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
P40423 UniProt NPD GO	MLRN_DROME	Myosin regulatory light chain, nonmuscle (MRLC-C) (Protein spaghetti-squash)	0.26	-	mit	0					174
Q9Z2C4 UniProt NPD GO	MTMR1_MOUSE	Myotubularin-related protein 1 (EC 3.1.3.-)	0.26	-	mit	0		cytoplasm [IDA] plasma membrane [IDA]			669
Q8BWP8 UniProt NPD GO	B3GN6_MOUSE	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase (EC 2.4.1.149) (Poly-N-acetyllactosam ...	0.26	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				415
P51098 UniProt NPD GO	NU5C_ATHGR	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.26	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				741
Q32131 UniProt NPD GO	NU5C_DIGGR	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.26	-	end	13 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				699
P33294 UniProt NPD GO	SIR2_KLULA	NAD-dependent histone deacetylase SIR2 (EC 3.5.1.-) (Regulatory protein SIR2) (Silent information re ...	0.26	-	nuc	0	Nucleus (Potential)				670
P41755 UniProt NPD GO	DHE2_ACHKL	NAD-specific glutamate dehydrogenase (EC 1.4.1.2) (NAD-GDH)	0.26	-	end	5 *					1063
Q9CQZ5 UniProt NPD GO	NDUA6_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.26	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side	mitochondrion [IDA]			131
P80261 UniProt NPD GO	NUGM_SOLTU	NADH-ubiquinone oxidoreductase 27 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-27KD) (CI-27KD) ...	0.26	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				190
Q5DUX5 UniProt NPD GO	NUCH_NYCOV	NADH-ubiquinone oxidoreductase 49 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (NADH dehydrogenase subunit ...	0.26	-	mit	0	Hydrogenosome				412
P41297 UniProt NPD GO	NU2M_BALMU	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.26	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P93401 UniProt NPD GO	NU2M_OENBE	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.26	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				488
O03204 UniProt NPD GO	NU4M_CERSI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.26	-	end	13 *					459
P92484 UniProt NPD GO	NU4M_EQUAS	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.26	-	end	12 *					459
P48655 UniProt NPD GO	NU4M_HORSE	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.26	-	end	12 *					459
P03909 UniProt NPD GO	NU4M_HYLLA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.26	-	end	12 *					459
Q2I3G4 UniProt NPD GO	NU5M_ELEMA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.26	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
P03915 UniProt NPD GO	NU5M_HUMAN	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.26	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)	respiratory chain complex I (sensu Eukaryota) [NAS]	535000		603
Q07994 UniProt NPD GO	NCPR_MUSDO	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.26	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Anchored to the ...				671
Q75AF2 UniProt NPD GO	UBC12_ASHGO	NEDD8-conjugating enzyme UBC12 (EC 6.3.2.-) (RUB1-conjugating enzyme) (RUB1-protein ligase) (Ubiquit ...	0.26	-	mit	0					184
O95944 UniProt NPD GO	NCTR2_HUMAN	Natural cytotoxicity triggering receptor 2 precursor (Natural killer cell p44-related protein) (NKp4 ...	0.26	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	604531	1HKF	276
Q13241 UniProt NPD GO	KLRD1_HUMAN	Natural killer cells antigen CD94 (NK cell receptor) (Killer cell lectin-like receptor subfamily D m ...	0.26	-	nuc	1 *	Membrane; single-pass type II membrane protein	plasma membrane [TAS]	602894	1B6E	179
Q96CW9 UniProt NPD GO	NTNG2_HUMAN	Netrin G2 precursor (Laminet-2)	0.26	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	anchored to plasma membrane [ISS]			530
Q94887 UniProt NPD GO	NRX4_DROME	Neurexin-4 precursor (Neurexin IV)	0.26	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [NAS] pleated septate junction [IDA]			1284
P54938 UniProt NPD GO	NFM_RABIT	Neurofilament triplet M protein (160 kDa neurofilament protein) (Neurofilament medium polypeptide) ( ...	0.26	-	nuc	0					644
