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
Q07322 UniProt NPD GO	ECP40_DAUCA	Embryogenic cell protein 40 (ECP40)	0.13	-	cyt	0					306
Q7M4E9 UniProt NPD GO	CUD3_SCHGR	Endocuticle structural glycoprotein SgAbd-3	0.13	-	nuc	0					119
O94919 UniProt NPD GO	ENDD1_HUMAN	Endonuclease domain-containing 1 protein precursor (EC 3.1.30.-)	0.13	-	end	3	Secreted protein (Potential)				500
Q6CWW7 UniProt NPD GO	ERV25_KLULA	Endoplasmic reticulum vesicle protein 25 precursor	0.13	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				212
Q74ZC0 UniProt NPD GO	YSH1_ASHGO	Endoribonuclease YSH1 (EC 3.1.27.-) (mRNA 3'-end-processing protein YSH1)	0.13	-	nuc	0	Nucleus (By similarity)				771
P32802 UniProt NPD GO	EMP70_YEAST	Endosomal P24A protein precursor (70 kDa endomembrane protein) (Pheromone alpha-factor transporter) ...	0.13	-	end	10 *	Endosome; endosomal membrane; multi-pass membrane protein (Probable)	endosome [TAS] membrane fraction [TAS]			667
P14604 UniProt NPD GO	ECHM_RAT	Enoyl-CoA hydratase, mitochondrial precursor (EC 4.2.1.17) (Short chain enoyl-CoA hydratase) (SCEH) ...	0.13	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]		2DUB	290
P35709 UniProt NPD GO	EMBP2_CAVPO	Eosinophil granule major basic protein 2 precursor (MBP-2)	0.13	-	exc	0	Matrix of eosinophil's large specific granule (crystalloid core)				234
Q61772 UniProt NPD GO	EPHA7_MOUSE	Ephrin type-A receptor 7 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EHK-3) (EPH homol ...	0.13	-	end	2 *	Membrane; single-pass type I membrane protein				998
Q15375 UniProt NPD GO	EPHA7_HUMAN	Ephrin type-A receptor 7 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EHK-3) (EPH homol ...	0.13	-	end	1	Membrane; single-pass type I membrane protein		602190		998
O60487 UniProt NPD GO	EVA1_HUMAN	Epithelial V-like antigen 1 precursor	0.13	-	end	2 *	Membrane; single-pass type I membrane protein (Probable)	cytoskeleton [TAS]	604873		215
O70255 UniProt NPD GO	EVA1_MOUSE	Epithelial V-like antigen 1 precursor	0.13	-	end	1	Membrane; single-pass type I membrane protein (Probable)				215
Q5R804 UniProt NPD GO	EVA1_PONPY	Epithelial V-like antigen 1 precursor	0.13	-	end	2 *	Membrane; single-pass type I membrane protein (Probable)				214
P70694 UniProt NPD GO	DHB5_MOUSE	Estradiol 17 beta-dehydrogenase 5 (EC 1.1.1.-) (17-beta-HSD 5)	0.13	-	cyt	0					323
P49889 UniProt NPD GO	ST1E3_RAT	Estrogen sulfotransferase, isoform 3 (EC 2.8.2.4) (EST-3) (Sulfotransferase, estrogen-preferring) (E ...	0.13	-	cyt	0	Cytoplasm				295
Q9M7M1 UniProt NPD GO	ETR1_PRUPE	Ethylene receptor (EC 2.7.13.3)	0.13	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				738
O82436 UniProt NPD GO	ETR1_CUCMR	Ethylene receptor (EC 2.7.13.3) (MEETR1) (Cm-ETR1)	0.13	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				740
Q9BMM3 UniProt NPD GO	ERF1_BLEAM	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.13	-	cyt	0	Cytoplasm				436
P47815 UniProt NPD GO	IF1A_WHEAT	Eukaryotic translation initiation factor 1A (EIF-1A) (EIF-4C)	0.13	-	nuc	0					143
P20460 UniProt NPD GO	IF2A_PIG	Eukaryotic translation initiation factor 2 subunit 1 (Eukaryotic translation initiation factor 2 sub ...	0.13	-	cyt	0					69
P04203 UniProt NPD GO	EXE1_HELSU	Exendin-1 (Helospectin-1) (Helospectin I) [Contains: Exendin-1b (Heloxspectin-2) (Helospectin II)]	0.13	-	nuc	0	Secreted protein				38
O59843 UniProt NPD GO	GUX1_ASPAC	Exoglucanase 1 precursor (EC 3.2.1.91) (Exoglucanase I) (Exocellobiohydrolase I) (1,4-beta-cellobioh ...	0.13	-	exc	0					540
Q00328 UniProt NPD GO	GUX1_COCCA	Exoglucanase 1 precursor (EC 3.2.1.91) (Exoglucanase I) (Exocellobiohydrolase I) (1,4-beta-cellobioh ...	0.13	-	mit	0					456
