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
Q86XN8 UniProt NPD GO	RKHD1_HUMAN	RING finger and KH domain-containing protein 1	0.26	-	nuc	0					485
Q84TF5 UniProt NPD GO	RHA4A_ARATH	RING-H2 zinc finger protein RHA4a	0.26	-	nuc	1 *					174
P29826 UniProt NPD GO	HB2B_RAT	RT1 class II histocompatibility antigen, B-1 beta chain precursor (RT1.B-beta(1))	0.26	-	end	1	Membrane; single-pass type I membrane protein (Potential)				263
Q8HXX7 UniProt NPD GO	GDIA_MACFA	Rab GDP dissociation inhibitor alpha (Rab GDI alpha) (Guanosine diphosphate dissociation inhibitor 1 ...	0.26	-	nuc	0	Cytoplasm (By similarity)				447
P50398 UniProt NPD GO	GDIA_RAT	Rab GDP dissociation inhibitor alpha (Rab GDI alpha) (Guanosine diphosphate dissociation inhibitor 1 ...	0.26	-	nuc	0	Cytoplasm	membrane fraction [IDA]			447
P21856 UniProt NPD GO	GDIA_BOVIN	Rab GDP dissociation inhibitor alpha (Rab GDI alpha) (Guanosine diphosphate dissociation inhibitor 1 ...	0.26	-	nuc	0				1LV0	447
P39958 UniProt NPD GO	GDI1_YEAST	Rab GDP-dissociation inhibitor (Rab GDI) (Secretory pathway GDP dissociation inhibitor)	0.26	-	nuc	0	Cytoplasm	membrane fraction [IDA] soluble fraction [IDA]		2BCG	451
P34022 UniProt NPD GO	RANG_MOUSE	Ran-specific GTPase-activating protein (Ran-binding protein 1) (RANBP1) (HpaII tiny fragments locus ...	0.26	+	nuc	0		centrosome [IDA] cytoplasm [IDA]			203
P10833 UniProt NPD GO	RRAS_MOUSE	Ras-related protein R-Ras (P23)	0.26	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Inner surface of plasma membrane poss ...				218
Q9BRK0 UniProt NPD GO	REEP2_HUMAN	Receptor expression-enhancing protein 2	0.26	-	nuc	2 *	Membrane; multi-pass membrane protein (By similarity)		609347		252
O45523 UniProt NPD GO	RGS10_CAEEL	Regulator of G-protein signaling rgs-10	0.26	-	cyt	0					270
Q9Z118 UniProt NPD GO	ROD1_RAT	Regulator of differentiation 1 (Rod1)	0.26	-	nuc	0					523
Q9JI58 UniProt NPD GO	RAE1D_MOUSE	Retinoic acid early inducible protein 1 delta precursor (RAE-1delta)	0.26	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [IDA]			249
Q9H1E1 UniProt NPD GO	RNAS7_HUMAN	Ribonuclease 7 precursor (EC 3.1.27.-) (RNase 7) (Skin-derived antimicrobial protein 2) (SAP-2)	0.26	-	exc	1 *	Secreted protein	extracellular region [NAS]			156
Q8L633 UniProt NPD GO	RNZC_ARATH	Ribonuclease Z, chloroplast precursor (EC 3.1.26.11) (RNase Z) (tRNase Z) (tRNA 3 endonuclease) (Zin ...	0.26	-	mit	0	Plastid; chloroplast (Potential)				354
P30374 UniProt NPD GO	RSFR_CHICK	Ribonuclease homolog precursor (EC 3.1.27.-) (RSFR)	0.26	-	exc	1 *	Secreted protein (Potential)				139
P00680 UniProt NPD GO	RNAS1_GALMU	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.26	-	nuc	0	Secreted protein				124
Q8SQ05 UniProt NPD GO	RNAS1_LAGLA	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.26	-	nuc	1 *	Secreted protein (By similarity)				156
Q9WUX6 UniProt NPD GO	RNAS1_URARU	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.26	-	exc	0	Secreted protein				149
P24717 UniProt NPD GO	RNAS1_CRIGR	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A) (Fragment)	0.26	-	nuc	0	Secreted protein				130
Q863J9 UniProt NPD GO	RNAS9_HYLSY	Ribonuclease-like protein 9 precursor	0.26	-	exc	0	Secreted protein (Probable)				204
Q7YRH3 UniProt NPD GO	RNAS9_MACMU	Ribonuclease-like protein 9 precursor	0.26	-	exc	0	Secreted protein (Probable)				204
P28005 UniProt NPD GO	POP5_YEAST	Ribonucleases P/MRP protein subunit POP5 (EC 3.1.26.5) (RNases P/MRP 19.6 kDa subunit) (RNA-processi ...	0.26	-	nuc	0	Nucleus (Potential)	nucleolar ribonuclease P complex [IDA] ribonuclease MRP complex [IDA]			173
P41831 UniProt NPD GO	KPRS_SCHPO	Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase)	0.26	-	cyt	0					409
Q93Z66 UniProt NPD GO	KPRS3_ARATH	Ribose-phosphate pyrophosphokinase 3 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 3)	0.26	-	mit	0					411
