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
P42930 UniProt NPD GO	HSPB1_RAT	Heat-shock protein beta-1 (HspB1) (Heat shock 27 kDa protein) (HSP 27)	0.15	-	mit	0		proteasome complex (sensu Eukaryota) [IDA]			206
P60057 UniProt NPD GO	THND_HELPU	Hellethionin D	0.15	-	mit	0	Secreted protein			1NBL	46
Q921L7 UniProt NPD GO	HEMK1_MOUSE	HemK methyltransferase family member 1 (EC 2.1.1.-)	0.15	-	mit	0					340
O78497 UniProt NPD GO	HO_GUITH	Heme oxygenase (EC 1.14.99.3)	0.15	-	cyt	0	Plastid; chloroplast				237
O70252 UniProt NPD GO	HMOX2_MOUSE	Heme oxygenase 2 (EC 1.14.99.3) (HO-2)	0.15	-	cyt	1	Microsome				315
P02241 UniProt NPD GO	HCYD_EURCA	Hemocyanin D chain (HcD)	0.15	-	cyt	0	Secreted protein; extracellular space	extracellular space [ISS]			626
P81044 UniProt NPD GO	HBAZ_MACEU	Hemoglobin subunit zeta (Hemoglobin zeta chain) (Zeta-globin) (Fragments)	0.15	-	cyt	0					79
P61148 UniProt NPD GO	FGF1_MOUSE	Heparin-binding growth factor 1 precursor (HBGF-1) (Acidic fibroblast growth factor) (aFGF)	0.15	-	nuc	0		extracellular matrix (sensu Metazoa) [IDA] extracellular space [IDA]			155
P61149 UniProt NPD GO	FGF1_RAT	Heparin-binding growth factor 1 precursor (HBGF-1) (Acidic fibroblast growth factor) (aFGF)	0.15	-	nuc	0					155
P48799 UniProt NPD GO	FGF2_RABIT	Heparin-binding growth factor 2 (HBGF-2) (Basic fibroblast growth factor) (BFGF) (Prostatropin) (Fra ...	0.15	-	nuc	0					137
P54854 UniProt NPD GO	HXT15_YEAST	Hexose transporter HXT15	0.15	-	end	12	Membrane; multi-pass membrane protein				567
P47185 UniProt NPD GO	HXT16_YEAST	Hexose transporter HXT16	0.15	-	end	12	Membrane; multi-pass membrane protein (Potential)				567
O59932 UniProt NPD GO	GHT4_SCHPO	High-affinity hexose transporter ght4 (Hexose transporter 4)	0.15	-	end	9 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			557
P37235 UniProt NPD GO	HPCL1_HUMAN	Hippocalcin-like protein 1 (Visinin-like protein 3) (VILIP-3) (Calcium-binding protein BDR-1) (HLP2) ...	0.15	-	nuc	0			600207		192
O13471 UniProt NPD GO	HIS2_KLULA	Histidine biosynthesis trifunctional protein [Includes: Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4. ...	0.15	-	cyt	0					795
Q9ZNV8 UniProt NPD GO	AHP2_ARATH	Histidine-containing phosphotransfer protein 2	0.15	-	nuc	0					156
Q9FEW2 UniProt NPD GO	HIS8_NICPL	Histidinol-phosphate aminotransferase, chloroplast precursor (EC 2.6.1.9) (Imidazole acetol-phosphat ...	0.15	-	cyt	0	Plastid; chloroplast (Potential)				413
Q75C22 UniProt NPD GO	H1_ASHGO	Histone H1	0.15	-	nuc	0	Nucleus (Potential)				225
P02269 UniProt NPD GO	H2A_ASTRU	Histone H2A	0.15	-	nuc	0	Nucleus				124
P21896 UniProt NPD GO	H2A_CHITH	Histone H2A	0.15	-	mit	0	Nucleus				124
P84052 UniProt NPD GO	H2A_DROER	Histone H2A	0.15	-	mit	0	Nucleus	nucleosome [ISS]			123
P84053 UniProt NPD GO	H2A_DROHY	Histone H2A	0.15	-	mit	0	Nucleus	nucleosome [NAS]			123
P84051 UniProt NPD GO	H2A_DROME	Histone H2A	0.15	-	mit	0	Nucleus	nucleosome [NAS] nucleus [IDA] polytene chromosome band [IDA]			123
P84054 UniProt NPD GO	H2A_DROSI	Histone H2A	0.15	-	mit	0	Nucleus	nucleosome [ISS]			123
P84055 UniProt NPD GO	H2A_DROYA	Histone H2A	0.15	-	mit	0	Nucleus	nucleosome [ISS]			123
