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
Q04964 UniProt NPD GO	SML1_YEAST	Ribonucleotide reductase inhibitor protein SML1	0.34	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			104
P37706 UniProt NPD GO	RRFC_DAUCA	Ribosome recycling factor, chloroplast precursor (Ribosome-releasing factor, chloroplast) (Nuclear l ...	0.34	-	nuc	0	Plastid; chloroplast (By similarity)				227
O14492 UniProt NPD GO	APS_HUMAN	SH2 and PH domain-containing adapter protein APS (Adapter protein with pleckstrin homology and Src h ...	0.34	-	nuc	0	Cytoplasm. Cell membrane. Cytoplasmic before PDGF stimulation. After PDGF stimulation, localized at ...	cytoplasm [IDA] plasma membrane [IDA]	605300	1Q2H	632
Q9SCY5 UniProt NPD GO	KINB2_ARATH	SNF1-related protein kinase regulatory subunit beta-2 (AKIN beta2) (AKINB2)	0.34	-	nuc	0					289
Q86TD4 UniProt NPD GO	SRCA_HUMAN	Sarcalumenin precursor	0.34	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen (By similarity). Associated through calcium wit ...		604992		932
Q8C850 UniProt NPD GO	SCAR3_MOUSE	Scavenger receptor class A member 3	0.34	-	nuc	1	Membrane; single-pass type II membrane protein. Endoplasmic reticulum and/or Golgi (By similarity)				606
Q10137 UniProt NPD GO	SEC14_SCHPO	Sec14 cytosolic factor (Phosphatidylinositol/phosphatidyl-choline transfer protein) (PI/PC TP) (Spor ...	0.34	-	nuc	0	Nucleus. Nuclear, during meiosis. Forespore; forespore membrane. Associated with the forespore membr ...	cell tip [IDA] nucleus [IDA] prospore membrane [IDA]			286
P10124 UniProt NPD GO	PGSG_HUMAN	Secretory granule proteoglycan core protein precursor (Platelet proteoglycan core protein) (P.PG) (H ...	0.34	-	exc	0			177040		158
Q8IZQ5 UniProt NPD GO	SELH_HUMAN	Selenoprotein H	0.34	-	nuc	0			607914		122
Q9Z2Q6 UniProt NPD GO	SEPT5_MOUSE	Septin-5 (Peanut-like protein 1) (Cell division control-related protein 1) (CDCrel-1)	0.34	-	nuc	0		plasma membrane [ISS] synaptic vesicle [ISS] synaptosome [IDA]			369
Q9JJM9 UniProt NPD GO	SEPT5_RAT	Septin-5 (Peanut-like protein 1) (Cell division control-related protein 1) (CDCrel-1)	0.34	-	nuc	0		plasma membrane [ISS] synaptic vesicle [ISS]			369
P69193 UniProt NPD GO	SERA_PLAFD	Serine-repeat antigen protein precursor (p126) (111 kDa antigen)	0.34	-	nuc	0	Vacuole. Exported antigen that accumulates in the parasitophorous vacuole				989
P69192 UniProt NPD GO	SERA_PLAFG	Serine-repeat antigen protein precursor (p126) (111 kDa antigen)	0.34	-	nuc	0	Vacuole. Exported antigen that accumulates in the parasitophorous vacuole				989
Q9LJF3 UniProt NPD GO	BRL3_ARATH	Serine/threonine-protein kinase BRI1-like 3 precursor (EC 2.7.11.1) (BRASSINOSTEROID INSENSITIVE 1-l ...	0.34	-	end	1	Cell membrane; single-pass type I membrane protein				1164
P43294 UniProt NPD GO	MHK_ARATH	Serine/threonine-protein kinase MHK (EC 2.7.11.22)	0.34	-	nuc	0					443
Q9ES74 UniProt NPD GO	NEK7_MOUSE	Serine/threonine-protein kinase Nek7 (EC 2.7.11.1) (NimA-related protein kinase 7)	0.34	-	cyt	0	Cytoplasm				302
O95747 UniProt NPD GO	OXSR1_HUMAN	Serine/threonine-protein kinase OSR1 (EC 2.7.11.1) (Oxidative stress-responsive 1 protein)	0.34	-	cyt	0			604046		527
P12965 UniProt NPD GO	MOS_XENLA	Serine/threonine-protein kinase mos (EC 2.7.11.1) (pp39-mos)	0.34	-	nuc	0					359
Q6NU47 UniProt NPD GO	PDK1A_XENLA	Serine/threonine-protein kinase pdik1l-A (EC 2.7.11.1)	0.34	-	nuc	0	Nucleus (By similarity)				339
Q61288 UniProt NPD GO	ACVL1_MOUSE	Serine/threonine-protein kinase receptor R3 precursor (EC 2.7.11.30) (SKR3) (Activin receptor-like k ...	0.34	-	end	0	Membrane; single-pass type I membrane protein				502
Q6FRQ9 UniProt NPD GO	PTPA1_CANGA	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.34	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				424
P48490 UniProt NPD GO	PP1_PHAVU	Serine/threonine-protein phosphatase PP1 (EC 3.1.3.16)	0.34	-	mit	0					314
P61287 UniProt NPD GO	PP1G_BOVIN	Serine/threonine-protein phosphatase PP1-gamma catalytic subunit (EC 3.1.3.16) (PP-1G) (Protein phos ...	0.34	-	cyt	0	Cytoplasm (By similarity)				323
P36873 UniProt NPD GO	PP1G_HUMAN	Serine/threonine-protein phosphatase PP1-gamma catalytic subunit (EC 3.1.3.16) (PP-1G) (Protein phos ...	0.34	-	cyt	0	Cytoplasm		176914	2BDX	323
