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
O18689 UniProt NPD GO	SRA18_CAEEL	Serpentine receptor class alpha-18 (Protein sra-18)	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				340
P02769 UniProt NPD GO	ALBU_BOVIN	Serum albumin precursor (Allergen Bos d 6) (BSA)	0.14	-	exc	0	Secreted protein	extracellular region [ISS] extracellular space [NAS] protein complex [ISS]			607
Q28522 UniProt NPD GO	ALBU_MACMU	Serum albumin precursor (Fragment)	0.14	-	nuc	0	Secreted protein	extracellular region [ISS] protein complex [ISS]			600
P31532 UniProt NPD GO	SAA4_MOUSE	Serum amyloid A-4 protein precursor (Amyloid A-5 protein)	0.14	-	exc	0					130
Q8VZD5 UniProt NPD GO	KSG5_ARATH	Shaggy-related protein kinase epsilon (EC 2.7.11.1) (ASK-epsilon)	0.14	-	cyt	0					410
P34075 UniProt NPD GO	NXS1_BOUAN	Short neurotoxin 1	0.14	-	nuc	0	Secreted protein				61
P01426 UniProt NPD GO	NXS1_NAJPA	Short neurotoxin 1 (Neurotoxin alpha)	0.14	-	nuc	0	Secreted protein			1NEA	61
P01420 UniProt NPD GO	NXS3_NAJHA	Short neurotoxin 3 (Toxin CM-10) (Toxin V-NH-I1)	0.14	-	nuc	0	Secreted protein				61
P79124 UniProt NPD GO	SPL2A_BOVIN	Short palate, lung and nasal epithelium carcinoma-associated protein 2A precursor (Common salivary p ...	0.14	-	end	0	Secreted protein (By similarity)				243
Q64627 UniProt NPD GO	NEUR2_RAT	Sialidase-2 (EC 3.2.1.18) (Cytosolic sialidase) (N-acetyl-alpha-neuraminidase 2)	0.14	-	cyt	0	Cytoplasm (By similarity)				379
Q91V61 UniProt NPD GO	SFXN3_MOUSE	Sideroflexin-3	0.14	-	cyt	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				321
Q756H7 UniProt NPD GO	SEC65_ASHGO	Signal recognition particle SEC65 subunit	0.14	-	nuc	0	Cytoplasm (By similarity)				261
P25063 UniProt NPD GO	CD24_HUMAN	Signal transducer CD24 precursor	0.14	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor	plasma membrane [NAS]	600074		80
Q9P1W8 UniProt NPD GO	SIRPG_HUMAN	Signal-regulatory protein gamma precursor (Signal-regulatory protein beta-2) (SIRP-beta-2) (SIRP-b2) ...	0.14	-	end	1	Membrane; single-pass type I membrane protein		605466		387
P32445 UniProt NPD GO	RIM1_YEAST	Single-stranded DNA-binding protein RIM1, mitochondrial precursor (Mitochondrial ssDNA-binding prote ...	0.14	-	nuc	0	Mitochondrion	mitochondrial nucleoid [IDA] mitochondrion [IDA]			135
P84826 UniProt NPD GO	SKSP1_ASCTR	Skin secreted peptide 1	0.14	-	mit	0	Secreted protein	extracellular region [IDA]			24
Q62401 UniProt NPD GO	CCL12_MOUSE	Small inducible cytokine A12 precursor (CCL12) (Monocyte chemotactic protein 5) (MCP-5) (MCP-1-relat ...	0.14	-	exc	0	Secreted protein				104
Q9TTQ3 UniProt NPD GO	CCL2_HORSE	Small inducible cytokine A2 precursor (CCL2) (Monocyte chemotactic protein 1) (MCP-1) (Monocyte chem ...	0.14	-	exc	0	Secreted protein				99
Q8HYS0 UniProt NPD GO	CCL5_CANFA	Small inducible cytokine A5 precursor (CCL5) (T-cell-specific RANTES protein)	0.14	-	exc	0	Secreted protein				91
Q03366 UniProt NPD GO	CCL7_MOUSE	Small inducible cytokine A7 precursor (CCL7) (Monocyte chemotactic protein 3) (MCP-3) (Monocyte chem ...	0.14	-	exc	1 *	Secreted protein				97
