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
P17221 UniProt NPD GO	FEM1_CAEEL	Sex-determining protein fem-1 (Feminization of XX and XO animals protein 1)	0.15	-	cyt	0	Cytoplasm (Potential)				656
Q39011 UniProt NPD GO	KSG7_ARATH	Shaggy-related protein kinase eta (EC 2.7.11.1) (ASK-eta) (BRASSINOSTEROID-INSENSITIVE 2) (ULTRACURV ...	0.15	-	cyt	0					380
P68414 UniProt NPD GO	NXSA_ACAPE	Short neurotoxin 1 (Major/minor neurotoxin)	0.15	-	nuc	0	Secreted protein				60
P01418 UniProt NPD GO	NXS1_DENVI	Short neurotoxin 1 (Neurotoxin 4.11.3)	0.15	-	nuc	0	Secreted protein				60
P01416 UniProt NPD GO	NXS1_DENPO	Short neurotoxin 1 (Neurotoxin alpha)	0.15	-	nuc	0	Secreted protein			1NTX	60
P68412 UniProt NPD GO	NXS1_ASTST	Short neurotoxin 1 (Toxin A)	0.15	-	nuc	0	Secreted protein				60
P68413 UniProt NPD GO	NXS1_HYDOR	Short neurotoxin 1 (Toxin A)	0.15	-	nuc	0	Secreted protein				60
Q9YGC4 UniProt NPD GO	NXS3_LATLA	Short neurotoxin OKI-01/OKI-19 precursor	0.15	-	nuc	0	Secreted protein				83
Q9YGC2 UniProt NPD GO	NXS1_LATLA	Short neurotoxin OKI-17/NCA-06 precursor	0.15	-	nuc	0	Secreted protein				83
P79125 UniProt NPD GO	SPL2B_BOVIN	Short palate, lung and nasal epithelium carcinoma-associated protein 2B precursor (Common salivary p ...	0.15	-	exc	0	Secreted protein (By similarity)				240
P16219 UniProt NPD GO	ACADS_HUMAN	Short-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.2) (SCAD) (Butyryl-C ...	0.15	-	mit	0	Mitochondrion; mitochondrial matrix		606885		412
O35657 UniProt NPD GO	NEUR1_MOUSE	Sialidase-1 precursor (EC 3.2.1.18) (Lysosomal sialidase) (N-acetyl-alpha-neuraminidase 1) (G9 siali ...	0.15	-	mit	0	Lysosome; lysosomal membrane; peripheral membrane; lumenal side. Lysosome; lysosomal lumen. Cell mem ...	lysosome [IDA]			409
O74395 UniProt NPD GO	STR1_SCHPO	Siderophore iron transporter 1	0.15	-	end	14	Membrane; multi-pass membrane protein (Probable)	membrane [TAS]			612
P46965 UniProt NPD GO	SPC1_YEAST	Signal peptidase complex subunit SPC1 (Microsomal signal peptidase subunit 1)	0.15	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	signal peptidase complex [IDA]			94
O04438 UniProt NPD GO	SRP09_MAIZE	Signal recognition particle 9 kDa protein (SRP9)	0.15	-	cyt	0	Cytoplasm (By similarity)				103
Q811Q1 UniProt NPD GO	SMUG1_RAT	Single-strand selective monofunctional uracil-DNA glycosylase (EC 3.2.2.-)	0.15	-	cyt	0	Nucleus (By similarity)	nucleolus [ISS]			278
P84827 UniProt NPD GO	SKSP2_ASCTR	Skin secreted peptide 2	0.15	-	nuc	0	Secreted protein	extracellular region [IDA]			24
P30222 UniProt NPD GO	HS22C_PETHY	Small heat shock protein, chloroplast precursor	0.15	-	mit	0	Plastid; chloroplast				241
Q16627 UniProt NPD GO	CCL14_HUMAN	Small inducible cytokine A14 precursor (CCL14) (Chemokine CC-1/CC-3) (HCC-1/HCC-3) (HCC-1(1-74)) (NC ...	0.15	-	nuc	0	Secreted protein	extracellular space [TAS]	601392		93
P17136 UniProt NPD GO	RSMB_RAT	Small nuclear ribonucleoprotein-associated protein B (snRNP-B) (Sm protein B) (Sm-B) (SmB) (SM11) (F ...	0.15	-	nuc	0	Nucleus	nucleus [TAS]			214
Q864L3 UniProt NPD GO	SCN2B_CANFA	Sodium channel beta-2 subunit precursor	0.15	-	end	1	Membrane; single-pass type I membrane protein				215
O60939 UniProt NPD GO	SCN2B_HUMAN	Sodium channel beta-2 subunit precursor	0.15	-	end	1	Membrane; single-pass type I membrane protein	voltage-gated sodium channel complex [TAS]	601327		215
P48762 UniProt NPD GO	SL9A1_PIG	Sodium/hydrogen exchanger 1 (Na(+)/H(+) exchanger 1) (NHE-1) (Solute carrier family 9 member 1)	0.15	-	end	12 *	Membrane; multi-pass membrane protein				818
Q8IVB4 UniProt NPD GO	SL9A9_HUMAN	Sodium/hydrogen exchanger 9 (Na(+)/H(+) exchanger 9) (NHE-9) (Solute carrier family 9 member 9)	0.15	-	end	10 *	Membrane; multi-pass membrane protein (By similarity)		608396		645
P53793 UniProt NPD GO	SC5A3_BOVIN	Sodium/myo-inositol cotransporter (Na(+)/myo-inositol cotransporter)	0.15	-	end	13 *	Membrane; multi-pass membrane protein				718
P31637 UniProt NPD GO	SC5A3_CANFA	Sodium/myo-inositol cotransporter (Na(+)/myo-inositol cotransporter)	0.15	-	end	14 *	Membrane; multi-pass membrane protein				718
Q9JKZ2 UniProt NPD GO	SC5A3_MOUSE	Sodium/myo-inositol cotransporter (Na(+)/myo-inositol cotransporter)	0.15	-	end	13 *	Membrane; multi-pass membrane protein				718
