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
Q9PUK8 UniProt NPD GO	FZD7_XENLA	Frizzled-7 precursor (Fz-7) (Xfz7)	0.03	-	end	6	Membrane; multi-pass membrane protein (Potential)				549
O75084 UniProt NPD GO	FZD7_HUMAN	Frizzled-7 precursor (Fz-7) (hFz7) (FzE3)	0.03	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	603410		574
Q61090 UniProt NPD GO	FZD7_MOUSE	Frizzled-7 precursor (Fz-7) (mFz7)	0.03	-	end	6 *	Membrane; multi-pass membrane protein				572
P14540 UniProt NPD GO	ALF_YEAST	Fructose-bisphosphate aldolase (EC 4.1.2.13)	0.03	-	mit	0		cytoplasm [IDA]			358
P91759 UniProt NPD GO	ALF_LYMST	Fructose-bisphosphate aldolase (EC 4.1.2.13) (Fragment)	0.03	-	end	0					101
P53449 UniProt NPD GO	ALDOC_CHICK	Fructose-bisphosphate aldolase C (EC 4.1.2.13) (Brain-type aldolase) (Fragment)	0.03	-	mit	0					137
P53446 UniProt NPD GO	ALF2_LAMJA	Fructose-bisphosphate aldolase, non-muscle type (EC 4.1.2.13)	0.03	-	cyt	0					364
P43393 UniProt NPD GO	K501_ACTCH	Fruit protein PKIWI501	0.03	-	cyt	0					184
Q9I929 UniProt NPD GO	FUCL3_ANGJA	Fucolectin-3 precursor	0.03	-	mit	0	Secreted protein; extracellular space	extracellular space [IDA]			180
Q41093 UniProt NPD GO	FCPE_PHATR	Fucoxanthin-chlorophyll a-c binding protein E, chloroplast precursor	0.03	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. FCPs are probably ...				197
Q39709 UniProt NPD GO	FCP_ISOGA	Fucoxanthin-chlorophyll a-c binding protein, chloroplast precursor (FCP)	0.03	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. FCPs are probably transported across the endop ...				208
P80349 UniProt NPD GO	FUC3_RAT	Fuctinin-3 (Fucosyltransferase inhibitor 3) (Fragment)	0.03	-	nuc	0	Cytoplasm				39
P97807 UniProt NPD GO	FUMH_MOUSE	Fumarate hydratase, mitochondrial precursor (EC 4.2.1.2) (Fumarase) (EF-3)	0.03	-	mit	0	Mitochondrion. Cytoplasm	mitochondrion [IDA]			507
P32614 UniProt NPD GO	FRDS_YEAST	Fumarate reductase (NADH) (EC 1.3.1.6) (NADH-dependent fumarate reductase) (FAD-dependent oxidoreduc ...	0.03	-	cyt	0	Mitochondrion. Cytoplasm	cytosol [IDA] mitochondrion [IDA]			470
Q00770 UniProt NPD GO	FAAA_EMENI	Fumarylacetoacetase (EC 3.7.1.2) (Fumarylacetoacetate hydrolase) (Beta-diketonase) (FAA)	0.03	-	cyt	0					431
Q8R0F8 UniProt NPD GO	FAHD1_MOUSE	Fumarylacetoacetate hydrolase domain-containing protein 1 (EC 3.-.-.-)	0.03	-	cyt	0		mitochondrial inner membrane [IDA] mitochondrion [IDA]			227
Q6AYQ8 UniProt NPD GO	FAHD1_RAT	Fumarylacetoacetate hydrolase domain-containing protein 1 (EC 3.-.-.-)	0.03	-	cyt	0					221
Q10731 UniProt NPD GO	FPIF_BOMMO	Fungal protease inhibitor F precursor (FPI-F)	0.03	-	exc	1 *	Secreted protein				77
Q2R1V8 UniProt NPD GO	GME2_ORYSA	GDP-mannose 3,5-epimerase 2 (EC 5.1.3.18) (GDP-Man 3,5-epimerase 2)	0.03	-	cyt	0					371
Q8K0C9 UniProt NPD GO	GMDS_MOUSE	GDP-mannose 4,6 dehydratase (EC 4.2.1.47) (GDP-D-mannose dehydratase) (GMD)	0.03	-	cyt	0					372
P83690 UniProt NPD GO	NFCP_MONEF	GFP-like non-fluorescent chromoprotein (Rtms 5) (Non-fluorescent pocilloporin)	0.03	-	cyt	0		host [TAS]		1MOV	221
Q9H3S5 UniProt NPD GO	PIGM_HUMAN	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Phosphatidylinositol- ...	0.03	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				423
Q5RAH7 UniProt NPD GO	PIGM_PONPY	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Phosphatidylinositol- ...	0.03	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				423
Q9EQY6 UniProt NPD GO	PIGM_RAT	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Phosphatidylinositol- ...	0.03	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				423
Q2GSI6 UniProt NPD GO	GPI18_CHAGB	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.03	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				471
Q5KJZ2 UniProt NPD GO	GPI18_CRYNE	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.03	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				423
