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
Q5RDM6 UniProt NPD GO	RAP1B_PONPY	Ras-related protein Rap-1b precursor	0.24	-	cyt	0	Cell membrane (By similarity). Cytoplasm; cytosol (By similarity). May shuttle between plasma membra ...				184
P61223 UniProt NPD GO	RAP1B_BOVIN	Ras-related protein Rap-1b precursor (GTP-binding protein smg p21B)	0.24	-	cyt	0	Cell membrane (By similarity). Cytoplasm; cytosol (By similarity). May shuttle between plasma membra ...	membrane [TAS]			184
P61224 UniProt NPD GO	RAP1B_HUMAN	Ras-related protein Rap-1b precursor (GTP-binding protein smg p21B)	0.24	-	cyt	0	Cell membrane. Cytoplasm; cytosol. May shuttle between plasma membrane and cytosol	membrane [TAS]	179530		184
Q99JI6 UniProt NPD GO	RAP1B_MOUSE	Ras-related protein Rap-1b precursor (GTP-binding protein smg p21B)	0.24	-	cyt	0	Cell membrane (By similarity). Cytoplasm; cytosol (By similarity). May shuttle between plasma membra ...				184
Q62636 UniProt NPD GO	RAP1B_RAT	Ras-related protein Rap-1b precursor (GTP-binding protein smg p21B)	0.24	-	cyt	0	Cell membrane (By similarity). Cytoplasm; cytosol (By similarity). May shuttle between plasma membra ...				184
P25183 UniProt NPD GO	RCC1_XENLA	Regulator of chromosome condensation	0.24	-	nuc	0	Nucleus. Cytoplasm. Becomes dispersed throughout the cytoplasm during mitosis				424
Q8TDU9 UniProt NPD GO	RL3R2_HUMAN	Relaxin-3 receptor 2 (Relaxin family peptide receptor 4) (G-protein coupled receptor 100) (GPCR142)	0.24	+	end	7 *	Membrane; multi-pass membrane protein		609043		374
P40339 UniProt NPD GO	RFC4_YEAST	Replication factor C subunit 4 (Replication factor C4) (Activator 1 37 kDa subunit)	0.24	-	cyt	0	Nucleus (Probable)	DNA replication factor C complex [IDA]		1SXJ	323
O15537 UniProt NPD GO	XLRS1_HUMAN	Retinoschisin precursor (X-linked juvenile retinoschisis protein)	0.24	-	end	0	Secreted protein	extracellular space [TAS]	312700		224
Q15669 UniProt NPD GO	RHOH_HUMAN	Rho-related GTP-binding protein RhoH (GTP-binding protein TTF)	0.24	+	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	cytoplasm [IDA]	602037		191
P24603 UniProt NPD GO	OPSD_LOLFO	Rhodopsin	0.24	-	end	6 *	Membrane; multi-pass membrane protein				452
Q17094 UniProt NPD GO	OPSD_LOLSU	Rhodopsin (Fragment)	0.24	-	end	6 *	Membrane; multi-pass membrane protein				439
O46531 UniProt NPD GO	RNAS6_MIOTA	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6)	0.24	-	exc	1 *	Secreted protein				150
Q9D244 UniProt NPD GO	RNAS6_MOUSE	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6)	0.24	-	nuc	0					153
Q969H6 UniProt NPD GO	POP5_HUMAN	Ribonuclease P/MRP protein subunit POP5 (EC 3.1.26.5) (hPop5)	0.24	-	cyt	0	Nucleus; nucleolus		609992		163
P04007 UniProt NPD GO	RNS2_NICAL	Ribonuclease S-2 precursor (EC 3.1.27.1) (Stylar glycoprotein 2) (S2-RNase)	0.24	-	exc	1 *	Secreted protein; extracellular space				214
Q8HZP9 UniProt NPD GO	RINI_PANTR	Ribonuclease inhibitor (Ribonuclease/angiogenin inhibitor 1)	0.24	-	nuc	0	Cytoplasm (By similarity)				460
P13489 UniProt NPD GO	RINI_HUMAN	Ribonuclease inhibitor (Ribonuclease/angiogenin inhibitor 1) (RAI) (Placental ribonuclease inhibitor ...	0.24	-	nuc	0	Cytoplasm		173320	2BEX	460
P00657 UniProt NPD GO	RNAS1_BUBBU	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.24	-	nuc	0	Secreted protein				124
Q29606 UniProt NPD GO	RNAS1_ORYLE	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A) (Fragment)	0.24	-	nuc	0	Secreted protein				75
Q9WUX3 UniProt NPD GO	RNS1B_RATEX	Ribonuclease pancreatic beta-type precursor (EC 3.1.27.5) (RNase 1 gamma)	0.24	-	exc	0	Secreted protein				152
Q7YRH4 UniProt NPD GO	RNAS9_PONPY	Ribonuclease-like protein 9 precursor	0.24	-	exc	0	Secreted protein (Probable)				204
Q9D6S7 UniProt NPD GO	RRFM_MOUSE	Ribosome recycling factor, mitochondrial precursor	0.24	-	mit	0	Mitochondrion (By similarity)			1WIH	262
P16132 UniProt NPD GO	RBS4_ACECL	Ribulose bisphosphate carboxylase small chain 4, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.24	-	mit	0	Plastid; chloroplast				182
P11541 UniProt NPD GO	PDE6A_BOVIN	Rod cGMP-specific 3',5'-cyclic phosphodiesterase alpha-subunit (EC 3.1.4.35) (GMP-PDE alpha) (PDE V- ...	0.24	+	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				858
