMP]			199
Q9P0Z9 UniProt NPD GO	SOX_HUMAN	Peroxisomal sarcosine oxidase (EC 1.5.3.1) (PSO) (L-pipecolate oxidase) (EC 1.5.3.7) (L-pipecolic ac ...	0.32	-	mit	1 *	Peroxisome	peroxisome [TAS]			390
Q9BE65 UniProt NPD GO	PEX26_MACFA	Peroxisome assembly protein 26 (Peroxin-26)	0.32	-	cyt	0	Peroxisome; peroxisomal membrane; single-pass type II membrane protein (By similarity)				305
P08425 UniProt NPD GO	SYFM_YEAST	Phenylalanyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.20) (Phenylalanine--tRNA ligase) (Ph ...	0.32	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			474
Q13371 UniProt NPD GO	PHLP_HUMAN	Phosducin-like protein (PHLP)	0.32	-	cyt	0			604421		301
P60483 UniProt NPD GO	PTEN_CANFA	Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase PTEN (EC 3.1.3.67) (Mutated in multiple advan ...	0.32	-	nuc	0		cytoplasm [ISS]			403
O08586 UniProt NPD GO	PTEN_MOUSE	Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase PTEN (EC 3.1.3.67) (Mutated in multiple advan ...	0.32	-	nuc	0		cytoplasm [ISS]			403
P60484 UniProt NPD GO	PTEN_HUMAN	Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN ...	0.32	-	nuc	0	Cytoplasm	cytoplasm [IDA]	137800	1D5R	403
Q9PUT6 UniProt NPD GO	PTEN_XENLA	Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN ...	0.32	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			402
Q9SUI2 UniProt NPD GO	PI5K7_ARATH	Phosphatidylinositol-4-phosphate 5-kinase 7 (EC 2.7.1.68) (AtPIP5K7) (1-phosphatidylinositol-4-phosp ...	0.32	-	cyt	0					754
Q8RY89 UniProt NPD GO	PI5K8_ARATH	Phosphatidylinositol-4-phosphate 5-kinase 8 (EC 2.7.1.68) (AtPIP5K8) (1-phosphatidylinositol-4-phosp ...	0.32	-	cyt	0					769
Q10949 UniProt NPD GO	PISD_CAEEL	Phosphatidylserine decarboxylase proenzyme (EC 4.1.1.65) [Contains: Phosphatidylserine decarboxylase ...	0.32	-	mit	0					377
Q12008 UniProt NPD GO	PMG2_YEAST	Phosphoglycerate mutase 2 (EC 5.4.2.1) (Phosphoglyceromutase 2) (PGAM 2) (MPGM 2) (BPG-dependent PGA ...	0.32	-	nuc	0	Cytoplasm	cytoplasm [IDA]			311
P56513 UniProt NPD GO	PLM_CANFA	Phospholemman precursor (FXYD domain-containing ion transport regulator 1)	0.32	-	end	1 *	Membrane; single-pass type I membrane protein				92
P00607 UniProt NPD GO	PA21B_NOTSC	Phospholipase A2 homolog 1 (Notechis II-1)	0.32	-	nuc	0	Secreted protein				119
P48650 UniProt NPD GO	PA2N_ECHCA	Phospholipase A2, neutral (EC 3.1.1.4) (Ecarpholin S) (Phosphatidylcholine 2-acylhydrolase)	0.32	-	nuc	0	Secreted protein				122
O43976 UniProt NPD GO	PMM_BABBO	Phosphomannomutase (EC 5.4.2.8)	0.32	-	cyt	0	Cytoplasm (By similarity)				246
Q9DB30 UniProt NPD GO	PHKG2_MOUSE	Phosphorylase b kinase gamma catalytic chain, testis/liver isoform (EC 2.7.11.19) (PHK-gamma-T) (Pho ...	0.32	-	cyt	0					406
P15372 UniProt NPD GO	ARRA_DROME	Phosrestin-2 (Phosrestin II) (Arrestin A) (Arrestin-1)	0.32	-	cyt	0		membrane fraction [IDA] rhabdomere [IDA]			364
Q70XZ2 UniProt NPD GO	YCF4_AMBTC	Photosystem I assembly protein ycf4	0.32	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				235
P15001 UniProt NPD GO	PHYA_PEA	Phytochrome A	0.32	-	mit	0					1124
P06594 UniProt NPD GO	PHYA4_AVESA	Phytochrome A type 4 (AP4)	0.32	-	nuc	0					1128
O24475 UniProt NPD GO	TPSD3_ABIGR	Pinene synthase, chloroplast precursor (EC 4.2.3.14) (Beta-geraniolene synthase) ((-)-(1S,5S)-pinene ...	0.32	-	cyt	0	Plastid; chloroplast				628
O35257 UniProt NPD GO	PRLPB_MOUSE	Placental prolactin-like protein B precursor (PRL-like protein B) (PLP-B)	0.32	-	cyt	0	Secreted protein (By similarity)				230
P03952 UniProt NPD GO	KLKB1_HUMAN	Plasma kallikrein precursor (EC 3.4.21.34) (Plasma prekallikrein) (Kininogenin) (Fletcher factor) [C ...	0.32	-	cyt	0		extracellular region [NAS]	229000	2ANY	638
P83970 UniProt NPD GO	PMA1_WHEAT	Plasma membrane ATPase (EC 3.6.3.6) (Proton pump)	0.32	-	end	8	Cell membrane; multi-pass membrane protein				951

You are viewing entries 38751 to 38800 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.