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
P43646 UniProt NPD GO	CATR_TETST	Caltractin (Centrin) (Fragment)	0.11	-	cyt	0					148
Q9UUQ6 UniProt NPD GO	LCPS_RHIRA	CarRP protein [Includes: Lycopene cyclase (EC 1.-.-.-); Phytoene synthase (EC 2.5.1.-)]	0.11	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			614
P31327 UniProt NPD GO	CPSM_HUMAN	Carbamoyl-phosphate synthase [ammonia], mitochondrial precursor (EC 6.3.4.16) (Carbamoyl-phosphate s ...	0.11	-	mit	0	Mitochondrion	mitochondrion [TAS]	608307		1500
P03965 UniProt NPD GO	CARB_YEAST	Carbamoyl-phosphate synthase arginine-specific large chain (EC 6.3.5.5) (Arginine-specific carbamoyl ...	0.11	-	cyt	0	Cytoplasm				1118
P40199 UniProt NPD GO	CEAM6_HUMAN	Carcinoembryonic antigen-related cell adhesion molecule 6 precursor (Normal cross-reacting antigen) ...	0.11	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor	integral to plasma membrane [TAS]	163980		344
P32331 UniProt NPD GO	YMC1_YEAST	Carrier protein YMC1, mitochondrial precursor	0.11	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				307
P21941 UniProt NPD GO	MATN1_HUMAN	Cartilage matrix protein precursor (Matrilin-1)	0.11	-	vac	0		extracellular matrix (sensu Metazoa) [TAS]	115437		496
P51942 UniProt NPD GO	MATN1_MOUSE	Cartilage matrix protein precursor (Matrilin-1)	0.11	-	exc	0		extracellular matrix (sensu Metazoa) [IDA]			500
Q01297 UniProt NPD GO	CATA1_RICCO	Catalase isozyme 1 (EC 1.11.1.6)	0.11	-	nuc	0	Peroxisome (Potential). Glyoxysome (Potential)				492
P80209 UniProt NPD GO	CATD_BOVIN	Cathepsin D precursor (EC 3.4.23.5)	0.11	-	mit	0	Lysosome				390
Q805F3 UniProt NPD GO	CATEA_XENLA	Cathepsin E-A precursor (EC 3.4.23.34)	0.11	-	mit	1 *	Endosome (By similarity). The proenzyme is localized to the endoplasmic reticulum and Golgi apparatu ...	endosome [ISS]			397
Q805F2 UniProt NPD GO	CATEB_XENLA	Cathepsin E-B precursor (EC 3.4.23.34)	0.11	-	exc	1 *	Endosome (By similarity). The proenzyme is localized to the endoplasmic reticulum and Golgi apparatu ...	endosome [ISS]			397
Q9R013 UniProt NPD GO	CATF_MOUSE	Cathepsin F precursor (EC 3.4.22.41)	0.11	-	vac	0	Lysosome				462
Q5E968 UniProt NPD GO	CATK_BOVIN	Cathepsin K precursor (EC 3.4.22.38)	0.11	-	cyt	0	Lysosome (By similarity)				329
Q02765 UniProt NPD GO	CATS_RAT	Cathepsin S precursor (EC 3.4.22.27)	0.11	-	cyt	0	Lysosome				330
Q8WY07 UniProt NPD GO	CTR3_HUMAN	Cationic amino acid transporter 3 (CAT-3) (Solute carrier family 7 member 3) (Cationic amino acid tr ...	0.11	-	end	14 *	Cell membrane; multi-pass membrane protein		300443		619
P61075 UniProt NPD GO	CDC2H_PLAF7	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23)	0.11	-	cyt	0	Cytoplasm (By similarity)				288
Q07785 UniProt NPD GO	CDC2H_PLAFK	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (PfPK5)	0.11	-	cyt	0	Cytoplasm			1V0P	288
Q41639 UniProt NPD GO	CDC2_VIGAC	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34cdc2)	0.11	-	cyt	0					294
P52389 UniProt NPD GO	CDC2_VIGUN	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34cdc2)	0.11	-	cyt	0					294
P24100 UniProt NPD GO	CDC2A_ARATH	Cell division control protein 2 homolog A (EC 2.7.11.22) (EC 2.7.11.23)	0.11	-	cyt	0					294
P23505 UniProt NPD GO	GP42_RAT	Cell surface glycoprotein gp42 precursor	0.11	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				233
Q6T499 UniProt NPD GO	RABP1_HIPCM	Cellular retinoic acid-binding protein 1 (Cellular retinoic acid-binding protein I) (CRABP-I) (Retin ...	0.11	-	nuc	0	Cytoplasm (By similarity)				136
P48389 UniProt NPD GO	CHSY_DIACA	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.11	-	cyt	0					391
