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
P34152 UniProt NPD GO	FAK1_MOUSE	Focal adhesion kinase 1 (EC 2.7.10.2) (FADK 1) (pp125FAK)	0.62	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side. Constituent of focal adhesion ...	focal adhesion [IDA] lamellipodium [IDA]		1KL0	1090
O35392 UniProt NPD GO	FOXD2_MOUSE	Forkhead box protein D2 (Mesoderm/mesenchyme forkhead 2) (MF-2)	0.62	-	nuc	0	Nucleus (Probable)				492
Q9C009 UniProt NPD GO	FOXQ1_HUMAN	Forkhead box protein Q1 (Hepatocyte nuclear factor 3 forkhead homolog 1) (HNF-3/forkhead-like protei ...	0.62	-	nuc	0	Nucleus (By similarity)				403
P34947 UniProt NPD GO	GRK5_HUMAN	G protein-coupled receptor kinase 5 (EC 2.7.11.16) (G protein-coupled receptor kinase GRK5)	0.62	+	cyt	0		cytoplasm [TAS] soluble fraction [TAS]	600870		590
P56581 UniProt NPD GO	TDG_MOUSE	G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.-) (C-JUN leucine zipper interactive protein ...	0.62	+	nuc	0	Nucleus				397
P43062 UniProt NPD GO	CG12_CANAL	G1/S-specific cyclin CLN2	0.62	+	nuc	0					465
Q9HEV5 UniProt NPD GO	ASD4_NEUCR	GATA type zinc finger protein Asd4 (Ascus development protein 4)	0.62	-	nuc	0	Nucleus				426
O93512 UniProt NPD GO	GFRA4_CHICK	GDNF family receptor alpha-4 precursor (GFR-alpha-4)	0.62	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				431
Q60865 UniProt NPD GO	GP137_MOUSE	GPI-anchored protein p137 (p137GPI)	0.62	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (Probable)				656
P70426 UniProt NPD GO	RIT1_MOUSE	GTP-binding protein Rit1 (Ras-like protein expressed in many tissues) (Ras-like without CAAX protein ...	0.62	+	nuc	0	Cell membrane	plasma membrane [IDA]			219
P48169 UniProt NPD GO	GBRA4_HUMAN	Gamma-aminobutyric-acid receptor alpha-4 subunit precursor (GABA(A) receptor)	0.62	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	137141		554
Q9BSJ2 UniProt NPD GO	GCP2_HUMAN	Gamma-tubulin complex component 2 (GCP-2) (Spindle pole body protein Spc97 homolog) (hSpc97) (hGCP2) ...	0.62	-	cyt	0	Centrosome	cytoplasmic microtubule [TAS] microtubule organizing center [TAS]			902
Q9SC88 UniProt NPD GO	GCP4_MEDTR	Gamma-tubulin complex component 4 homolog	0.62	-	cyt	0	Centrosome (Potential)				739
P35436 UniProt NPD GO	NMDE1_MOUSE	Glutamate [NMDA] receptor subunit epsilon 1 precursor (N-methyl D-aspartate receptor subtype 2A) (NR ...	0.62	-	end	4	Membrane; multi-pass membrane protein	postsynaptic membrane [IDA] presynaptic membrane [IEP] synapse [IDA]			1464
P48525 UniProt NPD GO	SYEM_YEAST	Glutamyl-tRNA synthetase, mitochondrial (EC 6.1.1.17) (Glutamate--tRNA ligase) (GluRS)	0.62	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			536
Q09453 UniProt NPD GO	GLRB4_CAEEL	Glycine receptor beta-type chain 4 precursor	0.62	-	end	4	Membrane; multi-pass membrane protein (Potential)				473
O95995 UniProt NPD GO	GAS8_HUMAN	Growth-arrest-specific protein 8 (Growth arrest-specific 11)	0.62	-	nuc	0	Cytoplasm (By similarity). Associates with microtubules. Flagellum (By similarity). In spermatozoa, ...	flagellum (sensu Eukaryota) [ISS] microtubule [IDA]	605178		478
Q61MQ8 UniProt NPD GO	GPA7_CAEBR	Guanine nucleotide-binding protein alpha-7 subunit	0.62	-	nuc	0					352
Q21917 UniProt NPD GO	GPA7_CAEEL	Guanine nucleotide-binding protein alpha-7 subunit	0.62	-	nuc	0					352
Q20907 UniProt NPD GO	GPA8_CAEEL	Guanine nucleotide-binding protein alpha-8 subunit	0.62	-	cyt	0					364
Q9ERL9 UniProt NPD GO	GCYA3_MOUSE	Guanylate cyclase soluble subunit alpha-3 (EC 4.6.1.2) (GCS-alpha-3) (Soluble guanylate cyclase larg ...	0.62	-	cyt	0	Cytoplasm				691
Q9QC07 UniProt NPD GO	POK7_HUMAN	HERV-K_1q23.3 provirus ancestral Pol protein (HERV-K18 Pol protein) (HERV-K110 Pol protein) (HERV-K( ...	0.62	-	mit	0					812
