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
P40351 UniProt NPD GO	ALG8_YEAST	Dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl-P-Glc:Gl ...	0.08	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IMP]			577
Q9C100 UniProt NPD GO	PMT2_SCHPO	Dolichyl-phosphate-mannose--protein mannosyltransferase 2 (EC 2.4.1.109)	0.08	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Nucleus; nuclear ...	dolichyl-phosphate-mannose-protein mannosyl... [IDA] endomembrane system [IDA]			739
Q10664 UniProt NPD GO	MEK2_CAEEL	Dual specificity mitogen-activated protein kinase kinase mek-2 (EC 2.7.12.2) (MAP kinase kinase mek- ...	0.08	-	cyt	0					387
Q5R8X2 UniProt NPD GO	DUS18_PONPY	Dual specificity protein phosphatase 18 (EC 3.1.3.48) (EC 3.1.3.16)	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				188
Q9NRW4 UniProt NPD GO	DUS22_HUMAN	Dual specificity protein phosphatase 22 (EC 3.1.3.48) (EC 3.1.3.16) (JNK-stimulatory phosphatase-1) ...	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)			1WRM	184
Q9QUI6 UniProt NPD GO	DUFFY_MOUSE	Duffy antigen/chemokine receptor (CD234 antigen)	0.08	-	end	7	Membrane; multi-pass membrane protein				334
Q8TF09 UniProt NPD GO	DLC2B_HUMAN	Dynein light chain 2B, cytoplasmic	0.08	-	cyt	0	Cytoplasm	cytoplasmic dynein complex [NAS]	607168		96
Q86SQ3 UniProt NPD GO	EMR4_HUMAN	EGF-like module-containing mucin-like hormone receptor-like 4 precursor (G-protein coupled receptor ...	0.08	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]			457
P18413 UniProt NPD GO	ERD2_KLULA	ER lumen protein retaining receptor	0.08	-	end	4 *	Membrane; multi-pass membrane protein				219
O75354 UniProt NPD GO	ENP6_HUMAN	Ectonucleoside triphosphate diphosphohydrolase 6 (EC 3.6.1.6) (NTPDase6) (CD39 antigen-like 2)	0.08	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein. Secreted protein. But also oc ...		603160		484
Q9UJA9 UniProt NPD GO	ENPP5_HUMAN	Ectonucleotide pyrophosphatase/phosphodiesterase 5 precursor (EC 3.1.-.-) (E-NPP5) (NPP-5)	0.08	-	end	1 *	Secreted protein (Potential)				477
Q5BKW7 UniProt NPD GO	ENPP6_BRARE	Ectonucleotide pyrophosphatase/phosphodiesterase 6 precursor (EC 3.1.-.-) (E-NPP6) (NPP-6)	0.08	-	cyt	1	Cell membrane; single-pass type I membrane protein (By similarity)				438
Q6DDP3 UniProt NPD GO	ENPP6_XENLA	Ectonucleotide pyrophosphatase/phosphodiesterase 6 precursor (EC 3.1.-.-) (E-NPP6) (NPP-6)	0.08	-	exc	0	Cell membrane; single-pass type I membrane protein (By similarity)				441
P00773 UniProt NPD GO	ELA1_RAT	Elastase-1 precursor (EC 3.4.21.36)	0.08	-	vac	0	Secreted protein				266
Q29461 UniProt NPD GO	ELA2A_BOVIN	Elastase-2A precursor (EC 3.4.21.71) (Elastase-2) (Elastase II)	0.08	-	exc	0	Secreted protein				269
P02993 UniProt NPD GO	EF1A_ARTSA	Elongation factor 1-alpha (EF-1-alpha)	0.08	-	cyt	0	Cytoplasm				461
P29520 UniProt NPD GO	EF1A_BOMMO	Elongation factor 1-alpha (EF-1-alpha)	0.08	-	cyt	0	Cytoplasm				463
Q92005 UniProt NPD GO	EF1A_BRARE	Elongation factor 1-alpha (EF-1-alpha)	0.08	-	cyt	0	Cytoplasm				462
P90519 UniProt NPD GO	EF1A_CRYPV	Elongation factor 1-alpha (EF-1-alpha)	0.08	-	cyt	0	Cytoplasm				435
Q9YIC0 UniProt NPD GO	EF1A_ORYLA	Elongation factor 1-alpha (EF-1-alpha)	0.08	-	cyt	0	Cytoplasm				461
P84321 UniProt NPD GO	EF1A_ADIBE	Elongation factor 1-alpha (EF-1-alpha) (Fragment)	0.08	-	cyt	0	Cytoplasm				413
P84322 UniProt NPD GO	EF1A_ANIIF	Elongation factor 1-alpha (EF-1-alpha) (Fragment)	0.08	-	cyt	0	Cytoplasm				413
P84319 UniProt NPD GO	EF1A_HELAL	Elongation factor 1-alpha (EF-1-alpha) (Fragment)	0.08	-	cyt	0	Cytoplasm				413
P84317 UniProt NPD GO	EF1A_HELAM	Elongation factor 1-alpha (EF-1-alpha) (Fragment)	0.08	-	cyt	0	Cytoplasm				413
P84320 UniProt NPD GO	EF1A_HELDI	Elongation factor 1-alpha (EF-1-alpha) (Fragment)	0.08	-	cyt	0	Cytoplasm				413
