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
Q4R5E2 UniProt NPD GO	NDUA2_MACFA	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.19	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				98
Q9NRX3 UniProt NPD GO	NUA4L_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4-like 2 (NADH-ubiquinone oxidoreductase ...	0.19	-	nuc	1 *					87
P25710 UniProt NPD GO	NUJM_NEUCR	NADH-ubiquinone oxidoreductase 21.3 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3)	0.19	-	cyt	3 *	Mitochondrion; mitochondrial inner membrane				200
O78693 UniProt NPD GO	NU1M_ATEPA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.19	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
P92718 UniProt NPD GO	NU1M_PONPP	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.19	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q94VC3 UniProt NPD GO	NU1M_VARRU	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.19	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
O63796 UniProt NPD GO	NU2M_ANACA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.19	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
O63775 UniProt NPD GO	NU2M_ANAFO	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.19	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
Q36346 UniProt NPD GO	NU2M_CAPHI	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.19	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
O21798 UniProt NPD GO	NU2M_PANTR	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.19	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
O79671 UniProt NPD GO	NU2M_PELSU	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.19	-	cyt	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
P48906 UniProt NPD GO	NU2M_PICCA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.19	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				567
O21398 UniProt NPD GO	NU2M_STRCA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.19	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
Q94VE5 UniProt NPD GO	NU2M_VARML	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.19	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				345
P41298 UniProt NPD GO	NU4M_BALMU	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.19	-	end	13 *					459
P05508 UniProt NPD GO	NU4M_RAT	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.19	-	end	13 *					459
P48921 UniProt NPD GO	NU5M_FELCA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.19	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
P13697 UniProt NPD GO	MAOX_RAT	NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME) (Malic enzyme 1)	0.19	-	mit	0	Cytoplasm	cytosol [IDA]			572
P37040 UniProt NPD GO	NCPR_MOUSE	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.19	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Anchored to the ...	microsome [IDA] soluble fraction [IDA]			677
Q02883 UniProt NPD GO	FMP30_YEAST	NAPE-hydrolyzing phospholipase D, mitochondrial precursor (EC 3.1.4.-) (Found in mitochondrial prote ...	0.19	-	mit	1	Mitochondrion; mitochondrial membrane; single-pass membrane protein (Potential)	mitochondrion [IDA]			468
Q4R3L6 UniProt NPD GO	ULA1_MACFA	NEDD8-activating enzyme E1 regulatory subunit (Amyloid protein-binding protein 1) (Amyloid beta prec ...	0.19	-	nuc	0	Cell membrane. Colocalizes with APP in lipid rafts (By similarity)				510
Q8VBW6 UniProt NPD GO	ULA1_MOUSE	NEDD8-activating enzyme E1 regulatory subunit (Amyloid protein-binding protein 1) (Amyloid beta prec ...	0.19	-	nuc	0	Cell membrane. Colocalizes with APP in lipid rafts (By similarity)				534
Q9Z1A5 UniProt NPD GO	ULA1_RAT	NEDD8-activating enzyme E1 regulatory subunit (Amyloid protein-binding protein 1) (Amyloid beta prec ...	0.19	-	nuc	0	Cell membrane. Colocalizes with APP in lipid rafts				534
Q6FVQ8 UniProt NPD GO	UBC12_CANGA	NEDD8-conjugating enzyme UBC12 (EC 6.3.2.-) (RUB1-conjugating enzyme) (RUB1-protein ligase) (Ubiquit ...	0.19	-	nuc	0					187
Q60778 UniProt NPD GO	IKBB_MOUSE	NF-kappa-B inhibitor beta (NF-kappa-BIB) (I-kappa-B-beta) (IkappaBbeta) (IKB-beta) (IKB-B)	0.19	-	nuc	0	Cytoplasm. Nucleus			1OY3	359
