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
Q5SCY2 UniProt NPD GO	NU2C_HUPLU	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.11	-	end	14 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				505
Q6EVY9 UniProt NPD GO	NU2C_NYMAL	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.11	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q6ENC2 UniProt NPD GO	NU2C_ORYNI	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.11	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q6ENN2 UniProt NPD GO	NU2C_SACOF	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.11	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
P06256 UniProt NPD GO	NU2C_TOBAC	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.11	-	end	14 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q70XV2 UniProt NPD GO	NU4C_AMBTC	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.11	-	end	12 *	Plastid; chloroplast				500
Q9M3J0 UniProt NPD GO	NU4C_SPIOL	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.11	-	end	13 *	Plastid; chloroplast				500
P69378 UniProt NPD GO	NU4LC_HORVU	NAD(P)H-quinone oxidoreductase chain 4L, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4L) ...	0.11	-	end	3 *	Plastid; chloroplast				101
P69379 UniProt NPD GO	NU4LC_WHEAT	NAD(P)H-quinone oxidoreductase chain 4L, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4L) ...	0.11	-	end	3 *	Plastid; chloroplast				101
Q95H60 UniProt NPD GO	NUGC_WHEAT	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.11	-	cyt	0	Plastid; chloroplast				159
P37221 UniProt NPD GO	MAOM_SOLTU	NAD-dependent malic enzyme 62 kDa isoform, mitochondrial precursor (EC 1.1.1.39) (NAD-ME)	0.11	-	mit	0	Mitochondrion; mitochondrial matrix				626
P23368 UniProt NPD GO	MAOM_HUMAN	NAD-dependent malic enzyme, mitochondrial precursor (EC 1.1.1.38) (NAD-ME) (Malic enzyme 2)	0.11	-	mit	0	Mitochondrion; mitochondrial matrix		154270	1QR6	584
Q4R5X8 UniProt NPD GO	NUMM_MACFA	NADH-ubiquinone oxidoreductase 13 kDa-A subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) ...	0.11	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				124
P22142 UniProt NPD GO	NUCM_NEUCR	NADH-ubiquinone oxidoreductase 49 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.11	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				478
Q9ZZZ0 UniProt NPD GO	NU2M_HIPAM	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.11	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q2TQ13 UniProt NPD GO	NU2M_MYOKI	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.11	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P92691 UniProt NPD GO	NU2M_PONPA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.11	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q330B2 UniProt NPD GO	NU2M_THYTR	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.11	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348
P12775 UniProt NPD GO	NU4M_PARLI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.11	-	end	13 *					464
Q8W9G4 UniProt NPD GO	NU4M_TACAC	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.11	-	end	13 *					459
O03710 UniProt NPD GO	NU4M_CROVC	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.11	-	end	6 *					231
O21521 UniProt NPD GO	NU4M_MICPE	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.11	-	end	6 *					208
O03772 UniProt NPD GO	NU4M_PORNA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.11	-	end	6 *					231
P38602 UniProt NPD GO	NU5M_HALGR	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.11	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				609
Q9ZZY1 UniProt NPD GO	NU5M_HIPAM	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.11	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				594
Q33635 UniProt NPD GO	NU6M_ANOAL	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.11	-	end	4 *					174