P50228 UniProt NPD GO	SCYB5_MOUSE	Small inducible cytokine B5 precursor (CXCL5) (Cytokine LIX) [Contains: GCP-2(1-78); GCP-2(9-78)]	0.14	-	exc	0	Secreted protein				132
Q9VR07 UniProt NPD GO	INE_DROME	Sodium- and chloride-dependent GABA transporter ine (Protein inebriated) (Protein receptor oscillati ...	0.14	-	end	11	Membrane; multi-pass membrane protein				943
Q28039 UniProt NPD GO	SC6A9_BOVIN	Sodium- and chloride-dependent glycine transporter 1 (GlyT1) (GlyT-1) (Solute carrier family 6 membe ...	0.14	-	end	12 *	Membrane; multi-pass membrane protein				638
Q5BL44 UniProt NPD GO	S20A1_XENTR	Sodium-dependent phosphate transporter 1 (Solute carrier family 20 member 1)	0.14	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				685
Q68F35 UniProt NPD GO	S20AA_XENLA	Sodium-dependent phosphate transporter 1-A (Solute carrier family 20 member 1-A)	0.14	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				685
P48765 UniProt NPD GO	NAC1_BOVIN	Sodium/calcium exchanger 1 precursor (Na(+)/Ca(2+)-exchange protein 1)	0.14	-	end	10 *	Cell membrane; multi-pass membrane protein				970
P23685 UniProt NPD GO	NAC1_CANFA	Sodium/calcium exchanger 1 precursor (Na(+)/Ca(2+)-exchange protein 1)	0.14	-	end	11 *	Cell membrane; multi-pass membrane protein			2FWU	970
P48766 UniProt NPD GO	NAC1_CAVPO	Sodium/calcium exchanger 1 precursor (Na(+)/Ca(2+)-exchange protein 1)	0.14	-	end	10 *	Cell membrane; multi-pass membrane protein				970
P48767 UniProt NPD GO	NAC1_FELCA	Sodium/calcium exchanger 1 precursor (Na(+)/Ca(2+)-exchange protein 1)	0.14	-	end	9 *	Cell membrane; multi-pass membrane protein				970
P32418 UniProt NPD GO	NAC1_HUMAN	Sodium/calcium exchanger 1 precursor (Na(+)/Ca(2+)-exchange protein 1)	0.14	-	end	11 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182305		973
Q8C3K6 UniProt NPD GO	SC5A1_MOUSE	Sodium/glucose cotransporter 1 (Na(+)/glucose cotransporter 1) (High affinity sodium-glucose cotrans ...	0.14	-	end	14 *	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] brush border [IDA]			665
Q8BLV3 UniProt NPD GO	SL9A7_MOUSE	Sodium/hydrogen exchanger 7 (Na(+)/H(+) exchanger 7) (NHE-7) (Solute carrier family 9 member 7)	0.14	-	end	12	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein (By ...	Golgi apparatus [ISS] Golgi trans face [ISS] integral to membrane [ISS]			726
Q8VDN2 UniProt NPD GO	AT1A1_MOUSE	Sodium/potassium-transporting ATPase alpha-1 chain precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ AT ...	0.14	-	end	10	Membrane; multi-pass membrane protein (By similarity)	basolateral plasma membrane [IDA] microsome [IDA] plasma membrane [IDA] sodium:potassium-exchanging ATPase complex [ISS]			1023
Q9WVL3 UniProt NPD GO	S12A7_MOUSE	Solute carrier family 12 member 7 (Electroneutral potassium-chloride cotransporter 4) (K-Cl cotransp ...	0.14	-	end	11	Membrane; multi-pass membrane protein				1083
