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
P35284 UniProt NPD GO	RAB12_RAT	Ras-related protein Rab-12 (Fragment)	0.22	-	nuc	0	Golgi apparatus; Golgi membrane; lipid-anchor (By similarity)	secretory granule [IDA]			197
P35283 UniProt NPD GO	RAB12_MOUSE	Ras-related protein Rab-12 (Rab-13) (Fragment)	0.22	-	nuc	0	Golgi apparatus; Golgi membrane; lipid-anchor (By similarity)				191
Q96E17 UniProt NPD GO	RAB3C_HUMAN	Ras-related protein Rab-3C	0.22	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				227
Q9NRW1 UniProt NPD GO	RAB6B_HUMAN	Ras-related protein Rab-6B	0.22	-	cyt	0	Golgi apparatus; Golgi membrane; lipid-anchor	Golgi apparatus [NAS]			208
P61294 UniProt NPD GO	RAB6B_MOUSE	Ras-related protein Rab-6B	0.22	-	cyt	0	Golgi apparatus; Golgi membrane; lipid-anchor (By similarity)				208
Q4R5P1 UniProt NPD GO	RAB8A_MACFA	Ras-related protein Rab-8A	0.22	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				207
P61007 UniProt NPD GO	RAB8A_CANFA	Ras-related protein Rab-8A (Oncogene c-mel)	0.22	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				207
P61006 UniProt NPD GO	RAB8A_HUMAN	Ras-related protein Rab-8A (Oncogene c-mel)	0.22	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		165040		207
Q2KI30 UniProt NPD GO	REEP2_BOVIN	Receptor expression-enhancing protein 2	0.22	-	nuc	2 *	Membrane; multi-pass membrane protein (By similarity)				254
Q9D8G5 UniProt NPD GO	REG4_MOUSE	Regenerating islet-derived protein 4 precursor	0.22	-	exc	0	Secreted protein (By similarity)				157
O08850 UniProt NPD GO	RGS5_MOUSE	Regulator of G-protein signaling 5 (RGS5)	0.22	-	nuc	0					181
P30986 UniProt NPD GO	RETO_ESCCA	Reticuline oxidase precursor (EC 1.21.3.3) (Berberine bridge-forming enzyme) (BBE) (Tetrahydroprotob ...	0.22	-	end	0	Cytoplasmic vesicle				538
O15973 UniProt NPD GO	OPSD1_PATYE	Rhodopsin, GQ-coupled (GQ-rhodopsin)	0.22	-	end	6	Membrane; multi-pass membrane protein				499
P81476 UniProt NPD GO	RNL2_CHICK	Ribonuclease CL2 (EC 3.1.27.-) (Poly C preferential ribonuclease) (RNase CL2)	0.22	-	nuc	0	Secreted protein				121
O70338 UniProt NPD GO	RNH1_MOUSE	Ribonuclease H1 (EC 3.1.26.4) (RNase H1)	0.22	+	mit	0	Cytoplasm (Potential)	mitochondrion [IDA]			285
P00663 UniProt NPD GO	RNAS1_CEREL	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.22	-	nuc	0	Secreted protein				124
P00665 UniProt NPD GO	RNAS1_DAMDA	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.22	-	nuc	0	Secreted protein				124
P07848 UniProt NPD GO	RNAS1_GAZTH	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.22	-	nuc	0	Secreted protein				124
P04059 UniProt NPD GO	RNAS1_PROGU	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.22	-	nuc	0	Secreted protein				128
P18652 UniProt NPD GO	KS6AA_CHICK	Ribosomal protein S6 kinase 2 alpha (EC 2.7.11.1) (Ribosomal protein S6 kinase II alpha) (S6KII-alph ...	0.22	-	cyt	0					752
P16131 UniProt NPD GO	RBS3_ACECL	Ribulose bisphosphate carboxylase small chain 3, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.22	-	mit	0	Plastid; chloroplast				183
Q6BI60 UniProt NPD GO	RUVB1_DEBHA	RuvB-like helicase 1 (EC 3.6.1.-)	0.22	-	cyt	0	Nucleus (By similarity)				457
Q8NEM2 UniProt NPD GO	SHCBP_HUMAN	SHC SH2 domain-binding protein 1	0.22	-	cyt	0					672
O75477 UniProt NPD GO	SPFH1_HUMAN	SPFH domain-containing protein 1 precursor (Protein KE04)	0.22	-	mit	1 *	Membrane; peripheral membrane protein (Probable)				346
Q99619 UniProt NPD GO	SPSB2_HUMAN	SPRY domain-containing SOCS box protein 2 (SSB-2) (Gene-rich cluster protein C9)	0.22	-	cyt	0	Cytoplasm (Probable)				263
