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
O43819 UniProt NPD GO	SCO2_HUMAN	SCO2 protein homolog, mitochondrial precursor	0.31	-	nuc	0	Mitochondrion	mitochondrion [TAS]	604377		266
Q3TYX3 UniProt NPD GO	SMYD5_MOUSE	SET and MYND domain-containing protein 5 (Protein NN8-4AG)	0.31	-	cyt	0					416
Q68F99 UniProt NPD GO	STAC3_XENTR	SH3 and cysteine-rich domain-containing protein 3	0.31	-	nuc	0					337
P36123 UniProt NPD GO	SA190_YEAST	SIT4-associating protein SAP190	0.31	-	nuc	0	Cytoplasm (Probable)	cytoplasm [IPI]			1033
O95295 UniProt NPD GO	S25BP_HUMAN	SNARE-associated protein Snapin (Synaptosomal-associated protein 25-binding protein) (SNAP-associate ...	0.31	-	cyt	0	Or: Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Or: Cytoplasmi ...	synaptic vesicle [TAS]	607007		136
Q90577 UniProt NPD GO	SRCA_CHICK	Sarcalumenin precursor	0.31	-	end	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen (By similarity). Associated through calcium wit ...				471
Q6AZY7 UniProt NPD GO	SCAR3_HUMAN	Scavenger receptor class A member 3 (Cellular stress response gene protein)	0.31	-	nuc	1	Membrane; single-pass type II membrane protein. Endoplasmic reticulum and/or Golgi		602728		606
Q9DEQ4 UniProt NPD GO	SFRP1_CHICK	Secreted frizzled-related protein 1 precursor (sFRP-1) (CsFRP1)	0.31	-	exc	1 *	Secreted protein. Cell membrane or extracellular matrix-associated. Released by heparin-binding (By ...				314
Q5RA66 UniProt NPD GO	SEPT2_PONPY	Septin-2	0.31	-	cyt	0					361
Q15019 UniProt NPD GO	SEPT2_HUMAN	Septin-2 (Protein NEDD5)	0.31	-	cyt	0		contractile ring [ISS] cytoplasm [IDA] nucleus [IDA]	601506		361
P48241 UniProt NPD GO	LCB2_KLULA	Serine palmitoyltransferase 2 (EC 2.3.1.50) (Long chain base biosynthesis protein 2) (SPT 2)	0.31	-	nuc	0	Membrane; single-pass membrane protein				562
Q63686 UniProt NPD GO	PCTK1_RAT	Serine/threonine-protein kinase PCTAIRE-1 (EC 2.7.11.22) (PCTAIRE-motif protein kinase 1)	0.31	-	cyt	0					496
Q5N942 UniProt NPD GO	SAPK4_ORYSA	Serine/threonine-protein kinase SAPK4 (EC 2.7.11.1) (Osmotic stress/abscisic acid-activated protein ...	0.31	-	nuc	0					360
Q9XT18 UniProt NPD GO	SGK1_RABIT	Serine/threonine-protein kinase Sgk1 (EC 2.7.11.1) (Serum/glucocorticoid-regulated kinase 1)	0.31	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Nuclear, upon phosphorylation (By similarity)				431
Q13362 UniProt NPD GO	2A5G_HUMAN	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform (PP2A, B subunit, B' ...	0.31	-	mit	0	Isoform 1, isoform 3: Nucleus	nucleus [IDA] protein phosphatase type 2A complex [NAS]	601645		524
Q60996 UniProt NPD GO	2A5G_MOUSE	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform (PP2A, B subunit, B' ...	0.31	-	cyt	0	Cytoplasm (By similarity)	nucleus [TAS]			524
Q5B6C5 UniProt NPD GO	PTPA1_EMENI	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.31	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				432
P12982 UniProt NPD GO	PP12_DROME	Serine/threonine-protein phosphatase alpha-2 isoform (EC 3.1.3.16)	0.31	-	cyt	0	Cytoplasm				302
P58006 UniProt NPD GO	SESN1_MOUSE	Sestrin-1 (p53-regulated protein PA26)	0.31	-	nuc	0	Nucleus (By similarity)				492
P40902 UniProt NPD GO	ISP7_SCHPO	Sexual differentiation process protein isp7	0.31	-	nuc	0					397
Q39019 UniProt NPD GO	KSG10_ARATH	Shaggy-related protein kinase kappa (EC 2.7.11.1) (ASK-kappa) (AtK-1)	0.31	-	cyt	0					421
P25495 UniProt NPD GO	NXSA_LATCR	Short neurotoxin A	0.31	-	nuc	0	Secreted protein				62
O43173 UniProt NPD GO	SIA8C_HUMAN	Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase (EC 2.4.99.-) (ST8 alpha-N-acetyl-ne ...	0.31	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)		609478		380
P61644 UniProt NPD GO	SIA8C_PANTR	Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase (EC 2.4.99.-) (ST8 alpha-N-acetyl-ne ...	0.31	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				380
