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
Q80YS5 UniProt NPD GO	LRC27_MOUSE	Leucine-rich repeat-containing protein 27	0.96	-	nuc	0					523
Q99090 UniProt NPD GO	CPRF2_PETCR	Light-inducible protein CPRF-2	0.96	+	nuc	0	Nucleus				401
Q8K1G2 UniProt NPD GO	LBN_MOUSE	Limbin	0.96	+	mit	1 *					1220
Q14693 UniProt NPD GO	LPIN1_HUMAN	Lipin-1	0.96	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]	605518		890
Q9V5M3 UniProt NPD GO	LOLA6_DROME	Longitudinals lacking protein, isoforms N/O/W/X/Y	0.96	+	nuc	0	Nucleus	nucleus [IDA]			878
P30310 UniProt NPD GO	MPIP2_XENLA	M-phase inducer phosphatase 2 (EC 3.1.3.48)	0.96	+	nuc	0					599
P30306 UniProt NPD GO	MPIP2_MOUSE	M-phase inducer phosphatase 2 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25B)	0.96	-	nuc	0	Centrosome (By similarity)				576
P30311 UniProt NPD GO	MPIP3_XENLA	M-phase inducer phosphatase 3 (EC 3.1.3.48)	0.96	+	nuc	0				1I8G	572
O44552 UniProt NPD GO	MPIP1_CAEEL	M-phase inducer phosphatase cdc-25.1 (EC 3.1.3.48) (Cell division cycle-related protein 25.1)	0.96	-	nuc	0		nucleus [IDA]			604
Q9M7J4 UniProt NPD GO	MFP1_TOBAC	MAR-binding filament-like protein 1-1	0.96	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix (By similarity)				722
Q91VE6 UniProt NPD GO	MK67I_MOUSE	MKI67 FHA domain-interacting nucleolar phosphoprotein (Nucleolar protein interacting with the FHA do ...	0.96	+	nuc	0	Nucleus; nucleolus. Localizes to mitotic chromosomes in conjunction with MKI67 (By similarity)				317
Q2Z1W2 UniProt NPD GO	MLFIP_CHICK	MLF1-interacting protein (Centromere protein p50) (CENP-50)	0.96	+	nuc	0	Nucleus. Localizes to the centromeres throughout the cell cycle				345
Q8BMD7 UniProt NPD GO	MORC4_MOUSE	MORC family CW-type zinc finger 4 (Zinc finger CW-type coiled-coil domain protein 2)	0.96	+	nuc	0					928
Q4V7D3 UniProt NPD GO	MACOI_RAT	Macoilin (Transmembrane protein 57)	0.96	+	nuc	4 *	Membrane; multi-pass membrane protein (Potential)				664
Q08269 UniProt NPD GO	ALR1_YEAST	Magnesium transporter ALR1 (Aluminum resistance protein 1)	0.96	-	nuc	1	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IMP]			859
P25159 UniProt NPD GO	STAU_DROME	Maternal effect protein staufen	0.96	-	nuc	0		apical cortex [IDA] basal cortex [TAS] cell cortex [IDA]		1STU	1026
P37935 UniProt NPD GO	MAAY4_SCHCO	Mating-type protein A-alpha Y4	0.96	+	nuc	0	Nucleus (Potential)				928
Q9HDS6 UniProt NPD GO	MTAL3_KLULA	Mating-type protein ALPHA3 (MATalpha3 protein) (HMLalpha3 protein)	0.96	+	nuc	0					897
Q7YR40 UniProt NPD GO	MDC1_PANTR	Mediator of DNA damage checkpoint protein 1	0.96	-	nuc	0	Nucleus (By similarity). Associated with chromatin. Relocalizes to discrete nuclear foci following D ...				2171
Q14676 UniProt NPD GO	MDC1_HUMAN	Mediator of DNA damage checkpoint protein 1 (Nuclear factor with BRCT domains 1)	0.96	-	nuc	0	Nucleus. Associated with chromatin. Relocalizes to discrete nuclear foci following DNA damage, this ...	nucleus [IDA]	607593	2ETX	2089
P25588 UniProt NPD GO	MRC1_YEAST	Mediator of replication checkpoint protein 1 (DNA replication checkpoint mediator MRC1)	0.96	-	nuc	0	Nucleus. Associated with chromatin during S phase	nuclear chromosome [IPI] nucleus [IDA] replication fork [IDA]			1096
Q09823 UniProt NPD GO	REC10_SCHPO	Meiotic recombination protein rec10	0.96	+	nuc	0		linear element [IDA]			791
Q6CK58 UniProt NPD GO	MSC3_KLULA	Meiotic sister-chromatid recombination protein 3	0.96	-	nuc	0	Cell membrane; peripheral membrane protein. Cell periphery (By similarity)				652
Q6RHR9 UniProt NPD GO	MAGI1_MOUSE	Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 (BAI1-associated protei ...	0.96	+	nuc	0	Isoform 2, isoform 3: Cytoplasm (Probable). Isoform 2, isoform 3: Membrane; peripheral membrane prot ...				1471
Q6ZPQ6 UniProt NPD GO	PITM2_MOUSE	Membrane-associated phosphatidylinositol transfer protein 2 (Phosphatidylinositol transfer protein, ...	0.96	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (Probable). May associate with the cytoskelet ...	intracellular [IDA] soluble fraction [IDA]			1335
