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
Q9QUR2 UniProt NPD GO	DCTN4_RAT	Dynactin subunit 4 (Dynactin subunit p62)	0.60	-	nuc	0	Overexpression in cultured mammalian cells revealed colocalization with cortical actin, stress fiber ...	cytoplasmic dynein complex [TAS]			467
Q05193 UniProt NPD GO	DYN1_HUMAN	Dynamin-1 (EC 3.6.5.5)	0.60	-	nuc	0	Cytoplasm. Microtubule-associated		602377	2DYN	864
Q8LF21 UniProt NPD GO	DRP1C_ARATH	Dynamin-related protein 1C (Dynamin-like protein C) (Dynamin-like protein 5) (Dynamin-like protein D ...	0.60	-	mit	0	Cytoplasm. Microtubule-associated				614
P21959 UniProt NPD GO	CMC17_EIMAC	EAMZP30-47 protein (Fragment)	0.60	-	nuc	0	Membrane. Surface membrane and internal rhoptries				79
Q9VJ26 UniProt NPD GO	EFHD_DROME	EF-hand domain-containing protein CG10641 (Swiprosin homolog)	0.60	-	nuc	0					217
P61553 UniProt NPD GO	EFR1_CALJA	ERV-FRD provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Syncytin-2) [Contains: ...	0.60	-	end	2					538
P17679 UniProt NPD GO	GATA1_MOUSE	Erythroid transcription factor (GATA-binding factor 1) (GATA-1) (Eryf1) (GF-1) (NF-E1 DNA-binding pr ...	0.60	+	nuc	0	Nucleus	nucleus [IDA]		1Y0J	413
P17678 UniProt NPD GO	GATA1_CHICK	Erythroid transcription factor (GATA-binding factor 1) (GATA-1) (Eryf1) (NF-E1 DNA-binding protein) ...	0.60	-	nuc	0	Nucleus			3GAT	304
Q8L9K1 UniProt NPD GO	ERF13_ARATH	Ethylene-responsive transcription factor 13 (Ethylene-responsive element-binding factor 13) (EREBP-1 ...	0.60	-	nuc	0	Nucleus (Probable)				226
Q9XZ08 UniProt NPD GO	EXT3_DROME	Exostosin-3 (EC 2.4.1.223) (Protein brother of tout-velu)	0.60	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	endoplasmic reticulum [IDA] Golgi apparatus [IDA] integral to membrane [NAS]			972
O95677 UniProt NPD GO	EYA4_HUMAN	Eyes absent homolog 4 (EC 3.1.3.48)	0.60	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		605362		639
Q9CQ24 UniProt NPD GO	FBX36_MOUSE	F-box only protein 36	0.60	-	cyt	0					188
Q3T0J1 UniProt NPD GO	FBX4_BOVIN	F-box only protein 4	0.60	-	nuc	0					387
Q8N531 UniProt NPD GO	FBXL6_HUMAN	F-box/LRR-repeat protein 6 (F-box and leucine-rich repeat protein 6) (F-box protein FBL6) (FBL6A)	0.60	-	nuc	0			609076		539
Q8H6B1 UniProt NPD GO	SPT16_MAIZE	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16) (Global trans ...	0.60	+	cyt	0	Nucleus (By similarity)				1055
Q5M7V7 UniProt NPD GO	FAKD2_RAT	FAST kinase domains-containing protein 2	0.60	-	mit	0					679
O42479 UniProt NPD GO	HEMH_CHICK	Ferrochelatase, mitochondrial precursor (EC 4.99.1.1) (Protoheme ferro-lyase) (Heme synthetase)	0.60	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side (By similarity ...				402
Q91WJ0 UniProt NPD GO	FRS3_MOUSE	Fibroblast growth factor receptor substrate 3 (FGFR substrate 3) (FRS2-beta)	0.60	-	nuc	0	Membrane; lipid-anchor				491
Q8R2I0 UniProt NPD GO	FOXE1_MOUSE	Forkhead box protein E1 (Thyroid transcription factor 2) (TTF-2)	0.60	-	nuc	0	Nucleus (Potential)				371
O88470 UniProt NPD GO	FOXL2_MOUSE	Forkhead box protein L2 (Pituitary forkhead factor) (P-Frk)	0.60	-	nuc	0	Nucleus (Potential)				375
P42777 UniProt NPD GO	GBF4_ARATH	G-box-binding factor 4 (AtbZIP40)	0.60	-	nuc	0	Nucleus				270
Q8K3V3 UniProt NPD GO	GPR56_RAT	G-protein coupled receptor 56 precursor	0.60	-	end	8 *	Membrane; multi-pass membrane protein				687
Q8BUY8 UniProt NPD GO	GASP2_MOUSE	G-protein coupled receptor-associated sorting protein 2 (GASP-2)	0.60	-	nuc	0					826
P39949 UniProt NPD GO	CCNE1_RAT	G1/S-specific cyclin-E1	0.60	-	nuc	0	Nucleus (By similarity)				396
P36630 UniProt NPD GO	CG22_SCHPO	G2/mitotic-specific cyclin cig2/cyc17	0.60	-	nuc	0					411
