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
P21760 UniProt NPD GO	EXFAB_CHICK	Extracellular fatty acid-binding protein precursor (Ex-FABP) (Quiescence-specific protein) (p20K) (C ...	0.07	-	exc	0	Secreted protein				178
P26914 UniProt NPD GO	GLB_PSEDC	Extracellular globin precursor	0.07	-	end	0	Secreted protein; extracellular space				333
O13529 UniProt NPD GO	ECM12_YEAST	Extracellular matrix protein 12	0.07	-	cyt	2 *	Membrane; multi-pass membrane protein (Potential)				151
P36156 UniProt NPD GO	ECM4_YEAST	Extracellular matrix protein 4	0.07	-	mit	0	Cytoplasm	cytoplasm [IDA]			370
Q93794 UniProt NPD GO	SEL10_CAEEL	F-box/WD repeat protein sel-10 (Suppressor/enhancer of lin-12) (Sel-10 protein)	0.07	-	cyt	0					587
Q6MV78 UniProt NPD GO	YFAS1_NEUCR	FAS1 domain-containing protein NCU02579 precursor	0.07	-	exc	0	Vacuole (By similarity)				228
Q6BP84 UniProt NPD GO	FKBP2_DEBHA	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.07	-	end	0	Endoplasmic reticulum (By similarity)				135
Q6CGG3 UniProt NPD GO	FKBP2_YARLI	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.07	-	end	1 *	Endoplasmic reticulum (By similarity)				144
Q41649 UniProt NPD GO	FKB15_VICFA	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.07	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				151
P43172 UniProt NPD GO	FAR9_ASCSU	FMRFamide-like neuropeptide AF9	0.07	-		0	Secreted protein				9
P58549 UniProt NPD GO	FXYD7_HUMAN	FXYD domain-containing ion transport regulator 7	0.07	-	nuc	1 *			606684		80
Q9SJ81 UniProt NPD GO	FLA7_ARATH	Fasciclin-like arabinogalactan protein 7 precursor	0.07	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			254
P54398 UniProt NPD GO	FBP2_DROME	Fat body protein 2 (Fat body protein P6)	0.07	-	cyt	0					256
Q9U1G6 UniProt NPD GO	FABP3_FASHE	Fatty acid-binding protein type 3	0.07	-	cyt	0					132
Q01469 UniProt NPD GO	FABPE_HUMAN	Fatty acid-binding protein, epidermal (E-FABP) (Psoriasis-associated fatty acid-binding protein homo ...	0.07	-	cyt	0	Cytoplasm	cytoplasm [TAS]	605168	1JJJ	134
P55050 UniProt NPD GO	FABPI_MOUSE	Fatty acid-binding protein, intestinal (I-FABP) (FABPI)	0.07	-	cyt	0	Cytoplasm				131
Q45KW7 UniProt NPD GO	FABPI_PIG	Fatty acid-binding protein, intestinal (I-FABP) (FABPI)	0.07	-	cyt	0	Cytoplasm (By similarity)				131
P81653 UniProt NPD GO	FABPL_HALBI	Fatty acid-binding protein, liver (L-FABP)	0.07	-	cyt	0	Cytoplasm (By similarity)				125
O08914 UniProt NPD GO	FAAH_MOUSE	Fatty-acid amide hydrolase (EC 3.1.-.-) (Oleamide hydrolase) (Anandamide amidohydrolase)	0.07	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Golgi apparatus ...				579
Q98U06 UniProt NPD GO	KRFB_CATAU	Feather beta keratin (F-ker)	0.07	-	nuc	0					97
P00455 UniProt NPD GO	FENR_SPIOL	Ferredoxin--NADP reductase, chloroplast precursor (EC 1.18.1.2) (FNR)	0.07	-	mit	0	Plastid; chloroplast; chloroplast stroma. Stromal side of the thylakoid membrane in the vicinity of ...			1FRQ	369
P00240 UniProt NPD GO	FER2_DUNSA	Ferredoxin-2 (Ferredoxin II)	0.07	-	nuc	0	Plastid; chloroplast				95
O42807 UniProt NPD GO	FAEA_ASPNG	Feruloyl esterase A precursor (EC 3.1.1.73) (Ferulic acid esterase A) (FAE-III) (Cinnamoyl esterase) ...	0.07	-	exc	0	Secreted protein	extracellular region [IDA]		2BJH	281
P12802 UniProt NPD GO	FIBB_ANAPL	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.07	-		0	Secreted protein				18
O59945 UniProt NPD GO	FIMB_SCHPO	Fimbrin	0.07	-	nuc	0	Localizes both to the cortical actin patches and to the medial ring in an F-actin-dependent manner	actin cortical patch [IDA] contractile ring (sensu Fungi) [IDA]		1RT8	614
P52839 UniProt NPD GO	FSTL_ARATH	Flavonol sulfotransferase-like (EC 2.8.2.-) (RaRO47)	0.07	-	cyt	0				1Q44	326
P42557 UniProt NPD GO	S19A1_CRIGR	Folate transporter 1 (Solute carrier family 19 member 1) (Folate carrier protein) (Methotrexate upta ...	0.07	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				518