P19178 UniProt NPD GO	H2A_PLADU	Histone H2A	0.15	-	nuc	0	Nucleus				123
P84056 UniProt NPD GO	H2A_RHYAM	Histone H2A	0.15	-	mit	0	Nucleus	nucleosome [ISS]			123
P02268 UniProt NPD GO	H2A_SEPOF	Histone H2A	0.15	-	nuc	0	Nucleus				124
P84057 UniProt NPD GO	H2A_TIGCA	Histone H2A	0.15	-	mit	0	Nucleus	nucleosome [ISS]			123
Q6BRG3 UniProt NPD GO	H2A2_DEBHA	Histone H2A.2	0.15	-	nuc	0	Nucleus (By similarity)				130
P02274 UniProt NPD GO	H2A2_TETPY	Histone H2A.2	0.15	-	nuc	0	Nucleus				132
Q12692 UniProt NPD GO	H2AZ_YEAST	Histone H2A.Z	0.15	-	nuc	0	Nucleus	chromatin assembly complex [IPI] nuclear chromatin [IDA]		2FSB	133
P16104 UniProt NPD GO	H2AX_HUMAN	Histone H2A.x (H2a/x)	0.15	-	nuc	0	Nucleus	nucleosome [NAS] nucleus [IDA]	601772	2D31	142
P27661 UniProt NPD GO	H2AX_MOUSE	Histone H2A.x (H2a/x)	0.15	-	nuc	0	Nucleus	chromatin [IDA] nucleus [IDA] replication fork [IDA]			142
P81904 UniProt NPD GO	H2B3_ICTPU	Histone H2B 3 (Antibacterial histone-like protein 3) (HLP-3) (Fragment)	0.15	-		0	Nucleus				17
P62789 UniProt NPD GO	H4_MEDSA	Histone H4 (Fragment)	0.15	-	nuc	0	Nucleus				24
P02260 UniProt NPD GO	H5_COLLI	Histone H5 (Fragment)	0.15	-	nuc	0	Nucleus				38
Q9GKU5 UniProt NPD GO	HDA11_MACFA	Histone deacetylase 11 (HD11)	0.15	-	cyt	0	Nucleus (By similarity)	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]			347
Q9FG08 UniProt NPD GO	ATXR4_ARATH	Histone-lysine N-methyltransferase ATXR4 precursor (EC 2.1.1.43) (Trithorax-related protein 4) (TRX- ...	0.15	-	mit	0	Nucleus (By similarity)				258
Q8MJD5 UniProt NPD GO	HOP_BOVIN	Homeodomain-only protein (Odd homeobox protein 1)	0.15	-	nuc	0	Nucleus (By similarity)				73
Q5RKG2 UniProt NPD GO	HCFC2_RAT	Host cell factor 2 (HCF-2) (C2 factor)	0.15	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				723
Q9QUP5 UniProt NPD GO	HPLN1_MOUSE	Hyaluronan and proteoglycan link protein 1 precursor (Proteoglycan link protein) (Cartilage link pro ...	0.15	-	exc	0		extracellular matrix (sensu Metazoa) [IDA]			356
P10859 UniProt NPD GO	HPLN1_PIG	Hyaluronan and proteoglycan link protein 1 precursor (Proteoglycan link protein) (Cartilage link pro ...	0.15	-	vac	0					354
Q62803 UniProt NPD GO	HYALP_RAT	Hyaluronidase PH-20 precursor (EC 3.2.1.35) (Hyal-PH20) (Sperm surface protein PH-20) (Sperm adhesio ...	0.15	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor				512
P24337 UniProt NPD GO	HPSE_SOYBN	Hydrophobic seed protein (HPS) (Allergen Gly m 1)	0.15	-	nuc	0				1HYP	80
P53225 UniProt NPD GO	YG1R_YEAST	Hypothetical 12.3 kDa protein in ORM1-KSS1 intergenic region	0.15	-	cyt	0					103
O19890 UniProt NPD GO	YCF54_CYACA	Hypothetical 12.4 kDa protein ycf54	0.15	-	cyt	0	Plastid; chloroplast				103
P53837 UniProt NPD GO	YN16_YEAST	Hypothetical 14.1 kDa protein in MET2-SEC2 intergenic region	0.15	-	nuc	0					131
P48275 UniProt NPD GO	YCF35_CYAPA	Hypothetical 15.3 kDa protein ycf35	0.15	-	cyt	0	Plastid; cyanelle				128
P38275 UniProt NPD GO	YBY4_YEAST	Hypothetical 15.5 kDa protein in AGP2-CKS1 intergenic region	0.15	-	cyt	0					133

You are viewing entries 57001 to 57050 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.