P09593 UniProt NPD GO	SANT_PLAFV	S-antigen protein precursor	0.24	-	nuc	0	Parasitophorous vacuole				375
O75880 UniProt NPD GO	SCO1_HUMAN	SCO1 protein homolog, mitochondrial precursor	0.24	-	mit	0	Mitochondrion	mitochondrion [TAS]	220110	2GVP	301
Q9Z200 UniProt NPD GO	APS_RAT	SH2 and PH domain-containing adapter protein APS (Adapter protein with pleckstrin homology and Src h ...	0.24	-	nuc	0	Cytoplasm. Membrane. Recruited to the membrane by binding to an autophosphorylated receptor after re ...			1YVH	621
Q8CIF6 UniProt NPD GO	SIDT2_MOUSE	SID1 transmembrane family member 2 precursor	0.24	-	end	9	Membrane; multi-pass membrane protein (Potential)				832
P40668 UniProt NPD GO	CH04_CHICK	SRY-related protein CH4 (Fragment)	0.24	-	nuc	0	Nucleus (Potential)				54
P30933 UniProt NPD GO	SVS5_MOUSE	Seminal vesicle secretory protein 5 precursor (Seminal vesicle secretory protein V) (SVS V) (SVS pro ...	0.24	-	exc	0	Secreted protein; extracellular space				122
P83111 UniProt NPD GO	LACTB_HUMAN	Serine beta-lactamase-like protein LACTB	0.24	-	mit	0			608440		547
O13425 UniProt NPD GO	GLYM_CANAL	Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine hy ...	0.24	-	mit	0	Mitochondrion				493
O43464 UniProt NPD GO	HTRA2_HUMAN	Serine protease HTRA2, mitochondrial precursor (EC 3.4.21.-) (High temperature requirement protein A ...	0.24	-	mit	1	Mitochondrion; mitochondrial intermembrane space. Predominantly present in the intermembrane space. ...	endoplasmic reticulum [NAS] endoplasmic reticulum membrane [TAS] mitochondrial intermembrane space [IDA] nucleus [TAS]	606441	1LCY	458
O77417 UniProt NPD GO	ASP2_ANISI	Serine protease inhibitor 2 precursor (ASPI-2)	0.24	-	exc	0	Secreted protein (By similarity)				77
Q6IE49 UniProt NPD GO	IPK2_RAT	Serine protease inhibitor Kazal-type 2 precursor	0.24	-	exc	0	Secreted protein (By similarity)				86
Q9LVE2 UniProt NPD GO	2A5Z_ARATH	Serine/threonine protein phosphatase 2A 59 kDa regulatory subunit B' zeta isoform (PP2A, B' subunit, ...	0.24	-	mit	0					518
Q9UHD2 UniProt NPD GO	TBK1_HUMAN	Serine/threonine-protein kinase TBK1 (EC 2.7.11.1) (TANK-binding kinase 1) (T2K) (NF-kappa-B-activat ...	0.24	-	cyt	0	Cytoplasm		604834		729
Q5K9U4 UniProt NPD GO	PTPA1_CRYNE	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.24	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				362
O62420 UniProt NPD GO	SRA39_CAEEL	Serpentine receptor class alpha-39 (Protein sra-39)	0.24	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				375
O01609 UniProt NPD GO	SRD33_CAEEL	Serpentine receptor class delta-33 (Protein srd-33)	0.24	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				342
Q19507 UniProt NPD GO	SRD47_CAEEL	Serpentine receptor class delta-47 (Protein srd-47)	0.24	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				317
Q09572 UniProt NPD GO	SRD55_CAEEL	Serpentine receptor class delta-55 (Protein srd-55)	0.24	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				334
O45300 UniProt NPD GO	SRE13_CAEEL	Serpentine receptor class epsilon-13 (Protein sre-13)	0.24	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				359
O45306 UniProt NPD GO	SRE21_CAEEL	Serpentine receptor class epsilon-21 (Protein sre-21)	0.24	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				365
O62269 UniProt NPD GO	SRE29_CAEEL	Serpentine receptor class epsilon-29 (Protein sre-29)	0.24	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				356
O61892 UniProt NPD GO	SRG31_CAEEL	Serpentine receptor class gamma-31 (Protein srg-31)	0.24	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				312
Q9D695 UniProt NPD GO	SPB7_MOUSE	Serpin B7 (Megsin)	0.24	-	mit	0	Cytoplasm (By similarity)				380
O75830 UniProt NPD GO	SPI2_HUMAN	Serpin I2 precursor (Myoepithelium-derived serine protease inhibitor) (Pancpin) (Protease inhibitor ...	0.24	-	nuc	0	Secreted protein (Probable)		605587		405
P21847 UniProt NPD GO	ALBU_RANCA	Serum albumin (Fragment)	0.24	-	cyt	0	Secreted protein				382

You are viewing entries 46801 to 46850 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.