Q6CTR7 UniProt NPD GO	RRF1_KLULA	Ribosomal recycling factor, mitochondrial precursor	0.26	-	nuc	0	Mitochondrion (By similarity)				241
O22024 UniProt NPD GO	RBS_CYAME	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.26	-	cyt	0	Plastid; chloroplast				138
P23756 UniProt NPD GO	RBS_GALSU	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.26	-	cyt	0	Plastid; chloroplast				138
P02879 UniProt NPD GO	RICI_RICCO	Ricin precursor [Contains: Ricin A chain (EC 3.2.2.22) (rRNA N-glycosidase); Linker peptide; Ricin B ...	0.26	-	mit	1 *				2AAI	576
P23440 UniProt NPD GO	PDE6B_MOUSE	Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta precursor (EC 3.1.4.35) (GMP-PDE beta) ...	0.26	-	cyt	0	Membrane; lipid-anchor				856
Q5M877 UniProt NPD GO	SPSB2_RAT	SPRY domain-containing SOCS box protein 2 (SSB-2)	0.26	-	mit	0	Cytoplasm (Probable)				264
P50623 UniProt NPD GO	UBC9_YEAST	SUMO-conjugating enzyme UBC9 (EC 6.3.2.19) (Ubiquitin-conjugating enzyme E2-18 kDa) (Ubiquitin-prote ...	0.26	-	nuc	0	Nucleus	nucleus [IDA]			157
Q757G5 UniProt NPD GO	SWC7_ASHGO	SWR1-complex protein 7	0.26	-	cyt	0	Nucleus (By similarity)				127
P32647 UniProt NPD GO	SECR_RABIT	Secretin	0.26	-	nuc	0	Secreted protein				27
Q9ERN0 UniProt NPD GO	SCAM2_MOUSE	Secretory carrier-associated membrane protein 2 (Secretory carrier membrane protein 2)	0.26	-	end	4	Membrane; multi-pass membrane protein (By similarity)				329
Q6S9C4 UniProt NPD GO	SELK_CHILA	Selenoprotein K	0.26	-	nuc	1 *					94
Q8VHC3 UniProt NPD GO	SELM_MOUSE	Selenoprotein M precursor (Protein SelM)	0.26	-	nuc	0	Cytoplasm; perinuclear region. Localized to perinuclear structures corresponding to Golgi and endopl ...	endoplasmic reticulum [IDA] Golgi apparatus [IDA]		2A2P	145
Q24323 UniProt NPD GO	SEM2A_DROME	Semaphorin-2A precursor (Semaphorin-II) (Sema II)	0.26	-	exc	0	Secreted protein (Potential)				724
Q9D2Z4 UniProt NPD GO	SENP8_MOUSE	Sentrin-specific protease 8 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP8) (NEDD8-specific pro ...	0.26	-	cyt	0					221
P40970 UniProt NPD GO	LCB2_YEAST	Serine palmitoyltransferase 2 (EC 2.3.1.50) (Long chain base biosynthesis protein 2) (SPT 2)	0.26	-	nuc	0	Membrane; multi-pass membrane protein (Potential)	membrane fraction [IDA] microsome [IPI] serine C-palmitoyltransferase complex [IMP]			561
Q75V63 UniProt NPD GO	SAPK3_ORYSA	Serine/threonine-protein kinase SAPK3 (EC 2.7.11.1) (Osmotic stress/abscisic acid-activated protein ...	0.26	-	cyt	0					334
P37023 UniProt NPD GO	ACVL1_HUMAN	Serine/threonine-protein kinase receptor R3 precursor (EC 2.7.11.30) (SKR3) (Activin receptor-like k ...	0.26	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	601284		503
O04857 UniProt NPD GO	PP12_TOBAC	Serine/threonine-protein phosphatase PP1 isozyme 2 (EC 3.1.3.16)	0.26	-	cyt	0					310
Q8WMS6 UniProt NPD GO	PP1A_CANFA	Serine/threonine-protein phosphatase PP1-alpha catalytic subunit (EC 3.1.3.16) (PP-1A)	0.26	-	cyt	0	Cytoplasm (By similarity)				330
Q05547 UniProt NPD GO	PP13_DROME	Serine/threonine-protein phosphatase alpha-3 isoform (EC 3.1.3.16)	0.26	-	cyt	0					302
P34551 UniProt NPD GO	SRX10_CAEEL	Serpentine receptor class XA 10 (Protein srxa-10)	0.26	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				319
O17844 UniProt NPD GO	SRA20_CAEEL	Serpentine receptor class alpha-20 (Protein sra-20)	0.26	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				339
Q9D7P9 UniProt NPD GO	SPB12_MOUSE	Serpin B12	0.26	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			423
O74453 UniProt NPD GO	SKB15_SCHPO	Shk1 kinase-binding protein 15	0.26	-	cyt	0		nucleus [IDA]			341
P01437 UniProt NPD GO	NXS1_HYDLA	Short neurotoxin 1 (Neurotoxin A)	0.26	-	nuc	0	Secreted protein				60

You are viewing entries 44651 to 44700 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.