P84318 UniProt NPD GO	EF1A_HELGL	Elongation factor 1-alpha (EF-1-alpha) (Fragment)	0.08	-	cyt	0	Cytoplasm				413
P84315 UniProt NPD GO	EF1A_HELVI	Elongation factor 1-alpha (EF-1-alpha) (Fragment)	0.08	-	cyt	0	Cytoplasm				413
P84316 UniProt NPD GO	EF1A_HELZE	Elongation factor 1-alpha (EF-1-alpha) (Fragment)	0.08	-	cyt	0	Cytoplasm				413
Q26487 UniProt NPD GO	EF1A_SPOFR	Elongation factor 1-alpha (EF-1-alpha) (Fragment)	0.08	-	cyt	0	Cytoplasm				413
Q32PH8 UniProt NPD GO	EF1A2_BOVIN	Elongation factor 1-alpha 2 (EF-1-alpha-2) (Elongation factor 1 A-2) (eEF1A-2)	0.08	-	cyt	0	Nucleus (By similarity)				463
Q05639 UniProt NPD GO	EF1A2_HUMAN	Elongation factor 1-alpha 2 (EF-1-alpha-2) (Elongation factor 1 A-2) (eEF1A-2) (Statin S1)	0.08	-	cyt	0	Nucleus (By similarity)		602959		463
Q71V39 UniProt NPD GO	EF1A2_RABIT	Elongation factor 1-alpha 2 (EF-1-alpha-2) (Elongation factor 1 A-2) (eEF1A-2) (Statin S1)	0.08	-	cyt	0	Nucleus				463
P17508 UniProt NPD GO	EF1A3_XENLA	Elongation factor 1-alpha, oocyte form (EF-1-alpha-O1) (EF-1AO1)	0.08	-	cyt	0	Cytoplasm				461
O81918 UniProt NPD GO	EF1D_BETVU	Elongation factor 1-delta (EF-1-delta) (Elongation factor 1B-beta) (eEF-1B beta)	0.08	-	cyt	0					230
Q4MYA4 UniProt NPD GO	EFTU_THEPA	Elongation factor Tu (EF-Tu)	0.08	-	cyt	0	Plastid; apicoplast				411
P68158 UniProt NPD GO	EFTU_TOBAC	Elongation factor Tu, chloroplast precursor (EF-Tu)	0.08	-	nuc	0	Plastid; chloroplast				478
O21245 UniProt NPD GO	EFTU_RECAM	Elongation factor Tu, mitochondrial	0.08	-	cyt	0	Mitochondrion				394
Q40450 UniProt NPD GO	EFTUA_NICSY	Elongation factor TuA, chloroplast precursor (EF-TuA)	0.08	-	nuc	0	Plastid; chloroplast				478
P24823 UniProt NPD GO	PPBE_MOUSE	Embryonic alkaline phosphatase precursor (EC 3.1.3.1) (EAP)	0.08	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				529
P35809 UniProt NPD GO	XYNA_SCHCO	Endo-1,4-beta-xylanase A (EC 3.2.1.8) (Xylanase A) (1,4-beta-D-xylan xylanohydrolase A)	0.08	-	nuc	0	Secreted protein				197
P54196 UniProt NPD GO	CHI1_COCIM	Endochitinase 1 precursor (EC 3.2.1.14) (Complement-fixation antigen) (CF-antigen) (CF-AG)	0.08	-	exc	0				1LL7	426
Q95NM6 UniProt NPD GO	NUCG_CAEEL	Endonuclease G, mitochondrial precursor (EC 3.1.30.-) (Endo G) (Ced-3 protease suppressor 6)	0.08	-	cyt	0	Mitochondrion	mitochondrion [IDA]			308
P81628 UniProt NPD GO	ERP29_CHICK	Endoplasmic reticulum protein ERp29 (Fragment)	0.08	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen				228
Q9CR89 UniProt NPD GO	ERGI2_MOUSE	Endoplasmic reticulum-Golgi intermediate compartment protein 2	0.08	-	mit	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...	ER-Golgi intermediate compartment [ISS]			377
Q66KH2 UniProt NPD GO	ERGI3_XENLA	Endoplasmic reticulum-Golgi intermediate compartment protein 3	0.08	-	end	2 *	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				389
Q95KI3 UniProt NPD GO	ESAM_MACFA	Endothelial cell-selective adhesion molecule precursor	0.08	-	exc	1	Cell membrane; cell-cell junction; adherens junction; single-pass type I membrane protein (By simila ...				390
P97682 UniProt NPD GO	ESM1_RAT	Endothelial cell-specific molecule 1 precursor (ESM-1 secretory protein) (ESM-1) (PG25)	0.08	-	exc	0	Secreted protein (By similarity)				184
Q90328 UniProt NPD GO	EDNRB_COTJA	Endothelin B receptor (ET-B) (Endothelin receptor non-selective type) (Fragment)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				347
Q6W3C0 UniProt NPD GO	ENO_TUBBO	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.08	-	cyt	0	Cytoplasm				440
P00924 UniProt NPD GO	ENO1_YEAST	Enolase 1 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 1) (2-phospho-D-glycerate hydro-lyase 1)	0.08	-	cyt	0	Cytoplasm	cytoplasm [IDA] phosphopyruvate hydratase complex [IDA]		7ENL	436

You are viewing entries 67951 to 68000 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.