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
P51776 UniProt NPD GO	PPDK_GIALA	Pyruvate, phosphate dikinase (EC 2.7.9.1) (Pyruvate, orthophosphate dikinase)	0.07	-	cyt	0					884
Q42910 UniProt NPD GO	PPDK_MESCR	Pyruvate, phosphate dikinase, chloroplast precursor (EC 2.7.9.1) (Pyruvate, orthophosphate dikinase) ...	0.07	-	cyt	0	Plastid; chloroplast				949
Q74ZQ0 UniProt NPD GO	TFB5_ASHGO	RNA polymerase II transcription factor B subunit 5 (General transcription and DNA repair factor IIH ...	0.07	-	nuc	0	Nucleus (By similarity)				72
Q9Z2B3 UniProt NPD GO	RGR_MOUSE	RPE-retinal G protein-coupled receptor	0.07	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			291
P15153 UniProt NPD GO	RAC2_HUMAN	Ras-related C3 botulinum toxin substrate 2 precursor (p21-Rac2) (Small G protein) (GX)	0.07	-	cyt	0	Cytoplasm. Membrane-associated when activated		602049	1DS6	192
Q9BZG1 UniProt NPD GO	RAB34_HUMAN	Ras-related protein Rab-34 (Rab-39) (Ras-related protein Rah)	0.07	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus (By similarity). Associates with the Golgi complex (By si ...				259
Q63941 UniProt NPD GO	RAB3B_RAT	Ras-related protein Rab-3B	0.07	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				219
Q40522 UniProt NPD GO	RB11D_TOBAC	Ras-related protein Rab11D	0.07	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				222
P36411 UniProt NPD GO	RAB7_DICDI	Ras-related protein Rab7	0.07	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				203
Q80ZJ1 UniProt NPD GO	RAP2A_MOUSE	Ras-related protein Rap-2a	0.07	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				183
Q5R988 UniProt NPD GO	RAP2A_PONPY	Ras-related protein Rap-2a	0.07	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				183
P10114 UniProt NPD GO	RAP2A_HUMAN	Ras-related protein Rap-2a (RbBP-30)	0.07	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	membrane [TAS]	179540	3RAP	183
Q9H902 UniProt NPD GO	REEP1_HUMAN	Receptor expression-enhancing protein 1	0.07	-	nuc	2 *	Membrane; multi-pass membrane protein (By similarity)		609139		201
Q8AYN0 UniProt NPD GO	OPSR2_BRARE	Red-sensitive opsin-2 (Red cone photoreceptor pigment 2) (Opsin-1, long-wave-sensitive 2) (Opsin LWS ...	0.07	-	end	7	Membrane; multi-pass membrane protein				356
P82943 UniProt NPD GO	REG1_BOVIN	Regakine-1 precursor	0.07	-	exc	0	Secreted protein				92
P49801 UniProt NPD GO	RGS6_RAT	Regulator of G-protein signaling 6 (RGS6) (Fragment)	0.07	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				66
P08424 UniProt NPD GO	RENI_RAT	Renin precursor (EC 3.4.23.15) (Angiotensinogenase)	0.07	-	end	0	Secreted protein (By similarity). Membrane (By similarity). Associated to membranes via binding to A ...				402
Q5R563 UniProt NPD GO	RENR_PONPY	Renin receptor precursor (Renin/prorenin receptor) (ATPase H(+)-transporting lysosomal accessory pro ...	0.07	-	end	1	Membrane; single-pass type I membrane protein (Potential)				350
O75787 UniProt NPD GO	RENR_HUMAN	Renin receptor precursor (Renin/prorenin receptor) (ATPase H(+)-transporting lysosomal accessory pro ...	0.07	-	end	1	Membrane; single-pass type I membrane protein (Potential)		300556		350
Q9WUK4 UniProt NPD GO	RFC2_MOUSE	Replication factor C subunit 2 (Replication factor C 40 kDa subunit) (RF-C 40 kDa subunit) (RFC40) ( ...	0.07	-	nuc	0	Nucleus (Probable)				349
P93479 UniProt NPD GO	RETO_PAPSO	Reticuline oxidase precursor (EC 1.21.3.3) (Berberine bridge-forming enzyme) (BBE) (Tetrahydroprotob ...	0.07	-	end	0	Cytoplasmic vesicle				535
Q9HBH5 UniProt NPD GO	RDH14_HUMAN	Retinol dehydrogenase 14 (EC 1.1.1.-) (Alcohol dehydrogenase PAN2)	0.07	-	nuc	1 *					336
P50169 UniProt NPD GO	RDH3_RAT	Retinol dehydrogenase 3 (EC 1.1.1.105) (Retinol dehydrogenase type I) (RODH I)	0.07	-	mit	0	Microsome				317
P43231 UniProt NPD GO	CARP2_RHINI	Rhizopuspepsin-2 precursor (EC 3.4.23.21) (Aspartate protease)	0.07	-	mit	0					391
Q642B3 UniProt NPD GO	RHBD3_RAT	Rhomboid domain-containing protein 3	0.07	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				385
O74926 UniProt NPD GO	RBD2_SCHPO	Rhomboid protein 2 (EC 3.4.21.-)	0.07	-	end	6 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity). Golgi apparatus; cis-G ...				248
