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
Q9HDF6 UniProt NPD GO	EF1A_PIRIN	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				462
O24534 UniProt NPD GO	EF1A_VICFA	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				447
Q03033 UniProt NPD GO	EF1A_WHEAT	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				447
O59949 UniProt NPD GO	EF1A_YARLI	Elongation factor 1-alpha (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				460
P18624 UniProt NPD GO	EF1A_DICDI	Elongation factor 1-alpha (EF-1-alpha) (50 kDa actin-binding protein) (ABP-50)	0.06	-	cyt	0	Cytoplasm				456
P02994 UniProt NPD GO	EF1A_YEAST	Elongation factor 1-alpha (EF-1-alpha) (Translation elongation factor 1A) (Eukaryotic elongation fac ...	0.06	-	cyt	0	Cytoplasm	ribosome [TAS]		1IJF	458
P43643 UniProt NPD GO	EF1A_TOBAC	Elongation factor 1-alpha (EF-1-alpha) (Vitronectin-like adhesion protein 1) (PVN1)	0.06	-	cyt	0	Localized in the cell wall of cortical and transmitting tissue cells of pollinated mature styles				447
P13905 UniProt NPD GO	EF1A_ARATH	Elongation factor 1-alpha (EF-1-alpha) (eEF-1A)	0.06	-	cyt	0	Cytoplasm				449
Q27139 UniProt NPD GO	EF11_EUPCR	Elongation factor 1-alpha 1 (EF-1-alpha-1)	0.06	-	cyt	0	Cytoplasm				442
P50256 UniProt NPD GO	EF1C_PORPU	Elongation factor 1-alpha C (EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				449
P50257 UniProt NPD GO	EF1S_PORPU	Elongation factor 1-alpha S (EF-1-alpha S) (Sporophyte-specific EF-1-alpha)	0.06	-	cyt	0	Cytoplasm				515
Q6DET9 UniProt NPD GO	EF1B_XENTR	Elongation factor 1-beta (EF-1-beta)	0.06	-	cyt	0					227
Q84WM9 UniProt NPD GO	EF1B1_ARATH	Elongation factor 1-beta 1 (EF-1-beta 1) (Elongation factor 1B-alpha 1) (eEF-1B alpha 1) (Elongation ...	0.06	-	cyt	0	Cell membrane; peripheral membrane protein (By similarity)				228
Q9FUM1 UniProt NPD GO	EF1G_PRUAV	Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma)	0.06	-	nuc	0					422
Q5Z627 UniProt NPD GO	EF1G3_ORYSA	Elongation factor 1-gamma 3 (EF-1-gamma 3) (eEF-1B gamma 3)	0.06	-	cyt	0					416
Q17152 UniProt NPD GO	EF2_BLAHO	Elongation factor 2 (EF-2)	0.06	-	cyt	0	Cytoplasm				867
P17746 UniProt NPD GO	EFTU_CHLRE	Elongation factor Tu (EF-Tu)	0.06	-	cyt	0	Plastid; chloroplast				418
O24310 UniProt NPD GO	EFTU_PEA	Elongation factor Tu, chloroplast precursor (EF-Tu)	0.06	-	mit	0	Plastid; chloroplast	chloroplast [IDA]			488
Q43364 UniProt NPD GO	EFTUB_NICSY	Elongation factor TuB, chloroplast precursor (EF-TuB)	0.06	-	nuc	0	Plastid; chloroplast				485
Q9HB03 UniProt NPD GO	ELOV3_HUMAN	Elongation of very long chain fatty acids protein 3 (Cold-inducible glycoprotein of 30 kDa)	0.06	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				270
P16476 UniProt NPD GO	PEPE_CHICK	Embryonic pepsinogen precursor (EC 3.4.23.-)	0.06	-	mit	0					383
Q9ZT66 UniProt NPD GO	E134_MAIZE	Endo-1,3;1,4-beta-D-glucanase precursor (EC 3.2.1.-)	0.06	-	exc	1	Secreted protein				303
P81536 UniProt NPD GO	XYNA_PAEVA	Endo-1,4-beta-xylanase (EC 3.2.1.8) (Xylanase) (1,4-beta-D-xylan xylanohydrolase) (PVX)	0.06	-	cyt	0				1PVX	194
P48824 UniProt NPD GO	XYNB_ASPKA	Endo-1,4-beta-xylanase B precursor (EC 3.2.1.8) (Xylanase B) (1,4-beta-D-xylan xylanohydrolase B)	0.06	-	vac	0					225
O43097 UniProt NPD GO	XYNA_THELA	Endo-1,4-beta-xylanase precursor (EC 3.2.1.8) (Xylanase) (1,4-beta-D-xylan xylanohydrolase)	0.06	-	mit	0				1YNA	225
Q12622 UniProt NPD GO	GUN1_HUMGT	Endoglucanase EG-1 precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase)	0.06	-	exc	0	Secreted protein				435
Q8C522 UniProt NPD GO	ENDD1_MOUSE	Endonuclease domain-containing 1 protein precursor (EC 3.1.30.-)	0.06	-	end	3 *	Secreted protein (Potential)				501
Q8NIP5 UniProt NPD GO	ERO1_KLULA	Endoplasmic oxidoreductin-1 precursor (EC 1.8.4.-)	0.06	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				561
