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
P07764 UniProt NPD GO	ALF_DROME	Fructose-bisphosphate aldolase (EC 4.1.2.13)	0.05	-	nuc	0				1FBA	360
Q5R1X4 UniProt NPD GO	ALDOC_PANTR	Fructose-bisphosphate aldolase C (EC 4.1.2.13) (Brain-type aldolase)	0.05	-	cyt	0					363
P46256 UniProt NPD GO	ALF1_PEA	Fructose-bisphosphate aldolase, cytoplasmic isozyme 1 (EC 4.1.2.13)	0.05	-	cyt	0	Cytoplasm				357
P46257 UniProt NPD GO	ALF2_PEA	Fructose-bisphosphate aldolase, cytoplasmic isozyme 2 (EC 4.1.2.13)	0.05	-	cyt	0	Cytoplasm				359
Q9I931 UniProt NPD GO	FUCL1_ANGJA	Fucolectin-1 precursor	0.05	-	cyt	0	Secreted protein; extracellular space	extracellular space [IDA]			178
Q9I930 UniProt NPD GO	FUCL2_ANGJA	Fucolectin-2 precursor	0.05	-	cyt	0	Secreted protein; extracellular space	extracellular space [IDA]			180
Q9I928 UniProt NPD GO	FUCL4_ANGJA	Fucolectin-4 precursor	0.05	-	mit	0	Secreted protein	extracellular space [IDA]			179
Q9FI53 UniProt NPD GO	FUM2_ARATH	Fumarate hydratase 2, chloroplast precursor (EC 4.2.1.2) (Fumarase 2)	0.05	-	cyt	0	Plastid; chloroplast (Potential)				499
Q6P587 UniProt NPD GO	FAHD1_HUMAN	Fumarylacetoacetate hydrolase domain-containing protein 1 (EC 3.-.-.-) (YISK-like)	0.05	-	cyt	0				1SAW	224
Q9JIL6 UniProt NPD GO	GPC5D_MOUSE	G-protein coupled receptor family C group 5 member D	0.05	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			344
P25012 UniProt NPD GO	CCNB2_SOYBN	G2/mitotic-specific cyclin S13-7 (B-like cyclin) (Fragment)	0.05	-	nuc	0					257
O45583 UniProt NPD GO	GMD2_CAEEL	GDP-mannose 4,6 dehydratase 2 (EC 4.2.1.47) (GDP-D-mannose dehydratase) (GMD)	0.05	-	cyt	0					382
Q7SAP1 UniProt NPD GO	MCD4_NEUCR	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-)	0.05	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				996
Q5H8A4 UniProt NPD GO	PIGG_HUMAN	GPI ethanolamine phosphate transferase 2 (EC 2.-.-.-) (Phosphatidylinositol-glycan biosynthesis clas ...	0.05	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			983
Q2TXB8 UniProt NPD GO	GPI14_ASPOR	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Glycosylphosphatidyli ...	0.05	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				415
Q6CRE7 UniProt NPD GO	GPI14_KLULA	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Glycosylphosphatidyli ...	0.05	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				402
Q5EA10 UniProt NPD GO	PIGM_BOVIN	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Phosphatidylinositol- ...	0.05	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				423
Q4R4E1 UniProt NPD GO	PIGM_MACFA	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Phosphatidylinositol- ...	0.05	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				423
Q59VN0 UniProt NPD GO	GPI18_CANAL	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.05	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				394
Q6CMW6 UniProt NPD GO	GPI18_KLULA	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.05	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				417
Q6BJ96 UniProt NPD GO	SMP3_DEBHA	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV)	0.05	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				410
Q4I785 UniProt NPD GO	SMP3_GIBZE	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV)	0.05	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				492
Q2UQH4 UniProt NPD GO	GWT1_ASPOR	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.05	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				500
Q6BTT3 UniProt NPD GO	GWT1_DEBHA	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.05	-	end	13 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				493
Q6CK18 UniProt NPD GO	GWT1_KLULA	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.05	-	end	13 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				446
