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
Q9Y283 UniProt NPD GO	INVS_HUMAN	Inversin (Inversion of embryo turning homolog) (Nephrocystin-2)	0.94	+	nuc	0	Cytoplasm (By similarity). Associates with several components of the cytoskeleton including ciliary, ...		602088		1065
Q8BW72 UniProt NPD GO	JHD3A_MOUSE	JmjC domain-containing histone demethylation protein 3A (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.94	+	nuc	0	Nucleus (By similarity)				1064
Q91VY5 UniProt NPD GO	JHD3B_MOUSE	JmjC domain-containing histone demethylation protein 3B (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.94	-	nuc	0	Nucleus (By similarity)				1086
P52732 UniProt NPD GO	KIF11_HUMAN	Kinesin-like protein KIF11 (Kinesin-related motor protein Eg5) (Kinesin-like spindle protein HKSP) ( ...	0.94	-	nuc	0		kinesin complex [TAS] spindle [TAS]	148760	2FL6	1057
Q8IR79 UniProt NPD GO	LIMK1_DROME	LIM domain kinase 1 (EC 2.7.11.1) (LIMK-1) (dLIMK)	0.94	-	nuc	0	Cytoplasm. Localizes to the cleavage furrow and the midbody at cytokinesis	cell cortex [IDA] contractile ring [IDA] cytoplasm [IDA]			1257
O43679 UniProt NPD GO	LDB2_HUMAN	LIM domain-binding protein 2 (Carboxyl-terminal LIM domain-binding protein 1) (CLIM-1) (LIM domain-b ...	0.94	+	nuc	0	Nucleus		603450		373
Q6ZQ58 UniProt NPD GO	LARP1_MOUSE	La-related protein 1 (La ribonucleoprotein domain family member 1) (Fragment)	0.94	+	nuc	0					364
P57016 UniProt NPD GO	LAD1_MOUSE	Ladinin 1 (Lad-1) (Linear IgA disease autoantigen)	0.94	-	nuc	0	Secreted protein; extracellular space; extracellular matrix. Localized to anchoring filaments underl ...				528
P48679 UniProt NPD GO	LMNA_RAT	Lamin-A	0.94	-	nuc	0	Nucleus				665
P48678 UniProt NPD GO	LMNA_MOUSE	Lamin-A/C	0.94	-	nuc	0	Nucleus	lamin filament [IDA] nucleus [IDA]		1UFG	665
P10999 UniProt NPD GO	LAML3_XENLA	Lamin-L(III) (Lamin-B3)	0.94	-	nuc	0	Nucleus; nuclear inner membrane; lipid-anchor; nucleoplasmic side				583
Q5XXA9 UniProt NPD GO	PSIP1_CHICK	Lens epithelium-derived growth factor	0.94	+	nuc	0	Nucleus (By similarity)				579
Q8AVS8 UniProt NPD GO	LRC59_XENLA	Leucine-rich repeat-containing protein 59	0.94	+	nuc	1	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				307
Q9HDV4 UniProt NPD GO	LID2_SCHPO	Lid2 complex component lid2 (Lid2C component lid2)	0.94	-	nuc	0	Nucleus (Probable)	Lid2 complex [IDA]			1513
P97412 UniProt NPD GO	LYST_MOUSE	Lysosomal-trafficking regulator (Beige protein) (CHS1 homolog)	0.94	+	end	0	Cytoplasm (Potential)				3788
P48965 UniProt NPD GO	MPIP1_RAT	M-phase inducer phosphatase 1 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25A)	0.94	-	nuc	0					525
Q2TLZ4 UniProt NPD GO	MACOI_MACMU	Macoilin (Transmembrane protein 57)	0.94	+	nuc	4 *	Membrane; multi-pass membrane protein (Potential)				664
P37936 UniProt NPD GO	MAAY1_SCHCO	Mating-type protein A-alpha Y1	0.94	+	nuc	0	Nucleus (Potential)				891
P38830 UniProt NPD GO	NDT80_YEAST	Meiosis-specific transcription factor NDT80	0.94	-	nuc	0	Nucleus	nuclear chromosome [IDA]		2EVJ	627
Q9UUB3 UniProt NPD GO	MEU18_SCHPO	Meiotic expression up-regulated protein 18	0.94	+	nuc	1 *					553
P61590 UniProt NPD GO	MCPH1_COLGU	Microcephalin	0.94	+	nuc	0	Centrosome (By similarity)				841
P61592 UniProt NPD GO	MCPH1_HYLLA	Microcephalin	0.94	-	nuc	0	Centrosome (By similarity)				840
P61594 UniProt NPD GO	MCPH1_PONPY	Microcephalin	0.94	+	nuc	0	Centrosome (By similarity)				839
Q12019 UniProt NPD GO	MDN1_YEAST	Midasin (MIDAS-containing protein)	0.94	+	end	0	Nucleus	mitochondrion [IDA] nucleoplasm [IDA] nucleus [IDA]			4910
Q8N4C8 UniProt NPD GO	MINK1_HUMAN	Misshapen-like kinase 1 (EC 2.7.11.1) (Mitogen-activated protein kinase kinase kinase kinase 6) (MAP ...	0.94	+	nuc	0			609426		1332
