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
Q5RFK0 UniProt NPD GO	ETFB_PONPY	Electron transfer flavoprotein subunit beta (Beta-ETF)	0.16	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				254
P29692 UniProt NPD GO	EF1D_HUMAN	Elongation factor 1-delta (EF-1-delta) (Antigen NY-CO-4)	0.16	-	cyt	0		eukaryotic translation elongation factor 1 ... [TAS]	130592		280
P32324 UniProt NPD GO	EF2_YEAST	Elongation factor 2 (EF-2) (Translation elongation factor 2) (Eukaryotic elongation factor 2) (eEF2) ...	0.16	-	cyt	0	Cytoplasm	ribosome [TAS]		1ZM9	842
Q5BEP0 UniProt NPD GO	YSH1_EMENI	Endoribonuclease ysh1 (EC 3.1.27.-) (mRNA 3'-end-processing protein ysh1)	0.16	-	mit	1	Nucleus (By similarity)				884
Q6AYD4 UniProt NPD GO	ESAM_RAT	Endothelial cell-selective adhesion molecule precursor	0.16	-	mit	2 *	Cell membrane; cell-cell junction; adherens junction; single-pass type I membrane protein (By simila ...				394
Q60629 UniProt NPD GO	EPHA5_MOUSE	Ephrin type-A receptor 5 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EHK-1) (EPH homol ...	0.16	-	nuc	0	Membrane; single-pass type I membrane protein				877
P54760 UniProt NPD GO	EPHB4_HUMAN	Ephrin type-B receptor 4 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor HTK)	0.16	-	end	1	Membrane; single-pass type I membrane protein	cell surface [IEP] integral to plasma membrane [TAS]	600011		987
O43921 UniProt NPD GO	EFNA2_HUMAN	Ephrin-A2 precursor (EPH-related receptor tyrosine kinase ligand 6) (LERK-6) (HEK7-ligand) (HEK7-L)	0.16	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)		602756		213
Q6JVE5 UniProt NPD GO	LCN12_HUMAN	Epididymal-specific lipocalin-12 precursor	0.16	-	exc	0	Secreted protein (Potential)				192
P80299 UniProt NPD GO	HYES_RAT	Epoxide hydrolase 2 (EC 3.3.2.3) (Soluble epoxide hydrolase) (SEH) (Epoxide hydratase) (Cytosolic ep ...	0.16	-	mit	0	Cytoplasm. Peroxisome	cytosol [TAS] peroxisome [TAS]			554
P54116 UniProt NPD GO	STOM_MOUSE	Erythrocyte band 7 integral membrane protein (Stomatin) (Protein 7.2b)	0.16	-	nuc	1 *	Cell membrane; single-pass membrane protein; lipid-anchor; cytoplasmic side. Exposed on the cytoplas ...				284
Q2KL21 UniProt NPD GO	EPOR_CANFA	Erythropoietin receptor precursor (EPO-R)	0.16	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				508
P21370 UniProt NPD GO	EST2_CULPI	Esterase B2 (EC 3.1.1.1) (Fragment)	0.16	-	cyt	0					215
P70385 UniProt NPD GO	DHB3_MOUSE	Estradiol 17-beta-dehydrogenase 3 (EC 1.1.1.62) (17-beta-HSD 3) (Testicular 17-beta-hydroxysteroid d ...	0.16	-	nuc	0					305
P49333 UniProt NPD GO	ETR1_ARATH	Ethylene receptor (EC 2.7.13.3)	0.16	-	vac	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein			1DCF	738
Q9C5I3 UniProt NPD GO	ERF11_ARATH	Ethylene-responsive transcription factor 11 (Ethylene-responsive element-binding factor 11) (EREBP-1 ...	0.16	-	nuc	0	Nucleus (Probable)				166
Q9LW49 UniProt NPD GO	ERF4_NICSY	Ethylene-responsive transcription factor 4 (Ethylene-responsive element-binding factor 4 homolog) (E ...	0.16	-	nuc	0	Nucleus (Probable)				227
P51971 UniProt NPD GO	EIF1_CHICK	Eukaryotic translation initiation factor 1 (eIF1) (Protein translation factor SUI1 homolog) (Fragmen ...	0.16	-	cyt	0					79
P56286 UniProt NPD GO	IF2A_SCHPO	Eukaryotic translation initiation factor 2 subunit alpha (eIF-2-alpha)	0.16	-	nuc	0					306
P46411 UniProt NPD GO	EAA1_BOVIN	Excitatory amino acid transporter 1 (Sodium-dependent glutamate/aspartate transporter 1) (GLAST1)	0.16	-	end	10 *	Membrane; multi-pass membrane protein				542
P24942 UniProt NPD GO	EAA1_RAT	Excitatory amino acid transporter 1 (Sodium-dependent glutamate/aspartate transporter 1) (Glial glut ...	0.16	-	end	10 *	Membrane; multi-pass membrane protein				543
P43003 UniProt NPD GO	EAA1_HUMAN	Excitatory amino acid transporter 1 (Sodium-dependent glutamate/aspartate transporter 1) (Glial glut ...	0.16	-	end	10 *	Membrane; multi-pass membrane protein	membrane fraction [TAS]	600111		542
Q9YH99 UniProt NPD GO	EYA3_CHICK	Eyes absent homolog 3 (EC 3.1.3.48) (Fragment)	0.16	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				119
