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
P51149 UniProt NPD GO	RAB7_HUMAN	Ras-related protein Rab-7	0.14	-	cyt	0	Endosome; late endosome. Lysosome. Phagosome	late endosome [IDA] lysosome [IDA]	600882	1T91	207
P51150 UniProt NPD GO	RAB7_MOUSE	Ras-related protein Rab-7	0.14	-	cyt	0	Endosome; late endosome (By similarity). Lysosome (By similarity). Phagosome (By similarity). Found ...	Golgi apparatus [IDA] late endosome [IDA]			207
P09527 UniProt NPD GO	RAB7_RAT	Ras-related protein Rab-7 (RAS-related protein P23) (RAS-related protein BRL-RAS)	0.14	-	cyt	0	Endosome; late endosome (By similarity). Lysosome (By similarity). Phagosome (By similarity)	late endosome [TAS]		1VG9	207
Q9XER8 UniProt NPD GO	RAB7_GOSHI	Ras-related protein Rab7	0.14	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				207
Q40787 UniProt NPD GO	RAB7_PENCL	Ras-related protein Rab7	0.14	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				206
P11234 UniProt NPD GO	RALB_HUMAN	Ras-related protein Ral-B	0.14	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		179551		206
Q9WUP0 UniProt NPD GO	RAMP2_MOUSE	Receptor activity-modifying protein 2 precursor	0.14	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				189
Q9Z2P5 UniProt NPD GO	RIPK3_RAT	Receptor-interacting serine/threonine-protein kinase 3 (EC 2.7.11.1) (RIP-like protein kinase 3) (Re ...	0.14	-	exc	0	Cytoplasm (Probable)				478
P35230 UniProt NPD GO	REG3B_MOUSE	Regenerating islet-derived protein 3 beta precursor (Reg III-beta) (Pancreatitis-associated protein ...	0.14	-	exc	0	Secreted protein. Found in the apical region of pancreatic acinar cells (By similarity)				175
Q6UW15 UniProt NPD GO	REG3G_HUMAN	Regenerating islet-derived protein 3 gamma precursor (Reg III-gamma) (Pancreatitis-associated protei ...	0.14	-	exc	0	Secreted protein		609933		175
P93788 UniProt NPD GO	REMO_SOLTU	Remorin (pp34)	0.14	-	nuc	0	Cell membrane; peripheral membrane protein	plasma membrane [IDA]			198
Q99J62 UniProt NPD GO	RFC4_MOUSE	Replication factor C subunit 4	0.14	-	cyt	0	Nucleus (Probable)				364
P26754 UniProt NPD GO	RFA2_YEAST	Replication factor-A protein 2 (RF-A) (DNA-binding protein BUF1) (Replication protein A 36 kDa subun ...	0.14	-	nuc	0	Nucleus	chromosome, telomeric region [IMP] DNA replication factor A complex [TAS]			273
O19179 UniProt NPD GO	GUC2D_CANFA	Retinal guanylyl cyclase 1 precursor (EC 4.6.1.2) (Guanylate cyclase 2D, retinal) (RETGC-1) (Rod out ...	0.14	-	end	2 *	Membrane; single-pass type I membrane protein				1109
P23820 UniProt NPD GO	REIS_TODPA	Retinochrome (Retinal photoisomerase)	0.14	-	end	7 *	Integral membrane protein. Myeloid membrane				301
P11367 UniProt NPD GO	POL3_MOUSE	Retrovirus-related Pol polyprotein (Endonuclease) (Fragment)	0.14	-	cyt	0					390
P58811 UniProt NPD GO	CXR_CONTU	Rho-conotoxin TIA (Rho-TIA)	0.14	-		0	Secreted protein			1IEN	19
Q8SPZ4 UniProt NPD GO	RNAS8_SAGOE	Ribonuclease 8 precursor (EC 3.1.27.-) (RNase 8)	0.14	-	exc	0	Secreted protein (Probable)				155
O46528 UniProt NPD GO	RNAS6_AOTTR	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6)	0.14	-	exc	0	Secreted protein				150
P15466 UniProt NPD GO	RNL1_PIG	Ribonuclease PL1 (EC 3.1.27.5) (Fragment)	0.14	-	mit	0	Lysosome (Probable)				34
Q5AKB1 UniProt NPD GO	RNY1B_CANAL	Ribonuclease T2-like 1-B precursor (EC 3.1.27.1) (RNase T2-like B)	0.14	-	exc	0	Secreted protein (By similarity)				413
P07849 UniProt NPD GO	RNAS1_BOSTR	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.14	-	nuc	0	Secreted protein				124
P19640 UniProt NPD GO	RNAS1_ODOVI	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A) (Fragment)	0.14	-	nuc	0	Secreted protein				30
P60154 UniProt NPD GO	RNAS9_MOUSE	Ribonuclease-like protein 9 precursor	0.14	-	exc	0	Secreted protein (Probable)				184
P79733 UniProt NPD GO	RIR2_BRARE	Ribonucleoside-diphosphate reductase M2 subunit (EC 1.17.4.1) (Ribonucleotide reductase small subuni ...	0.14	-	cyt	1	Cytoplasm				386
Q42583 UniProt NPD GO	KPRS2_ARATH	Ribose-phosphate pyrophosphokinase 2 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 2) (PRS I ...	0.14	-	mit	0					400
