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
P49914 UniProt NPD GO	MTHFS_HUMAN	5-formyltetrahydrofolate cyclo-ligase (EC 6.3.3.2) (5,10-methenyl-tetrahydrofolate synthetase) (Meth ...	0.39	-	nuc	0	Cytoplasm	cytosol [NAS]	604197		202
Q758S7 UniProt NPD GO	RL11_ASHGO	60S ribosomal protein L11	0.39	-	cyt	0					174
Q94300 UniProt NPD GO	RL11_CAEEL	60S ribosomal protein L11	0.39	-	cyt	0					196
Q6FTJ2 UniProt NPD GO	RL3_CANGA	60S ribosomal protein L3	0.39	+	mit	0	Cytoplasm (By similarity)				387
Q6NUH0 UniProt NPD GO	RL31_XENLA	60S ribosomal protein L31	0.39	-	nuc	0					125
P49207 UniProt NPD GO	RL34_HUMAN	60S ribosomal protein L34	0.39	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			116
Q9LJW6 UniProt NPD GO	RL343_ARATH	60S ribosomal protein L34-3	0.39	-	mit	0					120
P69201 UniProt NPD GO	RL40_LEIMA	60S ribosomal protein L40 (CEP52)	0.39	+	nuc	0					52
P69200 UniProt NPD GO	RL40_LEITA	60S ribosomal protein L40 (CEP52)	0.39	+	nuc	0					52
O35227 UniProt NPD GO	ADAM7_MOUSE	ADAM 7 precursor (A disintegrin and metalloproteinase domain 7)	0.39	-	nuc	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]			788
Q9UKP4 UniProt NPD GO	ATS7_HUMAN	ADAMTS-7 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 7) ...	0.39	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		605009		997
Q7TNK8 UniProt NPD GO	ADM2_MOUSE	ADM2 precursor (Intermedin) [Contains: Adrenomedullin-2 (Intermedin-long) (IMDL); Intermedin-short ( ...	0.39	-	nuc	1 *	Secreted protein				150
P49703 UniProt NPD GO	ARL4D_HUMAN	ADP-ribosylation factor-like protein 4D (ADP-ribosylation factor-like protein 4L)	0.39	-	mit	0	Nucleus; nucleolus (By similarity)		600732		201
O13939 UniProt NPD GO	AP3B_SCHPO	AP-3 complex subunit beta (Beta-adaptin) (Adapter-related protein complex 3 beta subunit) (Clathrin ...	0.39	-	nuc	0					745
Q6FLT7 UniProt NPD GO	HIS1_CANGA	ATP phosphoribosyltransferase (EC 2.4.2.17) (ATP-PRTase) (ATP-PRT)	0.39	-	cyt	0	Cytoplasm (By similarity)				306
Q9QY16 UniProt NPD GO	DDX25_RAT	ATP-dependent RNA helicase DDX25 (EC 3.6.1.-) (DEAD box protein 25) (Gonadotropin-regulated testicul ...	0.39	-	cyt	0	Cytoplasm				483
Q5B948 UniProt NPD GO	IF4A_EMENI	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.39	-	nuc	0	Cytoplasm (By similarity)				421
Q75BL8 UniProt NPD GO	IF4A_ASHGO	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.39	-	cyt	0	Cytoplasm (By similarity)				396
Q08409 UniProt NPD GO	AUS1_YEAST	ATP-dependent permease AUS1	0.39	-	end	13	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			1394
Q5ACU6 UniProt NPD GO	RRP3_CANAL	ATP-dependent rRNA helicase RRP3 (EC 3.6.1.-)	0.39	-	nuc	0	Nucleus (Probable)				399
P97794 UniProt NPD GO	IRK8_MOUSE	ATP-sensitive inward rectifier potassium channel 8 (Potassium channel, inwardly rectifying subfamily ...	0.39	-	end	2	Membrane; multi-pass membrane protein				424
Q63664 UniProt NPD GO	IRK8_RAT	ATP-sensitive inward rectifier potassium channel 8 (Potassium channel, inwardly rectifying subfamily ...	0.39	-	end	2	Membrane; multi-pass membrane protein				424
P25605 UniProt NPD GO	ILV6_YEAST	Acetolactate synthase small subunit, mitochondrial precursor (AHAS) (Acetohydroxy-acid synthase smal ...	0.39	-	mit	0	Mitochondrion	acetolactate synthase complex [IDA] mitochondrial nucleoid [IDA] mitochondrion [IDA]			309
P31562 UniProt NPD GO	ACCD_CUSRE	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.39	-	nuc	0	Plastid				497
Q9M3L7 UniProt NPD GO	ACCD_SPIOL	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.39	-	nuc	0	Plastid; chloroplast				522
P54247 UniProt NPD GO	ACHX_ONCVO	Acetylcholine receptor protein, non-alpha chain (Fragment)	0.39	-	vac	4	Membrane; multi-pass membrane protein				436
O35348 UniProt NPD GO	COLQ_MOUSE	Acetylcholinesterase collagenic tail peptide (AChE Q subunit) (Acetylcholinesterase-associated colla ...	0.39	-	nuc	0					236
