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
Q6L5D4 UniProt NPD GO	MPK9_ORYSA	Mitogen-activated protein kinase 9 (EC 2.7.11.24) (MAP kinase 9)	0.56	-	nuc	0					700
O54835 UniProt NPD GO	SMAD9_RAT	Mothers against decapentaplegic homolog 9 (SMAD 9) (Mothers against DPP homolog 9) (Smad9) (Smad8)	0.56	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...				434
Q8MI01 UniProt NPD GO	MUC15_BOVIN	Mucin-15 precursor (PASIII) (PAS3) (Glycoprotein C) (Glycoprotein 4) (Component II)	0.56	-	exc	1	Isoform 1: Cell membrane; single-pass type I membrane protein (Potential). Isoform 2: Secreted prote ...				330
O43196 UniProt NPD GO	MSH5_HUMAN	MutS protein homolog 5	0.56	-	mit	0			603382		834
Q62234 UniProt NPD GO	MYOM1_MOUSE	Myomesin-1 (Skelemin)	0.56	-	cyt	0		cytoskeleton [TAS] sarcomere [IDA]			1666
Q96MN2 UniProt NPD GO	NALP4_HUMAN	NACHT, LRR and PYD-containing protein 4 (PYRIN-containing APAF1-like protein 4) (PAAD and NACHT-cont ...	0.56	-	nuc	0			609645		994
Q6ENH0 UniProt NPD GO	NUKC_ORYNI	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.56	-	nuc	0	Plastid; chloroplast				246
P12159 UniProt NPD GO	NUKC_ORYSA	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.56	-	nuc	0	Plastid; chloroplast				246
Q6ENA3 UniProt NPD GO	NUIC_ORYNI	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.56	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				180
P12099 UniProt NPD GO	NUIC_ORYSA	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.56	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				180
P05312 UniProt NPD GO	NUIC_WHEAT	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.56	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				180
Q33994 UniProt NPD GO	NUGM_BETTR	NADH-ubiquinone oxidoreductase 27 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-27KD) (CI-27KD) ...	0.56	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				192
Q34011 UniProt NPD GO	NUGM_BETWE	NADH-ubiquinone oxidoreductase 27 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-27KD) (CI-27KD) ...	0.56	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				192
P27682 UniProt NPD GO	7B2_RAT	Neuroendocrine protein 7B2 precursor (Secretogranin-5) (Secretogranin V) (Secretory granule endocrin ...	0.56	-	exc	0	Neuroendocrine and endocrine secretory granules	secretory granule [ISS]			210
Q02038 UniProt NPD GO	NEUL_PIG	Neurolysin, mitochondrial precursor (EC 3.4.24.16) (Neurotensin endopeptidase) (Mitochondrial oligop ...	0.56	-	mit	0	Isoform 1: Mitochondrion. Isoform 2, isoform 3, isoform 4, isoform 5: Cytoplasm	cytosol [IDA] mitochondrion [IDA]			704
Q8N729 UniProt NPD GO	NPW_HUMAN	Neuropeptide W precursor (Preproprotein L8) (hPPL8) [Contains: Neuropeptide W-23 (NPW23) (hL8); Neur ...	0.56	-	nuc	0	Secreted protein		607997		165
O70342 UniProt NPD GO	NPY5R_MOUSE	Neuropeptide Y receptor type 5 (NPY5-R) (NPY-Y5 receptor) (Y5 receptor)	0.56	-	end	7	Membrane; multi-pass membrane protein	membrane [IDA]			466
P53204 UniProt NPD GO	NMA2_YEAST	Nicotinamide-nucleotide adenylyltransferase 2 (EC 2.7.7.1) (NAD(+) pyrophosphorylase 2) (NAD(+) diph ...	0.56	-	nuc	0	Nucleus	nucleus [IDA]			395
P04672 UniProt NPD GO	NO44_SOYBN	Nodulin 44 precursor (N-44) (Nodulin E27)	0.56	-	nuc	0					360
Q12129 UniProt NPD GO	NMD4_YEAST	Nonsense-mediated decay protein 4	0.56	-	nuc	0	Cytoplasm	cytoplasm [IDA]			218
Q4R4S6 UniProt NPD GO	NDEL1_MACFA	Nuclear distribution protein nudE-like 1 (Protein Nudel)	0.56	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				347
Q5R8T7 UniProt NPD GO	NDEL1_PONPY	Nuclear distribution protein nudE-like 1 (Protein Nudel)	0.56	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				345
Q9GZM8 UniProt NPD GO	NDEL1_HUMAN	Nuclear distribution protein nudE-like 1 (Protein Nudel) (Mitosin-associated protein 1)	0.56	-	nuc	0	Localizes to the cell body of the motor neurons and colocalizes with assembled neurofilaments within ...		607538		345
Q21878 UniProt NPD GO	NHR1_CAEEL	Nuclear hormone receptor family member nhr-1	0.56	-	nuc	0	Nucleus (Potential)				445
O16962 UniProt NPD GO	NHR55_CAEEL	Nuclear hormone receptor family member nhr-55	0.56	+	mit	0	Nucleus (Potential)				424
