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
Q26061 UniProt NPD GO	FRI_PACLE	Ferritin (EC 1.16.3.1)	0.29	-	nuc	0	Cytoplasm (Potential)				181
P30754 UniProt NPD GO	CAFF_RIFPA	Fibril-forming collagen alpha chain (Fragment)	0.29	-	nuc	0					1027
P24303 UniProt NPD GO	MO2X_MOROL	Flocculent-active proteins MO2.1 and MO2.2	0.29	-	mit	0					60
O13127 UniProt NPD GO	FLOT1_CARAU	Flotillin-1 (Reggie-2) (REG-2)	0.29	-	cyt	0	Cell membrane; caveola; peripheral membrane protein. Membrane-associated protein of caveolae				423
P10669 UniProt NPD GO	FST_PIG	Follistatin precursor (FS) (Activin-binding protein)	0.29	-	exc	0	Secreted protein				344
Q3UFD7 UniProt NPD GO	FFAR3_MOUSE	Free fatty acid receptor 3 (G-protein coupled receptor 41)	0.29	-	end	7 *	Membrane; multi-pass membrane protein				319
Q9H8T0 UniProt NPD GO	FTS1_HUMAN	Fused toes protein homolog (Ft1)	0.29	-	mit	0	Cytoplasm. Cell membrane; peripheral membrane protein		608483		292
P17053 UniProt NPD GO	G168_PARPR	G surface protein, allelic form 168 precursor	0.29	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				2704
Q6JAN0 UniProt NPD GO	GPR98_BRARE	G-protein coupled receptor 98 precursor (Monogenic audiogenic seizure susceptibility protein 1 homol ...	0.29	-	end	7	Membrane; multi-pass membrane protein (Potential)				6199
P55169 UniProt NPD GO	CCND1_CHICK	G1/S-specific cyclin-D1	0.29	-	cyt	0					292
P30282 UniProt NPD GO	CCND3_MOUSE	G1/S-specific cyclin-D3	0.29	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				292
P29332 UniProt NPD GO	CCNB2_CHICK	G2/mitotic-specific cyclin-B2	0.29	-	cyt	0					399
P49915 UniProt NPD GO	GUAA_HUMAN	GMP synthase [glutamine-hydrolyzing] (EC 6.3.5.2) (Glutamine amidotransferase) (GMP synthetase)	0.29	-	cyt	0	Cytoplasm		600358		693
Q4V7R2 UniProt NPD GO	PIGB_XENLA	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Phosphatidylinosi ...	0.29	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				531
Q4WTT7 UniProt NPD GO	SMP3_ASPFU	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV)	0.29	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				556
Q969N2 UniProt NPD GO	PIGT_HUMAN	GPI transamidase component PIG-T precursor (Phosphatidylinositol-glycan biosynthesis class T protein ...	0.29	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	GPI-anchor transamidase complex [TAS]			578
P52961 UniProt NPD GO	NAR1_HUMAN	GPI-linked NAD(P)(+)--arginine ADP-ribosyltransferase 1 precursor (EC 2.4.2.31) (Mono(ADP-ribosyl)tr ...	0.29	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum membrane; lipid-anchor; GPI-anchor	integral to plasma membrane [TAS] plasma membrane [NAS]	601625		327
P50139 UniProt NPD GO	GCH2_PICGU	GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)	0.29	-	nuc	0					344
Q8BWF2 UniProt NPD GO	GIMA5_MOUSE	GTPase, IMAP family member 5 (Immunity-associated nucleotide 4-like 1 protein) (Immunity-associated ...	0.29	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				308
Q5CB03 UniProt NPD GO	B3GA1_CANFA	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.29	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				335
P04342 UniProt NPD GO	CRGD_MOUSE	Gamma crystallin D (Gamma crystallin 1)	0.29	-	cyt	0					173
P33725 UniProt NPD GO	CXA5_CANFA	Gap junction alpha-5 protein (Connexin-40) (Cx40)	0.29	-	end	3 *	Membrane; multi-pass membrane protein				357
Q866T7 UniProt NPD GO	CXA9_BOVIN	Gap junction alpha-9 protein (Connexin-36) (Cx36)	0.29	-	end	4 *	Membrane; multi-pass membrane protein				321
O54851 UniProt NPD GO	CXA9_MOUSE	Gap junction alpha-9 protein (Connexin-36) (Cx36)	0.29	-	end	4 *	Membrane; multi-pass membrane protein				321
O70610 UniProt NPD GO	CXA9_RAT	Gap junction alpha-9 protein (Connexin-36) (Cx36)	0.29	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [TAS]			321
P09681 UniProt NPD GO	GIP_HUMAN	Gastric inhibitory polypeptide precursor (GIP) (Glucose-dependent insulinotropic polypeptide)	0.29	-	exc	0	Secreted protein	soluble fraction [TAS]	137240	2B4N	153