Q9JIA3 UniProt NPD GO	IKBB_RAT	NF-kappa-B inhibitor beta (NF-kappa-BIB) (I-kappa-B-beta) (IkappaBbeta) (IKB-beta) (IKB-B)	0.19	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				359
Q9CWS0 UniProt NPD GO	DDAH1_MOUSE	NG,NG-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18) (Dimethylargininase-1) (Dimethylargini ...	0.19	-	nuc	0					284
Q5IS82 UniProt NPD GO	NTRK3_SAIBB	NT-3 growth factor receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase receptor type 3)	0.19	-	nuc	2 *	Membrane; single-pass type I membrane protein (By similarity)				825
Q9R044 UniProt NPD GO	NPHN_RAT	Nephrin precursor (Renal glomerulus-specific cell adhesion receptor)	0.19	-	end	1	Cell membrane; single-pass type I membrane protein (Potential). Located at podocyte slit diaphragm b ...				1234
Q9Y2I2 UniProt NPD GO	NTNG1_HUMAN	Netrin G1 precursor (Laminet-1)	0.19	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	anchored to plasma membrane [ISS]	608818		539
P61602 UniProt NPD GO	NCALD_BOVIN	Neurocalcin delta	0.19	-	cyt	0		clathrin coat of trans-Golgi network vesicle [ISS] cytosol [ISS]		1BJF	192
P61601 UniProt NPD GO	NCALD_HUMAN	Neurocalcin delta	0.19	-	cyt	0		clathrin coat of trans-Golgi network vesicle [NAS] cytosol [NAS]	606722		192
Q91X97 UniProt NPD GO	NCALD_MOUSE	Neurocalcin delta	0.19	-	cyt	0					192
P08435 UniProt NPD GO	TKNK_RAT	Neurokinin-B precursor (NKB) (Neuromedin-K)	0.19	-	exc	0	Secreted protein				116
O55040 UniProt NPD GO	NMUR1_MOUSE	Neuromedin U receptor 1 (NMU-R1) (G-protein coupled receptor 66) (G-protein coupled receptor FM-3)	0.19	+	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IC]			405
P09483 UniProt NPD GO	ACHA4_RAT	Neuronal acetylcholine receptor protein subunit alpha-4 precursor	0.19	-	end	4 *	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [IMP]			630
P17787 UniProt NPD GO	ACHB2_HUMAN	Neuronal acetylcholine receptor protein subunit beta-2 precursor	0.19	+	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]	605375		502
P35331 UniProt NPD GO	NRCAM_CHICK	Neuronal cell adhesion molecule precursor (Nr-CAM) (NgCAM-related cell adhesion molecule) (Ng-CAM-re ...	0.19	-	nuc	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [ISS] integral to plasma membrane [ISS] intercellular junction [IDA] neuron projection [ISS]			1284
P41334 UniProt NPD GO	NPF_ARTTR	Neuropeptide F (NPF)	0.19	-	nuc	0	Secreted protein				36
Q90WF4 UniProt NPD GO	NEUY_PAROL	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.19	-	exc	1 *	Secreted protein				99
O88780 UniProt NPD GO	NRPN_RAT	Neuropsin precursor (EC 3.4.21.-) (NP) (Kallikrein-8) (Brain serine protease 1)	0.19	-	exc	1 *	Secreted protein (By similarity)				260
P83557 UniProt NPD GO	TXMG1_MACGS	Neurotoxin magi-1	0.19	-	nuc	0	Secreted protein				38
Q62715 UniProt NPD GO	DEF2_RAT	Neutrophil antibiotic peptide NP-2 precursor (Neutrophil defensin 2) (RatNP-2)	0.19	-	exc	0	Secreted protein				94
Q64365 UniProt NPD GO	DEF1B_CAVPO	Neutrophil cationic peptide 1 type B precursor (GNCP-1B) [Contains: Neutrophil cationic peptide 1 (N ...	0.19	-	exc	0	Secreted protein				93
P49112 UniProt NPD GO	DEF2_CAVPO	Neutrophil cationic peptide 2 precursor (CP-2) (GNCP-2)	0.19	-	exc	0	Secreted protein				93
Q92542 UniProt NPD GO	NICA_HUMAN	Nicastrin precursor	0.19	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	endoplasmic reticulum [IDA] Golgi apparatus [IDA] integral to plasma membrane [IDA]	605254		709
P16081 UniProt NPD GO	NIA1_ORYSA	Nitrate reductase [NADH] 1 (EC 1.7.1.1) (NR1)	0.19	-	cyt	0					916
P49102 UniProt NPD GO	NIA3_MAIZE	Nitrate reductase [NADH] 3 (EC 1.7.1.1) (NR)	0.19	-	cyt	0					889
P36858 UniProt NPD GO	NIA_ASPNG	Nitrate reductase [NADPH] (EC 1.7.1.3) (NR)	0.19	-	cyt	0					867
Q29498 UniProt NPD GO	NOS1_SHEEP	Nitric-oxide synthase, brain (EC 1.14.13.39) (NOS type I) (Neuronal NOS) (N-NOS) (NNOS) (Constitutiv ...	0.19	-	cyt	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein (By similarity). In skeletal muscle, N ...				186

You are viewing entries 52151 to 52200 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.