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
O13479 UniProt NPD GO	DPP5_ASPFU	Dipeptidyl-peptidase 5 precursor (EC 3.4.14.-) (Dipeptidyl-peptidase V) (DPP V) (DppV)	0.17	-	exc	0	Secreted protein				721
P83254 UniProt NPD GO	DISB_VIPLE	Disintegrin lebein-beta (Platelet aggregation activation inhibitor)	0.17	-	nuc	0	Secreted protein				64
Q12001 UniProt NPD GO	ALG6_YEAST	Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl-P-Glc:Man9Gl ...	0.17	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IMP]			544
O74189 UniProt NPD GO	PMT1_CANAL	Dolichyl-phosphate-mannose--protein mannosyltransferase 1 (EC 2.4.1.109)	0.17	-	end	11	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				877
P61849 UniProt NPD GO	NEMS_DROME	Dromyosuppressin precursor (TDVDHVFLRFamide)	0.17	-	exc	0	Secreted protein				100
Q9QYJ7 UniProt NPD GO	DUS13_MOUSE	Dual specificity protein phosphatase 13 (EC 3.1.3.48) (EC 3.1.3.16) (Testis- and skeletal muscle-spe ...	0.17	-	mit	1					198
P81160 UniProt NPD GO	DEJP_DROME	Ductus ejaculatorius peptide 99B precursor	0.17	-	vac	1 *	Secreted protein				54
Q29143 UniProt NPD GO	ELAC_TRIVU	Early lactation protein precursor	0.17	-	exc	0	Secreted protein				102
Q40361 UniProt NPD GO	NO12A_MEDSA	Early nodulin 12A precursor (N-12A) (Early nodulin NMS-8)	0.17	-	exc	1 *	Cell wall (By similarity)				93
Q29125 UniProt NPD GO	ELAF_PIG	Elafin precursor (WAP-1 protein)	0.17	-	mit	1 *					167
Q6UAQ8 UniProt NPD GO	ETFB_PIG	Electron transfer flavoprotein subunit beta	0.17	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				254
Q9DCW4 UniProt NPD GO	ETFB_MOUSE	Electron transfer flavoprotein subunit beta (Beta-ETF)	0.17	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)	electron transfer flavoprotein complex (sen... [TAS] mitochondrion [IDA]			254
Q68FU3 UniProt NPD GO	ETFB_RAT	Electron transfer flavoprotein subunit beta (Beta-ETF)	0.17	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				254
P84787 UniProt NPD GO	VSP2_TRIEL	Elegaxobin-2 (EC 3.4.21.-) (Elegaxobin II)	0.17	-	cyt	0	Secreted protein	extracellular region [IDA]			233
Q6FYA7 UniProt NPD GO	EF2_CANGA	Elongation factor 2 (EF-2)	0.17	-	cyt	0	Cytoplasm (By similarity)				842
Q8K0D5 UniProt NPD GO	EFG1_MOUSE	Elongation factor G 1, mitochondrial precursor (mEF-G 1) (Elongation factor G1)	0.17	-	nuc	0	Mitochondrion	mitochondrion [IDA]			751
P51248 UniProt NPD GO	EFTS_PORPU	Elongation factor Ts (EF-Ts)	0.17	-	nuc	0	Plastid; chloroplast				220
P05522 UniProt NPD GO	GUN1_PERAE	Endoglucanase 1 precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Abscission cellulase 1)	0.17	-	cyt	0					494
O08600 UniProt NPD GO	NUCG_MOUSE	Endonuclease G, mitochondrial precursor (EC 3.1.30.-) (Endo G)	0.17	-	end	0	Mitochondrion	mitochondrion [IDA]			294
P80230 UniProt NPD GO	ERH_PIG	Enhancer of rudimentary homolog [Contains: Antibacterial peptide 3910] (Fragment)	0.17	-	nuc	0					32
P22032 UniProt NPD GO	EMBP1_CAVPO	Eosinophil granule major basic protein 1 precursor (MBP-1)	0.17	-	exc	0	Matrix of eosinophil's large specific granule (crystalloid core)				233
P54757 UniProt NPD GO	EPHA5_RAT	Ephrin type-A receptor 5 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EHK-1) (EPH homol ...	0.17	-	nuc	0	Membrane; single-pass type I membrane protein				1005
P97553 UniProt NPD GO	EFNA1_RAT	Ephrin-A1 precursor (EPH-related receptor tyrosine kinase ligand 1) (LERK-1) (Immediate early respon ...	0.17	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				205
P56851 UniProt NPD GO	EP3B_HUMAN	Epididymal secretory protein E3 beta precursor (HE3 beta)	0.17	-	exc	1 *	Secreted protein (Potential)	extracellular region [NAS]			147
Q7YR43 UniProt NPD GO	DDR1_PANTR	Epithelial discoidin domain-containing receptor 1 precursor (EC 2.7.10.1) (Epithelial discoidin doma ...	0.17	-	nuc	1	Membrane; single-pass type I membrane protein				909
Q08345 UniProt NPD GO	DDR1_HUMAN	Epithelial discoidin domain-containing receptor 1 precursor (EC 2.7.10.1) (Epithelial discoidin doma ...	0.17	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600408		913