P01353 UniProt NPD GO	GAST_CANFA	Gastrin precursor [Contains: Big gastrin (Gastrin 34) (G34); Gastrin]	0.29	-	exc	0	Secreted protein				104
P18732 UniProt NPD GO	ZG64_XENLA	Gastrula zinc finger protein XLCGF64.1 (Fragment)	0.29	-	nuc	0	Nucleus (Potential)				196
P46689 UniProt NPD GO	GASA1_ARATH	Gibberellin-regulated protein 1 precursor	0.29	-	exc	0	Secreted protein				98
Q9Y692 UniProt NPD GO	GMEB1_HUMAN	Glucocorticoid modulatory element-binding protein 1 (GMEB-1) (Parvovirus initiation factor p96) (PIF ...	0.29	-	cyt	0	Nucleus. Cytoplasm. May be also cytoplasmic	nucleus [TAS]	604409	1OQJ	573
P18240 UniProt NPD GO	G6PI_PLAFA	Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose iso ...	0.29	-	nuc	0	Cytoplasm				591
Q8GXJ4 UniProt NPD GO	GLR34_ARATH	Glutamate receptor 3.4 precursor (Ligand-gated ion channel 3.4) (AtGLR4)	0.29	-	end	4	Membrane; multi-pass membrane protein				959
Q9SDQ4 UniProt NPD GO	GLR37_ARATH	Glutamate receptor 3.7 precursor (Ligand-gated ion channel 3.7) (Ionotropic glutamate receptor GLR5) ...	0.29	-	end	3	Membrane; multi-pass membrane protein				921
O43424 UniProt NPD GO	GRID2_HUMAN	Glutamate receptor delta-2 subunit precursor (GluR delta-2)	0.29	-	end	3	Membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]	602368		1007
P46432 UniProt NPD GO	GSTT3_MUSDO	Glutathione S-transferase 3 (EC 2.5.1.18) (GST class-theta)	0.29	-	cyt	0					210
P38088 UniProt NPD GO	SYG_YEAST	Glycyl-tRNA synthetase 1 (EC 6.1.1.14) (Glycine--tRNA ligase 1) (GlyRS 1) (GlyRS1)	0.29	+	cyt	0	Cytoplasm. Mitochondrion	cytoplasm [IMP] mitochondrion [IDA]			667
P50593 UniProt NPD GO	GPC1_CHICK	Glypican-1 precursor (Heparan sulfate proteoglycan core protein)	0.29	+	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				550
P49864 UniProt NPD GO	GRAK_RAT	Granzyme K precursor (EC 3.4.21.-) (NK-tryptase-2) (NK-Tryp-2)	0.29	-	nuc	0	Cytoplasmic granule				258
Q9UBI6 UniProt NPD GO	GBG12_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-12 subunit precursor	0.29	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				71
Q9DAS9 UniProt NPD GO	GBG12_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-12 subunit precursor	0.29	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				71
Q5RBQ0 UniProt NPD GO	GBG12_PONPY	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-12 subunit precursor	0.29	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				71
P51876 UniProt NPD GO	GNAI_HELTI	Guanine nucleotide-binding protein G(i) subunit alpha (Adenylate cyclase-inhibiting G alpha protein) ...	0.29	-	cyt	0					353
P38401 UniProt NPD GO	GNAI1_CAVPO	Guanine nucleotide-binding protein G(i), alpha-1 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.29	-	cyt	0					353
P50146 UniProt NPD GO	GNAI1_CHICK	Guanine nucleotide-binding protein G(i), alpha-1 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.29	-	cyt	0					353
P04899 UniProt NPD GO	GNAI2_HUMAN	Guanine nucleotide-binding protein G(i), alpha-2 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.29	-	gol	0			139360		354
P22454 UniProt NPD GO	GPA2_CAEEL	Guanine nucleotide-binding protein alpha-2 subunit	0.29	-	cyt	0					356
P38040 UniProt NPD GO	GBG1_DROME	Guanine nucleotide-binding protein gamma-1 subunit precursor	0.29	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	heterotrimeric G-protein complex [NAS]			70
Q6TL19 UniProt NPD GO	GUC2G_MOUSE	Guanylate cyclase 2G precursor (EC 4.6.1.2) (Guanylyl cyclase receptor G) (mGC-G)	0.29	-	end	0	Membrane; single-pass type I membrane protein (Potential)	external side of plasma membrane [IDA] membrane fraction [IDA]			1100
Q6AXM7 UniProt NPD GO	HBS1L_RAT	HBS1-like protein	0.29	-	mit	0					679
Q6ZVY0 UniProt NPD GO	ENK19_HUMAN	HERV-K_4p16.1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) [Includes: Truncat ...	0.29	-	nuc	1					342

You are viewing entries 41251 to 41300 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.