Q4R8X1 UniProt NPD GO	ERGI3_MACFA	Endoplasmic reticulum-Golgi intermediate compartment protein 3	0.06	-	end	2 *	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				382
Q9NQ30 UniProt NPD GO	ESM1_HUMAN	Endothelial cell-specific molecule 1 precursor (ESM-1 secretory protein) (ESM-1)	0.06	-	exc	0	Secreted protein	extracellular region [NAS]	601521		184
Q9QYC5 UniProt NPD GO	ETBR2_RAT	Endothelin B receptor-like protein 2 precursor (ETBR-LP-2) (G-protein coupled receptor 37-like 1) (G ...	0.06	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				481
P21450 UniProt NPD GO	EDNRA_BOVIN	Endothelin-1 receptor precursor (Endothelin A receptor) (ET-A)	0.06	-	end	7	Membrane; multi-pass membrane protein				427
P25696 UniProt NPD GO	ENO_ARATH	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.06	-	nuc	0	Cytoplasm				444
P15007 UniProt NPD GO	ENO_DROME	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.06	-	mit	0	Cytoplasm				500
Q43130 UniProt NPD GO	ENO_MESCR	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.06	-	nuc	0	Cytoplasm (By similarity)				444
Q96X30 UniProt NPD GO	ENO_ASPFU	Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase) (Allergen ...	0.06	-	nuc	0	Cytoplasm (By similarity)				437
P51555 UniProt NPD GO	ENO1_ENTHI	Enolase 1 (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.06	-	nuc	0	Cytoplasm				436
Q8WZM3 UniProt NPD GO	ETR1_CANTR	Enoyl-[acyl-carrier protein] reductase [NADPH, B-specific] 1, mitochondrial precursor (EC 1.3.1.10) ...	0.06	-	mit	0	Mitochondrion			1N9G	386
Q8WZM4 UniProt NPD GO	ETR2_CANTR	Enoyl-[acyl-carrier protein] reductase [NADPH, B-specific] 2, mitochondrial precursor (EC 1.3.1.10) ...	0.06	-	mit	0	Mitochondrion (By similarity)			1N9G	386
P80550 UniProt NPD GO	PERE_PIG	Eosinophil peroxidase (EC 1.11.1.7) (EPO) (Fragments)	0.06	-	nuc	0	Cytoplasmic granule. Cytoplasmic granules of eosinophils				38
P54756 UniProt NPD GO	EPHA5_HUMAN	Ephrin type-A receptor 5 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EHK-1) (EPH homol ...	0.06	-	nuc	0	Membrane; single-pass type I membrane protein	integral to membrane [TAS]	600004		1037
Q14507 UniProt NPD GO	EP3A_HUMAN	Epididymal secretory protein E3 alpha precursor (HE3 alpha)	0.06	-	exc	1 *	Secreted protein (Potential)	extracellular space [TAS]			147
O54699 UniProt NPD GO	S29A2_RAT	Equilibrative nucleoside transporter 2 (Equilibrative nitrobenzylmercaptopurine riboside-insensitive ...	0.06	-	end	10 *	Membrane; multi-pass membrane protein				456
Q14542 UniProt NPD GO	S29A2_HUMAN	Equilibrative nucleoside transporter 2 (Equilibrative nitrobenzylmercaptopurine riboside-insensitive ...	0.06	-	end	11 *	Isoform 1: Cell membrane; multi-pass membrane protein. Isoform 2: Nucleus; nuclear membrane; multi-p ...	integral to plasma membrane [TAS] nucleolus [TAS]	602110		456
Q61672 UniProt NPD GO	S29A2_MOUSE	Equilibrative nucleoside transporter 2 (Equilibrative nitrobenzylmercaptopurine riboside-insensitive ...	0.06	-	end	7 *	Nucleus; nuclear membrane; multi-pass membrane protein				327
P60994 UniProt NPD GO	ERVB_TABDI	Ervatamin-B (EC 3.4.22.-) (ERV-B)	0.06	-	mit	0	Secreted protein			1IWD	215
Q96PL5 UniProt NPD GO	ERMAP_HUMAN	Erythroid membrane-associated protein precursor (hERMAP) (Scianna blood group antigen) (Radin blood ...	0.06	-	nuc	2 *	Cell membrane; single-pass type I membrane protein. Cytoplasm. Also found in the cytoplasm	plasma membrane [IDA]	609017		475
Q2HJH3 UniProt NPD GO	CK054_BOVIN	Ester hydrolase C11orf54 homolog (EC 3.1.-.-)	0.06	-	cyt	0	Nucleus (By similarity)				315
Q9GJT2 UniProt NPD GO	ESTD_PIG	Esterase D (EC 3.1.1.1)	0.06	-	cyt	0	Cytoplasmic vesicle (By similarity)				282
O16520 UniProt NPD GO	ERF1_CAEEL	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.06	-	cyt	0	Cytoplasm (By similarity)				443

You are viewing entries 72001 to 72050 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.