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
Q9GP32 UniProt NPD GO	ALF_ECHMU	Fructose-bisphosphate aldolase (EC 4.1.2.13)	0.02	-	nuc	0					363
Q01516 UniProt NPD GO	ALFC_PEA	Fructose-bisphosphate aldolase 1, chloroplast precursor (EC 4.1.2.13) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				356
Q01517 UniProt NPD GO	ALFD_PEA	Fructose-bisphosphate aldolase 2, chloroplast (EC 4.1.2.13)	0.02	-	cyt	0	Plastid; chloroplast				349
P08440 UniProt NPD GO	ALF_MAIZE	Fructose-bisphosphate aldolase, cytoplasmic isozyme (EC 4.1.2.13)	0.02	-	cyt	0	Cytoplasm				355
P29356 UniProt NPD GO	ALF_SPIOL	Fructose-bisphosphate aldolase, cytoplasmic isozyme (EC 4.1.2.13)	0.02	-	mit	0	Cytoplasm				357
Q40296 UniProt NPD GO	FCPB_MACPY	Fucoxanthin-chlorophyll a-c binding protein B, chloroplast precursor	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. FCPs are probably ...				217
Q9NZH0 UniProt NPD GO	GPC5B_HUMAN	G-protein coupled receptor family C group 5 member B precursor (Retinoic acid-induced gene 2 protein ...	0.02	-	end	8 *	Cell membrane; multi-pass membrane protein. Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi ...		605948		403
P09609 UniProt NPD GO	GAL10_KLULA	GAL10 bifunctional protein [Includes: UDP-glucose 4-epimerase (EC 5.1.3.2) (Galactowaldenase); Aldos ...	0.02	-	cyt	0					688
O49213 UniProt NPD GO	FCL1_ARATH	GDP-L-fucose synthase 1 (EC 1.1.1.271) (GDP-4-keto-6-deoxy-D-mannose-3, 5-epimerase-4-reductase 1) ( ...	0.02	-	cyt	0					312
O60547 UniProt NPD GO	GMDS_HUMAN	GDP-mannose 4,6 dehydratase (EC 4.2.1.47) (GDP-D-mannose dehydratase) (GMD)	0.02	-	cyt	0		cytoplasm [IC]	602884	1T2A	372
Q9U6Y5 UniProt NPD GO	GFPL1_ZOASP	GFP-like fluorescent chromoprotein FP506 (zFP506)	0.02	-	cyt	0					231
Q9U6Y6 UniProt NPD GO	GFPL_ANEMA	GFP-like fluorescent chromoprotein amFP486	0.02	-	cyt	0				2A48	229
Q9GZ28 UniProt NPD GO	NFCP_ANESU	GFP-like non-fluorescent chromoprotein FP595 (asFP595) [Contains: GFP-like non-fluorescent chromopro ...	0.02	-	cyt	0				2A56	232
Q6FPB2 UniProt NPD GO	GPI7_CANGA	GPI ethanolamine phosphate transferase 2 (EC 2.-.-.-) (Glycosylphosphatidylinositol-anchor biosynthe ...	0.02	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				842
Q4WAH2 UniProt NPD GO	GPI14_ASPFU	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Glycosylphosphatidyli ...	0.02	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				425
Q757K7 UniProt NPD GO	GPI18_ASHGO	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.02	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				427
P51597 UniProt NPD GO	GCH1_EUGGR	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I) (Fragment)	0.02	-	nuc	0					80
P33519 UniProt NPD GO	RAN_DICDI	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.02	-	cyt	0	Nucleus (By similarity)				212
Q56JV3 UniProt NPD GO	RHEB_BOVIN	GTP-binding protein Rheb (Ras homolog enriched in brain)	0.02	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				184
Q921J2 UniProt NPD GO	RHEB_MOUSE	GTP-binding protein Rheb (Ras homolog enriched in brain)	0.02	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	spliceosome complex [IDA]			184
Q62639 UniProt NPD GO	RHEB_RAT	GTP-binding protein Rheb (Ras homolog enriched in brain)	0.02	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				184
P31584 UniProt NPD GO	YPTV1_VOLCA	GTP-binding protein yptV1	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				203
Q60529 UniProt NPD GO	RASH_MESAU	GTPase HRas (Transforming protein p21) (p21ras) (H-Ras-1) (c-H-ras) (Fragment)	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Golgi apparatus; Golgi membrane; lipi ...				96
P80395 UniProt NPD GO	GGN1_RANRU	Gaegurin-1	0.02	-	nuc	0	Secreted protein				33
P80398 UniProt NPD GO	GGN4_RANRU	Gaegurin-4 precursor	0.02	-	exc	0	Secreted protein				80
P56599 UniProt NPD GO	GAL1_CANMA	Galactokinase (EC 2.7.1.6) (Galactose kinase) (Fragment)	0.02	-	cyt	0					214
Q29043 UniProt NPD GO	FUT1_PIG	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.02	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				365
