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
Q9NSK0 UniProt NPD GO	KLC4_HUMAN	Kinesin light chain 4 (KLC 4) (Kinesin-like protein 8)	0.55	-	nuc	0					625
Q9DBS5 UniProt NPD GO	KLC4_MOUSE	Kinesin light chain 4 (KLC 4) (Kinesin-like protein 8)	0.55	-	nuc	0					619
Q9UTL2 UniProt NPD GO	KLP8_SCHPO	Kinesin-like protein 8	0.55	-	nuc	0					511
Q13118 UniProt NPD GO	KLF10_HUMAN	Krueppel-like factor 10 (Transforming growth factor-beta-inducible early growth response protein 1) ...	0.55	-	nuc	0	Nucleus	nucleus [TAS]	601878		480
O89091 UniProt NPD GO	KLF10_MOUSE	Krueppel-like factor 10 (Transforming growth factor-beta-inducible early growth response protein 1) ...	0.55	-	nuc	0	Nucleus (By similarity)				479
Q9Y2Y9 UniProt NPD GO	KLF13_HUMAN	Krueppel-like factor 13 (Transcription factor BTEB3) (Basic transcription element-binding protein 3) ...	0.55	-	nuc	0	Nucleus		605328		288
Q95198 UniProt NPD GO	LYAM1_MACMU	L-selectin precursor (Lymph node homing receptor) (Leukocyte adhesion molecule 1) (LAM-1) (Leukocyte ...	0.55	-	nuc	1	Membrane; single-pass type I membrane protein				372
Q28768 UniProt NPD GO	LYAM1_PAPHA	L-selectin precursor (Lymph node homing receptor) (Leukocyte adhesion molecule 1) (LAM-1) (Leukocyte ...	0.55	-	nuc	1	Membrane; single-pass type I membrane protein				372
P53776 UniProt NPD GO	LHX4_MOUSE	LIM/homeobox protein Lhx4	0.55	+	nuc	0	Nucleus (Potential)				367
Q6P4Z6 UniProt NPD GO	LCMT1_RAT	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-)	0.55	-	cyt	0					332
Q4IER0 UniProt NPD GO	LCMT2_GIBZE	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-)	0.55	-	mit	0					989
Q96DD0 UniProt NPD GO	LRC39_HUMAN	Leucine-rich repeat-containing protein 39 (Densin hlg)	0.55	-	nuc	0					335
Q8MJZ7 UniProt NPD GO	LIRB5_PANTR	Leukocyte immunoglobulin-like receptor subfamily B member 5 precursor (Leukocyte immunoglobulin-like ...	0.55	-	nuc	1	Membrane; single-pass type I membrane protein				643
P35617 UniProt NPD GO	XNIF_XENLA	Low molecular weight neuronal intermediate filament (XNIF)	0.55	-	nuc	0					470
O75581 UniProt NPD GO	LRP6_HUMAN	Low-density lipoprotein receptor-related protein 6 precursor	0.55	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [TAS] plasma membrane [TAS]	603507		1613
Q8BVN9 UniProt NPD GO	MAEL_MOUSE	Maelstrom homolog	0.55	-	nuc	0	Nucleus (Potential)				434
P48988 UniProt NPD GO	CENPB_CRIGR	Major centromere autoantigen B (Centromere protein B) (CENP-B)	0.55	-	nuc	0	Nucleus				606
P07199 UniProt NPD GO	CENPB_HUMAN	Major centromere autoantigen B (Centromere protein B) (CENP-B)	0.55	-	cyt	0	Nucleus	chromosome, pericentric region [NAS]	117140	1UFI	599
P27790 UniProt NPD GO	CENPB_MOUSE	Major centromere autoantigen B (Centromere protein B) (CENP-B)	0.55	-	nuc	0	Nucleus				599
Q9H239 UniProt NPD GO	MMP28_HUMAN	Matrix metalloproteinase-28 precursor (EC 3.4.24.-) (MMP-28) (Epilysin)	0.55	+	nuc	0	Secreted protein	extracellular matrix (sensu Metazoa) [NAS]			520
Q9MSR8 UniProt NPD GO	MATK_AMEAR	Maturase K (Intron maturase)	0.55	-	cyt	0	Plastid; chloroplast				509
Q7YJG1 UniProt NPD GO	MATK_ANTLI	Maturase K (Intron maturase)	0.55	-	nuc	0	Plastid; chloroplast				521
Q8MEW7 UniProt NPD GO	MATK_CEDDE	Maturase K (Intron maturase)	0.55	-	nuc	0	Plastid; chloroplast				515
Q8WHL4 UniProt NPD GO	MATK_LEMTR	Maturase K (Intron maturase)	0.55	-	cyt	0	Plastid; chloroplast				512
Q9TIR3 UniProt NPD GO	MATK_OROFA	Maturase K (Intron maturase)	0.55	-	nuc	0	Plastid; chloroplast				510
Q85V90 UniProt NPD GO	MATK_RHACA	Maturase K (Intron maturase)	0.55	-	cyt	0	Plastid; chloroplast				503