P28497 UniProt NPD GO	CAZA2_CHICK	F-actin capping protein alpha-2 subunit (CapZ 36/32) (Beta-actinin subunit I)	0.16	-	cyt	0	CapZ is located at the Z line in chicken muscle				286
Q2QL99 UniProt NPD GO	CAZA2_MONDO	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.16	-	cyt	0					285
Q78JE5 UniProt NPD GO	FBX22_MOUSE	F-box only protein 22	0.16	-	cyt	0					402
Q6GPC6 UniProt NPD GO	TB1RB_XENLA	F-box-like/WD repeat-containing protein TBL1XR1-B (Transducin beta-like 1X-related homolog 1-B) (Nuc ...	0.16	-	cyt	0	Nucleus (By similarity)				522
Q4INZ9 UniProt NPD GO	FKBP4_GIBZE	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.16	-	cyt	0	Nucleus; nucleolus (By similarity)				495
Q9XT11 UniProt NPD GO	FKBP5_AOTNA	FK506-binding protein 5 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (51 kDa FK506-binding imm ...	0.16	-	cyt	0	Cytoplasm				457
Q9XSH5 UniProt NPD GO	FKBP5_SAIBB	FK506-binding protein 5 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (51 kDa FK506-binding imm ...	0.16	-	cyt	0	Cytoplasm			1KT1	457
Q04433 UniProt NPD GO	FIT1_YEAST	Facilitator of iron transport 1 precursor	0.16	-	nuc	0	Cell wall; lipid-anchor; GPI-anchor	cell wall (sensu Fungi) [IDA]			528
P49945 UniProt NPD GO	FRIL2_MOUSE	Ferritin light chain 2 (Ferritin L subunit 2) (Ferritin subunit LG)	0.16	-	cyt	0					182
Q27200 UniProt NPD GO	FBRL_TETTH	Fibrillarin	0.16	+	cyt	0	Nucleus; nucleolus. Fibrillar region of the nucleolus				294
P22232 UniProt NPD GO	FBRL_XENLA	Fibrillarin	0.16	+	mit	0	Nucleus; nucleolus. Fibrillar region of the nucleolus				323
Q9JJN1 UniProt NPD GO	FGF21_MOUSE	Fibroblast growth factor 21 precursor (FGF-21)	0.16	-	exc	1 *	Secreted protein (Potential)				210
P05790 UniProt NPD GO	FIBH_BOMMO	Fibroin heavy chain precursor (Fib-H) (H-fibroin)	0.16	-	cyt	0					5263
O70497 UniProt NPD GO	FCN2_MOUSE	Ficolin-2 precursor (Collagen/fibrinogen domain-containing protein 2) (Ficolin-B) (Ficolin B) (Serum ...	0.16	-	exc	0	Secreted protein				306
O04395 UniProt NPD GO	FLS_MATIN	Flavonol synthase/flavanone 3-hydroxylase (EC 1.14.11.23) (EC 1.14.11.9) (FLS) (Fragment)	0.16	-	cyt	0	Cytoplasm				291
Q9Z2S9 UniProt NPD GO	FLOT2_RAT	Flotillin-2 (Reggie-1) (REG-1)	0.16	-	cyt	0	Membrane. In neuronal cells; associated with GPI-anchored cell-adhesion molecules	caveola [IDA] flotillin complex [IDA]			428
Q98TZ8 UniProt NPD GO	FLT2_BRARE	Flotillin-2a (Reggie-1a) (REG-1)	0.16	-	cyt	0	Membrane (By similarity). In neuronal cells; associated with GPI-anchored cell-adhesion molecules (B ...				428
P35376 UniProt NPD GO	FSHR_BOVIN	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.16	+	end	7	Membrane; multi-pass membrane protein				695
Q5GJ04 UniProt NPD GO	FSHR_FELCA	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.16	-	end	7	Membrane; multi-pass membrane protein				695
P35379 UniProt NPD GO	FSHR_SHEEP	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.16	-	end	7	Isoform FSH-R1, isoform FSH-R2: Cell membrane; multi-pass membrane protein. Isoform FSH-R3: Cell sur ...				695
Q8VCK6 UniProt NPD GO	FFAR2_MOUSE	Free fatty acid receptor 2 (G-protein coupled receptor 43) (Leukocyte-specific STAT-induced GPCR)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				330
P05062 UniProt NPD GO	ALDOB_HUMAN	Fructose-bisphosphate aldolase B (EC 4.1.2.13) (Liver-type aldolase)	0.16	-	cyt	0		cytoplasm [TAS]	229600	1XDM	363
Q8CG64 UniProt NPD GO	FKRP_MOUSE	Fukutin-related protein (EC 2.-.-.-)	0.16	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	Golgi apparatus [IDA]			494
Q96GU1 UniProt NPD GO	GGEE1_HUMAN	G antigen family E member 1 (Prostate-associated gene 5 protein) (PAGE-5)	0.16	-	mit	0					130
P41179 UniProt NPD GO	CCN1_TRYBB	G2/mitotic-specific cyclin-1	0.16	-	cyt	0					334
P46278 UniProt NPD GO	CCNB2_MEDVA	G2/mitotic-specific cyclin-2 (B-like cyclin) (CycMs2)	0.16	-	cyt	0					434
P13351 UniProt NPD GO	CCNB2_XENLA	G2/mitotic-specific cyclin-B2	0.16	-	mit	0					392

You are viewing entries 55601 to 55650 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.