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
P08183 UniProt NPD GO	MDR1_HUMAN	Multidrug resistance protein 1 (EC 3.6.3.44) (P-glycoprotein 1) (CD243 antigen)	0.30	-	end	10 *	Membrane; multi-pass membrane protein	cell surface [IEP] integral to membrane [TAS] membrane fraction [TAS]	171050		1280
Q9FHF1 UniProt NPD GO	MDR7_ARATH	Multidrug resistance protein 7 (P-glycoprotein 7)	0.30	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				1248
Q9R1S7 UniProt NPD GO	MRP6_MOUSE	Multidrug resistance-associated protein 6 (ATP-binding cassette sub-family C member 6)	0.30	-	end	14 *	Membrane; multi-pass membrane protein (By similarity)				1498
Q13465 UniProt NPD GO	MDS1_HUMAN	Myelodysplasia syndrome 1 protein (Myelodysplasia syndrome-associated protein 1)	0.30	-	nuc	0			600049		169
Q31791 UniProt NPD GO	NUKC_ANTFO	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.30	-	nuc	0	Plastid; chloroplast				247
Q5RBF1 UniProt NPD GO	SIRT2_PONPY	NAD-dependent deacetylase sirtuin-2 (EC 3.5.1.-)	0.30	-	mit	0	Cytoplasm. Colocalizes with microtubules (By similarity)				352
Q5RJQ4 UniProt NPD GO	SIRT2_RAT	NAD-dependent deacetylase sirtuin-2 (EC 3.5.1.-) (SIR2-like protein 2)	0.30	-	mit	0	Cytoplasm. Colocalizes with microtubules (By similarity)				350
Q19427 UniProt NPD GO	NPY1_CAEEL	NADH pyrophosphatase (EC 3.6.1.22)	0.30	-	cyt	0					348
P93306 UniProt NPD GO	NUCM_ARATH	NADH-ubiquinone oxidoreductase 49 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (NADH dehydrogenase subunit ...	0.30	-	cyt	0	Mitochondrion				394
Q94V92 UniProt NPD GO	NU2M_VARTI	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.30	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				345
O79555 UniProt NPD GO	NU4M_DINSE	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.30	-	end	10 *					445
O79436 UniProt NPD GO	NU4M_RABIT	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.30	-	end	13 *					459
O21233 UniProt NPD GO	NUIM_RECAM	NADH-ubiquinone oxidoreductase subunit 8 (EC 1.6.5.3)	0.30	-	cyt	0	Mitochondrion				162
Q9V6U8 UniProt NPD GO	UBA3_DROME	NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-) (Ubiquitin-activating enzyme 3 homolog)	0.30	-	cyt	0					450
Q08353 UniProt NPD GO	IKBA_PIG	NF-kappa-B inhibitor alpha (I-kappa-B-alpha) (IkappaBalpha) (IKB-alpha) (ECI-6)	0.30	-	nuc	0	Cytoplasm				314
Q8R4V1 UniProt NPD GO	NFAM1_MOUSE	NFAT activation molecule 1 precursor (Calcineurin/NFAT-activating ITAM-containing protein) (NFAT-act ...	0.30	+	nuc	1	Cell membrane; single-pass type I membrane protein (By similarity). Partially recruited to lipid raf ...	cell surface [IDA] integral to membrane [ISS] lipid raft [IDA]			264
P26718 UniProt NPD GO	NKG2D_HUMAN	NKG2-D type II integral membrane protein (NKG2-D-activating NK receptor) (NK cell receptor D) (Kille ...	0.30	-	mit	1	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]		1MPU	216
Q94JX9 UniProt NPD GO	NACA2_ARATH	Nascent polypeptide-associated complex subunit alpha-like protein 2 (NAC-alpha-like protein 2) (Alph ...	0.30	-	nuc	0					217
Q7ZZN8 UniProt NPD GO	CRVP2_NAJAT	Natrin-2 precursor (Cysteine-rich venom protein 2) (NA-CRVP2) (Protein G2b)	0.30	-	exc	0	Secreted protein				238
O76050 UniProt NPD GO	NEUL1_HUMAN	Neuralized-like protein 1 (h-neuralized 1) (h-neu) (RING finger protein 67)	0.30	-	nuc	0	Cytoplasm; perinuclear region		603804		574
P08949 UniProt NPD GO	NEUB_HUMAN	Neuromedin B-32 precursor [Contains: Neuromedin B]	0.30	-	exc	1 *	Secreted protein	soluble fraction [TAS]	162340	1C9A	121
P49581 UniProt NPD GO	ACHA6_CHICK	Neuronal acetylcholine receptor protein subunit alpha-6 precursor	0.30	-	end	4 *	Membrane; multi-pass membrane protein				494
P12392 UniProt NPD GO	ACHB4_RAT	Neuronal acetylcholine receptor protein subunit beta-4 precursor (Neuronal acetylcholine receptor no ...	0.30	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]			495
Q9Z1S5 UniProt NPD GO	SEPT3_MOUSE	Neuronal-specific septin-3	0.30	-	end	3					465
