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
Q8M9T5 UniProt NPD GO	NUCC_CHAGL	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.13	-	cyt	0	Plastid; chloroplast				391
Q9BBN8 UniProt NPD GO	NUCC_LOTJA	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.13	-	cyt	0	Plastid; chloroplast				393
P12131 UniProt NPD GO	NUCC_MARPO	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.13	-	cyt	0	Plastid; chloroplast				392
Q6ENA1 UniProt NPD GO	NUCC_ORYNI	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.13	-	cyt	0	Plastid; chloroplast				393
P12132 UniProt NPD GO	NUCC_ORYSA	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.13	-	cyt	0	Plastid; chloroplast				393
Q9M3I5 UniProt NPD GO	NUCC_SPIOL	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.13	-	cyt	0	Plastid; chloroplast				393
P53686 UniProt NPD GO	HST2_YEAST	NAD-dependent deacetylase HST2 (EC 3.5.1.-) (Homologous to SIR2 protein 2)	0.13	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA]		1SZD	357
Q9NTG7 UniProt NPD GO	SIRT3_HUMAN	NAD-dependent deacetylase sirtuin-3, mitochondrial precursor (EC 3.5.1.-) (SIR2-like protein 3) (hSI ...	0.13	-	mit	0	Mitochondrion; mitochondrial matrix		604481		399
P37225 UniProt NPD GO	MAON_SOLTU	NAD-dependent malic enzyme 59 kDa isoform, mitochondrial precursor (EC 1.1.1.39) (NAD-ME)	0.13	-	mit	0	Mitochondrion; mitochondrial matrix				601
Q9DCT2 UniProt NPD GO	NUGM_MOUSE	NADH-ubiquinone oxidoreductase 30 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.13	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity). Matrix and cytoplasmic side of the mito ...	mitochondrial inner membrane [IDA] mitochondrion [IDA]			263
Q37619 UniProt NPD GO	NUCM_PROWI	NADH-ubiquinone oxidoreductase 49 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (NADH dehydrogenase subunit ...	0.13	-	cyt	0	Mitochondrion				400
P38599 UniProt NPD GO	NU2M_HALGR	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.13	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
O21070 UniProt NPD GO	NU2M_LAMFL	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.13	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q330B4 UniProt NPD GO	NU2M_NATST	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.13	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q00540 UniProt NPD GO	NU2M_PHOVI	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.13	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P16673 UniProt NPD GO	NU2M_RANCA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.13	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				344
O21409 UniProt NPD GO	NU2M_SCYCA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.13	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348
O03692 UniProt NPD GO	NU4M_ATRNM	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.13	-	end	6 *					231
O03697 UniProt NPD GO	NU4M_BOTAS	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.13	-	exc	6 *					231
O21515 UniProt NPD GO	NU4M_PHOSU	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.13	-	end	6 *					208
Q9MIY0 UniProt NPD GO	NU5M_BRARE	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.13	-	end	18 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
Q94RJ2 UniProt NPD GO	NU5M_CHIMO	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.13	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				612
Q9ZZ44 UniProt NPD GO	NU5M_SQUAC	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.13	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				610
P03922 UniProt NPD GO	NU5M_XENLA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.13	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				604
P34105 UniProt NPD GO	MAOX_POPTR	NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME)	0.13	-	nuc	0	Cytoplasm (Potential)				591
P19618 UniProt NPD GO	NCPR_SALTR	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R) (Fragments)	0.13	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Anchored to the ...				601