Q9MZT2 UniProt NPD GO	S28A1_RABIT	Sodium/nucleoside cotransporter 1 (Na(+)/nucleoside cotransporter 1) (Sodium-coupled nucleoside tran ...	0.15	-	end	12	Membrane; multi-pass membrane protein (By similarity)				658
P30714 UniProt NPD GO	AT1A1_BUFMA	Sodium/potassium-transporting ATPase alpha-1 chain precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ AT ...	0.15	-	end	8	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]			1023
O13001 UniProt NPD GO	ATNG_XENLA	Sodium/potassium-transporting ATPase gamma chain (Sodium pump gamma chain) (Na+/K+ ATPase subunit ga ...	0.15	-	nuc	1 *	Membrane; single-pass type III membrane protein (Potential)				61
Q8C261 UniProt NPD GO	NCKX5_MOUSE	Sodium/potassium/calcium exchanger 5 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 5) (Solute carrie ...	0.15	-	end	11 *	Membrane; multi-pass membrane protein (By similarity)				501
O23979 UniProt NPD GO	IPYR_HORVD	Soluble inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.15	-	nuc	0	Cytoplasm				215
Q28677 UniProt NPD GO	S12A4_RABIT	Solute carrier family 12 member 4 (Electroneutral potassium-chloride cotransporter 1) (Erythroid K-C ...	0.15	-	end	12	Membrane; multi-pass membrane protein	integral to membrane [ISS]			1085
Q9Y666 UniProt NPD GO	S12A7_HUMAN	Solute carrier family 12 member 7 (Electroneutral potassium-chloride cotransporter 4) (K-Cl cotransp ...	0.15	-	end	11	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	604879		1083
Q922Q5 UniProt NPD GO	S35B3_MOUSE	Solute carrier family 35 member B3	0.15	-	end	10 *	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			369
Q9EPT5 UniProt NPD GO	SO2A1_MOUSE	Solute carrier organic anion transporter family member 2A1 (Solute carrier family 21 member 2) (Pros ...	0.15	-	end	11 *	Membrane; multi-pass membrane protein				643
P21780 UniProt NPD GO	SMS2_PLAFE	Somatostatin-2 precursor (Somatostatin II) [Contains: [Tyr21,Gly24]-somatostatin-28; [Tyr7,Gly10]-so ...	0.15	-	nuc	0	Secreted protein				73
P79682 UniProt NPD GO	SHH_AMBCH	Sonic hedgehog protein (SHH) (Fragments)	0.15	-	cyt	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
P79858 UniProt NPD GO	SHH_RASEL	Sonic hedgehog protein (SHH) (Fragments)	0.15	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
P79864 UniProt NPD GO	SHH_RASHE	Sonic hedgehog protein (SHH) (Fragments)	0.15	-	nuc	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
Q6P069 UniProt NPD GO	SORCN_MOUSE	Sorcin	0.15	-	cyt	0	Cytoplasm (By similarity)	intracellular [IDA] plasma membrane [IDA]			198
Q6PHU5 UniProt NPD GO	SORT_MOUSE	Sortilin precursor (Neurotensin receptor 3) (NTR3) (mNTR3)	0.15	-	end	1	Membrane; single-pass type I membrane protein (By similarity). Localized to membranes of the endopla ...	trans-Golgi network transport vesicle [IDA]			825
Q04519 UniProt NPD GO	ASM_MOUSE	Sphingomyelin phosphodiesterase precursor (EC 3.1.4.12) (Acid sphingomyelinase) (aSMase)	0.15	-	mit	1 *	Lysosome				627
P21453 UniProt NPD GO	EDG1_HUMAN	Sphingosine 1-phosphate receptor Edg-1 (Sphingosine 1-phosphate receptor 1) (S1P1)	0.15	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]	601974		381
Q8R0X7 UniProt NPD GO	SGPL1_MOUSE	Sphingosine-1-phosphate lyase 1 (EC 4.1.2.27) (SP-lyase) (mSPL) (Sphingosine-1-phosphate aldolase)	0.15	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...	integral to endoplasmic reticulum membrane [ISS]			568
Q99P55 UniProt NPD GO	SGPP1_RAT	Sphingosine-1-phosphate phosphatase 1 (EC 3.1.3.-) (Sphingosine-1-phosphatase 1) (SPPase1) (Spp1)	0.15	+	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				430
P09937 UniProt NPD GO	SPS4_YEAST	Sporulation-specific protein 4	0.15	-	nuc	0					338
P40031 UniProt NPD GO	SPO73_YEAST	Sporulation-specific protein 73	0.15	-	nuc	0	Cytoplasm. Punctate location throughout the cytosol in meiosis II cells and peripheral punctate stru ...	cytosol [IDA]			143
P29704 UniProt NPD GO	FDFT_YEAST	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.15	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	mitochondrial outer membrane [IDA]			444
P24805 UniProt NPD GO	TSJT1_TOBAC	Stem-specific protein TSJT1	0.15	-	cyt	0					149

You are viewing entries 57651 to 57700 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.