O21271 UniProt NPD GO	NUGM_RECAM	NADH-ubiquinone oxidoreductase subunit 9 (EC 1.6.5.3) (EC 1.6.99.3)	0.11	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity). Matrix and cytoplasmic side of the mito ...				204
Q8SPI4 UniProt NPD GO	N4BM_MACFA	NADH-ubiquinone oxidoreductase subunit B14.5b (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-B14.5b) (CI-B14. ...	0.11	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				119
P37222 UniProt NPD GO	MAOC_LYCES	NADP-dependent malic enzyme, chloroplast (EC 1.1.1.40) (NADP-ME) (Fragment)	0.11	-	mit	0	Plastid; chloroplast				573
Q9NYR9 UniProt NPD GO	KBRS2_HUMAN	NF-kappa-B inhibitor-interacting Ras-like protein 2 (I-kappa-B-interacting Ras-like protein 2) (Kapp ...	0.11	-	cyt	0	Cytoplasm (By similarity)		604497		191
Q9CR56 UniProt NPD GO	KBRS2_MOUSE	NF-kappa-B inhibitor-interacting Ras-like protein 2 (I-kappa-B-interacting Ras-like protein 2) (Kapp ...	0.11	-	cyt	0	Cytoplasm (By similarity)				191
O09043 UniProt NPD GO	NAPSA_MOUSE	Napsin-A precursor (EC 3.4.23.-) (Kidney-derived aspartic protease-like protein) (KDAP-1) (KAP)	0.11	-	end	0					419
P18291 UniProt NPD GO	NKP1_RAT	Natural killer cell protease 1 precursor (EC 3.4.21.-) (RNKP-1) (Fragmentin) (Granzyme B)	0.11	-	exc	0				1FI8	248
Q8IXH7 UniProt NPD GO	NELFD_HUMAN	Negative elongation factor C/D (NELF-C/D) (TH1-like protein)	0.11	-	cyt	0	Nucleus (Probable)		605297		590
P13596 UniProt NPD GO	NCAM1_RAT	Neural cell adhesion molecule 1, 140 kDa isoform precursor (N-CAM 140) (NCAM-140)	0.11	-	end	1	Membrane; single-pass type I membrane protein	growth cone [TAS] plasma membrane [TAS]		1QZ1	858
P13591 UniProt NPD GO	NCA11_HUMAN	Neural cell adhesion molecule 1, 140 kDa isoform precursor (N-CAM 140) (NCAM-140) (CD56 antigen)	0.11	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS] plasma membrane [TAS]	116930		848
Q09024 UniProt NPD GO	IMPL2_DROME	Neural/ectodermal development factor IMP-L2 precursor	0.11	-	exc	0	Secreted protein; extracellular space				267
O95156 UniProt NPD GO	NXPH2_HUMAN	Neurexophilin-2 precursor	0.11	-	mit	0	Secreted protein (Potential)	extracellular region [NAS]	604635		264
Q28145 UniProt NPD GO	NXPH2_BOVIN	Neurexophilin-2 precursor (Neurophilin-2)	0.11	-	mit	0	Secreted protein (Potential)				264
P42325 UniProt NPD GO	NCAH_DROME	Neurocalcin homolog (DrosNCa)	0.11	-	nuc	0					189
P28336 UniProt NPD GO	NMBR_HUMAN	Neuromedin-B receptor (NMB-R) (Neuromedin-B-preferring bombesin receptor)	0.11	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	162341		390
Q07263 UniProt NPD GO	ACHA3_BOVIN	Neuronal acetylcholine receptor protein subunit alpha-3 precursor	0.11	-	end	4	Membrane; multi-pass membrane protein				495
Q9Z0J8 UniProt NPD GO	NEGR1_RAT	Neuronal growth regulator 1 precursor (Kilon protein) (Kindred of IgLON)	0.11	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				348
P47970 UniProt NPD GO	NPTX2_CAVPO	Neuronal pentraxin-2 precursor (NP2) (Neuronal pentraxin II) (NP-II) (Apexin) (Acrosomal pentaxin-li ...	0.11	-	cyt	0	Acrosome; acrosomal lumen. Sperm acrosomal matrix				427
P11975 UniProt NPD GO	NEUH_CARCA	Neuropeptide H [Contains: Neuropeptide C; Neuropeptide D; Neuropeptide E; Neuropeptide F; Neuropepti ...	0.11	-	nuc	0					36
O60259 UniProt NPD GO	NRPN_HUMAN	Neuropsin precursor (EC 3.4.21.-) (NP) (Kallikrein-8) (Ovasin) (Serine protease TADG-14) (Tumor-asso ...	0.11	-	exc	0	Secreted protein		605644		260
P83911 UniProt NPD GO	TX37_PHORI	Neurotoxin PRTx3-7	0.11	-	cyt	0	Secreted protein				43
P84034 UniProt NPD GO	TX43_PHONI	Neurotoxin PnTx4-3	0.11	-	nuc	0	Secreted protein				48
P01534 UniProt NPD GO	TXA2_RADPA	Neurotoxin-2 (Neurotoxin II) (Toxin RpII) (Sodium channel toxin II)	0.11	-	nuc	0	Secreted protein. Found in nematocyst				48
Q80VU4 UniProt NPD GO	NT5_MOUSE	Neurotrophin-5 precursor (NT-5) (Neutrophic factor 5)	0.11	-	exc	0	Secreted protein (By similarity)	extracellular region [IDA]			209

You are viewing entries 63101 to 63150 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.