Q90691 UniProt NPD GO	HAND1_CHICK	Heart- and neural crest derivatives-expressed protein 1 (Extraembryonic tissues, heart, autonomic ne ...	0.62	+	nuc	0					202
P12861 UniProt NPD GO	HSP83_TRYBB	Heat shock protein 83	0.62	-	cyt	0	Cytoplasm	centrosome [NAS]			703
P46633 UniProt NPD GO	HS90A_CRIGR	Heat shock protein HSP 90-alpha (HSP 86)	0.62	-	nuc	0	Cytoplasm (By similarity)				732
O02705 UniProt NPD GO	HS90A_PIG	Heat shock protein HSP 90-alpha (HSP 86)	0.62	-	nuc	0	Cytoplasm				732
P07900 UniProt NPD GO	HS90A_HUMAN	Heat shock protein HSP 90-alpha (HSP 86) (NY-REN-38 antigen)	0.62	-	nuc	0	Cytoplasm	cytosol [NAS]	140571	2CDD	731
Q76LV1 UniProt NPD GO	HS90B_BOVIN	Heat shock protein HSP 90-beta	0.62	-	cyt	0	Cytoplasm (By similarity)				723
Q9GKX8 UniProt NPD GO	HS90B_HORSE	Heat shock protein HSP 90-beta (HSP 84)	0.62	-	nuc	0	Cytoplasm				723
P08238 UniProt NPD GO	HS90B_HUMAN	Heat shock protein HSP 90-beta (HSP 84) (HSP 90)	0.62	-	cyt	0	Cytoplasm	cytoplasm [NAS]	140572	1UYM	723
O08983 UniProt NPD GO	HPS1_MOUSE	Hermansky-Pudlak syndrome 1 protein homolog	0.62	-	cyt	0					704
Q03973 UniProt NPD GO	HMO1_YEAST	High mobility group protein 1 (High spontaneous mutagenesis protein 2)	0.62	+	nuc	0	Nucleus; nucleolus. Colocalizes with FOB1	cytoplasm [IDA] nucleolus [IDA] nucleus [IDA]			246
O88502 UniProt NPD GO	PDE8A_MOUSE	High-affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A (EC 3.1.4.17) (MM ...	0.62	-	nuc	0					823
Q7M4G7 UniProt NPD GO	H2B_ASTPE	Histone H2B	0.62	+	nuc	0	Nucleus				121
P19374 UniProt NPD GO	H2B_PLADU	Histone H2B	0.62	+	nuc	0	Nucleus				122
Q96A08 UniProt NPD GO	H2B1A_HUMAN	Histone H2B type 1-A (Histone H2B, testis) (Testis-specific histone H2B)	0.62	+	nuc	0	Nucleus		609904		126
P02286 UniProt NPD GO	H2B_ASTRU	Histone H2B, gonadal	0.62	+	nuc	0	Nucleus				121
Q6C710 UniProt NPD GO	ESA1_YARLI	Histone acetyltransferase ESA1 (EC 2.3.1.48)	0.62	+	cyt	0	Nucleus (By similarity)				469
Q6CN95 UniProt NPD GO	HAT1_KLULA	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.62	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				390
Q8GZB6 UniProt NPD GO	SUVH4_ARATH	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 (EC 2.1.1.43) (Histone H3-K9 methyltr ...	0.62	-	nuc	0	Nucleus. Associates with centromeric constitutive heterochromatin and at a lower level with regions ...				624
O82175 UniProt NPD GO	SUVH5_ARATH	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5 (EC 2.1.1.43) (Histone H3-K9 methyltr ...	0.62	-	nuc	0	Nucleus (By similarity). Associates with centromeric constitutive heterochromatin (By similarity)				794
Q04649 UniProt NPD GO	CDX2_MESAU	Homeobox protein CDX-2 (Caudal-type homeobox protein 2)	0.62	+	nuc	0	Nucleus				313
P53775 UniProt NPD GO	DLL4_XENLA	Homeobox protein DLL-4 (XDLL-4)	0.62	+	nuc	0	Nucleus (Potential)				285
P50575 UniProt NPD GO	DLX5_RAT	Homeobox protein DLX-5 (DLX-3) (RDLX)	0.62	+	nuc	0	Nucleus (Potential)				289
Q98875 UniProt NPD GO	DLX1A_BRARE	Homeobox protein Dlx1a (DLX-1) (Distal-less homeobox gene 1a)	0.62	+	nuc	0	Nucleus (Potential)				252
P50576 UniProt NPD GO	DLX5A_BRARE	Homeobox protein Dlx5a (DLX-4) (Distal-less homeobox protein 5a)	0.62	+	nuc	0	Nucleus (Potential)				283
P50210 UniProt NPD GO	HXA13_AMBME	Homeobox protein Hox-A13 (Fragment)	0.62	+	nuc	0	Nucleus				107
P31271 UniProt NPD GO	HXA13_HUMAN	Homeobox protein Hox-A13 (Hox-1J)	0.62	+	nuc	0	Nucleus		176305		388
O43364 UniProt NPD GO	HXA2_HUMAN	Homeobox protein Hox-A2	0.62	+	nuc	0	Nucleus		604685		376
P02831 UniProt NPD GO	HXA3_MOUSE	Homeobox protein Hox-A3 (Hox-1.5) (MO-10)	0.62	+	nuc	0	Nucleus				443

You are viewing entries 17901 to 17950 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.