Q91ZP6 UniProt NPD GO	NFIP2_MOUSE	NEDD4 family-interacting protein 2 (NEDD4 WW domain-binding protein 5A) (Fragment)	0.13	+	end	3	Golgi apparatus; Golgi membrane; multi-pass membrane protein. Endosome; endosomal membrane; multi-pa ...				311
Q9U3Z7 UniProt NPD GO	NHPX_DROME	NHP2-like protein (Hoi-polloi protein)	0.13	-	cyt	0	Nucleus (Potential)				127
Q9S818 UniProt NPD GO	FL3H_ARATH	Naringenin,2-oxoglutarate 3-dioxygenase (EC 1.14.11.9) (Flavanone 3-hydroxylase) (Naringenin 3-dioxy ...	0.13	-	cyt	0					358
P38879 UniProt NPD GO	NACA_YEAST	Nascent polypeptide-associated complex subunit alpha EGD2 (NAC-alpha) (Alpha-NAC) (GAL4 DNA-binding ...	0.13	-	cyt	0	Cytoplasm. Nucleus. Predominantly cytoplasmic, may also transiently localize to the nucleus. Nuclear ...	nascent polypeptide-associated complex [IDA]			173
Q66S03 UniProt NPD GO	NATTE_THANI	Nattectin precursor	0.13	-	mit	1 *	Secreted protein (By similarity)				159
P16170 UniProt NPD GO	NCA11_XENLA	Neural cell adhesion molecule 1-A precursor	0.13	-	end	1	Membrane; single-pass type I membrane protein				1088
Q15825 UniProt NPD GO	ACHA6_HUMAN	Neuronal acetylcholine receptor protein subunit alpha-6 precursor	0.13	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]	606888		494
Q9R0W9 UniProt NPD GO	ACHA6_MOUSE	Neuronal acetylcholine receptor protein subunit alpha-6 precursor	0.13	-	end	4	Membrane; multi-pass membrane protein				494
Q05901 UniProt NPD GO	ACHB3_HUMAN	Neuronal acetylcholine receptor protein subunit beta-3 precursor	0.13	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]	118508		458
Q5IS75 UniProt NPD GO	ACHB3_PANTR	Neuronal acetylcholine receptor protein subunit beta-3 precursor	0.13	-	end	4	Membrane; multi-pass membrane protein (By similarity)				458
P97738 UniProt NPD GO	NPTX2_RAT	Neuronal pentraxin-2 precursor (NP2) (Neuronal pentraxin II) (NP-II) (Neuronal activity-regulated pe ...	0.13	-	nuc	0	Secreted protein				432
Q9EQD2 UniProt NPD GO	NPFF2_RAT	Neuropeptide FF receptor 2 (Neuropeptide G-protein coupled receptor) (G-protein coupled receptor 74) ...	0.13	-	end	7 *	Membrane; multi-pass membrane protein				417
P80167 UniProt NPD GO	NEUY_GADMO	Neuropeptide Y (NPY)	0.13	-	nuc	0	Secreted protein				36
P34992 UniProt NPD GO	NPY1R_XENLA	Neuropeptide Y receptor type 1 (NPY1-R)	0.13	-	end	7 *	Membrane; multi-pass membrane protein				366
Q56UD9 UniProt NPD GO	NPBW1_RAT	Neuropeptides B/W receptor type 1 (G-protein coupled receptor 7)	0.13	-	end	7 *	Membrane; multi-pass membrane protein				329
Q8ITC7 UniProt NPD GO	CAPAR_DROME	Neuropeptides capa receptor (Cap2b receptor)	0.13	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			477
P32560 UniProt NPD GO	NEUT_CAVPO	Neurotensin (NT)	0.13	-		0	Secreted protein				13
P0C1F4 UniProt NPD GO	TX2_BUNGR	Neurotoxin Bg-2 (Bg II)	0.13	-	nuc	0	Secreted protein (Probable). Found in nematocyst (Probable)				48
P0C1F5 UniProt NPD GO	TX3_BUNGR	Neurotoxin Bg-3 (Bg III)	0.13	-	nuc	0	Secreted protein (Probable). Found in nematocyst (Probable)				48
Q62713 UniProt NPD GO	DEFA_RAT	Neutrophil antibiotic peptide NP-3 precursor (Neutrophil defensin 3) (RatNP-3a)	0.13	-	exc	0	Secreted protein				87
Q9Z1F1 UniProt NPD GO	DEFB_RAT	Neutrophil antibiotic peptide NP-3 precursor (Neutrophil defensin 3) (RatNP-3b)	0.13	-	exc	0	Secreted protein				87
P62511 UniProt NPD GO	NRK1_ASHGO	Nicotinamide riboside kinase 1 (EC 2.7.1.-)	0.13	-	cyt	0					241
Q8TDS4 UniProt NPD GO	G109A_HUMAN	Nicotinic acid receptor 1 (G-protein coupled receptor 109A) (G-protein coupled receptor HM74A)	0.13	-	end	7 *	Membrane; multi-pass membrane protein		609163		363
P34389 UniProt NPD GO	NPC2_CAEEL	Niemann-Pick C1 protein homolog 2 precursor	0.13	-	end	11	Membrane; multi-pass membrane protein (Potential)				1274

You are viewing entries 60051 to 60100 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.