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
P46060 UniProt NPD GO	RGP1_HUMAN	Ran GTPase-activating protein 1	0.13	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS] nuclear pore [TAS] soluble fraction [TAS]	602362	2GRR	587
P83663 UniProt NPD GO	RACYE_RANES	Ranacyclin-E	0.13	-		0	Secreted protein	extracellular region [IDA]			17
P52306 UniProt NPD GO	GDS1_HUMAN	Rap1 GTPase-GDP dissociation stimulator 1 (SMG P21 stimulatory GDP/GTP exchange protein) (SMG GDS pr ...	0.13	-	nuc	0			179502		607
O42785 UniProt NPD GO	RASL_COLTR	Ras-like protein (Ct-Ras)	0.13	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				214
P32252 UniProt NPD GO	RASB_DICDI	Ras-like protein rasB	0.13	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				197
P31583 UniProt NPD GO	RHN1_NICPL	Ras-related protein RHN1	0.13	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				200
P51152 UniProt NPD GO	RAB12_CANFA	Ras-related protein Rab-12 (Fragment)	0.13	-	cyt	0	Golgi apparatus; Golgi membrane; lipid-anchor				208
P55745 UniProt NPD GO	RAB21_CANFA	Ras-related protein Rab-21	0.13	-	cyt	0	Endosome; endosomal membrane; lipid-anchor. Cell membrane; lipid-anchor				222
Q9UL25 UniProt NPD GO	RAB21_HUMAN	Ras-related protein Rab-21	0.13	-	cyt	0	Golgi apparatus; Golgi membrane; lipid-anchor (By similarity)			1Z0I	224
Q504M8 UniProt NPD GO	RAB26_MOUSE	Ras-related protein Rab-26	0.13	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				260
Q9ERI2 UniProt NPD GO	RB27A_MOUSE	Ras-related protein Rab-27A	0.13	-	cyt	0	Membrane; lipid-anchor				221
Q8HZJ5 UniProt NPD GO	RB27B_BOVIN	Ras-related protein Rab-27B	0.13	-	cyt	0	Membrane; lipid-anchor (By similarity)				217
P63011 UniProt NPD GO	RAB3A_MOUSE	Ras-related protein Rab-3A	0.13	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	synaptic vesicle [IDA]			220
P63012 UniProt NPD GO	RAB3A_RAT	Ras-related protein Rab-3A	0.13	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)			3RAB	220
P20338 UniProt NPD GO	RAB4A_HUMAN	Ras-related protein Rab-4A	0.13	-	cyt	0	Membrane; peripheral membrane protein. Generally associated with membranes. Cytoplasm. Cytoplasmic w ...		179511	2BME	213
Q58DS9 UniProt NPD GO	RAB5C_BOVIN	Ras-related protein Rab-5C	0.13	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side. Endosome; early endosome; early endosome membrane; li ...				216
Q91YQ1 UniProt NPD GO	RAB7L_MOUSE	Ras-related protein Rab-7L1 (Rab-7-like protein 1)	0.13	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				204
P40792 UniProt NPD GO	RAC1_DROME	Ras-related protein Rac1	0.13	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	rhabdomere [IDA]			192
Q9QZL0 UniProt NPD GO	RIPK3_MOUSE	Receptor-interacting serine/threonine-protein kinase 3 (EC 2.7.11.1) (RIP-like protein kinase 3) (Re ...	0.13	-	nuc	0	Cytoplasm (Probable)	intracellular [IDA]			486
Q99279 UniProt NPD GO	CY41_TRYBB	Receptor-type adenylate cyclase GRESAG 4.1 (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase) ...	0.13	-	mit	0	Membrane; multi-pass membrane protein (Potential)			1FX2	1242
P32368 UniProt NPD GO	RSD1_YEAST	Recessive suppressor of secretory defect	0.13	-	cyt	2		integral to endoplasmic reticulum membrane [IDA] integral to Golgi membrane [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			623
O12948 UniProt NPD GO	OPSR_XENLA	Red-sensitive opsin (Red cone photoreceptor pigment)	0.13	-	end	7	Membrane; multi-pass membrane protein				365
O09049 UniProt NPD GO	REG3G_MOUSE	Regenerating islet-derived protein 3 gamma precursor (Reg III-gamma) (Pancreatitis-associated protei ...	0.13	-	exc	0	Secreted protein				174
Q5RC43 UniProt NPD GO	RFA2_PONPY	Replication protein A 32 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 2) (p32)	0.13	-	nuc	0	Nucleus. Also present in PML nuclear bodies. Redistributes to discrete nuclear foci upon DNA damage ...				270
