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
P69301 UniProt NPD GO	KM11_TRYBR	Kinetoplastid membrane protein 11 (KMP-11)	0.15	-	nuc	0	Cytoplasm. Associated with microtubules				92
Q16773 UniProt NPD GO	KAT1_HUMAN	Kynurenine--oxoglutarate transaminase 1 (EC 2.6.1.7) (Kynurenine--oxoglutarate transaminase I) (Kynu ...	0.15	-	cyt	0	Cytoplasm	cytosol [TAS]	600547	1W7N	422
Q8BTY1 UniProt NPD GO	KAT1_MOUSE	Kynurenine--oxoglutarate transaminase 1 (EC 2.6.1.7) (Kynurenine--oxoglutarate transaminase I) (Kynu ...	0.15	-	cyt	0	Cytoplasm (By similarity)				424
P23623 UniProt NPD GO	OXLA_NEUCR	L-amino-acid oxidase precursor (EC 1.4.3.2) (LAO)	0.15	-	mit	0					696
P40976 UniProt NPD GO	LYS2_SCHPO	L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (Alpha-aminoadipate reductase) (Alpha-AR)	0.15	-	mit	1					1419
Q75BB3 UniProt NPD GO	LYS2_ASHGO	L-aminoadipate-semialdehyde dehydrogenase large subunit (EC 1.2.1.31) (Alpha-aminoadipate reductase) ...	0.15	-	cyt	0					1385
Q8N0W3 UniProt NPD GO	FUK_HUMAN	L-fucose kinase (EC 2.7.1.52) (Fucokinase)	0.15	-	cyt	0			608675		1084
Q27797 UniProt NPD GO	LDH_TOXGO	L-lactate dehydrogenase (EC 1.1.1.27) (LDH)	0.15	-	mit	0				1SOW	326
Q6ZMG9 UniProt NPD GO	LASS6_HUMAN	LAG1 longevity assurance homolog 6	0.15	-	end	5 *	Nucleus; nuclear membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum; endoplasm ...				384
Q02079 UniProt NPD GO	LAC3_THACU	Laccase 3 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.15	-	vac	0	Secreted protein				572
Q6P7Q4 UniProt NPD GO	LGUL_RAT	Lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (Glx I) (Ke ...	0.15	-	cyt	0		cytoplasm [ISS]			183
P50107 UniProt NPD GO	LGUL_YEAST	Lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (Glx I) (Ke ...	0.15	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			326
Q5RDZ2 UniProt NPD GO	CRYL1_PONPY	Lambda-crystallin homolog	0.15	-	cyt	0					318
Q9BS40 UniProt NPD GO	LXN_HUMAN	Latexin (Endogenous carboxypeptidase inhibitor) (ECI) (Tissue carboxypeptidase inhibitor) (TCI) (MUM ...	0.15	-	cyt	0	Cytoplasm (Probable)		609305	2BO9	222
Q6ZSA7 UniProt NPD GO	LRC55_HUMAN	Leucine-rich repeat-containing protein 55	0.15	-	nuc	1	Membrane; single-pass membrane protein (Potential)				341
O08843 UniProt NPD GO	LST1_MOUSE	Leukocyte-specific transcript 1 protein (B144 protein)	0.15	-	nuc	1 *	Membrane; single-pass membrane protein (By similarity). Also detected in a perinuclear region corres ...	cytoplasm [ISS] Golgi apparatus [ISS] integral to membrane [ISS]			95
P19602 UniProt NPD GO	LKHA4_CAVPO	Leukotriene A-4 hydrolase (EC 3.3.2.6) (LTA-4 hydrolase) (Leukotriene A(4) hydrolase)	0.15	-	cyt	0	Cytoplasm				610
O88855 UniProt NPD GO	LT4R1_MOUSE	Leukotriene B4 receptor 1 (LTB4-R 1)	0.15	+	end	7 *	Membrane; multi-pass membrane protein				351
Q6VQA8 UniProt NPD GO	CHLB_CHLPR	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.15	-	cyt	0	Plastid; chloroplast				510
P56302 UniProt NPD GO	CHLB_CHLVU	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.15	-	cyt	0	Plastid; chloroplast				510
Q9P4E5 UniProt NPD GO	LIP10_CANAL	Lipase 10 precursor (EC 3.1.1.3)	0.15	-	end	0	Secreted protein				465
P30624 UniProt NPD GO	LCF1_YEAST	Long-chain-fatty-acid--CoA ligase 1 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 1) (Fatty acid acti ...	0.15	-	mit	0		lipid particle [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			700
P51890 UniProt NPD GO	LUM_CHICK	Lumican precursor (Keratan sulfate proteoglycan lumican) (KSPG lumican)	0.15	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				343
Q05443 UniProt NPD GO	LUM_BOVIN	Lumican precursor (Keratan sulfate proteoglycan) (KSPG) (Corneal keratan sulfate proteoglycan 37B co ...	0.15	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				342
