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
Q91WD0 UniProt NPD GO	GP108_MOUSE	Protein GPR108 precursor (Lung seven transmembrane receptor 2)	0.15	-	end	7	Membrane; multi-pass membrane protein				569
O76095 UniProt NPD GO	JTB_HUMAN	Protein JTB precursor (Jumping translocation breakpoint protein) (Prostate androgen-regulated protei ...	0.15	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS] membrane fraction [TAS]	604671		146
Q6ZQE4 UniProt NPD GO	K0286_MOUSE	Protein KIAA0286	0.15	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				437
Q6GQL1 UniProt NPD GO	NDRG3_XENLA	Protein NDRG3	0.15	-	cyt	0					375
Q08202 UniProt NPD GO	OPI10_YEAST	Protein OPI10 (Overproducer of inositol protein 10)	0.15	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			246
Q5ACR4 UniProt NPD GO	OS9_CANAL	Protein OS-9 homolog precursor	0.15	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				258
Q99220 UniProt NPD GO	OS9_YEAST	Protein OS-9 homolog precursor	0.15	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side	endoplasmic reticulum [TAS]			542
Q5KQ32 UniProt NPD GO	PNS1_CRYNE	Protein PNS1	0.15	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				551
Q9UHT9 UniProt NPD GO	P1768_HUMAN	Protein PRO1768	0.15	-	nuc	0					52
P36110 UniProt NPD GO	PRY2_YEAST	Protein PRY2 precursor (Pathogen related in Sc 2)	0.15	-	exc	0		extracellular region [IDA] vacuole (sensu Fungi) [IDA]			329
P38927 UniProt NPD GO	REV7_YEAST	Protein REV7	0.15	-	mit	0		mitochondrion [IDA] zeta DNA polymerase complex [IDA]			245
P05942 UniProt NPD GO	S10A4_RAT	Protein S100-A4 (S100 calcium-binding protein A4) (Metastasin) (Placental calcium-binding protein) ( ...	0.15	-	nuc	0		neuron projection [IDA]			101
P63084 UniProt NPD GO	S10A5_MOUSE	Protein S100-A5 (S100 calcium-binding protein A5) (Protein S-100D)	0.15	-	nuc	0					93
P63083 UniProt NPD GO	S10A5_RAT	Protein S100-A5 (S100 calcium-binding protein A5) (Protein S-100D)	0.15	-	nuc	0					93
P31151 UniProt NPD GO	S10A7_HUMAN	Protein S100-A7 (S100 calcium-binding protein A7) (Psoriasin)	0.15	-	nuc	0	Cytoplasm. Secreted protein. Also secreted by a non-classical secretory pathway	cytoplasm [IDA] cytosol [IDA] endoplasmic reticulum [IDA] extracellular region [IDA] focal adhesion [NAS] nucleus [IDA]	600353	3PSR	100
Q8WU66 UniProt NPD GO	TSEAR_HUMAN	Protein TSPEAR precursor (TSP-EAR)	0.15	-	end	0	Secreted protein (Probable)				669
Q3KPT3 UniProt NPD GO	TSSC1_XENLA	Protein TSSC1	0.15	-	cyt	0					387
P60985 UniProt NPD GO	U467_HUMAN	Protein UNQ467/PRO826 precursor	0.15	-	exc	0	Secreted protein (Potential)				99
Q8NJR5 UniProt NPD GO	URE2_CANGA	Protein URE2	0.15	-	cyt	0					355
P28139 UniProt NPD GO	WNT1_PITME	Protein Wnt-1 (Fragment)	0.15	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				126
P28114 UniProt NPD GO	WNT3_EPTST	Protein Wnt-3 (Fragment)	0.15	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P28125 UniProt NPD GO	WNT3A_MELGA	Protein Wnt-3a (Fragment)	0.15	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P28140 UniProt NPD GO	WNT3A_PITME	Protein Wnt-3a (Fragment)	0.15	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
Q06442 UniProt NPD GO	WNT5A_AMBME	Protein Wnt-5a precursor	0.15	-	exc	0	Secreted protein; extracellular space; extracellular matrix				359
P22725 UniProt NPD GO	WNT5A_MOUSE	Protein Wnt-5a precursor	0.15	-	exc	0	Secreted protein; extracellular space; extracellular matrix				379
Q1KYK4 UniProt NPD GO	WNT7A_AOTTR	Protein Wnt-7a precursor	0.15	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				349
Q1KYK6 UniProt NPD GO	WNT7A_CALJA	Protein Wnt-7a precursor	0.15	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				349
