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
Q920A0 UniProt NPD GO	OPT_MOUSE	Opticin precursor (Oculoglycan)	0.36	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				328
P83858 UniProt NPD GO	QRFPR_RAT	Orexigenic neuropeptide QRFP receptor (G-protein coupled receptor 103) (SP9155) (AQ27)	0.36	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]			433
P56719 UniProt NPD GO	OX2R_RAT	Orexin receptor type 2 (Ox2r) (Hypocretin receptor type 2)	0.36	-	end	7	Membrane; multi-pass membrane protein				460
P62045 UniProt NPD GO	NR1I3_PHOSI	Orphan nuclear receptor NR1I3 (Constitutive androstane receptor) (CAR)	0.36	-	cyt	0	Nucleus (By similarity)				348
Q99983 UniProt NPD GO	OMD_HUMAN	Osteomodulin precursor (Osteoadherin) (OSAD) (Keratan sulfate proteoglycan osteomodulin) (KSPG osteo ...	0.36	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				421
Q9H4Q3 UniProt NPD GO	PRD13_HUMAN	PR domain zinc finger protein 13 (PR domain-containing protein 13)	0.36	-	nuc	0	Nucleus (Potential)				717
Q80V63 UniProt NPD GO	PRDM4_MOUSE	PR domain zinc finger protein 4 (PR domain-containing protein 4)	0.36	-	nuc	0	Nucleus (Potential)				803
P37254 UniProt NPD GO	PABS_YEAST	Para-aminobenzoate synthase (EC 6.3.5.8) (P-aminobenzoic acid synthase) (PABA synthase)	0.36	-	cyt	0	Cytoplasm	cytoplasm [IDA]			787
Q8ND90 UniProt NPD GO	PNMA1_HUMAN	Paraneoplastic antigen Ma1 (Neuron- and testis-specific protein 1) (37 kDa neuronal protein)	0.36	+	cyt	0	Nucleus; nucleolus. In tumor cells, it is cytoplasmic	cytoplasm [TAS] nucleolus [TAS]	604010		353
Q9D0J8 UniProt NPD GO	PTMS_MOUSE	Parathymosin	0.36	-	nuc	0					100
P04550 UniProt NPD GO	PTMS_RAT	Parathymosin (Zinc-binding 11.5 kDa protein)	0.36	-	nuc	0					101
P82596 UniProt NPD GO	PLC_HALLA	Perlucin	0.36	-	nuc	0					155
Q9SI16 UniProt NPD GO	PER15_ARATH	Peroxidase 15 precursor (EC 1.11.1.7) (Atperox P15) (ATP36)	0.36	-	exc	0	Secreted protein (By similarity)				338
Q96522 UniProt NPD GO	PER45_ARATH	Peroxidase 45 precursor (EC 1.11.1.7) (Atperox P45) (ATP8a)	0.36	-	exc	0	Secreted protein (By similarity)				325
O23237 UniProt NPD GO	PER49_ARATH	Peroxidase 49 precursor (EC 1.11.1.7) (Atperox P49) (ATP31)	0.36	-	exc	0	Secreted protein (By similarity)				331
P41903 UniProt NPD GO	PTE1_YEAST	Peroxisomal acyl-coenzyme A thioester hydrolase 1 (EC 3.1.2.2) (Peroxisomal long-chain acyl-coA thio ...	0.36	-	cyt	0	Peroxisome	mitochondrion [IDA] peroxisome [IDA]		1TBU	349
P30263 UniProt NPD GO	CATA_PICAN	Peroxisomal catalase (EC 1.11.1.6)	0.36	-	cyt	0	Peroxisome				507
Q8BGI5 UniProt NPD GO	PEX26_MOUSE	Peroxisome assembly protein 26 (Peroxin-26)	0.36	-	nuc	0	Peroxisome; peroxisomal membrane; single-pass type II membrane protein (By similarity)				305
P24004 UniProt NPD GO	PEX1_YEAST	Peroxisome biosynthesis protein PAS1 (Peroxin-1)	0.36	-	nuc	0	Cytoplasm (Probable)	peroxisome [IDA]			1043
P37238 UniProt NPD GO	PPARG_MOUSE	Peroxisome proliferator-activated receptor gamma (PPAR-gamma)	0.36	+	cyt	0	Nucleus	cytosol [IDA] nucleus [IDA] transcriptional repressor complex [IC]			505
O88275 UniProt NPD GO	PPARG_RAT	Peroxisome proliferator-activated receptor gamma (PPAR-gamma)	0.36	+	cyt	0	Nucleus				505
P80463 UniProt NPD GO	PHS1_PHALU	Phaseolin precursor	0.36	-	gol	1 *	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies				428
P25055 UniProt NPD GO	PGKA_CRIFA	Phosphoglycerate kinase, glycosomal (EC 2.7.2.3) (Phosphoglycerate kinase A)	0.36	-	cyt	0	Glycosome				505
P84741 UniProt NPD GO	PBLFB_EUGGR	Photoactivated adenylate cyclase subunit beta-like protein FB	0.36	-	mit	0	Flagellum. Paraxonemal body. And paraxonemal bodies (PABs)	flagellum [IDA]			859
Q85FL9 UniProt NPD GO	YCF3_ADICA	Photosystem I assembly protein ycf3	0.36	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				183
