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
Q6YNB6 UniProt NPD GO	FSHR_MACEU	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.26	-	end	7	Membrane; multi-pass membrane protein				694
Q6R6L8 UniProt NPD GO	FSHR_MESAU	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.26	-	end	7	Membrane; multi-pass membrane protein				694
P31514 UniProt NPD GO	FST_SHEEP	Follistatin precursor (FS) (Activin-binding protein) (Fragment)	0.26	-	nuc	0	Secreted protein				337
Q9ER35 UniProt NPD GO	FN3K_MOUSE	Fructosamine-3-kinase (EC 2.7.1.-)	0.26	-	cyt	0					309
Q42796 UniProt NPD GO	F16P1_SOYBN	Fructose-1,6-bisphosphatase, chloroplast precursor (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phos ...	0.26	-	nuc	0	Plastid; chloroplast				402
P09195 UniProt NPD GO	F16P1_WHEAT	Fructose-1,6-bisphosphatase, chloroplast precursor (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phos ...	0.26	-	nuc	1	Plastid; chloroplast				409
Q60FY0 UniProt NPD GO	CCNB1_ANGJA	G2/mitotic-specific cyclin-B1	0.26	-	mit	0					403
Q9NJD8 UniProt NPD GO	GMPR_ONCVO	GMP reductase (EC 1.7.1.7) (Guanosine 5'-monophosphate oxidoreductase) (Guanosine monophosphate redu ...	0.26	-	cyt	0					364
Q1LZA0 UniProt NPD GO	PIGB_BOVIN	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Phosphatidylinosi ...	0.26	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				541
Q6CAW6 UniProt NPD GO	GWT1_YARLI	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.26	+	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				478
Q9CZU4 UniProt NPD GO	ERAL_MOUSE	GTP-binding protein era homolog (ERA-W) (Conserved ERA-like GTPase) (CEGA)	0.26	-	mit	0					437
O13876 UniProt NPD GO	YPT4_SCHPO	GTP-binding protein ypt4	0.26	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				234
Q9YGP1 UniProt NPD GO	LECG_TRIST	Galactose-binding lectin precursor (TSL)	0.26	-	exc	0	Secreted protein				158
Q99999 UniProt NPD GO	G3ST1_HUMAN	Galactosylceramide sulfotransferase (EC 2.8.2.11) (GalCer sulfotransferase) (Cerebroside sulfotransf ...	0.26	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to plasma membrane [TAS] membrane fraction [TAS]	602300		423
O88626 UniProt NPD GO	GALR3_RAT	Galanin receptor type 3 (GAL3-R) (GALR3)	0.26	-	end	7 *	Membrane; multi-pass membrane protein				370
P02530 UniProt NPD GO	CRG1_RANTE	Gamma crystallin 1 (Gamma crystallin I) (Fragment)	0.26	-	cyt	0					133
Q9XYP8 UniProt NPD GO	GCP3_DROME	Gamma-tubulin complex component 3 homolog (Gamma ring complex protein 91) (dGrip91) (d91p)	0.26	-	cyt	0	Centrosome (Potential)	gamma-tubulin small complex [IDA]			917
Q9Y6H8 UniProt NPD GO	CXA3_HUMAN	Gap junction alpha-3 protein (Connexin-46) (Cx46)	0.26	-	end	3 *	Membrane; multi-pass membrane protein		601885		434
Q95158 UniProt NPD GO	GBGT1_CANFA	Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (EC 2.4.1.88) (Forssman glycolipid synthetas ...	0.26	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				347
P58929 UniProt NPD GO	GMEB2_MOUSE	Glucocorticoid modulatory element-binding protein 2 (GMEB-2)	0.26	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). May be also cytoplasmic (By similarity)				530
O94808 UniProt NPD GO	GFPT2_HUMAN	Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (EC 2.6.1.16) (Hexosephosphate am ...	0.26	-	nuc	0			603865		681
Q9Z2Z9 UniProt NPD GO	GFPT2_MOUSE	Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (EC 2.6.1.16) (Hexosephosphate am ...	0.26	-	nuc	0					681
Q4KMC4 UniProt NPD GO	GFPT2_RAT	Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (EC 2.6.1.16) (Hexosephosphate am ...	0.26	-	nuc	0					681
P52417 UniProt NPD GO	GLGS2_VICFA	Glucose-1-phosphate adenylyltransferase small subunit 2, chloroplast precursor (EC 2.7.7.27) (ADP-gl ...	0.26	-	mit	0	Plastid; chloroplast (By similarity)				512
Q5IS68 UniProt NPD GO	DCE1_PANTR	Glutamate decarboxylase 1 (EC 4.1.1.15) (Glutamate decarboxylase, 67 kDa isoform) (GAD-67) (67 kDa g ...	0.26	-	cyt	0					594