Q8MP00 UniProt NPD GO	NPF_AEDAE	Neuropeptide F precursor (NPF) (AeaNPF)	0.30	-	nuc	0	Secreted protein				90
P01303 UniProt NPD GO	NEUY_HUMAN	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.30	-	exc	1 *	Secreted protein	cell [TAS]	162640	1RON	97
O60462 UniProt NPD GO	NRP2_HUMAN	Neuropilin-2 precursor (Vascular endothelial cell growth factor 165 receptor 2)	0.30	-	nuc	1	Membrane; single-pass type I membrane protein	membrane fraction [TAS]	602070		931
P97369 UniProt NPD GO	NCF4_MOUSE	Neutrophil cytosol factor 4 (NCF-4) (Neutrophil NADPH oxidase factor 4) (p40-phox) (p40phox)	0.30	-	nuc	0	Cytoplasm	cytoplasm [IDA]			339
Q6NZ07 UniProt NPD GO	NCLN_BRARE	Nicalin-1 precursor (Nicastrin-like protein 1)	0.30	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				572
Q9ET55 UniProt NPD GO	NOCT_RAT	Nocturnin (CCR4 protein homolog) (Fragment)	0.30	-	nuc	0					253
P05204 UniProt NPD GO	HMGN2_HUMAN	Nonhistone chromosomal protein HMG-17 (High-mobility group nucleosome-binding domain-containing prot ...	0.30	+	nuc	0	Nucleus	nucleus [NAS]	163910		89
Q4P9P9 UniProt NPD GO	NUDF_USTMA	Nuclear distribution protein PAC1 (nudF homolog)	0.30	-	nuc	0	Cytoplasm. Localizes to the plus ends of microtubules and the mitotic spindle poles (By similarity)				453
P31483 UniProt NPD GO	TIA1_HUMAN	Nucleolysin TIA-1 isoform p40 (RNA-binding protein TIA-1) (p40-TIA-1) [Contains: Nucleolysin TIA-1 i ...	0.30	-	cyt	0	Cytoplasmic granule. Cytoplasmic granules of cytolytic T-lymphocytes		603518		386
Q8IVD9 UniProt NPD GO	NUDC3_HUMAN	NudC domain-containing protein 3	0.30	-	cyt	0				1WGV	361
Q5RB75 UniProt NPD GO	NUDC3_PONPY	NudC domain-containing protein 3	0.30	-	cyt	0					361
Q28793 UniProt NPD GO	OCLN_POTTR	Occludin	0.30	-	end	6	Membrane; multi-pass membrane protein				489
O77408 UniProt NPD GO	OAR1_LYMST	Octopamine receptor 1 (OA1)	0.30	-	end	7 *	Membrane; multi-pass membrane protein				638
P81909 UniProt NPD GO	OR22A_DROME	Odorant receptor 22a	0.30	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	dendrite [IDA] integral to membrane [NAS]			397
Q8NGX0 UniProt NPD GO	O11L1_HUMAN	Olfactory receptor 11L1	0.30	-	end	7 *	Membrane; multi-pass membrane protein				322
P17408 UniProt NPD GO	TLM_MOUSE	Oncogene tlm	0.30	-	nuc	6 *					317
P60252 UniProt NPD GO	SCX1_OPICA	Opicalcin-1 precursor (Opicalcine-1)	0.30	-	nuc	1 *	Secreted protein				66
Q9NL83 UniProt NPD GO	ORCKA_PROCL	Orcokinin peptides type A precursor [Contains: Orcomyotropin-like peptide; Orcokinin; Orcokinin-like ...	0.30	-	vac	0	Secreted protein	extracellular region [IC]			251
Q95KC3 UniProt NPD GO	P2Y12_MACFA	P2Y purinoceptor 12 (P2Y12)	0.30	-	end	7 *	Membrane; multi-pass membrane protein				342
P70271 UniProt NPD GO	PDLI4_MOUSE	PDZ and LIM domain protein 4 (LIM protein RIL) (Reversion-induced LIM protein)	0.30	-	nuc	0					330
Q5RBI7 UniProt NPD GO	PDZD7_PONPY	PDZ domain-containing protein 7	0.30	-	nuc	0					528
Q6FSS4 UniProt NPD GO	ERFB_CANGA	Palmitoyltransferase ERF2 (EC 2.3.1.-) (DHHC cysteine-rich domain-containing protein ERF2) (Ras prot ...	0.30	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				326
Q6C890 UniProt NPD GO	ERFB_YARLI	Palmitoyltransferase ERF2 (EC 2.3.1.-) (DHHC cysteine-rich domain-containing protein ERF2) (Ras prot ...	0.30	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				408
Q9JK66 UniProt NPD GO	PRKN2_RAT	Parkin (EC 6.3.2.-) (Ubiquitin E3 ligase PRKN)	0.30	-	nuc	0	Cytoplasm (By similarity). Expressed in the endoplasmic reticulum, dendrites, some presynaptic termi ...				465
Q42534 UniProt NPD GO	PME2_ARATH	Pectinesterase-2 precursor (EC 3.1.1.11) (Pectin methylesterase 2) (PE 2)	0.30	-	mit	1 *					587
Q5PQ53 UniProt NPD GO	PEF1_XENLA	Peflin (PEF protein with a long N-terminal hydrophobic domain) (Penta-EF hand domain-containing prot ...	0.30	-	nuc	0	Cytoplasm (By similarity)				283

You are viewing entries 40551 to 40600 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.