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 152 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
Q15388 UniProt NPD GO	TOM20_HUMAN	Mitochondrial import receptor subunit TOM20 homolog (Mitochondrial 20 kDa outer membrane protein) (O ...	0.61	+	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (Potential)	mitochondrial outer membrane translocase co... [NAS]	601848		145
Q9UBC1 UniProt NPD GO	IKBL_HUMAN	NF-kappa-B inhibitor-like protein 1 (Inhibitor of kappa B-like) (I-kappa-B-like) (IkappaBL) (Nuclear ...	0.61	+	nuc	0			601022		381
Q02878 UniProt NPD GO	RL6_HUMAN	60S ribosomal protein L6 (TAX-responsive enhancer element-binding protein 107) (TAXREB107) (Neoplasm ...	0.60	+	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	603703		287
P16157 UniProt NPD GO	ANK1_HUMAN	Ankyrin-1 (Erythrocyte ankyrin) (Ankyrin-R)	0.60	+	nuc	0	Isoform Er1: Cytoplasm. Probably the other erythrocyte (Er) isoforms, are located near the surface o ...	basolateral plasma membrane [NAS] plasma membrane [NAS]	182900	1N11	1880
Q5FYB0 UniProt NPD GO	ARSJ_HUMAN	Arylsulfatase J precursor (EC 3.1.6.-) (ASJ)	0.60	+	nuc	0	Secreted protein (Potential)		610010		599
O14594 UniProt NPD GO	CSPG3_HUMAN	Neurocan core protein precursor (Chondroitin sulfate proteoglycan 3)	0.59	+	nuc	0			600826		1321
P61296 UniProt NPD GO	HAND2_HUMAN	Heart- and neural crest derivatives-expressed protein 2 (Deciduum, heart, autonomic nervous system a ...	0.57	+	nuc	0			602407		217
Q13474 UniProt NPD GO	DRP2_HUMAN	Dystrophin-related protein 2	0.56	+	nuc	0			300052		954
Q02575 UniProt NPD GO	HEN1_HUMAN	Helix-loop-helix protein 1 (HEN1) (Nescient helix loop helix 1) (NSCL-1)	0.55	+	nuc	0			162360		133
P04264 UniProt NPD GO	K2C1_HUMAN	Keratin, type II cytoskeletal 1 (Cytokeratin-1) (CK-1) (Keratin-1) (K1) (67 kDa cytokeratin) (Hair a ...	0.54	+	nuc	0		cytoskeleton [TAS] intermediate filament [TAS] membrane [IDA]	607654		643
P49006 UniProt NPD GO	MRP_HUMAN	MARCKS-related protein (MARCKS-like protein 1) (Macrophage myristoylated alanine-rich C kinase subst ...	0.54	+	nuc	0			602940		194
P62979 UniProt NPD GO	RS27A_HUMAN	40S ribosomal protein S27a	0.53	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	191343		80
Q9NQS1 UniProt NPD GO	AVEN_HUMAN	Cell death regulator Aven	0.53	+	nuc	0	Membrane; peripheral membrane protein. Associated with intracellular membranes	intracellular [IDA] membrane fraction [IDA]	605265		362
Q08116 UniProt NPD GO	RGS1_HUMAN	Regulator of G-protein signaling 1 (RGS1) (Early response protein 1R20) (B-cell activation protein B ...	0.53	+	nuc	0		plasma membrane [TAS]	600323	2BV1	196
P42677 UniProt NPD GO	RS27_HUMAN	40S ribosomal protein S27 (Metallopan-stimulin 1) (MPS-1)	0.52	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	603702		83
P49585 UniProt NPD GO	PCY1A_HUMAN	Choline-phosphate cytidylyltransferase A (EC 2.7.7.15) (Phosphorylcholine transferase A) (CTP:phosph ...	0.52	+	nuc	0	Cytoplasm; cytosol (By similarity). Membrane; peripheral membrane protein (By similarity). It can in ...	soluble fraction [TAS]	123695		367