Q8R0G9 UniProt NPD GO	NU133_MOUSE	Nuclear pore complex protein Nup133 (Nucleoporin Nup133) (133 kDa nucleoporin)	0.56	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity). Located on both the cytoplasmic and ...	nuclear pore [ISS]			1155
P37198 UniProt NPD GO	NUP62_HUMAN	Nuclear pore glycoprotein p62 (62 kDa nucleoporin)	0.56	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex. Central region of the nuclear pore, within the tran ...	cytoplasm [NAS] nuclear pore [IDA] nucleocytoplasmic shuttling complex [NAS]	605815		522
Q92753 UniProt NPD GO	RORB_HUMAN	Nuclear receptor ROR-beta (Nuclear receptor RZR-beta)	0.56	-	nuc	0	Nucleus (Probable)		601972		459
Q5E9X1 UniProt NPD GO	NFYC_BOVIN	Nuclear transcription factor Y subunit gamma (Nuclear transcription factor Y subunit C) (NF-YC) (CAA ...	0.56	+	nuc	0	Nucleus (By similarity)				335
Q5RA23 UniProt NPD GO	NFYC_PONPY	Nuclear transcription factor Y subunit gamma (Nuclear transcription factor Y subunit C) (NF-YC) (CAA ...	0.56	+	nuc	0	Nucleus (By similarity)				335
Q66IJ0 UniProt NPD GO	NUP53_XENTR	Nucleoporin NUP53 (Nuclear pore complex protein Nup53) (Nucleoporin Nup35) (35 kDa nucleoporin)	0.56	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity)				330
Q99457 UniProt NPD GO	NP1L3_HUMAN	Nucleosome assembly protein 1-like 3	0.56	+	nuc	0	Nucleus (By similarity)	chromatin assembly complex [TAS]	300117		506
Q6BTV5 UniProt NPD GO	SIL1_DEBHA	Nucleotide exchange factor SIL1 precursor	0.56	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				427
Q91049 UniProt NPD GO	OCLN_CHICK	Occludin	0.56	+	end	5	Membrane; multi-pass membrane protein				504
Q9YGP6 UniProt NPD GO	SLBP2_XENLA	Oocyte-specific histone RNA stem-loop-binding protein 2	0.56	-	nuc	0	Cytoplasm				250
O42690 UniProt NPD GO	CDR3_CANAL	Opaque-specific ABC transporter CDR3	0.56	-	end	13	Membrane; multi-pass membrane protein (Potential)				1501
P55094 UniProt NPD GO	TR4_RAT	Orphan nuclear receptor TR4	0.56	-	nuc	0	Nucleus (Potential)				596
Q9HC10 UniProt NPD GO	OTOF_HUMAN	Otoferlin (Fer-1-like protein 2)	0.56	+	nuc	1	Membrane; single-pass type II membrane protein (By similarity)	cytosol [TAS] integral to membrane [TAS] membrane [TAS] membrane fraction [TAS]	603681		1997
Q61999 UniProt NPD GO	ODFP_MOUSE	Outer dense fiber protein	0.56	-	nuc	0		outer dense fiber [IDA]			247
P21769 UniProt NPD GO	ODFP_RAT	Outer dense fiber protein (Protein RT7) (RTS 5/1)	0.56	-	nuc	0					245
P16109 UniProt NPD GO	LYAM3_HUMAN	P-selectin precursor (Granule membrane protein 140) (GMP-140) (PADGEM) (Leukocyte-endothelial cell a ...	0.56	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] membrane fraction [IDA] plasma membrane [TAS] platelet alpha granule membrane [IDA] soluble fraction [TAS]	173610	1KJD	830
P20266 UniProt NPD GO	PO4F1_RAT	POU domain, class 4, transcription factor 1 (Brain-specific homeobox/POU domain protein 3A) (Brn-3A) ...	0.56	+	nuc	0	Nucleus				128
Q5VXH5 UniProt NPD GO	PRAM7_HUMAN	PRAME family member 7	0.56	-	mit	0					474
Q5VWM5 UniProt NPD GO	PRAM9_HUMAN	PRAME family member 9	0.56	-	mit	0					478
Q4PE27 UniProt NPD GO	PFA4_USTMA	Palmitoyltransferase PFA4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.56	+	nuc	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				604
P49023 UniProt NPD GO	PAXI_HUMAN	Paxillin	0.56	-	nuc	0		microtubule associated complex [TAS]	602505	1KL0	591
O74711 UniProt NPD GO	PEX5_CANAL	Peroxisomal targeting signal receptor (Peroxin-5) (PTS1 receptor)	0.56	-	nuc	0	Cytoplasm (By similarity). Peroxisome; peroxisomal membrane; peripheral membrane protein (By similar ...				592
Q04370 UniProt NPD GO	PEX12_YEAST	Peroxisome assembly protein 12 (Peroxin-12)	0.56	-	cyt	1	Peroxisome; peroxisomal membrane; multi-pass membrane protein (Potential)				399
Q9ASU7 UniProt NPD GO	PPAN_ARATH	Peter Pan-like protein	0.56	-	nuc	0					345
P37297 UniProt NPD GO	STT4_YEAST	Phosphatidylinositol 4-kinase STT4 (EC 2.7.1.67) (PI4-kinase) (PtdIns-4-kinase)	0.56	-	mit	0		mitochondrion [IDA] plasma membrane [IDA]			1900

You are viewing entries 21501 to 21550 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.