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
O75449 UniProt NPD GO	KTNA1_HUMAN	Katanin p60 ATPase-containing subunit A1 (EC 3.6.4.3) (Katanin p60 subunit A1) (p60 katanin)	0.66	-	nuc	0	Cytoplasm. Predominantly. Centrosome. Also localized to the interphase centrosome. Spindle. Enhanced ...	spindle pole [IDA]	606696		491
O88447 UniProt NPD GO	KLC1_MOUSE	Kinesin light chain 1 (KLC 1)	0.66	-	nuc	0		axon [IDA] ciliary rootlet [IDA] cytoplasm [IDA] cytoplasmic vesicle [IDA] cytosol [IDA] kinesin complex [IDA]			537
P37285 UniProt NPD GO	KLC1_RAT	Kinesin light chain 1 (KLC 1)	0.66	-	nuc	0		kinesin complex [IDA]			556
O88448 UniProt NPD GO	KLC2_MOUSE	Kinesin light chain 2 (KLC 2)	0.66	+	nuc	0		ciliary rootlet [IDA] cytoplasm [IDA] cytosol [IDA] kinesin complex [IDA] neuron projection [IDA]			599
Q8J1G1 UniProt NPD GO	KIP2_ASHGO	Kinesin-like protein KIP2	0.66	-	nuc	0					685
P33399 UniProt NPD GO	LAH1_YEAST	La protein homolog (La ribonucleoprotein) (La autoantigen homolog)	0.66	-	nuc	0	Nucleus (Probable)	nucleolus [IDA] nucleoplasm [IDA] nucleus [IDA]			275
Q60675 UniProt NPD GO	LAMA2_MOUSE	Laminin alpha-2 chain precursor (Laminin M chain) (Merosin heavy chain)	0.66	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basement membrane [IDA]		1QU0	3106
P11047 UniProt NPD GO	LAMC1_HUMAN	Laminin gamma-1 chain precursor (Laminin B2 chain)	0.66	-	nuc	0	Secreted protein; extracellular space	basement membrane [TAS] laminin-1 [TAS]	150290		1609
Q5T751 UniProt NPD GO	LCE1C_HUMAN	Late cornified envelope protein 1C (Late envelope protein 3)	0.66	-	mit	0					118
O95970 UniProt NPD GO	LGI1_HUMAN	Leucine-rich glioma-inactivated protein 1 precursor (Epitempin-1)	0.66	-	mit	0	Secreted protein (Potential)		604619		557
Q5RFE9 UniProt NPD GO	LRC40_PONPY	Leucine-rich repeat-containing protein 40	0.66	-	nuc	0					602
Q9Y2L9 UniProt NPD GO	LRCH1_HUMAN	Leucine-rich repeats and calponin homology domain-containing protein 1 (Calponin homology domain-con ...	0.66	-	nuc	1					728
Q8N448 UniProt NPD GO	LNX2_HUMAN	Ligand of Numb-protein X 2 (Numb-binding protein 2) (PDZ domain-containing RING finger protein 1)	0.66	-	nuc	0			609733		690
P36775 UniProt NPD GO	LONM_YEAST	Lon protease homolog, mitochondrial precursor (EC 3.4.21.-)	0.66	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			1133
P12318 UniProt NPD GO	FCG2A_HUMAN	Low affinity immunoglobulin gamma Fc region receptor II-a precursor (Fc-gamma RII-a) (FcRII-a) (IgG ...	0.66	-	nuc	1	Membrane; single-pass type I membrane protein	plasma membrane [NAS]	146790	1FCG	317
Q99087 UniProt NPD GO	LDLR1_XENLA	Low-density lipoprotein receptor 1 precursor (LDL receptor 1)	0.66	-	exc	1	Membrane; single-pass type I membrane protein				909
P98164 UniProt NPD GO	LRP2_HUMAN	Low-density lipoprotein receptor-related protein 2 precursor (Megalin) (Glycoprotein 330) (gp330)	0.66	-	exc	1	Membrane; single-pass type I membrane protein	lysosome [TAS]	600073		4655
Q42498 UniProt NPD GO	CMB2_DIACA	MADS-box protein CMB2	0.66	-	nuc	0	Nucleus (By similarity)				214
Q84NC2 UniProt NPD GO	MAD31_ORYSA	MADS-box transcription factor 31 (OsMADS31)	0.66	-	nuc	0	Nucleus (Probable)				178
Q9SAR1 UniProt NPD GO	MADS8_ORYSA	MADS-box transcription factor 8 (OsMADS8) (MADS-box protein 24) (OsMADS24)	0.66	-	nuc	0	Nucleus (Probable)				248
Q7XJK8 UniProt NPD GO	PHE2_ARATH	MADS-box transcription factor PHERES2	0.66	+	nuc	0					278
Q96L34 UniProt NPD GO	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4 (EC 2.7.11.1) (MAP/microtubule affinity-regulating kina ...	0.66	-	nuc	0		centrosome [IDA] neuron projection [IDA]	606495		752