Q6GQ70 UniProt NPD GO	S35B1_XENLA	Solute carrier family 35 member B1 (Endoplasmic reticulum nucleotide sugar transporter 1)	0.14	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				320
Q96K37 UniProt NPD GO	SL35E_HUMAN	Solute carrier family 35 member E1	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				266
Q15465 UniProt NPD GO	SHH_HUMAN	Sonic hedgehog protein precursor (SHH) (HHG-1) [Contains: Sonic hedgehog protein N-product; Sonic he ...	0.14	-	cyt	1 *	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...	cell surface [ISS] extracellular space [ISS] lipid raft [ISS]	600725		462
O54861 UniProt NPD GO	SORT_RAT	Sortilin precursor (Neurotensin receptor 3) (NTR3) (Glycoprotein 110) (Gp110)	0.14	-	end	1	Membrane; single-pass type I membrane protein (By similarity). Localized to membranes of the endosom ...	cell soma [IDA] dendrite [IDA] integral to membrane [IDA] intracellular membrane-bound organelle [IDA] microsome [IDA] plasma membrane [IDA]			825
Q5E9P3 UniProt NPD GO	EDG1_BOVIN	Sphingosine 1-phosphate receptor Edg-1 (Sphingosine 1-phosphate receptor 1) (S1P1)	0.14	-	end	7 *	Membrane; multi-pass membrane protein				382
Q9C509 UniProt NPD GO	SGPL_ARATH	Sphingosine-1-phosphate lyase (EC 4.1.2.27) (SP-lyase) (SPL) (Sphingosine-1-phosphate aldolase)	0.14	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				544
Q8CHN6 UniProt NPD GO	SGPL1_RAT	Sphingosine-1-phosphate lyase 1 (EC 4.1.2.27) (SP-lyase) (SPL) (Sphingosine-1-phosphate aldolase)	0.14	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...	integral to endoplasmic reticulum membrane [ISS]			568
O14102 UniProt NPD GO	SAP49_SCHPO	Spliceosome-associated protein 49	0.14	-	nuc	0	Nucleus (Potential)				335
P08459 UniProt NPD GO	SPS2_YEAST	Sporulation-specific protein 2 precursor	0.14	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			502
O65727 UniProt NPD GO	ERG11_BRANA	Squalene monooxygenase 1,1 (EC 1.14.99.7) (Squalene epoxidase 1,1) (SE 1,1)	0.14	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				506
O65402 UniProt NPD GO	ERG12_ARATH	Squalene monooxygenase 1,2 (EC 1.14.99.7) (Squalene epoxidase 1,2) (SE 1,2)	0.14	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				517
O74165 UniProt NPD GO	FDFT_PICJA	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.14	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				443
Q496Z0 UniProt NPD GO	STTP1_RAT	Stat3-interacting protein (StIP1)	0.14	-	nuc	0					821
Q96WX4 UniProt NPD GO	ERG6_PNECA	Sterol 24-C-methyltransferase (EC 2.1.1.41) (Delta(24)-sterol C-methyltransferase)	0.14	-	cyt	0					377
P50427 UniProt NPD GO	STS_MOUSE	Steryl-sulfatase precursor (EC 3.1.6.2) (Steroid sulfatase) (Steryl-sulfate sulfohydrolase) (Arylsul ...	0.14	-	end	0	Microsome; microsomal membrane; multi-pass membrane protein. The sequence shows several membrane-spa ...				624
P51069 UniProt NPD GO	THS3_ARAHY	Stilbene synthase 3 (EC 2.3.1.95) (Resveratrol synthase 3) (RS3) (Trihydroxystilbene synthase 3)	0.14	-	nuc	0	Cytoplasm				389

You are viewing entries 59051 to 59100 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.