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
Q8TD33 UniProt NPD GO	SG1C1_HUMAN	Secretoglobin family 1C member 1 precursor (Secretoglobin RYD5)	0.03	-	exc	0	Secreted protein (By similarity)				95
Q9JKE3 UniProt NPD GO	SCAM5_RAT	Secretory carrier-associated membrane protein 5 (Secretory carrier membrane protein 5)	0.03	-	end	4 *	Cell membrane; multi-pass membrane protein. Highly enriched in synaptic vesicles (By similarity)				235
Q9Y876 UniProt NPD GO	SHR3_SCHPO	Secretory component protein psh3	0.03	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			215
P46283 UniProt NPD GO	S17P_ARATH	Sedoheptulose-1,7-bisphosphatase, chloroplast precursor (EC 3.1.3.37) (Sedoheptulose-bisphosphatase) ...	0.03	-	mit	0	Plastid; chloroplast				393
Q41161 UniProt NPD GO	LCS2_ROBPS	Seed agglutinin II precursor (RPSAII) (LECRPAS2)	0.03	-	exc	1 *					285
Q01881 UniProt NPD GO	RA05_ORYSA	Seed allergenic protein RA5 precursor	0.03	-	vac	1 *	Secreted protein (Potential)				160
Q9SWB6 UniProt NPD GO	PM36_SOYBN	Seed maturation protein PM36	0.03	-	cyt	0					229
Q41066 UniProt NPD GO	IBB2_PEA	Seed trypsin/chymotrypsin inhibitor TI5-72 precursor	0.03	-	exc	0					114
Q9STZ2 UniProt NPD GO	SELT_ARATH	SelT-like protein precursor	0.03	-	end	0					209
P49903 UniProt NPD GO	SPS1_HUMAN	Selenide, water dikinase 1 (EC 2.7.9.3) (Selenophosphate synthetase 1) (Selenium donor protein 1)	0.03	-	cyt	0			600902		392
Q8BH69 UniProt NPD GO	SPS1_MOUSE	Selenide, water dikinase 1 (EC 2.7.9.3) (Selenophosphate synthetase 1) (Selenium donor protein 1)	0.03	-	cyt	0					392
Q99611 UniProt NPD GO	SPS2_HUMAN	Selenide, water dikinase 2 (EC 2.7.9.3) (Selenophosphate synthetase 2) (Selenium donor protein 2)	0.03	-	cyt	0			606218		448
Q13228 UniProt NPD GO	SBP1_HUMAN	Selenium-binding protein 1	0.03	-	cyt	0	Cytoplasm (By similarity)		604188		472
O19097 UniProt NPD GO	SEPW1_SHEEP	Selenoprotein W	0.03	-	cyt	0	Cytoplasm	cytoplasm [ISS] plasma membrane [ISS]			86
P02784 UniProt NPD GO	SFP1_BOVIN	Seminal plasma protein PDC-109 precursor (Seminal vesicle secretory protein 109) (SVSP109) (BSP-A1 a ...	0.03	-	mit	0	Secreted protein			1PDC	134
P37891 UniProt NPD GO	CBP3_ORYSA	Serine carboxypeptidase 3 precursor (EC 3.4.16.5) (Serine carboxypeptidase III)	0.03	-	exc	0		vacuole [IEP]			500
P21529 UniProt NPD GO	CBP3_HORVU	Serine carboxypeptidase 3 precursor (EC 3.4.16.5) (Serine carboxypeptidase III) (CP-MIII)	0.03	-	exc	1 *	Secreted protein. Secreted into the endosperm				508
P11515 UniProt NPD GO	CBP3_WHEAT	Serine carboxypeptidase 3 precursor (EC 3.4.16.5) (Serine carboxypeptidase III) (CP-WIII)	0.03	-	exc	1 *					500
P55748 UniProt NPD GO	CBP22_HORVU	Serine carboxypeptidase II-2 precursor (EC 3.4.16.6) (CP-MII.2) [Contains: Serine carboxypeptidase I ...	0.03	-	cyt	0					436
Q9SZJ5 UniProt NPD GO	GLYM_ARATH	Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine hy ...	0.03	-	mit	0	Mitochondrion	mitochondrion [IDA]			517
Q41484 UniProt NPD GO	SPI5_SOLTU	Serine protease inhibitor 5 precursor (gCDI-B1)	0.03	-	exc	0	Vacuole (By similarity)				213
Q9GZT4 UniProt NPD GO	SRR_HUMAN	Serine racemase (EC 5.1.1.-)	0.03	-	nuc	0			606477		340
P52718 UniProt NPD GO	PEPF_ASPNG	Serine-type carboxypeptidase F precursor (EC 3.4.16.-) (Proteinase F) (CPD-II)	0.03	-	vac	0					531
Q86V86 UniProt NPD GO	PIM3_HUMAN	Serine/threonine-protein kinase Pim-3 (EC 2.7.11.1)	0.03	-	cyt	0					326
Q8AX02 UniProt NPD GO	MOS_ATHSQ	Serine/threonine-protein kinase mos (EC 2.7.11.1) (Oocyte maturation factor mos) (Fragment)	0.03	-	cyt	0					194
Q90XV8 UniProt NPD GO	MOS_CICNG	Serine/threonine-protein kinase mos (EC 2.7.11.1) (Oocyte maturation factor mos) (Fragment)	0.03	-	mit	0					200