P18427 UniProt NPD GO	FSHB_RAT	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.07	-	exc	0	Secreted protein				130
Q13642 UniProt NPD GO	FHL1_HUMAN	Four and a half LIM domains protein 1 (FHL-1) (Skeletal muscle LIM-protein 1) (SLIM 1) (SLIM)	0.07	-	nuc	0	Isoform 1, isoform 3: Cytoplasm. Isoform 2, isoform 3: Nucleus. Isoform 2: Cytoplasm; cytosol. Isofo ...		300163	2CUR	322
O14842 UniProt NPD GO	FFAR1_HUMAN	Free fatty acid receptor 1 (G-protein coupled receptor 40)	0.07	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603820		300
Q8K3T4 UniProt NPD GO	FFAR1_RAT	Free fatty acid receptor 1 (G-protein coupled receptor 40)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				300
Q24760 UniProt NPD GO	FRIZ_DROVI	Frizzled precursor (Frizzled-1) (dFz1)	0.07	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			583
Q9W742 UniProt NPD GO	FZ10B_XENLA	Frizzled-10-B precursor (Fz-10B) (Xfz10B) (Frizzled-9) (Xfz9)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				580
O93274 UniProt NPD GO	FZD8_XENLA	Frizzled-8 precursor (Fz-8) (Xfz8)	0.07	-	end	7	Membrane; multi-pass membrane protein				581
Q9MA79 UniProt NPD GO	F16P2_ARATH	Fructose-1,6-bisphosphatase, cytosolic (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.07	-	nuc	0	Cytoplasm (By similarity)				341
P53444 UniProt NPD GO	ALF_NEUCR	Fructose-bisphosphate aldolase (EC 4.1.2.13)	0.07	-	cyt	0					362
P53442 UniProt NPD GO	ALF_SCHMA	Fructose-bisphosphate aldolase (EC 4.1.2.13)	0.07	-	nuc	0					363
Q5NVR5 UniProt NPD GO	ALDOA_PONPY	Fructose-bisphosphate aldolase A (EC 4.1.2.13) (Muscle-type aldolase)	0.07	-	cyt	0					363
P05063 UniProt NPD GO	ALDOC_MOUSE	Fructose-bisphosphate aldolase C (EC 4.1.2.13) (Brain-type aldolase) (Aldolase 3) (Zebrin II) (Scrap ...	0.07	-	cyt	0		mitochondrion [IDA]			362
Q9I925 UniProt NPD GO	FUCL7_ANGJA	Fucolectin-7 precursor	0.07	-	mit	0	Secreted protein	extracellular space [IDA]			189
Q08584 UniProt NPD GO	FCPA_PHATR	Fucoxanthin-chlorophyll a-c binding protein A, chloroplast precursor	0.07	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. FCPs are probably ...				196
Q41094 UniProt NPD GO	FCPF_PHATR	Fucoxanthin-chlorophyll a-c binding protein F, chloroplast precursor	0.07	-	end	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. FCPs are probably ...				197
Q92806 UniProt NPD GO	IRK9_HUMAN	G protein-activated inward rectifier potassium channel 3 (GIRK3) (Potassium channel, inwardly rectif ...	0.07	+	end	3	Membrane; multi-pass membrane protein		600932		393
Q95NT6 UniProt NPD GO	MTH2_DROYA	G-protein coupled receptor Mth2 precursor (Protein methuselah-2)	0.07	-	end	7	Membrane; multi-pass membrane protein (Potential)				536
P23591 UniProt NPD GO	FCL_MOUSE	GDP-L-fucose synthetase (EC 1.1.1.271) (Protein FX) (Red cell NADP(H)-binding protein) (GDP-4-keto-6 ...	0.07	-	cyt	0					321
Q93VR3 UniProt NPD GO	GME_ARATH	GDP-mannose 3,5-epimerase (EC 5.1.3.18) (GDP-Man 3,5-epimerase)	0.07	-	cyt	0				2C5E	377
Q338B5 UniProt NPD GO	GME1_ORYSA	GDP-mannose 3,5-epimerase 1 (EC 5.1.3.18) (GDP-Man 3,5-epimerase 1) (OsGME-1)	0.07	-	cyt	0					378
Q2H0X9 UniProt NPD GO	MCD4_CHAGB	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-)	0.07	-	end	13	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				921
Q9R1S3 UniProt NPD GO	PIGN_MOUSE	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-) (Phosphatidylinositol-glycan biosynthesis clas ...	0.07	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				931
Q74ZS2 UniProt NPD GO	GPI13_ASHGO	GPI ethanolamine phosphate transferase 3 (EC 2.-.-.-) (Glycosylphosphatidylinositol-anchor biosynthe ...	0.07	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				1013

You are viewing entries 70001 to 70050 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.