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
Q6Z2L5 UniProt NPD GO	KPRS1_ORYSA	Ribose-phosphate pyrophosphokinase 1 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 1)	0.20	-	mit	0					396
Q8S2E5 UniProt NPD GO	KPRS3_ORYSA	Ribose-phosphate pyrophosphokinase 3 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 3)	0.20	-	mit	0					409
P10665 UniProt NPD GO	KS6AA_XENLA	Ribosomal protein S6 kinase 2 alpha (EC 2.7.11.1) (Ribosomal protein S6 kinase II alpha) (S6KII-alph ...	0.20	-	cyt	0					733
P25891 UniProt NPD GO	RIP3_MAIZE	Ribosome-inactivating protein 3 (rRNA N-glycosidase) (EC 3.2.2.22) (B-32 protein)	0.20	-	cyt	0	Cytoplasm				300
P28522 UniProt NPD GO	RIPX_MAIZE	Ribosome-inactivating protein precursor (EC 3.2.2.22) (rRNA N-glycosidase) [Contains: Ribosome-inact ...	0.20	-	cyt	0					301
P16129 UniProt NPD GO	RBS1_ACECL	Ribulose bisphosphate carboxylase small chain 1 (EC 4.1.1.39) (RuBisCO small subunit 1) (Fragment)	0.20	-	cyt	0	Plastid; chloroplast				126
P23439 UniProt NPD GO	PDE6B_BOVIN	Rod cGMP-specific 3',5'-cyclic phosphodiesterase beta-subunit precursor (EC 3.1.4.35) (GMP-PDE beta) ...	0.20	-	cyt	0	Membrane; lipid-anchor				853
Q9WTP3 UniProt NPD GO	SPDEF_MOUSE	SAM pointed domain-containing Ets transcription factor (Prostate-derived Ets factor) (Prostate epith ...	0.20	-	nuc	0	Nucleus (Probable)				325
P87378 UniProt NPD GO	CRK_XENLA	SH2/SH3 adaptor crk (Adapter molecule crk) (CRK2)	0.20	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocated to the plasma membrane upon c ...				296
P40643 UniProt NPD GO	AMA3_ALLMI	SRY-related protein AMA3 (Fragment)	0.20	-	nuc	0	Nucleus (Potential)				54
P63281 UniProt NPD GO	UBC9_RAT	SUMO-1-conjugating enzyme UBC9 (EC 6.3.2.19) (SUMO-1-protein ligase) (Ubiquitin-conjugating enzyme E ...	0.20	-	nuc	0					158
P63280 UniProt NPD GO	UBC9_MOUSE	SUMO-1-conjugating enzyme UBC9 (EC 6.3.2.19) (SUMO-1-protein ligase) (Ubiquitin-conjugating enzyme E ...	0.20	-	nuc	0				1U9B	158
P63279 UniProt NPD GO	UBC9_HUMAN	SUMO-1-conjugating enzyme UBC9 (EC 6.3.2.19) (SUMO-1-protein ligase) (Ubiquitin-conjugating enzyme E ...	0.20	-	nuc	0			601661	2GRR	158
P63283 UniProt NPD GO	UBC9_CHICK	SUMO-1-conjugating enzyme UBC9 (EC 6.3.2.19) (Ubiquitin-conjugating enzyme E2 I) (Ubiquitin-protein ...	0.20	-	nuc	0					158
P63282 UniProt NPD GO	UBC9_XENLA	SUMO-1-conjugating enzyme UBC9 (EC 6.3.2.19) (Ubiquitin-conjugating enzyme E2 I) (Ubiquitin-protein ...	0.20	-	nuc	0					158
P01144 UniProt NPD GO	SAUV_PHYSA	Sauvagin (Sauvagine) (SVG)	0.20	-	nuc	0	Secreted protein				40
Q39221 UniProt NPD GO	STLP2_ARATH	Sec12-like protein 2	0.20	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity). ...				393
P63296 UniProt NPD GO	SECR_BOVIN	Secretin	0.20	-	nuc	0	Secreted protein				27
P63297 UniProt NPD GO	SECR_CAVPO	Secretin	0.20	-	nuc	0	Secreted protein				27
P31299 UniProt NPD GO	SECR_SHEEP	Secretin	0.20	-	nuc	0	Secreted protein				27
O35609 UniProt NPD GO	SCAM3_MOUSE	Secretory carrier-associated membrane protein 3 (Secretory carrier membrane protein 3)	0.20	-	end	4	Membrane; multi-pass membrane protein	Golgi membrane [IDA]			349
Q17330 UniProt NPD GO	SEM1A_CAEEL	Semaphorin-1A precursor (CeSema)	0.20	-	end	1	Membrane; single-pass type I membrane protein				712
P08818 UniProt NPD GO	CBP2_HORVU	Serine carboxypeptidase 2 precursor (EC 3.4.16.6) (Serine carboxypeptidase II) (Carboxypeptidase D) ...	0.20	-	exc	1 *	Secreted protein. Secreted into the endosperm				476
P50432 UniProt NPD GO	GLYC_CAEEL	Serine hydroxymethyltransferase (EC 2.1.2.1) (Serine methylase) (Glycine hydroxymethyltransferase) ( ...	0.20	-	mit	0					507
Q91ZR4 UniProt NPD GO	NEK8_MOUSE	Serine/threonine-protein kinase Nek8 (EC 2.7.11.1) (Never in mitosis A-related kinase 8) (NimA-relat ...	0.20	-	cyt	0	Cytoplasm. Predominantly				698