Q9LFN5 UniProt NPD GO	GLR25_ARATH	Glutamate receptor 2.5 precursor (Ligand-gated ion channel 2.5)	0.26	-	end	4 *	Membrane; multi-pass membrane protein				918
P42263 UniProt NPD GO	GRIA3_HUMAN	Glutamate receptor 3 precursor (GluR-3) (GluR-C) (GluR-K3) (Glutamate receptor ionotropic, AMPA 3) ( ...	0.26	-	end	4 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]	305915		894
Q07075 UniProt NPD GO	AMPE_HUMAN	Glutamyl aminopeptidase (EC 3.4.11.7) (EAP) (Aminopeptidase A) (APA) (Differentiation antigen gp160) ...	0.26	-	mit	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS] plasma membrane [NAS]	138297		957
Q8HXX5 UniProt NPD GO	GSHB_MACFA	Glutathione synthetase (EC 6.3.2.3) (Glutathione synthase) (GSH synthetase) (GSH-S)	0.26	-	cyt	0					474
Q9SHJ5 UniProt NPD GO	GPAT1_ARATH	Glycerol-3-phosphate acyltransferase 1 (EC 2.3.1.15) (AtGPAT1)	0.26	-	vac	2	Membrane; multi-pass membrane protein. Ref.3: Mitochondrion. However, no clear transit peptide is pr ...	membrane [IDA] mitochondrion [IDA]			585
P32191 UniProt NPD GO	GPDM_YEAST	Glycerol-3-phosphate dehydrogenase, mitochondrial precursor (EC 1.1.99.5) (GPD-M) (GPDH-M)	0.26	-	cyt	0	Mitochondrion; mitochondrial inner membrane	integral to mitochondrial outer membrane [IDA] mitochondrion [IDA]			649
P26969 UniProt NPD GO	GCSP_PEA	Glycine dehydrogenase [decarboxylating], mitochondrial precursor (EC 1.4.4.2) (Glycine decarboxylase ...	0.26	-	mit	0	Mitochondrion				1057
Q01157 UniProt NPD GO	GRW10_LYCES	Glycine-rich cell wall structural protein (Clone W10-1) (Fragment)	0.26	+	cyt	0	Cell wall				43
Q38896 UniProt NPD GO	GRP2B_ARATH	Glycine-rich protein 2b (AtGRP2b)	0.26	+	cyt	0					201
Q5MIB5 UniProt NPD GO	PYGL_SHEEP	Glycogen phosphorylase, liver form (EC 2.4.1.1)	0.26	-	nuc	0					850
Q9WV60 UniProt NPD GO	GSK3B_MOUSE	Glycogen synthase kinase-3 beta (EC 2.7.11.26) (GSK-3 beta)	0.26	-	nuc	0		cytosol [IDA] nucleus [IDA]			420
Q08193 UniProt NPD GO	GAS5_YEAST	Glycolipid-anchored surface protein 5 precursor	0.26	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			484
P02726 UniProt NPD GO	GLP_HORSE	Glycophorin HA	0.26	-	nuc	1 *	Membrane; single-pass type I membrane protein				120
P14743 UniProt NPD GO	NMT_YEAST	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.26	-	cyt	0	Cytoplasm	cytosol [IDA]		2NMT	455
P82358 UniProt NPD GO	GOME_ACAGO	Gomesin precursor	0.26	-	exc	0	Secreted protein			1KFP	84
P46577 UniProt NPD GO	GOP2_CAEEL	Gro-1 operon protein 2	0.26	-	cyt	0					355
P19941 UniProt NPD GO	GHR_RABIT	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.26	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				638
P11862 UniProt NPD GO	GAS2_MOUSE	Growth-arrest-specific protein 2 (GAS-2)	0.26	-	nuc	0	Component of the microfilament system. Colocalizes with actin fibers at the cell border and along th ...			1V5R	314
P50147 UniProt NPD GO	GNAI2_CHICK	Guanine nucleotide-binding protein G(i), alpha-2 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.26	-	gol	0					354
P59216 UniProt NPD GO	GNAO1_CRILO	Guanine nucleotide-binding protein G(o) subunit alpha 1	0.26	-	cyt	0					353
P59215 UniProt NPD GO	GNAO1_RAT	Guanine nucleotide-binding protein G(o) subunit alpha 1	0.26	-	cyt	0					353
P34044 UniProt NPD GO	GPA6_DICDI	Guanine nucleotide-binding protein alpha-6 subunit (G alpha-6) (Fragment)	0.26	-	nuc	0					153
P20595 UniProt NPD GO	GCYB1_RAT	Guanylate cyclase soluble subunit beta-1 (EC 4.6.1.2) (GCS-beta-1) (Soluble guanylate cyclase small ...	0.26	-	cyt	0	Cytoplasm				619
P06339 UniProt NPD GO	HA15_MOUSE	H-2 class I histocompatibility antigen, D-37 alpha chain precursor	0.26	-	end	1	Membrane; single-pass type I membrane protein				357
Q69ZS7 UniProt NPD GO	HBS1L_MOUSE	HBS1-like protein	0.26	-	mit	0				1UFZ	682

You are viewing entries 44201 to 44250 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.