P36435 UniProt NPD GO	MATK_SAXIN	Maturase K (Intron maturase)	0.55	-	cyt	0	Plastid; chloroplast				505
Q9MVV8 UniProt NPD GO	MATK_TAXBA	Maturase K (Intron maturase)	0.55	-	cyt	0	Plastid; chloroplast				504
Q9MSS1 UniProt NPD GO	MATK_THUPL	Maturase K (Intron maturase)	0.55	-	cyt	0	Plastid; chloroplast				510
Q9MVV7 UniProt NPD GO	MATK_TORCL	Maturase K (Intron maturase)	0.55	-	cyt	0	Plastid; chloroplast				495
Q7JEW7 UniProt NPD GO	MATK_TRICT	Maturase K (Intron maturase)	0.55	-	cyt	0	Plastid; chloroplast				521
Q9XPP0 UniProt NPD GO	MATK_TRILU	Maturase K (Intron maturase)	0.55	-	cyt	0	Plastid; chloroplast				515
Q8WHK8 UniProt NPD GO	MATK_WOLGL	Maturase K (Intron maturase)	0.55	-	nuc	0	Plastid; chloroplast				512
Q9MSV6 UniProt NPD GO	MATK_CHALA	Maturase K (Intron maturase) (Fragment)	0.55	-	cyt	0	Plastid; chloroplast				444
O74438 UniProt NPD GO	MCP2_SCHPO	Meiotic coiled-coil protein 2	0.55	-	nuc	0					703
Q9NWG9 UniProt NPD GO	MAGH1_MOUSE	Melanoma-associated antigen H1 (MAGE-H1 antigen)	0.55	-	nuc	1					218
Q14833 UniProt NPD GO	MGR4_HUMAN	Metabotropic glutamate receptor 4 precursor (mGluR4)	0.55	-	end	7 *	Membrane; multi-pass membrane protein	cytoplasmic vesicle [IDA] integral to plasma membrane [IDA] intracellular [IDA]	604100		912
Q8WWY6 UniProt NPD GO	MB3L1_HUMAN	Methyl-CpG-binding domain protein 3-like 1 (MBD3-like 1)	0.55	-	mit	0	Nucleus. Nuclear, in large foci		607963		194
P18409 UniProt NPD GO	MDM10_YEAST	Mitochondrial inheritance component MDM10	0.55	-	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrial sorting and assembly machiner... [IPI]			493
Q67C40 UniProt NPD GO	MPK7_ORYSA	Mitogen-activated protein kinase 7 (EC 2.7.11.24) (MAP kinase 7) (OsMAPK6) (MAP kinase 6)	0.55	-	nuc	0					569
Q9R1X5 UniProt NPD GO	MRP5_MOUSE	Multidrug resistance-associated protein 5 (ABC transporter MOAT-C) (SMRP)	0.55	-	end	11	Membrane; multi-pass membrane protein				1436
P04761 UniProt NPD GO	ACM1_PIG	Muscarinic acetylcholine receptor M1	0.55	-	end	7 *	Membrane; multi-pass membrane protein				460
P22366 UniProt NPD GO	MYD88_MOUSE	Myeloid differentiation primary response protein MyD88	0.55	-	cyt	0	Cytoplasm (Probable)	cytoplasm [TAS]			296
O94832 UniProt NPD GO	MYO1D_HUMAN	Myosin Id	0.55	-	nuc	0			606539		1006
Q8TDZ2 UniProt NPD GO	MICA1_HUMAN	NEDD9-interacting protein with calponin homology and LIM domains (Molecule interacting with CasL pro ...	0.55	-	nuc	0	Cytoplasm	cytoplasm [IDA] intermediate filament [NAS]	607129	2CO8	1067
Q8NET5 UniProt NPD GO	NFAM1_HUMAN	NFAT activation molecule 1 precursor (Calcineurin/NFAT-activating ITAM-containing protein) (NFAT-act ...	0.55	-	nuc	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Partially recruited to lipid raf ...	integral to membrane [IDA]	608740		270
Q9NQX5 UniProt NPD GO	NPDC1_HUMAN	Neural proliferation differentiation and control protein 1 precursor (NPDC-1 protein)	0.55	-	mit	1			605798		325
P12285 UniProt NPD GO	AGNY_APLSP	Neuroactive polyprotein R15-2 precursor [Contains: R15 alpha-1 peptide; R15 beta peptide; R15 gamma ...	0.55	-	nuc	1 *	Secreted protein				156
P12036 UniProt NPD GO	NFH_HUMAN	Neurofilament triplet H protein (200 kDa neurofilament protein) (Neurofilament heavy polypeptide) (N ...	0.55	-	nuc	0		axon [TAS] neurofilament [NAS]	162230		1026
Q9Y5X5 UniProt NPD GO	NPFF2_HUMAN	Neuropeptide FF receptor 2 (Neuropeptide G-protein coupled receptor) (G-protein coupled receptor 74) ...	0.55	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	607449		522

You are viewing entries 22051 to 22100 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.