O00445 UniProt NPD GO	SYT5_HUMAN	Synaptotagmin-5 (Synaptotagmin V) (SytV)	0.52	+	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity). Endosome; ...		600782		386
Q14694 UniProt NPD GO	UBP10_HUMAN	Ubiquitin carboxyl-terminal hydrolase 10 (EC 3.1.2.15) (Ubiquitin thioesterase 10) (Ubiquitin-specif ...	0.52	+	nuc	0			609818		798
P35221 UniProt NPD GO	CTN1_HUMAN	Alpha-1 catenin (Cadherin-associated protein) (Alpha E-catenin) (NY-REN-13 antigen)	0.51	+	nuc	0	Cell membrane; cell-cell junction. Cell membrane; cell-matrix junction. Found at cell-cell boundarie ...		116805	1L7C	906
Q99962 UniProt NPD GO	SH3G2_HUMAN	SH3-containing GRB2-like protein 2 (EC 2.3.1.-) (SH3 domain protein 2A) (Endophilin 1) (EEN-B1)	0.51	+	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Concentrated in presynaptic nerve terminals in neu ...		604465	1X04	352
Q9NVD7 UniProt NPD GO	PARVA_HUMAN	Alpha-parvin (Calponin-like integrin-linked kinase-binding protein) (CH-ILKBP)	0.50	+	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side. Constituent of focal adhesion ...		608120		372
P62861 UniProt NPD GO	RS30_HUMAN	40S ribosomal protein S30	0.49	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	134690		59
Q9H2B2 UniProt NPD GO	SYT4_HUMAN	Synaptotagmin-4 (Synaptotagmin IV) (SytIV)	0.49	+	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein	integral to membrane [ISS]	600103	1UGK	425
O96018 UniProt NPD GO	APBA3_HUMAN	Amyloid beta A4 precursor protein-binding family A member 3 (Neuron-specific X11L2 protein) (Neurona ...	0.48	+	nuc	0		membrane [NAS]	604262		575
O15524 UniProt NPD GO	SOCS1_HUMAN	Suppressor of cytokine signaling 1 (SOCS-1) (JAK-binding protein) (JAB) (STAT-induced STAT inhibitor ...	0.47	+	nuc	0		cytoplasm [TAS]	603597		211
Q92845 UniProt NPD GO	KIFA3_HUMAN	Kinesin-associated protein 3 (Smg GDS-associated protein)	0.45	+	nuc	0		endoplasmic reticulum [TAS] kinesin II complex [ISS]	601836		792
Q9NYL9 UniProt NPD GO	TMOD3_HUMAN	Tropomodulin-3 (Ubiquitous tropomodulin) (U-Tmod)	0.45	+	nuc	0			605112		352
Q96BY2 UniProt NPD GO	MOAP1_HUMAN	Modulator of apoptosis 1 (MAP-1) (MAP1) (Paraneoplastic antigen MA4)	0.43	+	nuc	0			609485		351
P29966 UniProt NPD GO	MARCS_HUMAN	Myristoylated alanine-rich C-kinase substrate (MARCKS) (Protein kinase C substrate, 80 kDa protein, ...	0.43	+	nuc	0		actin cytoskeleton [TAS]	177061		331
Q9BZA7 UniProt NPD GO	PC11X_HUMAN	Protocadherin-11 X-linked precursor (Protocadherin-11) (Protocadherin on the X chromosome) (PCDH-X) ...	0.42	+	nuc	0	Membrane; single-pass type I membrane protein (Potential)		300246		1347
Q6QNY0 UniProt NPD GO	BL1S3_HUMAN	Biogenesis of lysosome-related organelles complex-1 subunit 3 (BLOC subunit 3)	0.41	+	nuc	0	Cytoplasm (By similarity)		609762		202
Q9BT88 UniProt NPD GO	SYT11_HUMAN	Synaptotagmin-11 (Synaptotagmin XI) (SytXI)	0.40	+	nuc	1 *	Membrane; single-pass membrane protein. In substantia nigra, observed in neuronal cell bodies and ne ...		608741		431
Q7L8A9 UniProt NPD GO	VASH_HUMAN	Vasohibin	0.40	+	nuc	0	Secreted protein (Probable)		609011		365
O60443 UniProt NPD GO	DFNA5_HUMAN	Non-syndromic hearing impairment protein 5 (Inversely correlated with estrogen receptor expression 1 ...	0.38	+	nuc	0			600994		496