Q9TTC7 UniProt NPD GO	FUT2_HYLLA	Galactoside 2-alpha-L-fucosyltransferase 2 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.02	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				343
Q10981 UniProt NPD GO	FUT2_HUMAN	Galactoside 2-alpha-L-fucosyltransferase 2 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.02	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...	Golgi apparatus [TAS] integral to Golgi membrane [NAS]	182100		343
Q10983 UniProt NPD GO	FUT2_RABIT	Galactoside 2-alpha-L-fucosyltransferase 2 (EC 2.4.1.69) (Secretor blood group alpha-2-fucosyltransf ...	0.02	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				354
P47214 UniProt NPD GO	GALA_AMICA	Galanin	0.02	-	cyt	0	Secreted protein				29
Q06100 UniProt NPD GO	CGL1_COPCI	Galectin-1 (Galectin I) (Cgl-I)	0.02	-	cyt	0	Detected in extracellular matrix, cell wall and cytoplasmic membrane-bound bodies	cell wall [IDA] cytoplasmic membrane-bound vesicle [IDA] extracellular matrix (sensu Metazoa) [IDA]			150
P81184 UniProt NPD GO	LEG1_SHEEP	Galectin-1 (Lectin galactoside-binding soluble 1) (Beta-galactoside-binding lectin L-14-I) (Lactose- ...	0.02	-	cyt	0					134
P11762 UniProt NPD GO	LEG1_RAT	Galectin-1 (Lectin galactoside-binding soluble 1) (Beta-galactoside-binding lectin L-14-I) (Lactose- ...	0.02	-	cyt	0					134
P17931 UniProt NPD GO	LEG3_HUMAN	Galectin-3 (Galactose-specific lectin 3) (Mac-2 antigen) (IgE-binding protein) (35 kDa lectin) (Carb ...	0.02	-	nuc	0	Nucleus. Cytoplasmic in adenomas and carcinomas. May be secreted by a non-classical secretory pathwa ...	cytoplasm [IDA] nucleus [IDA] plasma membrane [TAS]	153619	1KJR	249
P07323 UniProt NPD GO	ENOG_RAT	Gamma-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Neural enolase) (Neuron-specific en ...	0.02	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Can translocate to the plasma membrane in ...				433
Q92820 UniProt NPD GO	GGH_HUMAN	Gamma-glutamyl hydrolase precursor (EC 3.4.19.9) (Gamma-Glu-X carboxypeptidase) (Conjugase) (GH)	0.02	-	mit	0	Secreted protein; extracellular space. Lysosome. While its intracellular location is primarily the l ...		601509	1L9X	318
Q8L9G7 UniProt NPD GO	APH1_ARATH	Gamma-secretase subunit APH1-like	0.02	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				250
Q63544 UniProt NPD GO	SYUG_RAT	Gamma-synuclein (Persyn) (Sensory neuron synuclein)	0.02	-	cyt	0	Cytoplasm; perinuclear region (By similarity). Centrosome (By similarity). Spindle (By similarity). ...				123
Q29458 UniProt NPD GO	LIPG_BOVIN	Gastric triacylglycerol lipase precursor (EC 3.1.1.3) (Gastric lipase) (GL) (Pregastric esterase) (P ...	0.02	+	cyt	0	Secreted protein				397
P30879 UniProt NPD GO	PEPC_PIG	Gastricsin precursor (EC 3.4.23.3) (Pepsinogen C) (Fragment)	0.02	-	cyt	0	Secreted protein				73
P08989 UniProt NPD GO	GRP_CANFA	Gastrin-releasing peptide (GRP) [Contains: Neuromedin C (GRP-10)]	0.02	-	cyt	0	Secreted protein				27
P31418 UniProt NPD GO	OBP1_MANSE	General odorant-binding protein 1 precursor (GOBP 1)	0.02	-	exc	1 *					166
Q9VR94 UniProt NPD GO	OB19A_DROME	General odorant-binding protein 19a precursor	0.02	-	nuc	0	Secreted protein (By similarity)	extracellular region [ISS]			159
P84159 UniProt NPD GO	GLP1_CITSI	Germin-like protein (Allergen Cit s 1) (Fragment)	0.02	-	cyt	0	Secreted protein; extracellular space; apoplast (By similarity)				25
Q9FIC6 UniProt NPD GO	GL117_ARATH	Germin-like protein subfamily 1 member 17 precursor	0.02	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				221
Q9FL89 UniProt NPD GO	GL119_ARATH	Germin-like protein subfamily 1 member 19 precursor	0.02	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				221
Q9SFF9 UniProt NPD GO	GL17_ARATH	Germin-like protein subfamily 1 member 7 precursor	0.02	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				229
Q9SR72 UniProt NPD GO	GL32_ARATH	Germin-like protein subfamily 3 member 2 precursor	0.02	-	mit	0	Secreted protein; extracellular space; apoplast (By similarity)				227
P20413 UniProt NPD GO	GLB4_LAMSP	Giant hemoglobin AIV chain (Fragment)	0.02	-	cyt	0					32

You are viewing entries 83551 to 83600 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.