Q9BXM7 UniProt NPD GO	PINK1_HUMAN	Serine/threonine-protein kinase PINK1, mitochondrial precursor (EC 2.7.11.1) (PTEN-induced putative ...	0.20	-	mit	0	Mitochondrion	mitochondrion [IEP]	608309		581
Q08209 UniProt NPD GO	PP2BA_HUMAN	Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform (EC 3.1.3.16) (Calmodulin-de ...	0.20	-	cyt	0	Nucleus (By similarity). Colocalizes with ACTN1 and MYOZ2 at the Z line in heart and skeletal muscle ...	calcineurin complex [NAS]	114105	1MF8	521
P53041 UniProt NPD GO	PPP5_HUMAN	Serine/threonine-protein phosphatase 5 (EC 3.1.3.16) (PP5) (Protein phosphatase T) (PP-T) (PPT)	0.20	-	cyt	0	Nucleus. Predominantly. Cytoplasm. But also present in the cytoplasm	nucleus [TAS]	600658	1WAO	499
P48489 UniProt NPD GO	PP1_ORYSA	Serine/threonine-protein phosphatase PP1 (EC 3.1.3.16)	0.20	-	cyt	0					322
O04858 UniProt NPD GO	PP13_TOBAC	Serine/threonine-protein phosphatase PP1 isozyme 3 (EC 3.1.3.16)	0.20	-	cyt	0					304
Q07100 UniProt NPD GO	PP2A3_ARATH	Serine/threonine-protein phosphatase PP2A-3 catalytic subunit (EC 3.1.3.16)	0.20	-	nuc	0	Cytoplasm				313
Q16613 UniProt NPD GO	SNAT_HUMAN	Serotonin N-acetyltransferase (EC 2.3.1.87) (Aralkylamine N-acetyltransferase) (AA-NAT) (Serotonin a ...	0.20	-	nuc	0			600950		207
Q92079 UniProt NPD GO	TRFE_GADMO	Serotransferrin (Fragment)	0.20	-	cyt	0	Secreted protein				642
P79815 UniProt NPD GO	TRFE_ONCKI	Serotransferrin precursor	0.20	-	exc	0	Secreted protein				687
Q20405 UniProt NPD GO	SRA10_CAEEL	Serpentine receptor class alpha-10 (Protein sra-10)	0.20	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				336
Q09210 UniProt NPD GO	SRA8_CAEEL	Serpentine receptor class alpha-8 (Protein sra-8)	0.20	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				329
Q09273 UniProt NPD GO	SRE2_CAEEL	Serpentine receptor class epsilon-2 (Protein sre-2)	0.20	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				309
P46571 UniProt NPD GO	SRG2_CAEEL	Serpentine receptor class gamma-2 (Protein srg-2)	0.20	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				327
P91994 UniProt NPD GO	SRG46_CAEEL	Serpentine receptor class gamma-46 (Protein srg-46)	0.20	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				283
Q96P63 UniProt NPD GO	SPB12_HUMAN	Serpin B12	0.20	-	mit	0	Cytoplasm (By similarity)	cytoplasm [NAS]			405
Q9UN30 UniProt NPD GO	SCML1_HUMAN	Sex comb on midleg-like protein 1	0.20	-	nuc	0	Nucleus (Probable)		300227		208
P01427 UniProt NPD GO	NXS1_NAJOX	Short neurotoxin 1 (Neurotoxin alpha) (Neurotoxin II) (NTX II)	0.20	-	nuc	0	Secreted protein			1NOR	61
Q8TD22 UniProt NPD GO	SFXN5_HUMAN	Sideroflexin-5	0.20	-	end	5	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				340
P61010 UniProt NPD GO	SRP54_CANFA	Signal recognition particle 54 kDa protein (SRP54)	0.20	-	cyt	0	Cytoplasm				504
Q8MZJ6 UniProt NPD GO	SRP54_GEOCY	Signal recognition particle 54 kDa protein (SRP54)	0.20	-	cyt	0	Cytoplasm (By similarity)				499
P61011 UniProt NPD GO	SRP54_HUMAN	Signal recognition particle 54 kDa protein (SRP54)	0.20	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle. Cytoplasmic		604857	1QB2	504
Q4R965 UniProt NPD GO	SRP54_MACFA	Signal recognition particle 54 kDa protein (SRP54)	0.20	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Cytoplasm (By similarity)				504
P14576 UniProt NPD GO	SRP54_MOUSE	Signal recognition particle 54 kDa protein (SRP54)	0.20	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Cytoplasm			1WGW	504
Q5R4R6 UniProt NPD GO	SRP54_PONPY	Signal recognition particle 54 kDa protein (SRP54)	0.20	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Cytoplasm (By similarity)				504
Q6AYB5 UniProt NPD GO	SRP54_RAT	Signal recognition particle 54 kDa protein (SRP54)	0.20	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Cytoplasm (By similarity)				504

You are viewing entries 51201 to 51250 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.