Q9Y215 UniProt NPD GO	COLQ_HUMAN	Acetylcholinesterase collagenic tail peptide precursor (AChE Q subunit) (Acetylcholinesterase-associ ...	0.39	-	nuc	0		basal lamina [TAS] extracellular space [TAS]	603033	1VZJ	456
Q3SZC6 UniProt NPD GO	AN32B_BOVIN	Acidic leucine-rich nuclear phosphoprotein 32 family member B	0.39	-	nuc	0	Nucleus. Accumulates in the nuclei at the S phase (By similarity)				261
Q43593 UniProt NPD GO	STAD_OLEEU	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.39	-	cyt	0	Plastid; chloroplast (By similarity). In green tissue, found in chloroplasts. Plastid (By similarity ...				390
Q9VW60 UniProt NPD GO	ADCY2_DROME	Adenylate cyclase type 2 (EC 4.6.1.1) (ATP pyrophosphate-lyase 2) (Adenylyl cyclase 76E)	0.39	-	end	10	Membrane; multi-pass membrane protein (Potential)	plasma membrane [ISS]			1307
O43306 UniProt NPD GO	ADCY6_HUMAN	Adenylate cyclase type 6 (EC 4.6.1.1) (Adenylate cyclase type VI) (ATP pyrophosphate-lyase 6) (Ca(2+ ...	0.39	-	end	12	Membrane; multi-pass membrane protein		600294		1168
P26364 UniProt NPD GO	KAD2_YEAST	Adenylate kinase 2 (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.39	-	nuc	0	Mitochondrion	mitochondrial inner membrane [IDA]			225
O89020 UniProt NPD GO	AFAM_MOUSE	Afamin precursor (Alpha-albumin) (Alpha-Alb)	0.39	-	mit	0	Secreted protein				611
Q28343 UniProt NPD GO	PGCA_CANFA	Aggrecan core protein precursor (Cartilage-specific proteoglycan core protein) (CSPCP)	0.39	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				2333
O00468 UniProt NPD GO	AGRN_HUMAN	Agrin precursor	0.39	-	exc	0	Synaptic basal lamina at the neuromuscular junction (By similarity)	basal lamina [IDA]	103320		2045
Q9D8F1 UniProt NPD GO	ALKB4_MOUSE	Alkylated repair protein alkB homolog 4	0.39	-	cyt	0					300
Q8C0I1 UniProt NPD GO	ADAS_MOUSE	Alkyldihydroxyacetonephosphate synthase, peroxisomal precursor (EC 2.5.1.26) (Alkyl-DHAP synthase) ( ...	0.39	-	cyt	0	Peroxisome (By similarity)				645
P15322 UniProt NPD GO	ALL1_SINAL	Allergen Sin a 1 precursor (Sin a I) [Contains: Allergen Sin a 1 small chain; Allergen Sin a 1 large ...	0.39	-	nuc	0					145
P02498 UniProt NPD GO	CRYAA_LOXAF	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.39	-	nuc	0					173
P56434 UniProt NPD GO	FUT6_PANTR	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.65) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferas ...	0.39	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				359
Q9DBE8 UniProt NPD GO	ALG2_MOUSE	Alpha-1,3-mannosyltransferase ALG2 (EC 2.4.1.-) (GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransfe ...	0.39	-	mit	0					415
Q9YH85 UniProt NPD GO	TECTA_CHICK	Alpha-tectorin precursor	0.39	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor; extracellular side (Probable). Found in the non-collagenous ...				2120
P04722 UniProt NPD GO	GDA2_WHEAT	Alpha/beta-gliadin A-II precursor (Prolamin)	0.39	-	exc	0					291
P04723 UniProt NPD GO	GDA3_WHEAT	Alpha/beta-gliadin A-III precursor (Prolamin)	0.39	-	exc	0					282
P04725 UniProt NPD GO	GDA5_WHEAT	Alpha/beta-gliadin A-V precursor (Prolamin)	0.39	-	exc	0					319
O46547 UniProt NPD GO	SCNND_PANTR	Amiloride-sensitive sodium channel subunit delta (Epithelial Na+ channel subunit delta) (Delta ENaC) ...	0.39	-	end	1	Membrane; multi-pass membrane protein				638
P28337 UniProt NPD GO	GCST_CHICK	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.39	-	mit	0	Mitochondrion				392
Q60495 UniProt NPD GO	A4_CAVPO	Amyloid beta A4 protein precursor (APP) (ABPP) (Alzheimer disease amyloid protein homolog) [Contains ...	0.39	-	end	1	Membrane; single-pass type I membrane protein (By similarity). Cell surface protein that rapidly bec ...				770
Q95LR4 UniProt NPD GO	ASB17_MACFA	Ankyrin repeat and SOCS box protein 17 (ASB-17)	0.39	-	mit	0					295

You are viewing entries 32351 to 32400 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.