Q9JM52 UniProt NPD GO	MINK1_MOUSE	Misshapen-like kinase 1 (EC 2.7.11.1) (Mitogen-activated protein kinase kinase kinase kinase 6) (MAP ...	0.94	+	nuc	0					1308
Q95UN8 UniProt NPD GO	M3KSL_DROME	Mitogen-activated protein kinase kinase kinase (EC 2.7.11.25) (Mixed lineage kinase) (dMLK) (Protein ...	0.94	-	nuc	0					1161
P32944 UniProt NPD GO	SWE1_YEAST	Mitosis inhibitor protein kinase SWE1 (EC 2.7.11.1)	0.94	-	nuc	0		bud neck [IDA] nucleus [IDA]			819
Q9UT79 UniProt NPD GO	MSC1_SCHPO	Multicopy suppressor of chk1 protein 1	0.94	+	nuc	0	Nucleus. Associates with chromatin	chromatin [IDA]			1588
Q6CQR6 UniProt NPD GO	MRD1_KLULA	Multiple RNA-binding domain-containing protein 1	0.94	-	nuc	0	Nucleus (By similarity)				878
Q05935 UniProt NPD GO	MYBA_XENLA	Myb-related protein A (A-Myb) (XAMYB) (MYB-related protein 2) (XMYB2)	0.94	+	nuc	0	Nucleus				728
P10244 UniProt NPD GO	MYBB_HUMAN	Myb-related protein B (B-Myb)	0.94	+	nuc	0	Nucleus		601415		700
P49033 UniProt NPD GO	MYC_HYLLA	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.94	+	nuc	0	Nucleus				439
P01108 UniProt NPD GO	MYC_MOUSE	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.94	+	nuc	0	Nucleus	nucleus [IDA] spindle [IDA]			439
Q29031 UniProt NPD GO	MYC_PIG	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.94	+	nuc	0	Nucleus				439
P09416 UniProt NPD GO	MYC_RAT	Myc proto-oncogene protein (c-Myc) (Transcription factor p64)	0.94	+	nuc	0	Nucleus	nucleus [TAS]			439
P01109 UniProt NPD GO	MYC_CHICK	Myc proto-oncogene protein (c-myc)	0.94	+	nuc	0	Nucleus				416
P13540 UniProt NPD GO	MYH7_MESAU	Myosin heavy chain, cardiac muscle beta isoform (MyHC-beta)	0.94	+	nuc	0	Thick filaments of the myofibrils				1934
P02564 UniProt NPD GO	MYH7_RAT	Myosin heavy chain, cardiac muscle beta isoform (MyHC-beta)	0.94	+	nuc	0	Thick filaments of the myofibrils				1935
P12847 UniProt NPD GO	MYH3_RAT	Myosin heavy chain, fast skeletal muscle, embryonic	0.94	+	nuc	0	Thick filaments of the myofibrils				1940
Q99323 UniProt NPD GO	MYSN_DROME	Myosin heavy chain, non-muscle (Zipper protein) (Myosin II) (Non-muscle MHC)	0.94	-	nuc	0		apical cortex [TAS] cytoskeleton [NAS] unconventional myosin [NAS] Z disc [IDA]			2057
Q9UKX2 UniProt NPD GO	MYH2_HUMAN	Myosin heavy chain, skeletal muscle, adult 2 (Myosin heavy chain IIa) (MyHC-IIa)	0.94	+	nuc	0	Thick filaments of the myofibrils	muscle myosin [TAS]	160740		1941
Q9USI6 UniProt NPD GO	MYO2_SCHPO	Myosin type-2 heavy chain 1 (Myosin type II heavy chain 1)	0.94	+	nuc	0		contractile ring (sensu Fungi) [IDA] myosin II [IDA]			1526
Q9HD67 UniProt NPD GO	MYO10_HUMAN	Myosin-10 (Myosin X)	0.94	-	nuc	0			601481		2058
Q63862 UniProt NPD GO	MYH11_RAT	Myosin-11 (Myosin heavy chain, smooth muscle isoform) (SMMHC) (Fragments)	0.94	-	nuc	0	Thick filaments of the myofibrils	muscle myosin [NAS]			1327
Q9UKN7 UniProt NPD GO	MYO15_HUMAN	Myosin-15 (Myosin XV) (Unconventional myosin-15)	0.94	+	nuc	0	Cytoplasm		602666		3530
Q29RW1 UniProt NPD GO	MYH4_RAT	Myosin-4	0.94	+	nuc	0	Thick filaments of the myofibrils				1939
Q28641 UniProt NPD GO	MYH4_RABIT	Myosin-4 (Myosin heavy chain, skeletal muscle, juvenile)	0.94	+	nuc	0	Thick filaments of the myofibrils				1938
Q13402 UniProt NPD GO	MYO7A_HUMAN	Myosin-7A (Myosin VIIa)	0.94	+	nuc	0	Cytoplasm (Probable). In the photoreceptor cells, mainly localized in the inner and base of outer se ...		601317		2215
Q9EPI6 UniProt NPD GO	NELF_RAT	Nasal embryonic luteinizing hormone-releasing hormone factor (Nasal embryonic LHRH factor) (Juxtasyn ...	0.94	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Found on the outside of the LHRH cell me ...				532

You are viewing entries 2351 to 2400 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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