Q12277 UniProt NPD GO	RRP42_YEAST	Exosome complex exonuclease RRP42 (EC 3.1.13.-) (Ribosomal RNA-processing protein 42)	0.13	-	cyt	0	Cytoplasm. Nucleus; nucleolus	cytoplasmic exosome (RNase complex) [IDA] nuclear exosome (RNase complex) [IDA]			265
Q38913 UniProt NPD GO	EXTN1_ARATH	Extensin-1 precursor (AtExt1) (AtExt4)	0.13	-	mit	0	Secreted protein; extracellular space; extracellular matrix				373
Q9FS16 UniProt NPD GO	EXTN3_ARATH	Extensin-3 precursor (AtExt3) (AtExt5)	0.13	-	mit	0	Secreted protein; extracellular space; extracellular matrix				427
Q4R5G1 UniProt NPD GO	CAZA2_MACFA	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.13	-	nuc	0					285
P47754 UniProt NPD GO	CAZA2_MOUSE	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.13	-	nuc	0					285
Q7TPD1 UniProt NPD GO	FBX11_MOUSE	F-box only protein 11 (Fragment)	0.13	-	cyt	0					521
Q3SYW0 UniProt NPD GO	FBX15_BOVIN	F-box only protein 15	0.13	-	nuc	0					466
Q9BQ87 UniProt NPD GO	TBL1Y_HUMAN	F-box-like/WD repeat protein TBL1Y (Transducin beta-like 1Y protein) (Transducin-beta-like 1, Y-link ...	0.13	-	cyt	0	Nucleus (By similarity)		400033		522
Q4WMV5 UniProt NPD GO	FKBP4_ASPFU	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.13	+	cyt	0	Nucleus; nucleolus (By similarity)				489
Q4PIN7 UniProt NPD GO	FKBP4_USTMA	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.13	-	nuc	0	Nucleus; nucleolus (By similarity)				375
Q9XSI2 UniProt NPD GO	FKBP5_SAGOE	FK506-binding protein 5 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (51 kDa FK506-binding imm ...	0.13	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				457
Q5RET2 UniProt NPD GO	FKBP7_PONPY	FK506-binding protein 7 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.13	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				222
Q8WT54 UniProt NPD GO	FAR1_WUCBA	Fatty-acid and retinol-binding protein 1 precursor (Wb-FAR-1)	0.13	-	cyt	0	Secreted protein (By similarity)	extracellular region [ISS]			178
O93500 UniProt NPD GO	KRF3_COLLI	Feather keratin Cos2-2 (F-ker)	0.13	-	nuc	0					100
P51386 UniProt NPD GO	FTRC_PORPU	Ferredoxin-thioredoxin reductase, catalytic chain (EC 1.18.-.-) (FTR-C) (Ferredoxin-thioredoxin redu ...	0.13	-	nuc	0	Plastid; chloroplast				118
Q6FN88 UniProt NPD GO	FBRL_CANGA	Fibrillarin	0.13	+	cyt	0	Nucleus; nucleolus (By similarity). Fibrillar region of the nucleolus (By similarity)				323
P02677 UniProt NPD GO	FIBB_CANFA	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.13	-	nuc	0	Secreted protein				31
P11450 UniProt NPD GO	FCP3C_DROME	Follicle cell protein 3C-1	0.13	-	nuc	0					213
P20395 UniProt NPD GO	FSHR_RAT	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.13	+	end	7	Membrane; multi-pass membrane protein				692
P81437 UniProt NPD GO	FORM2_MYRGU	Formaecin-2	0.13	-		0	Secreted protein				16
Q91XD4 UniProt NPD GO	FTCD_MOUSE	Formimidoyltransferase-cyclodeaminase (Formiminotransferase-cyclodeaminase) (FTCD) [Includes: Glutam ...	0.13	-	nuc	0					541
O00757 UniProt NPD GO	F16P2_HUMAN	Fructose-1,6-bisphosphatase isozyme 2 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.13	-	cyt	0			603027		339
Q9N0J6 UniProt NPD GO	F16P2_RABIT	Fructose-1,6-bisphosphatase isozyme 2 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.13	-	cyt	0					339
Q9Z1N1 UniProt NPD GO	F16P2_RAT	Fructose-1,6-bisphosphatase isozyme 2 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.13	-	cyt	0					339
P70695 UniProt NPD GO	F16P2_MOUSE	Fructose-1,6-bisphosphatase isozyme 2 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.13	-	cyt	0					339
P79226 UniProt NPD GO	ALDOB_RABIT	Fructose-bisphosphate aldolase B (EC 4.1.2.13) (Liver-type aldolase)	0.13	-	cyt	0				1FDJ	363
P35794 UniProt NPD GO	SC7_SCHCO	Fruiting body protein SC7 precursor	0.13	-	exc	0	Secreted protein				204

You are viewing entries 59651 to 59700 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.