P38689 UniProt NPD GO	KPR3_YEAST	Ribose-phosphate pyrophosphokinase 3 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 3)	0.14	-	cyt	0		cytoplasm [IDA]			320
Q08052 UniProt NPD GO	RBS_PLECA	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.14	-	cyt	0	Plastid; chloroplast				139
P16136 UniProt NPD GO	RBS3_ACEME	Ribulose bisphosphate carboxylase small chain 3, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.14	-	cyt	0	Plastid; chloroplast				182
Q02980 UniProt NPD GO	RBS_MALSP	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.14	-	cyt	0	Plastid; chloroplast				183
Q40073 UniProt NPD GO	RCAA_HORVU	Ribulose bisphosphate carboxylase/oxygenase activase A, chloroplast precursor (RuBisCO activase A) ( ...	0.14	-	mit	0	Plastid; chloroplast; chloroplast stroma				464
P21238 UniProt NPD GO	RUBA_ARATH	RuBisCO large subunit-binding protein subunit alpha, chloroplast precursor (60 kDa chaperonin subuni ...	0.14	-	mit	0	Plastid; chloroplast				586
Q06151 UniProt NPD GO	DCPS_YEAST	Scavenger mRNA decapping enzyme DcpS (EC 3.-.-.-) (DCS-1) (Hint-related 7meGMP-directed hydrolase 1) ...	0.14	-	cyt	0	Cytoplasm. Predominantly	cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			350
O09126 UniProt NPD GO	SEM4D_MOUSE	Semaphorin-4D precursor (Semaphorin J) (Sema J) (Semaphorin C-like 2) (M-Sema G)	0.14	-	end	1 *	Membrane; single-pass type I membrane protein				861
Q29539 UniProt NPD GO	RNS_CEPSI	Seminal ribonuclease (EC 3.1.27.5) (Seminal RNase) (Fragment)	0.14	-	nuc	0	Secreted protein				103
Q09098 UniProt NPD GO	SVS7_MOUSE	Seminal vesicle protein 7 precursor (SVS VII) (Caltrin) (Calcium transport inhibitor)	0.14	-	exc	1 *	Secreted protein				99
Q12884 UniProt NPD GO	SEPR_HUMAN	Seprase (EC 3.4.21.-) (Fibroblast activation protein alpha) (Integral membrane serine protease) (170 ...	0.14	-	exc	1 *	Cell membrane; single-pass type II membrane protein. Found in cell surface lamellipodia, invadopodia ...	integral to membrane [NAS] lamellipodium [IDA]	600403	1Z68	760
Q8N165 UniProt NPD GO	PDK1L_HUMAN	Serine/threonine-protein kinase PDIK1L (EC 2.7.11.1) (PDLIM1-interacting kinase 1-like)	0.14	-	nuc	0	Nucleus				341
Q5RER6 UniProt NPD GO	PDK1L_PONPY	Serine/threonine-protein kinase PDIK1L (EC 2.7.11.1) (PDLIM1-interacting kinase 1-like)	0.14	-	nuc	0	Nucleus (By similarity)				340
P10741 UniProt NPD GO	MOS_CHICK	Serine/threonine-protein kinase mos (EC 2.7.11.1) (Oocyte maturation factor mos)	0.14	-	cyt	0					349
Q9Y5P8 UniProt NPD GO	2ACC_HUMAN	Serine/threonine-protein phosphatase 2A 48 kDa regulatory subunit B (PP2A, subunit B, PR48 isoform)	0.14	-	cyt	0	Nucleus	nucleus [TAS] protein phosphatase type 2A complex [ISS]			414
P48483 UniProt NPD GO	PP13_ARATH	Serine/threonine-protein phosphatase PP1 isozyme 3 (EC 3.1.3.16)	0.14	-	cyt	0					322
P23696 UniProt NPD GO	PP2A_DROME	Serine/threonine-protein phosphatase PP2A (EC 3.1.3.16) (Protein microtubule star)	0.14	-	cyt	0					309
P48580 UniProt NPD GO	PP2A1_NEUCR	Serine/threonine-protein phosphatase PP2A catalytic subunit (EC 3.1.3.16)	0.14	-	cyt	0					327
Q06009 UniProt NPD GO	PP2A_MEDSA	Serine/threonine-protein phosphatase PP2A catalytic subunit (EC 3.1.3.16)	0.14	-	nuc	0					313
Q9XGH7 UniProt NPD GO	PP2A_TOBAC	Serine/threonine-protein phosphatase PP2A catalytic subunit (EC 3.1.3.16)	0.14	-	nuc	0	Cytoplasm (By similarity)				312
P23594 UniProt NPD GO	PP2A1_YEAST	Serine/threonine-protein phosphatase PP2A-1 catalytic subunit (EC 3.1.3.16)	0.14	-	cyt	0		protein phosphatase type 2A complex [TAS]			369
Q07099 UniProt NPD GO	PP2A2_ARATH	Serine/threonine-protein phosphatase PP2A-2 catalytic subunit (EC 3.1.3.16)	0.14	-	cyt	0	Cytoplasm				306
O04860 UniProt NPD GO	PP2A5_TOBAC	Serine/threonine-protein phosphatase PP2A-5 catalytic subunit (EC 3.1.3.16)	0.14	-	nuc	0	Cytoplasm (By similarity)				314
Q29495 UniProt NPD GO	SNAT_SHEEP	Serotonin N-acetyltransferase (EC 2.3.1.87) (Aralkylamine N-acetyltransferase) (AA-NAT) (Serotonin a ...	0.14	-	mit	0				1L0C	207

You are viewing entries 59001 to 59050 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.