Q90XV6 UniProt NPD GO	MOS_GYMCA	Serine/threonine-protein kinase mos (EC 2.7.11.1) (Oocyte maturation factor mos) (Fragment)	0.03	-	mit	0					200
Q90XV9 UniProt NPD GO	MOS_NYCNY	Serine/threonine-protein kinase mos (EC 2.7.11.1) (Oocyte maturation factor mos) (Fragment)	0.03	-	mit	0					200
Q90XV7 UniProt NPD GO	MOS_VULGR	Serine/threonine-protein kinase mos (EC 2.7.11.1) (Oocyte maturation factor mos) (Fragment)	0.03	-	mit	0					200
Q75BY1 UniProt NPD GO	PTPA2_ASHGO	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.03	-	mit	0	Cytoplasm (By similarity)				359
Q6BU97 UniProt NPD GO	PTPA2_DEBHA	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.03	-	nuc	0	Cytoplasm (By similarity)				367
Q6CNT6 UniProt NPD GO	PP4C_KLULA	Serine/threonine-protein phosphatase 4 catalytic subunit (EC 3.1.3.16) (PP4C)	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				308
P49576 UniProt NPD GO	PPX1_PARTE	Serine/threonine-protein phosphatase PP-X homolog (EC 3.1.3.16)	0.03	-	cyt	0					303
P48528 UniProt NPD GO	PPX2_ARATH	Serine/threonine-protein phosphatase PP-X isozyme 2 (EC 3.1.3.16)	0.03	-	cyt	0					305
Q95ZY0 UniProt NPD GO	SRB1_CAEEL	Serpentine receptor class beta-1 (Protein srb-1)	0.03	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				341
P54142 UniProt NPD GO	SRB7_CAEEL	Serpentine receptor class beta-7 (Protein srb-7)	0.03	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				348
P92015 UniProt NPD GO	SRD26_CAEEL	Serpentine receptor class delta-26 (Protein srd-26)	0.03	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				317
O17240 UniProt NPD GO	SRD3_CAEEL	Serpentine receptor class delta-3 (Protein srd-3)	0.03	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				344
O17816 UniProt NPD GO	SRE38_CAEEL	Serpentine receptor class epsilon-38 (Protein sre-38)	0.03	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				365
O02739 UniProt NPD GO	SPB6_BOVIN	Serpin B6 (Serine proteinase inhibitor B-43)	0.03	-	end	0	Cytoplasm (By similarity)				378
P02739 UniProt NPD GO	SAA2_MUSVI	Serum amyloid A-2 protein precursor [Contains: Amyloid protein A (Amyloid fibril protein AA)]	0.03	-	exc	0					129
P50160 UniProt NPD GO	TS2_MAIZE	Sex determination protein tasselseed-2	0.03	-	mit	0					336
P83752 UniProt NPD GO	JANA_DROTE	Sex-regulated protein janus-A	0.03	-	cyt	0					135
P83753 UniProt NPD GO	JANA_DROYA	Sex-regulated protein janus-A	0.03	-	cyt	0					135
P20349 UniProt NPD GO	JANB_DROME	Sex-regulated protein janus-B	0.03	-	cyt	0					140
Q8BN82 UniProt NPD GO	S17A5_MOUSE	Sialin (Solute carrier family 17 member 5) (Sodium/sialic acid cotransporter)	0.03	-	end	11 *	Lysosome; lysosomal membrane; multi-pass membrane protein (Potential)	cytoplasmic membrane-bound vesicle [IDA] plasma membrane [IDA]			495
Q63965 UniProt NPD GO	SFXN1_RAT	Sideroflexin-1 (Tricarboxylate carrier protein) (TCC)	0.03	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein				321
P49458 UniProt NPD GO	SRP09_HUMAN	Signal recognition particle 9 kDa protein (SRP9)	0.03	-	nuc	0	Cytoplasm	signal recognition particle receptor complex [TAS]	600707	1RY1	85
O13950 UniProt NPD GO	SRPB_SCHPO	Signal recognition particle receptor subunit beta (SR-beta)	0.03	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane				227
Q8HYP9 UniProt NPD GO	CCL17_MACMU	Small inducible cytokine A17 precursor (CCL17) (Thymus and activation-regulated chemokine) (CC chemo ...	0.03	-	exc	0	Secreted protein (By similarity)				94

You are viewing entries 81651 to 81700 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.