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
P51180 UniProt NPD GO	MIP_MOUSE	Lens fiber major intrinsic protein (Aquaporin-0) (MIP26) (MP26)	0.02	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			263
P09011 UniProt NPD GO	MIP_RAT	Lens fiber major intrinsic protein (Aquaporin-0) (MIP26) (MP26) (Fragment)	0.02	-	end	6 *	Membrane; multi-pass membrane protein				261
P20274 UniProt NPD GO	LMIP_BOVIN	Lens fiber membrane intrinsic protein (MP18) (MP19) (MP21) (MP23)	0.02	-	end	4 *	Membrane; multi-pass membrane protein				173
P81761 UniProt NPD GO	SCIT_MESTA	Lepidopteran-selective toxin precursor (ButaIT) (BTChl2)	0.02	-	exc	1 *	Secreted protein	extracellular region [IDA]			62
Q9NDA6 UniProt NPD GO	COW3_CONTE	Leu-contryphan-Tx precursor	0.02	-	exc	0	Secreted protein				63
Q3UY51 UniProt NPD GO	LRC55_MOUSE	Leucine-rich repeat-containing protein 55	0.02	-	end	1	Membrane; single-pass membrane protein (Potential)				311
Q4KLL3 UniProt NPD GO	LRC55_RAT	Leucine-rich repeat-containing protein 55	0.02	-	end	1	Membrane; single-pass membrane protein (Potential)				311
P05087 UniProt NPD GO	PHAL_PHAVU	Leucoagglutinating phytohemagglutinin precursor (PHA-L)	0.02	-	exc	0				1G8W	272
P04428 UniProt NPD GO	LSK1_LEUMA	Leucosulfakinin-1 (Leucosulfakinin-I) (LSK-I)	0.02	-		0					11
O62644 UniProt NPD GO	LECT2_BOVIN	Leukocyte cell-derived chemotaxin 2 precursor (bLECT2) (Chondromodulin II) (bChM-II)	0.02	-	exc	0	Secreted protein				151
O14960 UniProt NPD GO	LECT2_HUMAN	Leukocyte cell-derived chemotaxin 2 precursor (hLECT2)	0.02	-	exc	0	Cytoplasm. Secreted protein	cytoplasm [TAS] extracellular space [TAS]	602882		151
Q5REL0 UniProt NPD GO	CD47_PONPY	Leukocyte surface antigen CD47 precursor (Integrin-associated protein) (IAP)	0.02	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				323
Q08722 UniProt NPD GO	CD47_HUMAN	Leukocyte surface antigen CD47 precursor (Integrin-associated protein) (IAP) (Antigenic surface dete ...	0.02	-	end	6 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	601028		323
Q8LU58 UniProt NPD GO	CHLL_CHAGL	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.02	-	nuc	0	Plastid; chloroplast				290
Q6VQA9 UniProt NPD GO	CHLL_CHLPR	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.02	-	nuc	0	Plastid; chloroplast				300
P56291 UniProt NPD GO	CHLL_CHLVU	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.02	-	nuc	0	Plastid; chloroplast				300
P06267 UniProt NPD GO	CHLL_MARPO	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.02	-	nuc	0	Plastid; chloroplast				289
Q9MUM2 UniProt NPD GO	CHLL_MESVI	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.02	-	nuc	0	Plastid; chloroplast				296
Q9T399 UniProt NPD GO	CHLL_NEPOL	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.02	-	cyt	0	Plastid; chloroplast				287
P41645 UniProt NPD GO	CHLL_PINTH	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.02	-	nuc	0	Plastid; chloroplast				291
P51187 UniProt NPD GO	CHLL_PORPU	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.02	-	nuc	0	Plastid; chloroplast				290
P36439 UniProt NPD GO	CHLL_POLAC	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.02	-	nuc	0	Plastid; chloroplast				160
P37847 UniProt NPD GO	CHLB_LYCAN	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.02	-	cyt	0	Plastid; chloroplast				103
P37848 UniProt NPD GO	CHLB_LYCCO	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.02	-	cyt	0	Plastid; chloroplast				103
Q33076 UniProt NPD GO	CHLB_SPHCO	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.02	-	cyt	0	Plastid; chloroplast				103
Q03200 UniProt NPD GO	LIRP1_ORYSA	Light-regulated protein precursor	0.02	-	mit	0					128