Q3ZBG7 UniProt NPD GO	SRP19_BOVIN	Signal recognition particle 19 kDa protein (SRP19)	0.31	-	nuc	0	Cytoplasm (By similarity)				144
Q95MM9 UniProt NPD GO	SLAF1_CANFA	Signaling lymphocytic activation molecule precursor (CD150 antigen homolog)	0.31	+	exc	1	Cell membrane; single-pass type I membrane protein. Present on the surface of B-cells and T-cells (B ...				342
Q566B0 UniProt NPD GO	BURS2_APIME	Single-chain bursicon precursor	0.31	-	nuc	1 *	Secreted protein				269
P15807 UniProt NPD GO	MET8_YEAST	Siroheme biosynthesis protein MET8 [Includes: Precorrin-2 dehydrogenase (EC 1.3.1.76); Sirohydrochlo ...	0.31	-	cyt	0				1KYQ	274
Q99731 UniProt NPD GO	CCL19_HUMAN	Small inducible cytokine A19 precursor (CCL19) (Macrophage inflammatory protein 3 beta) (MIP-3-beta) ...	0.31	-	exc	0	Secreted protein		602227		98
Q9WUQ5 UniProt NPD GO	SCYBE_MOUSE	Small inducible cytokine B14 precursor (CXCL14) (Chemokine BRAK) (Kidney-expressed chemokine CXC)	0.31	-	mit	0	Secreted protein (Potential)				99
Q925F0 UniProt NPD GO	SMPX_RAT	Small muscular protein (Stretch-responsive skeletal muscle protein)	0.31	-	mit	0					85
P13587 UniProt NPD GO	ATN1_YEAST	Sodium transport ATPase 1 (EC 3.6.3.7)	0.31	-	end	10	Cell membrane; multi-pass membrane protein	plasma membrane [IDA]			1091
Q49SH1 UniProt NPD GO	NCKX5_BRARE	Sodium/potassium/calcium exchanger 5 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 5) (Solute carrie ...	0.31	-	end	12 *	Intracytoplasmic membrane; multi-pass membrane protein. Localizes to intracellular membranes, likely ...				513
P42577 UniProt NPD GO	FRIS_LYMST	Soma ferritin (EC 1.16.3.1)	0.31	-	nuc	0	Cytoplasm				173
P20392 UniProt NPD GO	SOMA_LOXAF	Somatotropin (Growth hormone)	0.31	-	mit	0	Secreted protein				190
P10766 UniProt NPD GO	SOMA_VULVU	Somatotropin (Growth hormone)	0.31	-	mit	0	Secreted protein				190
Q7YRR6 UniProt NPD GO	SOMA_CAMDR	Somatotropin precursor (Growth hormone)	0.31	-	exc	0	Secreted protein				216
Q9JKM4 UniProt NPD GO	SOMA_CAVPO	Somatotropin precursor (Growth hormone)	0.31	-	vac	0	Secreted protein				216
Q7YQD2 UniProt NPD GO	SOMA_GIRCA	Somatotropin precursor (Growth hormone)	0.31	-	exc	1 *	Secreted protein				217
P01245 UniProt NPD GO	SOMA_HORSE	Somatotropin precursor (Growth hormone)	0.31	-	exc	0	Secreted protein				216
Q9W6J5 UniProt NPD GO	SOMA_MISMI	Somatotropin precursor (Growth hormone)	0.31	-	nuc	0	Secreted protein				210
P01244 UniProt NPD GO	SOMA_RAT	Somatotropin precursor (Growth hormone)	0.31	-	mit	0	Secreted protein				216
Q91VH2 UniProt NPD GO	SNX9_MOUSE	Sorting nexin-9	0.31	-	nuc	0		cytoplasm [IDA] microsome [IDA] plasma membrane [IDA] soluble fraction [IDA]			595
Q7SXP4 UniProt NPD GO	SF1L1_BRARE	Splicing factor, arginine/serine-rich 1-like protein 1	0.31	+	nuc	0	Nucleus (By similarity)				245
Q9D0B0 UniProt NPD GO	SFRS9_MOUSE	Splicing factor, arginine/serine-rich 9	0.31	-	nuc	0	Nucleus (By similarity)			1WG4	222
Q5PPI1 UniProt NPD GO	SFRS9_RAT	Splicing factor, arginine/serine-rich 9	0.31	-	nuc	0	Nucleus (By similarity)				221
O65726 UniProt NPD GO	ERG12_BRANA	Squalene monooxygenase 1,2 (EC 1.14.99.7) (Squalene epoxidase 1,2) (SE 1,2)	0.31	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				518
P53798 UniProt NPD GO	FDFT_MOUSE	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.31	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				416
Q08264 UniProt NPD GO	STC_ONCKI	Stanniocalcin precursor (STC) (Corpuscles of Stannius protein) (CS) (Hypocalcin) (Teleocalcin)	0.31	-	cyt	0	Secreted protein				256
Q5RAT2 UniProt NPD GO	STC2_PONPY	Stanniocalcin-2 precursor (STC-2)	0.31	-	exc	0	Secreted protein (Potential)				302

You are viewing entries 39851 to 39900 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.