Q707Y6 UniProt NPD GO	MATA1_PICAN	Mating-type protein A1 (MATa1 transcription factor)	0.66	+	nuc	0	Nucleus (By similarity)				181
Q9TKS1 UniProt NPD GO	MATK_ABRPR	Maturase K (Intron maturase)	0.66	-	cyt	0	Plastid; chloroplast				508
Q7HKI2 UniProt NPD GO	MATK_ACEPL	Maturase K (Intron maturase)	0.66	-	nuc	0	Plastid; chloroplast				512
Q8WKN0 UniProt NPD GO	MATK_ACEPM	Maturase K (Intron maturase)	0.66	-	nuc	0	Plastid; chloroplast				514
Q8MEC9 UniProt NPD GO	MATK_ANCDI	Maturase K (Intron maturase)	0.66	-	cyt	0	Plastid; chloroplast				511
Q8MC94 UniProt NPD GO	MATK_AUCJA	Maturase K (Intron maturase)	0.66	-	nuc	0	Plastid; chloroplast				504
Q95EE0 UniProt NPD GO	MATK_AUSVS	Maturase K (Intron maturase)	0.66	-	nuc	0	Plastid; chloroplast				509
Q9MUZ6 UniProt NPD GO	MATK_AVESA	Maturase K (Intron maturase)	0.66	-	cyt	0	Plastid; chloroplast				511
Q8WJ32 UniProt NPD GO	MATK_BACMR	Maturase K (Intron maturase)	0.66	-	nuc	0	Plastid; chloroplast				503
Q7YM30 UniProt NPD GO	MATK_CANOD	Maturase K (Intron maturase)	0.66	-	cyt	0	Plastid; chloroplast				507
Q5YJX4 UniProt NPD GO	MATK_GYMCH	Maturase K (Intron maturase)	0.66	-	cyt	0	Plastid; chloroplast				499
Q5GF76 UniProt NPD GO	MATK_IRIDA	Maturase K (Intron maturase)	0.66	-	cyt	0	Plastid; chloroplast				522
O47129 UniProt NPD GO	MATK_LYOFE	Maturase K (Intron maturase)	0.66	-	nuc	0	Plastid; chloroplast				507
Q95DP4 UniProt NPD GO	MATK_NICBI	Maturase K (Intron maturase)	0.66	-	cyt	0	Plastid; chloroplast				509
Q70D37 UniProt NPD GO	MATK_NICCL	Maturase K (Intron maturase)	0.66	-	cyt	0	Plastid; chloroplast				509
O98635 UniProt NPD GO	MATK_NUPVA	Maturase K (Intron maturase)	0.66	-	cyt	0	Plastid; chloroplast				505
Q9MUZ4 UniProt NPD GO	MATK_PHLPR	Maturase K (Intron maturase)	0.66	-	cyt	0	Plastid; chloroplast				511
Q9MV59 UniProt NPD GO	MATK_PINAR	Maturase K (Intron maturase)	0.66	-	nuc	0	Plastid; chloroplast				515
Q5J2V8 UniProt NPD GO	MATK_RIVHU	Maturase K (Intron maturase)	0.66	-	nuc	0	Plastid; chloroplast				503
Q9G1H4 UniProt NPD GO	MATK_RORAM	Maturase K (Intron maturase)	0.66	-	mit	0	Plastid; chloroplast				504
Q7IZ70 UniProt NPD GO	MATK_RORPA	Maturase K (Intron maturase)	0.66	-	mit	0	Plastid; chloroplast				504
Q14582 UniProt NPD GO	MAD4_HUMAN	Max-interacting transcriptional repressor MAD4 (Max-associated protein 4) (MAX dimerization protein ...	0.66	-	nuc	0	Nucleus (By similarity)				209
P08965 UniProt NPD GO	MEI2_SCHPO	Meiosis protein mei2	0.66	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			750
Q64230 UniProt NPD GO	MEP1A_RAT	Meprin A subunit alpha precursor (EC 3.4.24.18) (Endopeptidase-2) (MEP-1) (Endopeptidase-24.18 subun ...	0.66	-	end	1	Membrane; single-pass type I membrane protein	meprin A complex [IDA]			748
P82457 UniProt NPD GO	TRI18_MUSSP	Midline-1 (Tripartite motif-containing protein 18)	0.66	-	nuc	0	Cytoplasm (By similarity). Microtubule-associated (By similarity)				667
Q91573 UniProt NPD GO	MCR_XENLA	Mineralocorticoid receptor (MR) (Fragment)	0.66	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic and nuclear in the absence of ligand ...				612
Q03246 UniProt NPD GO	RTS17_YEAST	Mitochondrial 40S ribosomal protein MRPS17	0.66	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [IPI]			237
Q4I2W2 UniProt NPD GO	GEM1_GIBZE	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.66	-	cyt	0	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				627

You are viewing entries 15851 to 15900 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.