Q4I0K3 UniProt NPD GO	GPI18_GIBZE	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.03	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				423
Q7TPN3 UniProt NPD GO	PIGV_MOUSE	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Phosphatidylinosito ...	0.03	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				493
Q5AK24 UniProt NPD GO	GPI10_CANAL	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.03	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				482
Q8CHJ0 UniProt NPD GO	PIGU_CRIGR	GPI transamidase component PIG-U (Phosphatidylinositol-glycan biosynthesis class U protein) (Cell di ...	0.03	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	GPI-anchor transamidase complex [ISS]			434
Q9H490 UniProt NPD GO	PIGU_HUMAN	GPI transamidase component PIG-U (Phosphatidylinositol-glycan biosynthesis class U protein) (Cell di ...	0.03	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	GPI-anchor transamidase complex [IMP]	608528		434
Q8K358 UniProt NPD GO	PIGU_MOUSE	GPI transamidase component PIG-U (Phosphatidylinositol-glycan biosynthesis class U protein) (Cell di ...	0.03	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	GPI-anchor transamidase complex [ISS]			433
Q8CHJ1 UniProt NPD GO	PIGU_RAT	GPI transamidase component PIG-U (Phosphatidylinositol-glycan biosynthesis class U protein) (Cell di ...	0.03	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	GPI-anchor transamidase complex [ISS]			434
P51600 UniProt NPD GO	GCH1_PHYBL	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I) (Fragment)	0.03	-	cyt	0					94
Q15382 UniProt NPD GO	RHEB_HUMAN	GTP-binding protein Rheb (Ras homolog enriched in brain)	0.03	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	membrane [TAS]	601293	1XTS	184
Q9VND8 UniProt NPD GO	RHEB_DROME	GTP-binding protein Rheb homolog	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				182
P36536 UniProt NPD GO	SAR1A_MOUSE	GTP-binding protein SAR1a	0.03	-	cyt	0		sarcoplasmic reticulum [IDA]			198
P38146 UniProt NPD GO	YPT10_YEAST	GTP-binding protein YPT10	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	cytoplasm [IDA]			199
Q9HDU2 UniProt NPD GO	GAL1_SCHPO	Galactokinase (EC 2.7.1.6) (Galactose kinase)	0.03	-	mit	0					519
Q9SEE5 UniProt NPD GO	GALK1_ARATH	Galactokinase (EC 2.7.1.6) (Galactose kinase)	0.03	-	nuc	0					496
Q866D6 UniProt NPD GO	FUT1_LEOCY	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.03	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				365
Q10982 UniProt NPD GO	FUT2_PIG	Galactoside 2-alpha-L-fucosyltransferase 2 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.03	-	nuc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				340
O77487 UniProt NPD GO	FUT2_PONPY	Galactoside 2-alpha-L-fucosyltransferase 2 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.03	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				343
P47213 UniProt NPD GO	GALA_ONCMY	Galanin	0.03	-	cyt	0	Secreted protein				29
P47216 UniProt NPD GO	GALA_RANRI	Galanin	0.03	-	cyt	0	Secreted protein				29
P31234 UniProt NPD GO	GALA_SHEEP	Galanin	0.03	-	cyt	0	Secreted protein				29
Q9W6M9 UniProt NPD GO	GALA_COTJA	Galanin precursor [Contains: Galanin; Galanin message-associated peptide (GMAP)]	0.03	-	exc	1 *	Secreted protein				117
P33710 UniProt NPD GO	GALA_CANFA	Galanin precursor [Contains: Galanin; Galanin message-associated peptide (GMAP)] (Fragment)	0.03	-	nuc	0	Secreted protein				54
P05162 UniProt NPD GO	LEG2_HUMAN	Galectin-2 (Beta-galactoside-binding lectin L-14-II) (Lactose-binding lectin 2) (S-Lac lectin 2) (HL ...	0.03	-	cyt	0			150571	1HLC	132
P47845 UniProt NPD GO	LEG3_RABIT	Galectin-3 (Galactose-specific lectin 3) (Mac-2 antigen) (IgE-binding protein) (35 kDa lectin) (Carb ...	0.03	-	nuc	0	Nucleus (By similarity). Cytoplasmic in adenomas and carcinomas. May be secreted by a non-classical ...				241

You are viewing entries 79951 to 80000 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.