P63087 UniProt NPD GO	PP1G_MOUSE	Serine/threonine-protein phosphatase PP1-gamma catalytic subunit (EC 3.1.3.16) (PP-1G) (Protein phos ...	0.34	-	cyt	0	Cytoplasm (By similarity)	mitochondrial outer membrane [IDA] mitochondrion [IDA]			323
P63088 UniProt NPD GO	PP1G_RAT	Serine/threonine-protein phosphatase PP1-gamma catalytic subunit (EC 3.1.3.16) (PP-1G) (Protein phos ...	0.34	-	cyt	0	Cytoplasm				323
Q09206 UniProt NPD GO	SRA4_CAEEL	Serpentine receptor class alpha-4 (Protein sra-4)	0.34	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				329
Q09209 UniProt NPD GO	SRA7_CAEEL	Serpentine receptor class alpha-7 (Protein sra-7)	0.34	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				329
O17823 UniProt NPD GO	SRD44_CAEEL	Serpentine receptor class delta-44 (Protein srd-44)	0.34	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				317
Q19505 UniProt NPD GO	SRD45_CAEEL	Serpentine receptor class delta-45 (Protein srd-45)	0.34	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				316
Q9JK88 UniProt NPD GO	SPI2_MOUSE	Serpin I2 precursor (Serine protease inhibitor 14)	0.34	-	exc	0	Secreted protein (Probable)				405
P10808 UniProt NPD GO	NXS1_BUNFA	Short neurotoxin 1 (Toxin V-II-1)	0.34	-	nuc	0	Secreted protein				64
P01422 UniProt NPD GO	NXS2_NAJHA	Short neurotoxin 2 (Toxin CM-14) (Toxin V-N-I2)	0.34	-	nuc	0	Secreted protein				61
P01433 UniProt NPD GO	NXS2_HEMHA	Short neurotoxin 2 (Toxin IV)	0.34	-	nuc	0	Secreted protein				61
Q9Y336 UniProt NPD GO	SIGL9_HUMAN	Sialic acid-binding Ig-like lectin 9 precursor (Siglec-9) (Protein FOAP-9)	0.34	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	605640		463
Q99150 UniProt NPD GO	SRP54_YARLI	Signal recognition particle 54 kDa protein homolog (SRP54)	0.34	-	cyt	0	Cytoplasm				536
Q9CUN6 UniProt NPD GO	SMUF1_MOUSE	Smad ubiquitination regulatory factor 1 (EC 6.3.2.-) (Ubiquitin--protein ligase SMURF1) (Smad-specif ...	0.34	-	mit	0		intracellular [ISS]			731
P22362 UniProt NPD GO	CCL1_HUMAN	Small inducible cytokine A1 precursor (CCL1) (T lymphocyte-secreted protein I-309)	0.34	-	nuc	0	Secreted protein	extracellular space [TAS]	182281	1EL0	96
Q9Y4X3 UniProt NPD GO	CCL27_HUMAN	Small inducible cytokine A27 precursor (CCL27) (CC chemokine ILC) (IL-11 R-alpha-locus chemokine) (S ...	0.34	-	exc	0			604833		112
Q8LPW2 UniProt NPD GO	RT13_SOYBN	Small ribosomal subunit protein S13, mitochondrial precursor	0.34	-	mit	0	Mitochondrion				148
Q7ZVA0 UniProt NPD GO	SMU1_BRARE	Smu-1 suppressor of mec-8 and unc-52 protein homolog	0.34	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				513
Q99M63 UniProt NPD GO	SMU1_RAT	Smu-1 suppressor of mec-8 and unc-52 protein homolog (Brain-enriched WD repeat protein)	0.34	-	cyt	0	Cytoplasm. Nucleus				513
O46669 UniProt NPD GO	SC10A_CANFA	Sodium channel protein type 10 subunit alpha (Sodium channel protein type X subunit alpha) (Voltage- ...	0.34	-	end	19	Membrane; multi-pass membrane protein (By similarity). It can be translocated to the extracellular m ...				1962
P26433 UniProt NPD GO	SL9A3_RAT	Sodium/hydrogen exchanger 3 (Na(+)/H(+) exchanger 3) (NHE-3) (Solute carrier family 9 member 3)	0.34	+	end	12	Membrane; multi-pass membrane protein	brush border [IDA]			831
Q28139 UniProt NPD GO	NCKX1_BOVIN	Sodium/potassium/calcium exchanger 1 (Na(+)/K(+)/Ca(2+)-exchange protein 1) (Retinal rod Na-Ca+K exc ...	0.34	-	end	11 *	Membrane; multi-pass membrane protein				1216
P55019 UniProt NPD GO	S12A3_PSEAM	Solute carrier family 12 member 3 (Thiazide-sensitive sodium-chloride cotransporter) (Na-Cl symporte ...	0.34	-	end	10	Membrane; multi-pass membrane protein				1023
P63292 UniProt NPD GO	SLIB_BOVIN	Somatoliberin precursor (Growth hormone-releasing factor) (GRF) (Growth hormone-releasing hormone) ( ...	0.34	-	mit	0	Secreted protein				106
P34005 UniProt NPD GO	SOMA_CHEMY	Somatotropin (Growth hormone)	0.34	-	nuc	0	Secreted protein				191
Q91221 UniProt NPD GO	SOMA2_ONCNE	Somatotropin-2 precursor (Somatotropin II) (Growth hormone II)	0.34	-	exc	0	Secreted protein				210
Q4WWS3 UniProt NPD GO	SNX3_ASPFU	Sorting nexin-3	0.34	-	cyt	0	Cytoplasm (By similarity)				149

You are viewing entries 37101 to 37150 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.