P15927 UniProt NPD GO	RFA2_HUMAN	Replication protein A 32 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 2) (p32) (p34)	0.13	-	nuc	0	Nucleus. Also present in PML nuclear bodies. Redistributes to discrete nuclear foci upon DNA damage	DNA replication factor A complex [TAS]	179836	1Z1D	270
Q8BHL4 UniProt NPD GO	RAI3_MOUSE	Retinoic acid-induced protein 3 (G-protein coupled receptor family C group 5 member A) (Retinoic aci ...	0.13	-	end	7 *	Membrane; multi-pass membrane protein				356
Q03272 UniProt NPD GO	PO14_NASVI	Retrovirus-related Pol polyprotein from type-1 retrotransposable element R1 4 (Retrovirus-related Po ...	0.13	+	cyt	0					392
P25378 UniProt NPD GO	RHEB_YEAST	Rheb-like protein RHB1 (GTP-binding protein RSG1)	0.13	-	cyt	0	Cell membrane; peripheral membrane protein. Cell periphery, adjacent to the plasma membrane	extrinsic to plasma membrane [IGI]			209
P19803 UniProt NPD GO	GDIR_BOVIN	Rho GDP-dissociation inhibitor 1 (Rho GDI 1) (Rho-GDI alpha)	0.13	-	cyt	0	Cytoplasm			1GDF	203
Q8SPN3 UniProt NPD GO	RNS1B_PYGNE	Ribonuclease 1B pancreatic precursor (EC 3.1.27.5) (RNase 1B)	0.13	-	exc	1 *	Secreted protein (By similarity)				156
Q8SPZ7 UniProt NPD GO	RNAS8_MIOTA	Ribonuclease 8 precursor (EC 3.1.27.-) (RNase 8)	0.13	-	nuc	0	Secreted protein (Probable)				154
Q9CQ01 UniProt NPD GO	RNT2_MOUSE	Ribonuclease T2 precursor (EC 3.1.27.-) (Ribonuclease 6)	0.13	-	mit	1 *	Secreted protein (Potential)	mitochondrion [IDA]			259
Q9XG98 UniProt NPD GO	KPRS1_SPIOL	Ribose-phosphate pyrophosphokinase 1 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 1)	0.13	-	mit	0					336
Q5I0R6 UniProt NPD GO	RL22L_XENTR	Ribosomal protein L22-like 1	0.13	-	nuc	0					120
P23029 UniProt NPD GO	RIP2_TRIKI	Ribosome-inactivating protein TAP-29 (EC 3.2.2.22) (rRNA N-glycosidase) (Fragment)	0.13	-	nuc	0					45
P00865 UniProt NPD GO	RBS1_SOYBN	Ribulose bisphosphate carboxylase small chain 1, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.13	-	cyt	0	Plastid; chloroplast				178
P16133 UniProt NPD GO	RBS5_ACECL	Ribulose bisphosphate carboxylase small chain 5, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.13	-	cyt	0	Plastid; chloroplast				184
P16138 UniProt NPD GO	RBS5_ACEME	Ribulose bisphosphate carboxylase small chain 5, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.13	-	mit	0	Plastid; chloroplast				183
P31333 UniProt NPD GO	RBS_GOSHI	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.13	-	mit	0	Plastid; chloroplast				182
P29684 UniProt NPD GO	RBS_HEVBR	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.13	-	mit	0	Plastid; chloroplast				183
Q5KPZ8 UniProt NPD GO	RUVB1_CRYNE	RuvB-like helicase 1 (EC 3.6.1.-)	0.13	-	mit	0	Nucleus (By similarity)				484
Q43820 UniProt NPD GO	DCAM_PEA	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.13	-	cyt	0					353
O09486 UniProt NPD GO	METK_AMOPR	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.13	-	cyt	0	Cytoplasm	cytoplasm [NAS]			426
P79260 UniProt NPD GO	ARRS_PIG	S-arrestin (Retinal S-antigen) (48 kDa protein) (S-AG) (Rod photoreceptor arrestin)	0.13	-	cyt	0					405
Q9WTX5 UniProt NPD GO	SKP1_MOUSE	S-phase kinase-associated protein 1A (Cyclin A/CDK2-associated protein p19) (p19A) (p19skp1)	0.13	-	cyt	0		SCF ubiquitin ligase complex [IDA]			162
Q6PEC4 UniProt NPD GO	SKP1_RAT	S-phase kinase-associated protein 1A (Cyclin A/CDK2-associated protein p19) (p19A) (p19skp1)	0.13	-	cyt	0					162
Q71U00 UniProt NPD GO	SKP1_XENLA	S-phase kinase-associated protein 1A (Cyclin A/CDK2-associated protein p19) (p19A) (p19skp1)	0.13	-	cyt	0					162
P63209 UniProt NPD GO	SKP1_CAVPO	S-phase kinase-associated protein 1A (Cyclin A/CDK2-associated protein p19) (p19A) (p19skp1) (Organ ...	0.13	-	cyt	0					162
P63208 UniProt NPD GO	SKP1_HUMAN	S-phase kinase-associated protein 1A (Cyclin A/CDK2-associated protein p19) (p19A) (p19skp1) (RNA po ...	0.13	-	cyt	0			601434	2AST	162
Q8R5A0 UniProt NPD GO	SMYD2_MOUSE	SET and MYND domain-containing protein 2	0.13	-	cyt	0					433

You are viewing entries 60351 to 60400 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.