O88838 UniProt NPD GO	SPSB2_MOUSE	SPRY domain-containing SOCS box protein 2 (SSB-2) (Gene-rich cluster protein C9)	0.22	-	mit	0	Cytoplasm (Probable)			2AFJ	264
Q5R8K3 UniProt NPD GO	SLIRP_PONPY	SRA stem-loop-interacting RNA-binding protein, mitochondrial precursor	0.22	-	mit	0	Mitochondrion; predominantly. Nucleus; some fraction is nuclear. In the nucleus, it is recruited to ...				109
P40671 UniProt NPD GO	CH32_CHICK	SRY-related protein CH32 (Fragment)	0.22	-	nuc	0	Nucleus (Potential)				54
P40669 UniProt NPD GO	CH07_CHICK	SRY-related protein CH7 (Fragment)	0.22	-	nuc	0	Nucleus (Potential)				54
Q5YCU7 UniProt NPD GO	STH_GORGO	Saitohin	0.22	-	nuc	0					128
Q5YCU8 UniProt NPD GO	STH_PANTR	Saitohin	0.22	-	nuc	0					128
Q94424 UniProt NPD GO	CTF1_CTEFE	Salivary antigen 1 precursor (FS-I) (Allergen Cte f 1)	0.22	-	nuc	0	Secreted protein				176
Q2VLH6 UniProt NPD GO	C163A_MOUSE	Scavenger receptor cysteine-rich type 1 protein M130 precursor (CD163 antigen) [Contains: Soluble CD ...	0.22	-	end	2 *	Cell membrane; single-pass type I membrane protein (By similarity). Soluble CD163: Secreted protein ...				1121
Q8WU76 UniProt NPD GO	SCFD2_HUMAN	Sec1 family domain-containing protein 2 (Syntaxin-binding protein 1-like 1)	0.22	-	end	0					684
Q95117 UniProt NPD GO	SFRP3_BOVIN	Secreted frizzled-related protein 3 precursor (sFRP-3) (Frizzled-related protein 1) (FrzB-1)	0.22	-	exc	1 *	Secreted protein (Probable)	extracellular region [ISS]			325
O15127 UniProt NPD GO	SCAM2_HUMAN	Secretory carrier-associated membrane protein 2 (Secretory carrier membrane protein 2)	0.22	-	end	4	Membrane; multi-pass membrane protein		606912		329
P00999 UniProt NPD GO	IACA_PIG	Seminal plasma acrosin inhibitor A1	0.22	-	mit	0	Secreted protein				65
Q9EP89 UniProt NPD GO	LACTB_MOUSE	Serine beta-lactamase-like protein LACTB	0.22	-	cyt	1 *					551
P43292 UniProt NPD GO	ASK2_ARATH	Serine/threonine-protein kinase ASK2 (EC 2.7.11.1)	0.22	-	cyt	0					353
O00141 UniProt NPD GO	SGK1_HUMAN	Serine/threonine-protein kinase Sgk1 (EC 2.7.11.1) (Serum/glucocorticoid-regulated kinase 1)	0.22	-	cyt	0	Cytoplasm. Nucleus. Nuclear, upon phosphorylation		602958		431
O74456 UniProt NPD GO	PEF1_SCHPO	Serine/threonine-protein kinase pef1 (EC 2.7.11.22) (Cyclin-dependent kinase pef1) (PHO85 homolog)	0.22	-	cyt	0					288
Q38951 UniProt NPD GO	2AAG_ARATH	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A gamma isoform (PP2A, subunit A, ...	0.22	-	cyt	0					587
Q4WMU5 UniProt NPD GO	PTPA1_ASPFU	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.22	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				473
P48481 UniProt NPD GO	PP12_ACECL	Serine/threonine-protein phosphatase PP1 isozyme 2 (EC 3.1.3.16)	0.22	-	cyt	0					319
P20233 UniProt NPD GO	TRFE_XENLA	Serotransferrin precursor	0.22	-	exc	0	Secreted protein				701
Q09204 UniProt NPD GO	SRA2_CAEEL	Serpentine receptor class alpha-2 (Protein sra-2)	0.22	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				329
Q09208 UniProt NPD GO	SRA6_CAEEL	Serpentine receptor class alpha-6 (Protein sra-6)	0.22	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				329
O17800 UniProt NPD GO	SRD63_CAEEL	Serpentine receptor class delta-63 (Protein srd-63)	0.22	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				321
P46567 UniProt NPD GO	SRG13_CAEEL	Serpentine receptor class gamma-13 (Protein srg-13)	0.22	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				336
P54127 UniProt NPD GO	SRG5_CAEEL	Serpentine receptor class gamma-5 (Protein srg-5)	0.22	-	end	5 *	Membrane; multi-pass membrane protein (Probable)				317

You are viewing entries 48901 to 48950 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.