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
Q4UB16 UniProt NPD GO	RAB1_THEAN	Ras-related protein Rab-1 (Small GTP-binding protein rab1)	0.03	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				220
P61026 UniProt NPD GO	RAB10_HUMAN	Ras-related protein Rab-10	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				200
P61027 UniProt NPD GO	RAB10_MOUSE	Ras-related protein Rab-10	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	Golgi apparatus [IDA]			200
Q9NP72 UniProt NPD GO	RAB18_HUMAN	Ras-related protein Rab-18	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		602207	1X3S	206
Q5R5H5 UniProt NPD GO	RAB18_PONPY	Ras-related protein Rab-18	0.03	-	cyt	0					206
P51154 UniProt NPD GO	RB22A_CANFA	Ras-related protein Rab-22A (Rab-22)	0.03	-	cyt	0	Endosome; endosomal membrane; lipid-anchor. Cell membrane; lipid-anchor				194
Q9WTL2 UniProt NPD GO	RAB25_MOUSE	Ras-related protein Rab-25	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
P25228 UniProt NPD GO	RAB3_DROME	Ras-related protein Rab-3	0.03	-	nuc	0	Synaptic vesicles	synaptic vesicle [NAS]			220
P97950 UniProt NPD GO	RB33A_MOUSE	Ras-related protein Rab-33A (Small GTP-binding protein S10)	0.03	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				237
Q8QZZ8 UniProt NPD GO	RAB38_MOUSE	Ras-related protein Rab-38	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				211
P51151 UniProt NPD GO	RAB9A_HUMAN	Ras-related protein Rab-9A (Rab-9)	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	late endosome [IDA] lysosome [IDA]	300284	1WMS	201
P61225 UniProt NPD GO	RAP2B_HUMAN	Ras-related protein Rap-2b precursor	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		179541		183
P61226 UniProt NPD GO	RAP2B_MOUSE	Ras-related protein Rap-2b precursor	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				183
P61227 UniProt NPD GO	RAP2B_RAT	Ras-related protein Rap-2b precursor	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				183
O42819 UniProt NPD GO	SEC4_CANGA	Ras-related protein SEC4	0.03	-	cyt	0	Secretory vesicle; secretory vesicle membrane; lipid-anchor; cytoplasmic side (By similarity). Cell ...				215
Q9JJ74 UniProt NPD GO	RAMP1_RAT	Receptor activity-modifying protein 1 precursor	0.03	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				148
Q8ISF8 UniProt NPD GO	RFP_PARAC	Red fluorescent protein eqFP611 (GFP-like chromoprotein)	0.03	-	cyt	0				1UIS	231
P87367 UniProt NPD GO	OPSR_ORYLA	Red-sensitive opsin (Red cone photoreceptor pigment) (KFH-R)	0.03	-	end	7	Membrane; multi-pass membrane protein				357
O09037 UniProt NPD GO	REG3A_MOUSE	Regenerating islet-derived protein 3 alpha precursor (Reg III-alpha) (Pancreatitis-associated protei ...	0.03	-	end	0	Secreted protein				175
Q9TTJ5 UniProt NPD GO	RGN_BOVIN	Regucalcin (RC) (Senescence marker protein 30) (SMP-30)	0.03	-	nuc	0	Cytoplasm (By similarity)				299
Q9TTJ6 UniProt NPD GO	RGN_RABIT	Regucalcin (RC) (Senescence marker protein 30) (SMP-30)	0.03	-	cyt	0	Cytoplasm (By similarity)				299
Q7M3C4 UniProt NPD GO	RELX_PHODA	Relaxin B chain	0.03	-	cyt	0	Secreted protein				31
P01349 UniProt NPD GO	RELX_ODOTA	Relaxin [Contains: Relaxin B chain; Relaxin A chain] (Fragments)	0.03	-	mit	0	Secreted protein				44
Q61983 UniProt NPD GO	NPT1_MOUSE	Renal sodium-dependent phosphate transport protein 1 (Sodium/phosphate cotransporter 1) (Na(+)/PI co ...	0.03	-	end	10 *	Membrane; multi-pass membrane protein				465
P11760 UniProt NPD GO	SAP2_ARBPU	Resact (Sperm-activating peptide) (SAP-IIA)	0.03	-		0					14
Q9HD89 UniProt NPD GO	RSN_HUMAN	Resistin precursor (Cysteine-rich secreted protein FIZZ3) (Adipose tissue-specific secretory factor) ...	0.03	-	exc	0	Secreted protein	extracellular region [NAS]	605565	1LV6	108
Q9EP95 UniProt NPD GO	RSNA_MOUSE	Resistin-like alpha precursor (RELMalpha) (Cysteine-rich secreted protein FIZZ1) (Parasite-induced m ...	0.03	-	nuc	0	Secreted protein	extracellular region [IDA]			111