O65872 UniProt NPD GO	CHSY_PINST	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.11	-	cyt	0					395
Q41436 UniProt NPD GO	CHSA_SOLTU	Chalcone synthase 1A (EC 2.3.1.74) (Naringenin-chalcone synthase 1A)	0.11	-	mit	0					389
Q43163 UniProt NPD GO	CHSB_SOLTU	Chalcone synthase 1B (EC 2.3.1.74) (Naringenin-chalcone synthase 1B)	0.11	-	mit	0					389
P51077 UniProt NPD GO	CHS3_MEDSA	Chalcone synthase 4-1 (EC 2.3.1.74) (Naringenin-chalcone synthase 4-1)	0.11	-	nuc	0					389
P51078 UniProt NPD GO	CHS5_MEDSA	Chalcone synthase 4-2 (EC 2.3.1.74) (Naringenin-chalcone synthase 4-2)	0.11	-	nuc	0					389
Q01288 UniProt NPD GO	CHS6_PEA	Chalcone synthase 6 (EC 2.3.1.74) (Naregenin-chalcone synthase 6)	0.11	-	mit	0					389
P30076 UniProt NPD GO	CHS8_MEDSA	Chalcone synthase 8 (EC 2.3.1.74) (Naringenin-chalcone synthase 8)	0.11	-	nuc	0					389
P30077 UniProt NPD GO	CHS9_MEDSA	Chalcone synthase 9 (EC 2.3.1.74) (Naringenin-chalcone synthase 9)	0.11	-	nuc	0					389
Q8BMP4 UniProt NPD GO	CML2_MOUSE	Chemokine receptor-like 2 (G-protein coupled receptor 30)	0.11	-	end	7	Membrane; multi-pass membrane protein				375
P29025 UniProt NPD GO	CHI1_RHINI	Chitinase 1 precursor (EC 3.2.1.14)	0.11	-	mit	0					493
Q6FLZ2 UniProt NPD GO	ALG1_CANGA	Chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) (GDP-mannose-dolichol diphospho ...	0.11	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				450
Q924C9 UniProt NPD GO	S26A3_RAT	Chloride anion exchanger (Protein DRA) (Down-regulated in adenoma) (Solute carrier family 26 member ...	0.11	-	end	11	Membrane; multi-pass membrane protein (Probable)	integral to membrane [IEP]			757
Q4PKH3 UniProt NPD GO	CLCN7_BOVIN	Chloride channel protein 7 (ClC-7)	0.11	-	end	11	Membrane; multi-pass membrane protein				809
O15247 UniProt NPD GO	CLIC2_HUMAN	Chloride intracellular channel protein 2 (XAP121)	0.11	-	mit	0		cytoplasm [TAS] nucleus [TAS]	300138		247
Q9T2K9 UniProt NPD GO	CB22_SPIOL	Chlorophyll a-b binding protein (LHCII type II CAB) (LHCP) (Fragment)	0.11	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein	thylakoid membrane (sensu Viridiplantae) [IDA]			9
O22527 UniProt NPD GO	CLH1_ARATH	Chlorophyllase-1 (EC 3.1.1.14) (AtCLH1) (Chlorophyll-chlorophyllido hydrolase 1) (Chlase 1) (Coronat ...	0.11	-	cyt	0					324
P36207 UniProt NPD GO	RR16_GINBI	Chloroplast 30S ribosomal protein S16 (Fragment)	0.11	-		0	Plastid; chloroplast				12
P33954 UniProt NPD GO	RR19_SECCE	Chloroplast 30S ribosomal protein S19	0.11	-	nuc	0	Plastid; chloroplast				92
P60577 UniProt NPD GO	RR19_WHEAT	Chloroplast 30S ribosomal protein S19	0.11	-	nuc	0	Plastid; chloroplast				92
Q9MUS8 UniProt NPD GO	RR2_MESVI	Chloroplast 30S ribosomal protein S2	0.11	-	mit	0	Plastid; chloroplast				228
P51299 UniProt NPD GO	RK18_PORPU	Chloroplast 50S ribosomal protein L18	0.11	-	nuc	0	Plastid; chloroplast				120
P21434 UniProt NPD GO	RK2_NICDE	Chloroplast 50S ribosomal protein L2	0.11	-	mit	0	Plastid; chloroplast				266
Q8M9U9 UniProt NPD GO	RK22_CHAGL	Chloroplast 50S ribosomal protein L22	0.11	-	nuc	0	Plastid; chloroplast				119
Q9TLT3 UniProt NPD GO	RK4_CYACA	Chloroplast 50S ribosomal protein L4	0.11	-	cyt	0	Plastid; chloroplast				219
P58155 UniProt NPD GO	CEMA_LOTJA	Chloroplast envelope membrane protein	0.11	-	end	2 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				229
Q9MUN7 UniProt NPD GO	CEMA_MESVI	Chloroplast envelope membrane protein	0.11	-	end	4 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				236

You are viewing entries 62451 to 62500 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.