P49118 UniProt NPD GO	BIP_LYCES	Luminal-binding protein precursor (BiP) (78 kDa glucose-regulated protein homolog) (GRP 78)	0.15	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				666
Q61790 UniProt NPD GO	LAG3_MOUSE	Lymphocyte activation gene 3 protein precursor (LAG-3)	0.15	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			521
O95711 UniProt NPD GO	LY86_HUMAN	Lymphocyte antigen 86 precursor (MD-1 protein)	0.15	-	end	0	Secreted protein; extracellular space. Associated with CD180 at the cell surface	plasma membrane [TAS]	605241		162
Q14210 UniProt NPD GO	LY6D_HUMAN	Lymphocyte antigen Ly-6D precursor (E48 antigen)	0.15	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor	membrane fraction [TAS]	606204		128
P35460 UniProt NPD GO	LY6F_MOUSE	Lymphocyte antigen Ly-6F.1 precursor	0.15	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				134
P79180 UniProt NPD GO	LYSC_HYLLA	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.15	-	vac	0					148
Q9DFS4 UniProt NPD GO	MLN64_BRARE	MLN64-like protein (START domain-containing protein 3)	0.15	-	end	3					448
P13369 UniProt NPD GO	CSF1R_FELCA	Macrophage colony-stimulating factor 1 receptor precursor (CSF-1-R) (EC 2.7.10.1) (Fms proto-oncogen ...	0.15	-	end	1	Membrane; single-pass type I membrane protein				980
P07333 UniProt NPD GO	CSF1R_HUMAN	Macrophage colony-stimulating factor 1 receptor precursor (CSF-1-R) (EC 2.7.10.1) (Fms proto-oncogen ...	0.15	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	164770		972
P53017 UniProt NPD GO	MSP19_CAEEL	Major sperm protein 19/31/40/45/50/51/53/59/61/65/81/113/142 (MSP)	0.15	-	cyt	0				1GRW	126
P53019 UniProt NPD GO	MSP33_CAEEL	Major sperm protein 33 (MSP)	0.15	-	cyt	0					126
P53020 UniProt NPD GO	MSP38_CAEEL	Major sperm protein 38 (MSP)	0.15	-	cyt	0					126
Q17856 UniProt NPD GO	MSP55_CAEEL	Major sperm protein 55/57 (MSP)	0.15	-	cyt	0					126
P52426 UniProt NPD GO	MDHP_SPIOL	Malate dehydrogenase [NADP], chloroplast precursor (EC 1.1.1.82) (NADP-MDH)	0.15	-	cyt	0	Plastid; chloroplast				435
P49081 UniProt NPD GO	MASY_MAIZE	Malate synthase, glyoxysomal (EC 2.3.3.9)	0.15	-	cyt	0	Glyoxysome				559
Q29407 UniProt NPD GO	MEA1_BOVIN	Male-enhanced antigen 1 (Mea-1)	0.15	-	cyt	0					174
Q01645 UniProt NPD GO	MS84D_DROME	Male-specific sperm protein Mst84Dd	0.15	-	nuc	0					72
O16098 UniProt NPD GO	MAL1_DROVI	Maltase 1 precursor (EC 3.2.1.20)	0.15	-	exc	0					586
P29952 UniProt NPD GO	MANA_YEAST	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.15	-	nuc	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			428
Q8J0Q0 UniProt NPD GO	MNS1_CANAL	Mannosyl-oligosaccharide 1,2-alpha-mannosidase (EC 3.2.1.113) (Man(9)-alpha-mannosidase)	0.15	-	cyt	0					565
Q9UUB7 UniProt NPD GO	SWI5_SCHPO	Mating-type switching protein swi5 (DNA repair protein swi5)	0.15	-	nuc	0					85
P14780 UniProt NPD GO	MMP9_HUMAN	Matrix metalloproteinase-9 precursor (EC 3.4.24.35) (MMP-9) (92 kDa type IV collagenase) (92 kDa gel ...	0.15	-	exc	0		extracellular space [IDA]	120361	1LKG	707
Q58T59 UniProt NPD GO	M6H10_BOMMX	Maximins 6/H10 precursor [Contains: Maximin-6; Maximin-H10]	0.15	-	end	0	Secreted protein				144
Q9JI70 UniProt NPD GO	MKKS_MOUSE	McKusick-Kaufman/Bardet-Biedl syndromes putative chaperonin	0.15	-	mit	0					570
P41367 UniProt NPD GO	ACADM_PIG	Medium-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.3) (MCAD)	0.15	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [ISS] mitochondrion [ISS]		3MDE	421
P83419 UniProt NPD GO	MRN3_MEGVI	Megourin-3	0.15	-	nuc	0	Secreted protein				63

You are viewing entries 57151 to 57200 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.