P79066 UniProt NPD GO	LIP1_GEOFE	Lipase 1 precursor (EC 3.1.1.3) (Lipase I) (TFL I)	0.02	-	exc	0	Secreted protein				563
O88956 UniProt NPD GO	LPP1_CAVPO	Lipid phosphate phosphohydrolase 1 (EC 3.1.3.4) (Phosphatidic acid phosphatase 2a) (Phosphatidate ph ...	0.02	-	end	5 *	Cell membrane; multi-pass membrane protein (By similarity)	membrane fraction [ISS]			285
Q9DAX2 UniProt NPD GO	LPP2_MOUSE	Lipid phosphate phosphohydrolase 2 (EC 3.1.3.4) (Phosphatidic acid phosphatase 2c) (Phosphatidate ph ...	0.02	-	end	6 *	Membrane; multi-pass membrane protein				276
P11181 UniProt NPD GO	ODB2_BOVIN	Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitocho ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix				482
P11182 UniProt NPD GO	ODB2_HUMAN	Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitocho ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix	alpha-ketoglutarate dehydrogenase complex (... [TAS] mitochondrion [TAS]	248600	2COO	482
Q5PRC1 UniProt NPD GO	LHFP_BRARE	Lipoma HMGIC fusion partner homolog precursor	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				200
Q9Y693 UniProt NPD GO	LHFP_HUMAN	Lipoma HMGIC fusion partner precursor	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)		606710		200
Q8BM86 UniProt NPD GO	LHFP_MOUSE	Lipoma HMGIC fusion partner precursor	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				200
Q5BJS2 UniProt NPD GO	LHFP_RAT	Lipoma HMGIC fusion partner precursor	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				200
Q6DHB5 UniProt NPD GO	LHPL3_BRARE	Lipoma HMGIC fusion partner-like 3 protein homolog	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				216
P23953 UniProt NPD GO	ESTN_MOUSE	Liver carboxylesterase N precursor (EC 3.1.1.1) (PES-N) (Lung surfactant convertase)	0.02	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Microsomal membrane, lumen of endoplasmic reticu ...				554
P41488 UniProt NPD GO	LPK2_LOCMI	Locustapyrokinin-2 (Lom-PK-2) (FXPRL-amide)	0.02	-		0	Secreted protein				10
P30249 UniProt NPD GO	TKL3_LOCMI	Locustatachykinin-3 (Locustatachykinin III) (TK-III)	0.02	-		0	Secreted protein				10
P30250 UniProt NPD GO	TKL4_LOCMI	Locustatachykinin-4 (Locustatachykinin IV) (TK-IV)	0.02	-		0	Secreted protein				10
P01397 UniProt NPD GO	NXL2_DENPO	Long neurotoxin 2 (Neurotoxin delta) (Toxin TN2)	0.02	-	nuc	0	Secreted protein				72
P14896 UniProt NPD GO	ELI6_HORVU	Low molecular mass early light-inducible protein HV60, chloroplast precursor (ELIP)	0.02	-	nuc	0	Plastid; chloroplast. Associated with both photosystems I and II				167
P32466 UniProt NPD GO	HXT3_YEAST	Low-affinity glucose transporter HXT3	0.02	-	end	11	Membrane; multi-pass membrane protein				567
P38734 UniProt NPD GO	MUP3_YEAST	Low-affinity methionine permease	0.02	-	end	12	Membrane; multi-pass membrane protein (Potential)				546
P82745 UniProt NPD GO	LCR30_ARATH	Low-molecular-weight cysteine-rich protein LCR30 precursor	0.02	-	exc	0					76
P17554 UniProt NPD GO	LUCI_VARHI	Luciferin 2-monooxygenase precursor (EC 1.13.12.6) (Cypridina-type luciferase)	0.02	-	nuc	0					555
P13129 UniProt NPD GO	LUCI_LUCCR	Luciferin 4-monooxygenase (EC 1.13.12.7) (Luciferase)	0.02	-	nuc	0	Peroxisome (By similarity)			2D1T	548
P08659 UniProt NPD GO	LUCI_PHOPY	Luciferin 4-monooxygenase (EC 1.13.12.7) (Luciferase)	0.02	-	mit	0	Peroxisome	peroxisome [IDA]		1LCI	550
P05938 UniProt NPD GO	LBP_RENRE	Luciferin-binding protein (LBP)	0.02	-	cyt	0					184
P45646 UniProt NPD GO	LSHB_MELGA	Lutropin beta chain precursor (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.02	-	end	0	Secreted protein				159

You are viewing entries 84201 to 84250 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.