P12357 UniProt NPD GO	PSAG_SPIOL	Photosystem I reaction center subunit V, chloroplast precursor (PSI-G) (Photosystem I 9 kDa protein) ...	0.36	-	mit	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				167
P36505 UniProt NPD GO	PHY1_PHYPA	Phytochrome 1	0.36	-	mit	0					1132
P19862 UniProt NPD GO	PHYA1_MAIZE	Phytochrome A	0.36	-	mit	0					1131
P10931 UniProt NPD GO	PHYA_ORYSA	Phytochrome A	0.36	-	mit	0					1128
O49934 UniProt NPD GO	PHYA_POPTM	Phytochrome A	0.36	-	mit	0					1125
P37272 UniProt NPD GO	PSY_CAPAN	Phytoene synthase, chloroplast precursor (EC 2.5.1.-)	0.36	-	cyt	0	Plastid; chloroplast				419
P49763 UniProt NPD GO	PLGF_HUMAN	Placenta growth factor precursor (PlGF)	0.36	-	nuc	0	Secreted protein. The three forms are secreted but PlGF-2 appears to remain cell attached unless rel ...		601121	1RV6	221
P34770 UniProt NPD GO	RK22_ASTLO	Plastid 50S ribosomal protein L22	0.36	-	nuc	0	Plastid				115
P48532 UniProt NPD GO	PTB1_XENLA	Pleiotrophic factor-beta-1 precursor (PTF-beta-1)	0.36	-	nuc	1 *	Secreted protein (By similarity)				161
Q76CU2 UniProt NPD GO	PDR1_TOBAC	Pleiotropic drug resistance protein 1 (NtPDR1)	0.36	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1434
Q7PC87 UniProt NPD GO	PDR6_ARATH	Pleiotropic drug resistance protein 6	0.36	-	end	12	Membrane; multi-pass membrane protein (By similarity)				1453
Q8GU87 UniProt NPD GO	PDR6_ORYSA	Pleiotropic drug resistance protein 6	0.36	-	end	13					1450
Q9M5J8 UniProt NPD GO	PGIP2_ARATH	Polygalacturonase inhibitor 2 precursor (Polygalacturonase-inhibiting protein) (PGIP-2)	0.36	-	exc	0	Cell wall; peripheral membrane protein				330
O70570 UniProt NPD GO	PIGR_MOUSE	Polymeric-immunoglobulin receptor precursor (Poly-Ig receptor) (PIGR) [Contains: Secretory component ...	0.36	-	exc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein				771
Q29099 UniProt NPD GO	PTBP1_PIG	Polypyrimidine tract-binding protein 1 (PTB) (Heterogeneous nuclear ribonucleoprotein I) (hnRNP I)	0.36	-	nuc	0	Nucleus				557
Q6FNR4 UniProt NPD GO	HEM3_CANGA	Porphobilinogen deaminase (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyri ...	0.36	-	mit	0					329
Q09899 UniProt NPD GO	HEM3_SCHPO	Porphobilinogen deaminase (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyri ...	0.36	-	cyt	0					336
P57789 UniProt NPD GO	KCNKA_HUMAN	Potassium channel subfamily K member 10 (Outward rectifying potassium channel protein TREK-2) (TREK- ...	0.36	-	end	6	Membrane; multi-pass membrane protein (Potential)		605873		538
P19024 UniProt NPD GO	KCNA5_RAT	Potassium voltage-gated channel subfamily A member 5 (Voltage-gated potassium channel subunit Kv1.5) ...	0.36	-	end	3	Membrane; multi-pass membrane protein				602
P22462 UniProt NPD GO	KCNC2_RAT	Potassium voltage-gated channel subfamily C member 2 (Voltage-gated potassium channel subunit Kv3.2) ...	0.36	+	end	6	Membrane; multi-pass membrane protein				638
Q63472 UniProt NPD GO	KCNH1_RAT	Potassium voltage-gated channel subfamily H member 1 (Voltage-gated potassium channel subunit Kv10.1 ...	0.36	-	end	4	Membrane; multi-pass membrane protein				962
P27112 UniProt NPD GO	ATP4A_RABIT	Potassium-transporting ATPase alpha chain 1 (EC 3.6.3.10) (Proton pump) (Gastric H+/K+ ATPase subuni ...	0.36	-	end	8	Membrane; multi-pass membrane protein				1034
Q6BMD1 UniProt NPD GO	SLT11_DEBHA	Pre-mRNA-splicing factor SLT11	0.36	-	nuc	0	Nucleus (By similarity)				359
Q5BE22 UniProt NPD GO	PRP46_EMENI	Pre-mRNA-splicing factor prp46 (Pre-mRNA-processing protein 46)	0.36	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				452
Q9UJX0 UniProt NPD GO	OKL38_HUMAN	Pregnancy-induced growth inhibitor OKL38 (huOKL38) (Ovary, kidney and liver protein 38)	0.36	-	end	0			607975		560

You are viewing entries 35201 to 35250 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.