Q8JZP9 UniProt NPD GO	GA2L1_MOUSE	GAS2-like protein 1 (Growth arrest-specific 2-like 1)	0.60	-	nuc	0					678
Q10351 UniProt NPD GO	PIGS_SCHPO	GPI transamidase component PIG-S homolog	0.60	+	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				554
Q9PWA3 UniProt NPD GO	GRIN2_CHICK	GRIN2-like protein (G protein-regulated inducer of neurite outgrowth 2-like protein) (G(o) alpha-int ...	0.60	-	nuc	0					518
Q5R6S2 UniProt NPD GO	DIRA2_PONPY	GTP-binding protein Di-Ras2 (Distinct subgroup of the Ras family member 2)	0.60	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				199
Q92963 UniProt NPD GO	RIT1_HUMAN	GTP-binding protein Rit1 (Ras-like protein expressed in many tissues) (Ras-like without CAAX protein ...	0.60	+	mit	0	Cell membrane	plasma membrane [TAS]	609591		219
P27681 UniProt NPD GO	GBRG3_MOUSE	Gamma-aminobutyric-acid receptor gamma-3 subunit precursor (GABA(A) receptor)	0.60	-	end	4	Membrane; multi-pass membrane protein				467
P28476 UniProt NPD GO	GBRR2_HUMAN	Gamma-aminobutyric-acid receptor rho-2 subunit precursor (GABA(A) receptor)	0.60	+	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	137162		465
P14922 UniProt NPD GO	SSN6_YEAST	Glucose repression mediator protein	0.60	-	nuc	0	Nucleus	nucleus [IPI]			966
P04776 UniProt NPD GO	GLYG1_SOYBN	Glycinin G1 precursor [Contains: Glycinin A1a subunit; Glycinin Bx subunit]	0.60	-	exc	0				1UD1	495
P35052 UniProt NPD GO	GPC1_HUMAN	Glypican-1 precursor	0.60	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	extracellular space [TAS] integral to plasma membrane [TAS]	600395		558
Q8N158 UniProt NPD GO	GPC2_HUMAN	Glypican-2 precursor	0.60	+	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				579
P29992 UniProt NPD GO	GNA11_HUMAN	Guanine nucleotide-binding protein subunit alpha-11 (G alpha-11) (Guanine nucleotide-binding protein ...	0.60	-	cyt	0		cytoplasm [TAS] plasma membrane [TAS]	139313		359
Q07553 UniProt NPD GO	GCY3E_DROME	Guanylate cyclase 32E precursor (EC 4.6.1.2)	0.60	-	end	0	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]			1163
Q4ZHS0 UniProt NPD GO	GCYA3_CANFA	Guanylate cyclase soluble subunit alpha-3 (EC 4.6.1.2) (GCS-alpha-3) (Soluble guanylate cyclase larg ...	0.60	-	cyt	0	Cytoplasm (By similarity)				690
Q9CPX5 UniProt NPD GO	HRSL5_MOUSE	HRAS-like suppressor 5 (H-rev107-like protein 5)	0.60	-	nuc	0					270
Q04619 UniProt NPD GO	HS90B_CHICK	Heat shock cognate protein HSP 90-beta	0.60	-	cyt	0	Cytoplasm	cytosol [IDA]			725
P40292 UniProt NPD GO	HSP90_ASPFU	Heat shock protein 90 (Heat shock protein hsp1) (65 kDa IgE-binding protein) (Allergen Asp f 12)	0.60	-	cyt	0					706
P40673 UniProt NPD GO	HMGB2_BOVIN	High mobility group protein B2 (High mobility group protein 2) (HMG-2)	0.60	-	nuc	0	Nucleus				208
P26583 UniProt NPD GO	HMGB2_HUMAN	High mobility group protein B2 (High mobility group protein 2) (HMG-2)	0.60	-	nuc	0	Nucleus	condensed chromosome [IDA] cytoplasm [IDA] nuclear chromosome [TAS] nucleus [IDA] perinuclear region [IDA]	163906		208
Q18336 UniProt NPD GO	H1X_CAEEL	Histone H1.X (Histone H1-like protein 1)	0.60	-	nuc	0	Nucleus (By similarity)				232
P59781 UniProt NPD GO	H2B_DROER	Histone H2B	0.60	+	nuc	0	Nucleus	nucleosome [ISS]			122
P17271 UniProt NPD GO	H2B_DROHY	Histone H2B	0.60	+	nuc	0	Nucleus	nucleosome [ISS]			122
Q76FE5 UniProt NPD GO	H2B_DROMA	Histone H2B	0.60	+	nuc	0	Nucleus	nucleosome [ISS]			122
P02283 UniProt NPD GO	H2B_DROME	Histone H2B	0.60	+	nuc	0	Nucleus	nucleosome [NAS]			122
Q76FE9 UniProt NPD GO	H2B_DROOR	Histone H2B	0.60	+	nuc	0	Nucleus	nucleosome [ISS]			122

You are viewing entries 19001 to 19050 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.