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
Q8BH95 UniProt NPD GO	ECHM_MOUSE	Enoyl-CoA hydratase, mitochondrial precursor (EC 4.2.1.17) (Short chain enoyl-CoA hydratase) (SCEH) ...	0.14	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			290
P54755 UniProt NPD GO	EPHA5_CHICK	Ephrin type-A receptor 5 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor CEK7)	0.14	-	end	0	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			1013
P54759 UniProt NPD GO	EPHA7_RAT	Ephrin type-A receptor 7 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EHK-3) (EPH homol ...	0.14	-	end	2 *	Membrane; single-pass type I membrane protein				998
P79728 UniProt NPD GO	EFNA5_BRARE	Ephrin-A5b precursor (EPH-related receptor tyrosine kinase ligand 7) (LERK-7) (AL-1) (ZfEPHL4)	0.14	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				228
Q63474 UniProt NPD GO	DDR1_RAT	Epithelial discoidin domain-containing receptor 1 precursor (EC 2.7.10.1) (Epithelial discoidin doma ...	0.14	-	end	1	Membrane; single-pass type I membrane protein				910
O95925 UniProt NPD GO	EPPI_HUMAN	Eppin precursor (Epididymal protease inhibitor) (Serine protease inhibitor-like with Kunitz and WAP ...	0.14	-	exc	0	Secreted protein (Potential)		609031		133
P16854 UniProt NPD GO	EST1_CULPI	Esterase B1 precursor (EC 3.1.1.1)	0.14	-	nuc	0					540
P49891 UniProt NPD GO	ST1E1_MOUSE	Estrogen sulfotransferase, testis isoform (EC 2.8.2.4) (Sulfotransferase, estrogen-preferring)	0.14	-	cyt	0	Cytoplasm			1BO6	295
Q9XH58 UniProt NPD GO	ETR1_PELHO	Ethylene receptor 1 (EC 2.7.13.3) (PhETR1)	0.14	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				740
Q9XH57 UniProt NPD GO	ETR2_PELHO	Ethylene receptor 2 (EC 2.7.13.3) (PhETR2)	0.14	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				741
Q5CD95 UniProt NPD GO	ERF1_BLEMU	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.14	-	cyt	0	Cytoplasm (By similarity)				436
Q9VPH7 UniProt NPD GO	ERF1_DROME	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.14	-	cyt	0	Cytoplasm (By similarity)				438
Q9D1M4 UniProt NPD GO	MCA3_MOUSE	Eukaryotic translation elongation factor 1 epsilon-1 (Multisynthetase complex auxiliary component p1 ...	0.14	-	cyt	0	Cytoplasm. Nucleus. Cytoplasmic under growth arrest conditions. Translocated into the nucleus when g ...	aminoacyl-tRNA synthetase multienzyme complex [NAS] cytoplasm [IDA] nucleus [IDA]			174
Q04067 UniProt NPD GO	IF34_YEAST	Eukaryotic translation initiation factor 3 RNA-binding subunit (eIF-3 RNA-binding subunit) (eIF3 p33 ...	0.14	-	nuc	0		eukaryotic translation initiation factor 3 ... [IDA]			274
P56570 UniProt NPD GO	IF4E5_CAEEL	Eukaryotic translation initiation factor 4E-5 (eIF4E-5) (eIF-4E-5) (mRNA cap-binding protein) (eIF-4 ...	0.14	-	cyt	0					240
P24152 UniProt NPD GO	EXTN_SORBI	Extensin precursor (Proline-rich glycoprotein)	0.14	-	exc	0					283
O74232 UniProt NPD GO	CAPZA_KLULA	F-actin capping protein subunit alpha	0.14	-	cyt	0					262
Q7SZM9 UniProt NPD GO	TB1RA_XENLA	F-box-like/WD repeat-containing protein TBL1XR1-A (Transducin beta-like 1X-related protein 1-A) (Nuc ...	0.14	-	cyt	0	Nucleus (By similarity)				519
Q5MJ12 UniProt NPD GO	FXL16_RAT	F-box/LRR-repeat protein 16 (F-box and leucine-rich repeat protein 16) (Spinal cord injury and regen ...	0.14	-	cyt	0					479
P30416 UniProt NPD GO	FKBP4_MOUSE	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (p59 ...	0.14	-	cyt	0	Cytoplasm. Nucleus	nucleus [IDA]			457
P83319 UniProt NPD GO	FAR4_PENMO	FMRFamide-like neuropeptide FLP4 (SQPSMRLRF-amide)	0.14	-		0	Secreted protein				9
P81456 UniProt NPD GO	FAB1_VICFA	Fabatin-1	0.14	-	nuc	0					47
P81457 UniProt NPD GO	FAB2_VICFA	Fabatin-2	0.14	-	nuc	0					47
Q92250 UniProt NPD GO	FPPS_NEUCR	Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes ...	0.14	-	cyt	1	Cytoplasm				347
P37261 UniProt NPD GO	FRM2_YEAST	Fatty acid repression mutant protein 2	0.14	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			193
P34731 UniProt NPD GO	FAS1_CANAL	Fatty acid synthase subunit beta (EC 2.3.1.86) [Includes: 3-hydroxypalmitoyl-[acyl-carrier-protein] ...	0.14	-	nuc	0					2037