Q9Y5I0 UniProt NPD GO	PCDAD_HUMAN	Protocadherin alpha 13 precursor (PCDH-alpha13)	0.35	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)		606319		950
Q9Y5H9 UniProt NPD GO	PCDA2_HUMAN	Protocadherin alpha 2 precursor (PCDH-alpha2)	0.34	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606308		948
P35527 UniProt NPD GO	K1C9_HUMAN	Keratin, type I cytoskeletal 9 (Cytokeratin-9) (CK-9) (Keratin-9) (K9)	0.32	+	nuc	0			607606		623
Q9Y5H8 UniProt NPD GO	PCDA3_HUMAN	Protocadherin alpha 3 precursor (PCDH-alpha3)	0.32	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606309		950
O60829 UniProt NPD GO	GAGC1_HUMAN	G antigen family C member 1 (Prostate-associated gene 4 protein) (PAGE-4) (PAGE-1) (GAGE-9)	0.30	+	nuc	0			300287		102
P62851 UniProt NPD GO	RS25_HUMAN	40S ribosomal protein S25	0.28	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	180465		125
Q15506 UniProt NPD GO	SP17_HUMAN	Sperm surface protein Sp17 (Sperm autoantigenic protein 17) (Sperm protein 17) (Sp17-1)	0.28	+	nuc	0	Membrane; peripheral membrane protein (Potential)		608621		151
Q9Y5I3 UniProt NPD GO	PCDA1_HUMAN	Protocadherin alpha 1 precursor (PCDH-alpha1)	0.26	+	nuc	0	Isoform 1: Cell membrane; single-pass type I membrane protein (By similarity). Isoform 2: Secreted p ...	integral to plasma membrane [TAS]	606307		950
Q9UN72 UniProt NPD GO	PCDA7_HUMAN	Protocadherin alpha 7 precursor (PCDH-alpha7)	0.26	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606313		937
Q9BXN1 UniProt NPD GO	ASPN_HUMAN	Asporin precursor (Periodontal ligament-associated protein 1) (PLAP-1)	0.25	+	nuc	0	Secreted protein; extracellular space; extracellular matrix		608135		379
Q96RP9 UniProt NPD GO	EFG1_HUMAN	Elongation factor G 1, mitochondrial precursor (mEF-G 1) (Elongation factor G1)	0.23	+	nuc	0	Mitochondrion		609060		751
Q8NBV8 UniProt NPD GO	SYT8_HUMAN	Synaptotagmin-8 (Synaptotagmin VIII) (SytVIII)	0.23	+	nuc	1 *	Cell membrane; single-pass type III membrane protein (By similarity). Acrosome (By similarity)		607719		172
P16435 UniProt NPD GO	NCPR_HUMAN	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.22	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Anchored to the ...	endoplasmic reticulum [TAS]	124015	1B1C	676
P62263 UniProt NPD GO	RS14_HUMAN	40S ribosomal protein S14	0.19	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	130620		150
P32320 UniProt NPD GO	CDD_HUMAN	Cytidine deaminase (EC 3.5.4.5) (Cytidine aminohydrolase)	0.16	+	nuc	0		cytosol [TAS] extracellular region [TAS]	123920	1MQ0	146
O75688 UniProt NPD GO	PP2CB_HUMAN	Protein phosphatase 2C isoform beta (EC 3.1.3.16) (PP2C-beta)	0.11	+	nuc	0			603770		479
P21741 UniProt NPD GO	MK_HUMAN	Midkine precursor (MK) (Neurite outgrowth-promoting protein) (Midgestation and kidney protein) (Amph ...	0.10	+	nuc	1 *	Secreted protein		162096	1MKN	143
P15880 UniProt NPD GO	RS2_HUMAN	40S ribosomal protein S2 (S4) (LLRep3 protein)	0.05	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	603624		293

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.