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
Q5AWS1 UniProt NPD GO	DCN1_EMENI	Defective in cullin neddylation protein 1	0.23	-	mit	0					308
Q56Y11 UniProt NPD GO	DDPS2_ARATH	Dehydrodolichyl diphosphate synthase 2 (EC 2.5.1.-) (Dedol-PP synthase 2)	0.23	-	cyt	0					310
Q6PDY0 UniProt NPD GO	DIPA_MOUSE	Delta-interacting protein A homolog (Coiled-coil domain-containing protein 85B)	0.23	-	nuc	0					202
Q62651 UniProt NPD GO	ECH1_RAT	Delta3,5-delta2,4-dienoyl-CoA isomerase, mitochondrial precursor (EC 5.3.3.-)	0.23	-	pox	0	Mitochondrion. Peroxisome			1DCI	327
Q9CQJ6 UniProt NPD GO	DENR_MOUSE	Density-regulated protein (DRP)	0.23	-	cyt	0					198
Q39017 UniProt NPD GO	DGK1_ARATH	Diacylglycerol kinase 1 (EC 2.7.1.107) (Diglyceride kinase 1) (DGK 1) (DAG kinase 1)	0.23	-	nuc	1 *					728
P59906 UniProt NPD GO	DICT_DICLA	Dicentracin precursor (Dicentracine)	0.23	-	cyt	0	Secreted protein (Potential)				79
Q566C7 UniProt NPD GO	NUDT3_RAT	Diphosphoinositol polyphosphate phosphohydrolase 1 (EC 3.6.1.52) (DIPP-1) (Diadenosine 5',5'''-P1,P6 ...	0.23	-	nuc	0	Cytoplasm (Probable)				168
Q5KN81 UniProt NPD GO	DPH1_CRYNE	Diphthamide biosynthesis protein 1	0.23	-	cyt	0	Cytoplasm (By similarity)				529
P22826 UniProt NPD GO	DISI_ERIMA	Disintegrin eristicophin (Platelet aggregation activation inhibitor)	0.23	-	nuc	0	Secreted protein				51
P31984 UniProt NPD GO	DISI_CROMM	Disintegrin molossin (Platelet aggregation activation inhibitor)	0.23	-	nuc	0	Secreted protein				73
Q8K2A8 UniProt NPD GO	ALG3_MOUSE	Dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase (EC 2.4.1.-) (Dol-P-Man-dependent alp ...	0.23	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				438
P80219 UniProt NPD GO	DDN1_BOVIN	Duodenase-1 precursor (EC 3.4.21.-) (Duodenase I) (Duodenum serine protease)	0.23	-	exc	0				1EUF	251
P98107 UniProt NPD GO	LYAM2_BOVIN	E-selectin precursor (Endothelial leukocyte adhesion molecule 1) (ELAM-1) (Leukocyte-endothelial cel ...	0.23	-	exc	1	Membrane; single-pass type I membrane protein				485
Q42377 UniProt NPD GO	EC2_ARATH	EC protein homolog 2	0.23	-	nuc	0					85
P61551 UniProt NPD GO	EFC1_GORGO	ERV-F(c)1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (GorERV-Fc1env envelop ...	0.23	-	exc	0					179
Q96L15 UniProt NPD GO	NAR5_HUMAN	Ecto-ADP-ribosyltransferase 5 precursor (EC 2.4.2.31) (NAD(P)(+)--arginine ADP-ribosyltransferase 5) ...	0.23	-	end	0	Secreted protein (Potential)				292
Q3SYU2 UniProt NPD GO	EF2_BOVIN	Elongation factor 2 (EF-2)	0.23	-	nuc	0	Cytoplasm (By similarity)				857
Q90705 UniProt NPD GO	EF2_CHICK	Elongation factor 2 (EF-2)	0.23	-	nuc	0	Cytoplasm				857
P13639 UniProt NPD GO	EF2_HUMAN	Elongation factor 2 (EF-2)	0.23	-	nuc	0	Cytoplasm		130610		857
Q5R8Z3 UniProt NPD GO	EF2_PONPY	Elongation factor 2 (EF-2)	0.23	-	nuc	0	Cytoplasm (By similarity)				857
Q96RP9 UniProt NPD GO	EFG1_HUMAN	Elongation factor G 1, mitochondrial precursor (mEF-G 1) (Elongation factor G1)	0.23	+	nuc	0	Mitochondrion		609060		751
Q6B8R4 UniProt NPD GO	EFTS_GRATL	Elongation factor Ts (EF-Ts)	0.23	-	cyt	0	Plastid; chloroplast				208
O78481 UniProt NPD GO	EFTS_GUITH	Elongation factor Ts (EF-Ts)	0.23	-	nuc	0	Plastid; chloroplast				219
P55335 UniProt NPD GO	XYN2_MAGGR	Endo-1,4-beta-xylanase 22 precursor (EC 3.2.1.8) (Xylanase 22) (1,4-beta-D-xylan xylanohydrolase 22) ...	0.23	-	exc	1 *					233
P82186 UniProt NPD GO	GUN_MYTED	Endoglucanase (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase) (CMCase)	0.23	-	mit	0				1WC2	181