Q8MZJ8 UniProt NPD GO	FAR1_ACAVI	Fatty-acid and retinol-binding protein 1 precursor (Av-FAR-1) (Av20)	0.14	-	gol	0	Secreted protein	extracellular region [IDA]			178
P07521 UniProt NPD GO	KRFT_COLLI	Feather keratin B-4 (F-ker)	0.14	-	nuc	0					95
Q9PSV3 UniProt NPD GO	KRF4_COLLI	Feather keratin Cos2-3 (F-ker)	0.14	-	nuc	0					100
Q91X85 UniProt NPD GO	FLVC2_MOUSE	Feline leukemia virus subgroup C receptor-related protein 2 (Calcium-chelate transporter) (CCT)	0.14	-	end	12	Cell membrane; multi-pass membrane protein				551
O04397 UniProt NPD GO	FENR2_TOBAC	Ferredoxin--NADP reductase, root-type isozyme, chloroplast precursor (EC 1.18.1.2) (FNR)	0.14	-	nuc	0	Plastid; chloroplast; chloroplast stroma. Stromal side of the thylakoid membrane in the vicinity of ...				375
O46119 UniProt NPD GO	FRIH_ECHGR	Ferritin heavy chain (EC 1.16.3.1)	0.14	-	cyt	0					173
O04921 UniProt NPD GO	HEMH2_ARATH	Ferrochelatase-2, chloroplast precursor (EC 4.99.1.1) (Ferrochelatase II) (Protoheme ferro-lyase 2) ...	0.14	-	nuc	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Plastid; chloroplast; chlor ...				512
Q756P0 UniProt NPD GO	FBRL_ASHGO	Fibrillarin	0.14	+	cyt	0	Nucleus; nucleolus (By similarity). Fibrillar region of the nucleolus (By similarity)				326
Q6BQ34 UniProt NPD GO	FBRL_DEBHA	Fibrillarin	0.14	+	cyt	0	Nucleus; nucleolus (By similarity). Fibrillar region of the nucleolus (By similarity)				329
P35549 UniProt NPD GO	FBRL_LEIMA	Fibrillarin	0.14	+	mit	0	Nucleus; nucleolus. Fibrillar region of the nucleolus				297
P68118 UniProt NPD GO	FIBB_CEREL	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.14	-	nuc	0	Secreted protein				21
P68119 UniProt NPD GO	FIBB_CEREN	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.14	-	nuc	0	Secreted protein				21
P22455 UniProt NPD GO	FGFR4_HUMAN	Fibroblast growth factor receptor 4 precursor (EC 2.7.10.1) (FGFR-4) (CD334 antigen)	0.14	-	end	0	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	134935	1QCT	802
Q9SBQ9 UniProt NPD GO	F3PH_PETHY	Flavonoid 3'-monooxygenase (EC 1.14.13.21) (Flavonoid 3'-hydroxylase) (Cytochrome P450 75B2)	0.14	-	end	1 *	Membrane; single-pass type III membrane protein (Potential)				512
P47799 UniProt NPD GO	FSHR_HORSE	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.14	-	end	7	Membrane; multi-pass membrane protein				694
O95633 UniProt NPD GO	FSTL3_HUMAN	Follistatin-related protein 3 precursor (Follistatin-like 3) (Follistatin-related gene protein)	0.14	-	exc	0	Secreted protein (Potential). Ref.3: Nucleus	extracellular space [TAS]	605343		263
P81438 UniProt NPD GO	FORM1_MYRGU	Formaecin-1	0.14	-		0	Secreted protein				16
Q2KJJ9 UniProt NPD GO	F16P2_BOVIN	Fructose-1,6-bisphosphatase isozyme 2 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.14	-	cyt	0					339
Q9XF47 UniProt NPD GO	F16P2_MUSAC	Fructose-1,6-bisphosphatase, cytosolic (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.14	-	nuc	0	Cytoplasm (By similarity)				341
P08417 UniProt NPD GO	FUMH_YEAST	Fumarate hydratase, mitochondrial precursor (EC 4.2.1.2) (Fumarase)	0.14	-	mit	0	Mitochondrion; mitochondrial matrix. Cytoplasm. Both fumarases are encoded by a single nuclear gene	cytosol [IDA] mitochondrial matrix [IDA]		1YFM	488
P35505 UniProt NPD GO	FAAA_MOUSE	Fumarylacetoacetase (EC 3.7.1.2) (Fumarylacetoacetate hydrolase) (Beta-diketonase) (FAA)	0.14	-	cyt	0				1QQJ	419
Q862A8 UniProt NPD GO	GPBAR_RABIT	G-protein coupled bile acid receptor 1	0.14	-	end	7 *	Cell membrane; multi-pass membrane protein (By similarity)				330
Q80SS6 UniProt NPD GO	GPBAR_MOUSE	G-protein coupled bile acid receptor 1 (Membrane-type receptor for bile acids) (M-BAR)	0.14	-	end	7 *	Cell membrane; multi-pass membrane protein (By similarity)				329
Q8TDU6 UniProt NPD GO	GPBAR_HUMAN	G-protein coupled bile acid receptor 1 (Membrane-type receptor for bile acids) (M-BAR) (hGPCR19) (BG ...	0.14	-	end	7 *	Cell membrane; multi-pass membrane protein				330

You are viewing entries 58301 to 58350 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.