Q9Z2D7 UniProt NPD GO	MBD4_MOUSE	Methyl-CpG-binding domain protein 4 (EC 3.2.2.-) (Methyl-CpG-binding protein MBD4) (Mismatch-specifi ...	0.96	+	nuc	0	Nucleus. Nuclear, in discrete foci	chromatin [IDA] nucleus [IDA]		1NGN	554
Q9P267 UniProt NPD GO	MBD5_HUMAN	Methyl-CpG-binding domain protein 5 (Methyl-CpG-binding protein MBD5)	0.96	-	nuc	0	Nucleus (Probable)				1494
Q99L90 UniProt NPD GO	MCRS1_MOUSE	Microspherule protein 1 (58 kDa microspherule protein)	0.96	-	nuc	0	Nucleus (By similarity)				462
Q96EZ8 UniProt NPD GO	MCRS1_HUMAN	Microspherule protein 1 (58 kDa microspherule protein) (Cell cycle-regulated factor p78) (MCRS2)	0.96	-	nuc	0	Nucleus. Nucleus; nucleolus. In microspherules in the nucleolus	cytoplasm [TAS] nucleoplasm [TAS]	609504		462
Q5TCX8 UniProt NPD GO	M3KL4_HUMAN	Mitogen-activated protein kinase kinase kinase (EC 2.7.11.25) (Mixed lineage kinase 4)	0.96	-	nuc	0					1036
Q5R8X7 UniProt NPD GO	M3K13_PONPY	Mitogen-activated protein kinase kinase kinase 13 (EC 2.7.11.25)	0.96	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	membrane fraction [ISS]			966
P87050 UniProt NPD GO	CDR2_SCHPO	Mitosis inducer protein kinase cdr2 (EC 2.7.11.1)	0.96	-	nuc	0		medial ring [IDA]			775
Q5M9I6 UniProt NPD GO	MMTA2_RAT	Multiple myeloma tumor-associated protein 2 homolog	0.96	+	nuc	0					260
P49578 UniProt NPD GO	ACM3_CHICK	Muscarinic acetylcholine receptor M3	0.96	+	end	7	Membrane; multi-pass membrane protein				639
P51960 UniProt NPD GO	MYBA_MOUSE	Myb-related protein A (A-Myb)	0.96	+	nuc	0	Nucleus				751
P54697 UniProt NPD GO	MYOJ_DICDI	Myosin IJ heavy chain	0.96	-	nuc	0					2245
P29616 UniProt NPD GO	MYSC_CHICK	Myosin heavy chain, cardiac muscle isoform (Fragment)	0.96	+	nuc	0	Thick filaments of the myofibrils				1102
Q5SX40 UniProt NPD GO	MYH1_MOUSE	Myosin-1 (Myosin heavy chain, skeletal muscle, adult 1)	0.96	+	nuc	0	Thick filaments of the myofibrils				1942
P08964 UniProt NPD GO	MYO1_YEAST	Myosin-1 (Type II myosin)	0.96	-	nuc	0		contractile ring (sensu Saccharomyces) [IDA]			1928
Q9UKX3 UniProt NPD GO	MYH13_HUMAN	Myosin-13 (Myosin heavy chain, skeletal muscle, extraocular) (MyHC-eo)	0.96	-	nuc	0	Thick filaments of the myofibrils	muscle myosin [TAS]	603487		1938
P08799 UniProt NPD GO	MYS2_DICDI	Myosin-2 heavy chain, non muscle (Myosin II heavy chain, non muscle)	0.96	+	nuc	0	Cytoplasm; cell cortex. Highest concentration in the posterior cell cortex			2AKA	2116
P12844 UniProt NPD GO	MYO3_CAEEL	Myosin-3 (Myosin heavy chain A) (MHC A)	0.96	-	nuc	0	Thick filaments of the myofibrils				1969
Q64331 UniProt NPD GO	MYO6_MOUSE	Myosin-6 (Myosin VI)	0.96	+	nuc	0					1265
P13535 UniProt NPD GO	MYH8_HUMAN	Myosin-8 (Myosin heavy chain, skeletal muscle, perinatal) (MyHC-perinatal)	0.96	+	nuc	0	Thick filaments of the myofibrils	muscle myosin [TAS]	608837		1937
Q8WXH0 UniProt NPD GO	SYNE2_HUMAN	Nesprin-2 (Nuclear envelope spectrin repeat protein 2) (Syne-2) (Synaptic nuclear envelope protein 2 ...	0.96	-	nuc	0	Nucleus; nuclear membrane; single-pass type IV membrane protein (Potential). The largest part of the ...		608442		6885
Q5I2W8 UniProt NPD GO	NBN_BRARE	Nibrin (Nijmegen breakage syndrome protein 1 homolog)	0.96	-	nuc	0	Nucleus (By similarity)				818
Q9JIL9 UniProt NPD GO	NBN_RAT	Nibrin (Nijmegen breakage syndrome protein 1 homolog)	0.96	-	nuc	0	Nucleus (By similarity)	Mre11 complex [ISS] nuclear inclusion body [ISS]			750
P78688 UniProt NPD GO	AREA_GIBFU	Nitrogen regulatory protein areA	0.96	-	nuc	0	Nucleus				971
O13824 UniProt NPD GO	NMD2_SCHPO	Nonsense-mediated mRNA decay protein 2 (Up-frameshift suppressor 2)	0.96	-	nuc	0	Cytoplasm				1049
O35892 UniProt NPD GO	SP100_MOUSE	Nuclear autoantigen Sp-100 (Speckled 100 kDa) (Nuclear dot-associated Sp100 protein)	0.96	+	nuc	0	Nucleus (By similarity). Found in the nuclear body, also known as nuclear domain 10 (ND10), PML onco ...				482

You are viewing entries 1451 to 1500 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.)

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