Q9GZQ4 UniProt NPD GO	NMUR2_HUMAN	Neuromedin U receptor 2 (NMU-R2) (G-protein coupled receptor TGR-1) (G-protein coupled receptor FM-4 ...	0.26	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IDA]	605108		415
Q4PL64 UniProt NPD GO	HPCA_BOVIN	Neuron-specific calcium-binding protein hippocalcin	0.26	-	nuc	0					192
P84075 UniProt NPD GO	HPCA_MOUSE	Neuron-specific calcium-binding protein hippocalcin	0.26	-	nuc	0					192
P84074 UniProt NPD GO	HPCA_HUMAN	Neuron-specific calcium-binding protein hippocalcin (Calcium-binding protein BDR-2)	0.26	-	nuc	0			142622		192
P84076 UniProt NPD GO	HPCA_RAT	Neuron-specific calcium-binding protein hippocalcin (P23K)	0.26	-	nuc	0					192
P12390 UniProt NPD GO	ACHB2_RAT	Neuronal acetylcholine receptor protein subunit beta-2 precursor (Neuronal acetylcholine receptor no ...	0.26	+	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [IDA]			500
Q810U4 UniProt NPD GO	NRCAM_MOUSE	Neuronal cell adhesion molecule precursor (Nr-CAM) (NgCAM-related cell adhesion molecule) (Ng-CAM-re ...	0.26	-	end	1 *	Membrane; single-pass type I membrane protein	external side of plasma membrane [ISS] integral to plasma membrane [ISS] neuron projection [ISS]			1256
P97686 UniProt NPD GO	NRCAM_RAT	Neuronal cell adhesion molecule precursor (Nr-CAM) (NgCAM-related cell adhesion molecule) (Ng-CAM-re ...	0.26	-	nuc	1	Cell membrane; single-pass type I membrane protein. Localized to axonal membranes at the node of Ran ...	external side of plasma membrane [ISS] integral to plasma membrane [ISS] neuron projection [ISS]			1214
O95502 UniProt NPD GO	NPTXR_HUMAN	Neuronal pentraxin receptor	0.26	-	end	1 *	Membrane; single-pass type II membrane protein (Potential)		609474		499
P79795 UniProt NPD GO	NRP1_CHICK	Neuropilin-1 precursor (A5 protein)	0.26	-	nuc	1	Membrane; single-pass type I membrane protein				914
P84470 UniProt NPD GO	TX2B_BUNCA	Neurotoxin T2 B chain (Fragment)	0.26	-		0	Secreted protein				15
Q5G270 UniProt NPD GO	NETR_GORGO	Neurotrypsin precursor (EC 3.4.21.-)	0.26	-	end	0	Secreted protein				876
Q5G267 UniProt NPD GO	NETR_MACMU	Neurotrypsin precursor (EC 3.4.21.-)	0.26	-	end	0	Secreted protein				875
Q5G269 UniProt NPD GO	NETR_PONPY	Neurotrypsin precursor (EC 3.4.21.-)	0.26	-	end	0	Secreted protein				877
Q5G265 UniProt NPD GO	NETR_SAGLB	Neurotrypsin precursor (EC 3.4.21.-)	0.26	-	end	0	Secreted protein				875
Q9NR71 UniProt NPD GO	ASAH2_HUMAN	Neutral ceramidase (EC 3.5.1.23) (NCDase) (N-CDase) (Acylsphingosine deacylase 2) (N-acylsphingosine ...	0.26	-	end	1 *	Cell membrane; single-pass type II membrane protein. The neutral ceramidase soluble form is a secret ...	mitochondrion [TAS]			780
P49381 UniProt NPD GO	TREA_KLULA	Neutral trehalase (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.26	-	nuc	0	Cytoplasm (By similarity)				754
O70138 UniProt NPD GO	MMP8_MOUSE	Neutrophil collagenase precursor (EC 3.4.24.34) (Matrix metalloproteinase-8) (MMP-8) (Collagenase 2) ...	0.26	-	exc	0	Stored in intracellular granules and released during inflammatory conditions	extracellular space [ISS]			465
P22894 UniProt NPD GO	MMP8_HUMAN	Neutrophil collagenase precursor (EC 3.4.24.34) (Matrix metalloproteinase-8) (MMP-8) (PMNL collagena ...	0.26	-	nuc	0	Stored in intracellular granules	extracellular space [IDA]	120355	1ZVX	467
P81467 UniProt NPD GO	DEF3_MESAU	Neutrophil defensin 3 (HANP-3)	0.26	-	nuc	0	Secreted protein				33
Q23316 UniProt NPD GO	NICA_CAEEL	Nicastrin precursor (Anterior-pharynx-defective protein 2)	0.26	-	end	1	Membrane; single-pass type I membrane protein (Potential)				723
Q9NPI5 UniProt NPD GO	NRK2_HUMAN	Nicotinamide riboside kinase 2 (EC 2.7.1.-) (Integrin beta-1-binding protein 3) (Muscle integrin-bin ...	0.26	-	cyt	0			608705		230
O88322 UniProt NPD GO	NID2_MOUSE	Nidogen-2 precursor (NID-2) (Entactin-2)	0.26	-	end	0	Secreted protein; extracellular space; extracellular matrix	basement membrane [IDA]			1403
Q86X76 UniProt NPD GO	NIT1_HUMAN	Nitrilase homolog 1 (EC 3.5.-.-)	0.26	-	mit	0			604618		327
Q9XFS7 UniProt NPD GO	NLTP5_ARATH	Nonspecific lipid-transfer protein 5 precursor (LTP 5)	0.26	-	exc	0					118

You are viewing entries 44401 to 44450 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.