Q1KYL3 UniProt NPD GO	WNT7A_CERAE	Protein Wnt-7a precursor	0.15	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				349
Q1KYK7 UniProt NPD GO	WNT7A_GORGO	Protein Wnt-7a precursor	0.15	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				349
Q1KYK9 UniProt NPD GO	WNT7A_MACFA	Protein Wnt-7a precursor	0.15	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				349
P24383 UniProt NPD GO	WNT7A_MOUSE	Protein Wnt-7a precursor	0.15	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix				349
Q1KYL1 UniProt NPD GO	WNT7A_PANTR	Protein Wnt-7a precursor	0.15	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				349
Q1KYK5 UniProt NPD GO	WNT7A_PONPY	Protein Wnt-7a precursor	0.15	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				349
Q9U6Y9 UniProt NPD GO	CSUL_DROME	Protein arginine N-methyltransferase capsuleen (EC 2.1.1.-) (Arginine N-methyltransferase 5) (JBP1 h ...	0.15	-	cyt	0	Cytoplasm (Probable)	nucleus [IDA]			610
P41991 UniProt NPD GO	PES10_CAEEL	Protein pes-10	0.15	-	mit	0					407
P36875 UniProt NPD GO	2AAA_PEA	Protein phosphatase PP2A regulatory subunit A (PR65) (Fragment)	0.15	-	cyt	0					395
P38389 UniProt NPD GO	SC61B_ARATH	Protein transport protein Sec61 subunit beta	0.15	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				82
P70708 UniProt NPD GO	PADI3_RAT	Protein-arginine deiminase type-3 (EC 3.5.3.15) (Protein-arginine deiminase type III) (Peptidylargin ...	0.15	-	cyt	0	Cytoplasm (By similarity)				664
Q8BMT9 UniProt NPD GO	HHAT_MOUSE	Protein-cysteine N-palmitoyltransferase HHAT (EC 2.3.1.-) (Hedgehog acyltransferase) (Skinny hedgeho ...	0.15	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				499
Q9VZU2 UniProt NPD GO	HHAT_DROME	Protein-cysteine N-palmitoyltransferase Rasp (EC 2.3.1.-) (Protein skinny hedgehog) (Protein sightle ...	0.15	-	end	11 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			500
P52181 UniProt NPD GO	TGM2_PAGMA	Protein-glutamine gamma-glutamyltransferase 2 (EC 2.3.2.13) (Tissue transglutaminase) (TGase C) (TGC ...	0.15	-	cyt	0				1G0D	695
O95932 UniProt NPD GO	TGM3L_HUMAN	Protein-glutamine gamma-glutamyltransferase 6 (EC 2.3.2.13) (Transglutaminase-3-like) (TGase-3-like) ...	0.15	-	end	0					706
Q9JLF6 UniProt NPD GO	TGM1_MOUSE	Protein-glutamine gamma-glutamyltransferase K (EC 2.3.2.13) (Transglutaminase K) (TGase K) (TGK) (TG ...	0.15	-	cyt	0	Membrane; peripheral membrane protein (By similarity)	cell-cell adherens junction [IDA]			815
O88856 UniProt NPD GO	TPS2_MOUSE	Protein-tyrosine sulfotransferase 2 (EC 2.8.2.20) (Tyrosylprotein sulfotransferase-2) (TPST-2)	0.15	-	exc	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				376
P56703 UniProt NPD GO	WNT3_HUMAN	Proto-oncogene protein Wnt-3 precursor	0.15	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix	extracellular region [NAS]	165330		355
P09769 UniProt NPD GO	FGR_HUMAN	Proto-oncogene tyrosine-protein kinase FGR (EC 2.7.10.2) (P55-FGR) (C-FGR)	0.15	-	nuc	0			164940		529
Q02977 UniProt NPD GO	YRK_CHICK	Proto-oncogene tyrosine-protein kinase Yrk (EC 2.7.10.2) (p60-Yrk) (Yes-related kinase)	0.15	-	cyt	0					535
Q9Y5G8 UniProt NPD GO	PCDG5_HUMAN	Protocadherin gamma A5 precursor (PCDH-gamma-A5)	0.15	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		606292		931
Q41578 UniProt NPD GO	PORA_WHEAT	Protochlorophyllide reductase A, chloroplast precursor (EC 1.3.1.33) (PCR A) (NADPH-protochlorophyll ...	0.15	-	cyt	0	Plastid; chloroplast				388
P50336 UniProt NPD GO	PPOX_HUMAN	Protoporphyrinogen oxidase (EC 1.3.3.4) (PPO)	0.15	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...	intrinsic to mitochondrial inner membrane [ISS] mitochondrial membrane [IMP]	600923		477

You are viewing entries 57501 to 57550 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.