Q94529 UniProt NPD GO	GS1_DROME	GS1-like protein	0.05	-	cyt	0					231
Q6GM84 UniProt NPD GO	GFRP_XENLA	GTP cyclohydrolase 1 feedback regulatory protein (GTP cyclohydrolase I feedback regulatory protein) ...	0.05	-	cyt	0					84
P32234 UniProt NPD GO	128UP_DROME	GTP-binding protein 128up	0.05	-	cyt	0					368
O95661 UniProt NPD GO	DIRA3_HUMAN	GTP-binding protein Di-Ras3 (Distinct subgroup of the Ras family member 3) (Rho-related GTP-binding ...	0.05	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		605193		229
Q23445 UniProt NPD GO	SAR1_CAEEL	GTP-binding protein SAR1	0.05	-	cyt	0					193
P32939 UniProt NPD GO	YPT7_YEAST	GTP-binding protein YPT7	0.05	-	cyt	0	Vacuole	mitochondrial outer membrane [IDA] vacuole [IDA]		1KY3	208
P36862 UniProt NPD GO	YPTV3_VOLCA	GTP-binding protein yptV3	0.05	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				203
P56091 UniProt NPD GO	GAL1_CANAL	Galactokinase (EC 2.7.1.6) (Galactose kinase)	0.05	-	mit	0					515
Q866D9 UniProt NPD GO	FUT1_CALHU	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.05	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				365
Q866D2 UniProt NPD GO	FUT1_SAGFU	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.05	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				365
Q8N1C3 UniProt NPD GO	GBRG1_HUMAN	Gamma-aminobutyric-acid receptor gamma-1 subunit precursor (GABA(A) receptor)	0.05	-	end	4	Membrane; multi-pass membrane protein		137166		465
Q29559 UniProt NPD GO	CXA4_PIG	Gap junction alpha-4 protein (Connexin-37) (Cx37) (Fragment)	0.05	-	cyt	2 *	Membrane; multi-pass membrane protein				138
P04073 UniProt NPD GO	PEPC_RAT	Gastricsin precursor (EC 3.4.23.3) (Pepsinogen C)	0.05	-	exc	0	Secreted protein				392
P33713 UniProt NPD GO	GAST_DIDMA	Gastrin precursor [Contains: Big gastrin (Gastrin 33) (G33); Gastrin]	0.05	-	cyt	0	Secreted protein				33
P51162 UniProt NPD GO	ILBP_MOUSE	Gastrotropin (GT) (Ileal lipid-binding protein) (ILBP)	0.05	-	cyt	0	Cytoplasm				127
P80020 UniProt NPD GO	ILBP_RAT	Gastrotropin (GT) (Ileal lipid-binding protein) (ILBP) (Intestinal 15 kDa protein) (I-15P) (14 kDa b ...	0.05	-	cyt	0	Cytoplasm	cytosol [IDA]			127
P43548 UniProt NPD GO	AGP3_YEAST	General amino acid permease AGP3	0.05	-	end	12	Membrane; multi-pass membrane protein (Probable)				558
Q9LUD9 UniProt NPD GO	GGPP3_ARATH	Geranylgeranyl pyrophosphate synthetase 3, chloroplast precursor (GGPP synthetase 3) (GGPS3) [Includ ...	0.05	-	mit	0	Plastid; chloroplast				360
P15469 UniProt NPD GO	GLB3_LAMSP	Giant hemoglobin AIII chain	0.05	-	nuc	0					144
Q61606 UniProt NPD GO	GLR_MOUSE	Glucagon receptor precursor (GL-R)	0.05	-	end	7	Membrane; multi-pass membrane protein				485
P52396 UniProt NPD GO	E13I_TOBAC	Glucan endo-1,3-beta-glucosidase, acidic isoform PR-N (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolas ...	0.05	-	cyt	0	Secreted protein; extracellular space				275
P23431 UniProt NPD GO	E13B_NICPL	Glucan endo-1,3-beta-glucosidase, basic vacuolar isoform precursor (EC 3.2.1.39) ((1->3)-beta-glucan ...	0.05	-	exc	1 *	Vacuole				365
P08019 UniProt NPD GO	AMYG_YEAST	Glucoamylase, intracellular sporulation-specific (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-al ...	0.05	-	exc	1 *		vacuole (sensu Fungi) [IDA]			549
Q17427 UniProt NPD GO	GNA1_CAEEL	Glucosamine 6-phosphate N-acetyltransferase (EC 2.3.1.4) (Phosphoglucosamine transacetylase) (Phosph ...	0.05	-	cyt	0					165
P81156 UniProt NPD GO	GOX_PENAG	Glucose oxidase (EC 1.1.3.4) (Glucose oxyhydrase) (GOD) (Beta-D-glucose:oxygen 1-oxido-reductase)	0.05	-	cyt	0	Secreted protein			1GPE	587

You are viewing entries 74451 to 74500 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.