Q6GPQ6 UniProt NPD GO	EDF1_XENLA	Endothelial differentiation-related factor 1 homolog (EDF-1)	0.23	-	nuc	0	Nucleus (By similarity)				147
Q28469 UniProt NPD GO	EDN1_MACFA	Endothelin-1 (ET-1) (Fragment)	0.23	-	nuc	0	Secreted protein				76
P14138 UniProt NPD GO	EDN3_HUMAN	Endothelin-3 precursor (ET-3) (Preproendothelin-3) (PPET3)	0.23	-	nuc	0	Secreted protein	soluble fraction [TAS]	277580		238
P28693 UniProt NPD GO	EPHB2_CHICK	Ephrin type-B receptor 2 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor CEK5)	0.23	-	end	1	Membrane; single-pass type I membrane protein			1SGG	1004
O13147 UniProt NPD GO	EPHB3_BRARE	Ephrin type-B receptor 3 (EC 2.7.10.1) (Tyrosine-protein kinase receptor ZEK3) (EPH-like kinase 3) ( ...	0.23	-	nuc	1	Membrane; single-pass type I membrane protein				500
P20827 UniProt NPD GO	EFNA1_HUMAN	Ephrin-A1 precursor (EPH-related receptor tyrosine kinase ligand 1) (LERK-1) (Immediate early respon ...	0.23	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor	integral to plasma membrane [TAS]	191164		205
P81755 UniProt NPD GO	CXET_CONTE	Epsilon-conotoxin TxIX precursor (Conotoxin tx5a)	0.23	-	exc	0	Secreted protein			1WCT	67
Q01799 UniProt NPD GO	ESCA_SCICO	Escargot/snail protein homolog (Fragment)	0.23	-	nuc	0	Nucleus (Probable)				82
P49887 UniProt NPD GO	ST1E1_CAVPO	Estrogen sulfotransferase (EC 2.8.2.4) (Sulfotransferase, estrogen-preferring) (ST1E3)	0.23	-	cyt	0	Cytoplasm				296
Q9U8U5 UniProt NPD GO	ERF1_TETTH	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.23	-	nuc	0	Cytoplasm				435
Q9C5Z1 UniProt NPD GO	IF39_ARATH	Eukaryotic translation initiation factor 3 subunit 9 (eIF-3 eta) (eIF3 p110) (eIF3b) (p82)	0.23	-	cyt	0					712
Q8VBV3 UniProt NPD GO	EXOS2_MOUSE	Exosome complex exonuclease RRP4 (EC 3.1.13.-) (Ribosomal RNA-processing protein 4) (Exosome compone ...	0.23	-	cyt	0					293
P38195 UniProt NPD GO	ECM13_YEAST	Extracellular matrix protein 13	0.23	-	nuc	0					257
Q5NVM0 UniProt NPD GO	CAZA1_PONPY	F-actin capping protein alpha-1 subunit (CapZ alpha-1)	0.23	-	nuc	0					285
Q2QL88 UniProt NPD GO	CAZA2_MICMU	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.23	-	nuc	0					285
Q9WUV6 UniProt NPD GO	CAZA3_RAT	F-actin capping protein alpha-3 subunit (CapZ alpha-3)	0.23	-	cyt	0		F-actin capping protein complex [IPI]			299
P70190 UniProt NPD GO	CAZA3_MOUSE	F-actin capping protein alpha-3 subunit (CapZ alpha-3) (Germ cell-specific protein 3)	0.23	-	cyt	0					299
Q9W2N0 UniProt NPD GO	CAPZA_DROME	F-actin capping protein subunit alpha	0.23	-	cyt	0					286
P47757 UniProt NPD GO	CAPZB_MOUSE	F-actin capping protein subunit beta (CapZ beta)	0.23	-	nuc	0		lamellipodium [IDA]			276
Q96EF6 UniProt NPD GO	FBX17_HUMAN	F-box only protein 17 (F-box only protein 26)	0.23	-	mit	0			609094		278
Q8BK26 UniProt NPD GO	FBX44_MOUSE	F-box only protein 44 (F-box only protein 6a)	0.23	-	cyt	0					255
O94529 UniProt NPD GO	POB3_SCHPO	FACT complex subunit pob3 (Facilitates chromatin transcription complex subunit pob3)	0.23	-	nuc	0	Nucleus (By similarity)				512
Q62446 UniProt NPD GO	FKBP3_MOUSE	FK506-binding protein 3 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (25 k ...	0.23	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			224
Q07418 UniProt NPD GO	PEX19_YEAST	Farnesylated protein PEX19 (Peroxin-19)	0.23	-	nuc	0	Peroxisome. Cytoplasm	cytosol [IDA]			350

You are viewing entries 47301 to 47350 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.