Q6CRT6 UniProt NPD GO	RNY1_KLULA	Ribonuclease T2-like precursor (EC 3.1.27.1) (RNase T2-like)	0.07	-	mit	0	Secreted protein (By similarity)				425
P00658 UniProt NPD GO	RNAS1_TRAOR	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.07	-	nuc	0	Secreted protein				124
Q9D5A9 UniProt NPD GO	RNS10_MOUSE	Ribonuclease-like protein 10 precursor (Protein Train A)	0.07	-	exc	1 *	Secreted protein (By similarity)				208
P38208 UniProt NPD GO	POP8_YEAST	Ribonucleases P/MRP protein subunit POP8 (EC 3.1.26.5) (RNases P/MRP 15.5 kDa subunit) (RNA-processi ...	0.07	-	mit	0	Nucleus (Potential)	nucleolar ribonuclease P complex [IDA] ribonuclease MRP complex [IDA]			133
Q6ZFT5 UniProt NPD GO	KPRS4_ORYSA	Ribose-phosphate pyrophosphokinase 4 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 4)	0.07	-	mit	0					325
P38788 UniProt NPD GO	SSZ1_YEAST	Ribosome-associated complex subunit SSZ1 (Heat shock protein 70 homolog SSZ1) (DnaK-related protein ...	0.07	-	cyt	0	Cytoplasm	cytoplasm [IDA]			538
P24817 UniProt NPD GO	RIP3_MOMCH	Ribosome-inactivating protein beta-momorcharin precursor (EC 3.2.2.22) (rRNA N-glycosidase) (MAP 30) ...	0.07	-	cyt	0				1D8V	286
P29339 UniProt NPD GO	RIP2_MOMBA	Ribosome-inactivating protein momordin II precursor (EC 3.2.2.22) (rRNA N-glycosidase)	0.07	-	cyt	0					286
P48074 UniProt NPD GO	RBL_EUGST	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.07	-	cyt	0	Plastid; chloroplast				436
P56647 UniProt NPD GO	RBL_SETIT	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.07	-	cyt	0	Plastid; chloroplast				476
Q04450 UniProt NPD GO	RBS2_MESCR	Ribulose bisphosphate carboxylase small chain 2, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.07	-	cyt	0	Plastid; chloroplast				180
Q08183 UniProt NPD GO	RBS3_MESCR	Ribulose bisphosphate carboxylase small chain 3, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.07	-	mit	0	Plastid; chloroplast				183
P10798 UniProt NPD GO	RBS3B_ARATH	Ribulose bisphosphate carboxylase small chain 3B, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.07	-	mit	0	Plastid; chloroplast				181
O65194 UniProt NPD GO	RBS_MEDSA	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.07	-	mit	0	Plastid; chloroplast				180
P08135 UniProt NPD GO	RBS_RAPSA	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.07	-	mit	0	Plastid; chloroplast				181
Q40281 UniProt NPD GO	RCA_MALDO	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA)	0.07	-	mit	0	Plastid; chloroplast; chloroplast stroma				437
P93431 UniProt NPD GO	RCA_ORYSA	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA)	0.07	-	mit	0	Plastid; chloroplast; chloroplast stroma				466
Q9M4H4 UniProt NPD GO	GRI22_VITVI	Ripening-related protein grip22 precursor	0.07	-	exc	1 *	Secreted protein (Potential)				220
P08824 UniProt NPD GO	RUBA_RICCO	RuBisCO large subunit-binding protein subunit alpha (60 kDa chaperonin subunit alpha) (CPN-60 alpha) ...	0.07	-	cyt	0	Plastid; chloroplast				495
P08823 UniProt NPD GO	RUBA_WHEAT	RuBisCO large subunit-binding protein subunit alpha, chloroplast precursor (60 kDa chaperonin subuni ...	0.07	-	cyt	0	Plastid; chloroplast				543
Q43831 UniProt NPD GO	RUBB_SECCE	RuBisCO large subunit-binding protein subunit beta, chloroplast (60 kDa chaperonin subunit beta) (CP ...	0.07	-	cyt	0	Plastid; chloroplast				499
P60122 UniProt NPD GO	RUVB1_MOUSE	RuvB-like 1 (EC 3.6.1.-) (49 kDa TATA box-binding protein-interacting protein) (49 kDa TBP-interacti ...	0.07	-	cyt	0	Nucleus (By similarity)				456
P60123 UniProt NPD GO	RUVB1_RAT	RuvB-like 1 (EC 3.6.1.-) (49 kDa TATA box-binding protein-interacting protein) (49 kDa TBP-interacti ...	0.07	-	cyt	0	Nucleus (By similarity)				456
Q9Y265 UniProt NPD GO	RUVB1_HUMAN	RuvB-like 1 (EC 3.6.1.-) (49 kDa TATA box-binding protein-interacting protein) (49 kDa TBP-interacti ...	0.07	-	cyt	0	Nucleus; nuclear matrix. Nucleus; nucleoplasm. Mainly localized in the nucleus, associated with nucl ...	nucleus [IDA] TIP60 histone acetyltransferase complex [IDA]	603449		456

You are viewing entries 70951 to 71000 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.