Q9MYZ9 UniProt NPD GO	EPOR_PIG	Erythropoietin receptor precursor (EPO-R)	0.17	-	end	1	Membrane; single-pass type I membrane protein				509
Q01800 UniProt NPD GO	ESCA_TRICA	Escargot/snail protein homolog (Fragment)	0.17	-	nuc	0	Nucleus (Probable)				46
P49886 UniProt NPD GO	ESR1_MACMU	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha) (Fragment)	0.17	-	nuc	0	Nucleus				121
Q39097 UniProt NPD GO	ERF1X_ARATH	Eukaryotic peptide chain release factor subunit 1-1 (eRF1-1) (Eukaryotic release factor 1-1) (Omnipo ...	0.17	-	cyt	0	Cytoplasm				436
Q9DBZ5 UniProt NPD GO	IF3C_MOUSE	Eukaryotic translation initiation factor 3 subunit 12 (eIF-3 p25) (eIF3k)	0.17	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				218
Q9PW28 UniProt NPD GO	IF4EB_BRARE	Eukaryotic translation initiation factor 4E-1B (eIF4E-1B) (eIF4E)	0.17	-	nuc	0	Cytoplasm. Nucleus				214
Q22888 UniProt NPD GO	IF4E4_CAEEL	Eukaryotic translation initiation factor 4E-4 (eIF4E-4) (eIF-4E-4) (mRNA cap-binding protein) (eIF-4 ...	0.17	-	cyt	0					212
P55876 UniProt NPD GO	IF5_MAIZE	Eukaryotic translation initiation factor 5 (eIF-5)	0.17	-	nuc	0					451
P56564 UniProt NPD GO	EAA1_MOUSE	Excitatory amino acid transporter 1 (Sodium-dependent glutamate/aspartate transporter) (High-affinit ...	0.17	-	end	10 *	Membrane; multi-pass membrane protein				543
P38676 UniProt NPD GO	GUX1_NEUCR	Exoglucanase 1 precursor (EC 3.2.1.91) (Exocellobiohydrolase 1) (1,4-beta-cellobiohydrolase)	0.17	-	mit	0	Secreted protein				516
P19355 UniProt NPD GO	GUX1_TRIVI	Exoglucanase 1 precursor (EC 3.2.1.91) (Exoglucanase I) (Exocellobiohydrolase) (1,4-beta-cellobiohyd ...	0.17	-	exc	0					514
Q9NQT5 UniProt NPD GO	EXOS3_HUMAN	Exosome complex exonuclease RRP40 (EC 3.1.13.-) (Ribosomal RNA-processing protein 40) (Exosome compo ...	0.17	-	cyt	0	Cytoplasm. Nucleus; nucleolus	cytoplasmic exosome (RNase complex) [IDA] nuclear exosome (RNase complex) [IDA]	606489		274
Q9NQT4 UniProt NPD GO	EXOS5_HUMAN	Exosome complex exonuclease RRP46 (EC 3.1.13.-) (Ribosomal RNA-processing protein 46) (Exosome compo ...	0.17	-	mit	0	Nucleus; nucleolus	cytoplasm [NAS] nucleolus [NAS]	606492		235
P16412 UniProt NPD GO	RNF2_GIBBA	Extracellular guanyl-specific ribonuclease Fl2 (EC 3.1.27.3) (RNase Fl2)	0.17	-	nuc	0					105
Q2QLD1 UniProt NPD GO	CAZA2_CARPS	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.17	-	nuc	0					285
Q2QL78 UniProt NPD GO	CAZA2_DIDMA	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.17	-	cyt	0					285
Q2QLA8 UniProt NPD GO	CAZA2_HORSE	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.17	-	nuc	0					285
P28495 UniProt NPD GO	CAPZA_YEAST	F-actin capping protein subunit alpha	0.17	-	nuc	0		actin cortical patch [IDA] actin filament [IPI] F-actin capping protein complex [IDA]			268
Q9UKT6 UniProt NPD GO	FXL21_HUMAN	F-box/LRR-repeat protein 21 (F-box and leucine-rich repeat protein 21) (F-box/LRR-repeat protein 3B) ...	0.17	-	cyt	0		ubiquitin ligase complex [NAS]	609087		434
Q96AY3 UniProt NPD GO	FKB10_HUMAN	FK506-binding protein 10 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rota ...	0.17	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)		607063		582
P0C1B0 UniProt NPD GO	FKBP4_EMENI	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.17	+	cyt	0	Nucleus; nucleolus (By similarity)				478
Q02790 UniProt NPD GO	FKBP4_HUMAN	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (p59 ...	0.17	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [TAS] intracellular [NAS]	600611	1QZ2	458
Q64378 UniProt NPD GO	FKBP5_MOUSE	FK506-binding protein 5 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (51 k ...	0.17	-	cyt	0	Cytoplasm. Nucleus				456
P41854 UniProt NPD GO	FARP_ASCSU	FMRFamide-like neuropeptides precursor [Contains: Neuropeptide AF10 (GFGDEMSMPGVLRF-amide); Neuropep ...	0.17	-	mit	0	Secreted protein				161

You are viewing entries 54251 to 54300 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.