Q99P86 UniProt NPD GO	RSNB_MOUSE	Resistin-like beta precursor (RELMbeta) (Cysteine-rich secreted protein FIZZ2) (Cysteine-rich secret ...	0.03	-	exc	0	Secreted protein	extracellular region [IDA]		1RH7	105
O95197 UniProt NPD GO	RTN3_HUMAN	Reticulon-3 (Neuroendocrine-specific protein-like 2) (NSP-like protein II) (NSPLII)	0.03	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	extracellular space [TAS]	604249		236
Q8MI17 UniProt NPD GO	AL1A1_RABIT	Retinal dehydrogenase 1 (EC 1.2.1.36) (RalDH1) (RALDH 1) (Aldehyde dehydrogenase family 1 member A1) ...	0.03	-	cyt	0	Cytoplasm (By similarity)				496
Q9YI25 UniProt NPD GO	RPE65_AMBTI	Retinal pigment epithelium-specific 65 kDa protein	0.03	-	mit	0					532
O88350 UniProt NPD GO	RBBP9_RAT	Retinoblastoma-binding protein 9 (RBBP-9) (B5T overexpressed gene protein) (Bog protein)	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				186
Q9UL19 UniProt NPD GO	TIG3_HUMAN	Retinoic acid receptor responder protein 3 (Tazarotene-induced gene 3 protein) (RAR-responsive prote ...	0.03	-	cyt	1			605092		164
Q920A6 UniProt NPD GO	RISC_RAT	Retinoid-inducible serine carboxypeptidase precursor (EC 3.4.16.-) (Serine carboxypeptidase 1)	0.03	-	exc	1 *	Secreted protein (Potential)	cytosol [IDA]			452
Q9QYF1 UniProt NPD GO	RDH11_MOUSE	Retinol dehydrogenase 11 (EC 1.1.1.-) (Retinal reductase 1) (RalR1) (Prostate short-chain dehydrogen ...	0.03	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	intracellular [ISS]			316
Q8NBN7 UniProt NPD GO	RDH13_HUMAN	Retinol dehydrogenase 13 (EC 1.1.1.-)	0.03	-	exc	0					331
Q00001 UniProt NPD GO	RHGA_ASPAC	Rhamnogalacturonase A precursor (EC 3.2.1.-) (RGase A) (RHG A)	0.03	-	end	0				1RMG	440
P06026 UniProt NPD GO	CARP_RHICH	Rhizopuspepsin precursor (EC 3.4.23.21)	0.03	-	cyt	0				6APR	393
P80237 UniProt NPD GO	GDIR_CAVPO	Rho GDP-dissociation inhibitor 1 (Rho GDI 1) (Rho-GDI alpha) (Fragments)	0.03	-	cyt	0	Cytoplasm				111
Q61599 UniProt NPD GO	GDIS_MOUSE	Rho GDP-dissociation inhibitor 2 (Rho GDI 2) (Rho-GDI beta) (D4)	0.03	-	cyt	0	Cytoplasm				199
Q62160 UniProt NPD GO	GDIT_MOUSE	Rho GDP-dissociation inhibitor 3 (Rho GDI 3) (Rho-GDI gamma) (Rho-GDI2)	0.03	-	mit	0	Cytoplasm (Potential)				225
P17081 UniProt NPD GO	RHOQ_HUMAN	Rho-related GTP-binding protein RhoQ (Ras-related GTP-binding protein TC10)	0.03	-	cyt	0	Cytoplasm. Cell membrane; lipid-anchor	plasma membrane [NAS]	605857	2ATX	205
Q8R527 UniProt NPD GO	RHOQ_MOUSE	Rho-related GTP-binding protein RhoQ (Ras-related GTP-binding protein TC10)	0.03	-	cyt	0	Cytoplasm (By similarity). Cell membrane; lipid-anchor (By similarity)				205
Q9JJL4 UniProt NPD GO	RHOQ_RAT	Rho-related GTP-binding protein RhoQ (Ras-related GTP-binding protein TC10)	0.03	-	cyt	0	Cytoplasm (By similarity). Cell membrane; lipid-anchor (By similarity)				205
Q874X5 UniProt NPD GO	RBD2_PODAN	Rhomboid protein 2 (EC 3.4.21.-)	0.03	-	end	6 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity). Golgi apparatus; cis-G ...				289
O74866 UniProt NPD GO	RIFK_SCHPO	Riboflavin kinase (EC 2.7.1.26) (ATP:riboflavin 5'-phosphotransferase) (Flavokinase)	0.03	-	cyt	0				1N08	163
Q5U209 UniProt NPD GO	RNHL_RAT	Ribonuclease HI large subunit (EC 3.1.26.4) (RNase HI large subunit) (Ribonuclease H2) (RNase H2)	0.03	-	cyt	0					301
Q7M456 UniProt NPD GO	RNOY_CRAGI	Ribonuclease Oy (EC 3.1.27.-) (RNase Oy)	0.03	-	cyt	0	Secreted protein				213
P36603 UniProt NPD GO	RIR2_SCHPO	Ribonucleoside-diphosphate reductase small chain (EC 1.17.4.1) (Ribonucleotide reductase small subun ...	0.03	-	cyt	0	Nucleus. Cytoplasm. Localization to the cytoplasm is CSN- and checkpoint-dependent and is required f ...	cytoplasm [IDA] nucleus [IGI] ribonucleoside-diphosphate reductase complex [TAS]			391
O15910 UniProt NPD GO	RIR2_TRYBB	Ribonucleoside-diphosphate reductase small chain (EC 1.17.4.1) (Ribonucleotide reductase small subun ...	0.03	-	nuc	1					337

You are viewing entries 81551 to 81600 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.