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
P15828 UniProt NPD GO	GUX1_HUMGT	Exoglucanase 1 precursor (EC 3.2.1.91) (Exoglucanase I) (Exocellobiohydrolase I) (1,4-beta-cellobioh ...	0.15	-	exc	0					525
Q92400 UniProt NPD GO	GUX2_AGABI	Exoglucanase precursor (EC 3.2.1.91) (Exocellobiohydrolase) (1,4-beta-cellobiohydrolase) (Beta-gluca ...	0.15	-	exc	0					506
Q9NH13 UniProt NPD GO	RP43_RIFPA	Exoskeleton protein RP43 precursor	0.15	-	cyt	0					421
P80022 UniProt NPD GO	RNLE_LYCES	Extracellular ribonuclease LE precursor (EC 3.1.27.1) (RNase LE)	0.15	-	exc	1 *	Secreted protein; extracellular space. Cell wall			1DIX	230
P34461 UniProt NPD GO	SODE_CAEEL	Extracellular superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1) (EC-SOD)	0.15	-	exc	0	Isoform 1: Secreted protein; extracellular space. Isoform 2: Membrane; peripheral membrane protein ( ...				221
P47755 UniProt NPD GO	CAZA2_HUMAN	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.15	-	nuc	0		F-actin capping protein complex [TAS]	601571		285
Q2QLF0 UniProt NPD GO	CAZA2_PANTR	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.15	-	nuc	0					285
Q5R4P6 UniProt NPD GO	CAZA2_PONPY	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.15	-	nuc	0					285
Q8NI29 UniProt NPD GO	FBX27_HUMAN	F-box only protein 27 (F-box/G-domain protein 5)	0.15	-	mit	0			609099		283
Q9QXE7 UniProt NPD GO	TBLX_MOUSE	F-box-like/WD repeat protein TBL1X (Transducin beta-like 1X protein)	0.15	-	cyt	0	Nucleus (By similarity)	transcription factor complex [IDA]			527
O60907 UniProt NPD GO	TBL1X_HUMAN	F-box-like/WD repeat protein TBL1X (Transducin beta-like 1X protein) (Transducin-beta-like 1, X-link ...	0.15	-	cyt	0	Nucleus (Probable)		300196		526
Q2UN37 UniProt NPD GO	FKBP4_ASPOR	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.15	+	cyt	0	Nucleus; nucleolus (By similarity)				470
P08022 UniProt NPD GO	FMR4_APLCA	FMRFamide neuropeptides type FMRF-4 precursor [Contains: FMRFamide] (Fragment)	0.15	-	cyt	0	Secreted protein				196
O42633 UniProt NPD GO	FAT1_COCHE	Fatty acid transporter protein	0.15	-	cyt	0	Membrane; multi-pass membrane protein (Potential)				643
Q8MUC1 UniProt NPD GO	FABP_CLOSI	Fatty acid-binding protein	0.15	-	cyt	0					133
P97612 UniProt NPD GO	FAAH_RAT	Fatty-acid amide hydrolase (EC 3.1.-.-) (Oleamide hydrolase) (Anandamide amidohydrolase)	0.15	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Golgi apparatus ...	integral to membrane [TAS]		1MT5	579
Q962W7 UniProt NPD GO	FAR1_LOALO	Fatty-acid and retinol-binding protein 1 precursor (Ll-FAR-1) (Ll20)	0.15	-	exc	1 *	Secreted protein (By similarity)	extracellular region [ISS]			178
P07797 UniProt NPD GO	FRI3_RANCA	Ferritin, lower subunit (Ferritin L)	0.15	-	nuc	0				1RCI	173
P25319 UniProt NPD GO	FRIH1_SCHMA	Ferritin-1 heavy chain (EC 1.16.3.1)	0.15	-	cyt	0					173
Q08830 UniProt NPD GO	FGL1_HUMAN	Fibrinogen-like protein 1 precursor (Hepatocyte-derived fibrinogen-related protein 1) (HFREP-1) (Hep ...	0.15	-	cyt	0	Secreted protein	fibrinogen complex [TAS]	605776		312
O70165 UniProt NPD GO	FCN1_MOUSE	Ficolin-1 precursor (Collagen/fibrinogen domain-containing protein 1) (Ficolin-A) (Ficolin A) (M-Fic ...	0.15	-	exc	0	Secreted protein. Found on the monocyte surface (By similarity)				334
Q9WTS8 UniProt NPD GO	FCN1_RAT	Ficolin-1 precursor (Collagen/fibrinogen domain-containing protein 1) (Ficolin-A) (Ficolin A) (M-Fic ...	0.15	-	exc	0	Secreted protein. Found on the monocyte surface (By similarity)				335
P82659 UniProt NPD GO	THGF_HELAN	Flower-specific gamma-thionin precursor (Defensin SD2)	0.15	-	exc	1 *	Or: Cell wall (Potential). Or: Vacuole (Potential)				78
O13492 UniProt NPD GO	FOLE_NEUCR	Folylpolyglutamate synthase (EC 6.3.2.17) (Folylpoly-gamma-glutamate synthetase) (FPGS) (Tetrahydrof ...	0.15	-	mit	0					528
Q76JV1 UniProt NPD GO	FFAR1_MACFA	Free fatty acid receptor 1 (G-protein coupled receptor 40)	0.15	-	end	7 *	Membrane; multi-pass membrane protein				300
Q5RFA6 UniProt NPD GO	ALDOB_PONPY	Fructose-bisphosphate aldolase B (EC 4.1.2.13) (Liver-type aldolase)	0.15	-	cyt	0					363
Q91Y97 UniProt NPD GO	ALDOB_MOUSE	Fructose-bisphosphate aldolase B (EC 4.1.2.13) (Liver-type aldolase) (Aldolase 2)	0.15	-	cyt	0					363
P34800 UniProt NPD GO	CCN1_ANTMA	G2/mitotic-specific cyclin-1	0.15	-	nuc	0					473
Q9DG97 UniProt NPD GO	CCNB1_ORYLU	G2/mitotic-specific cyclin-B1	0.15	-	mit	0					401
Q6MG59 UniProt NPD GO	G6B_RAT	G6b protein precursor	0.15	-	end	1	Membrane; multi-pass membrane protein				232
Q95W86 UniProt NPD GO	NFCP_CONGI	GFP-like non-fluorescent chromoprotein (cgCP)	0.15	-	cyt	0		host [ISS]			227
Q95W11 UniProt NPD GO	NFCP_CONPS	GFP-like non-fluorescent chromoprotein (cpCP)	0.15	-	cyt	0		host [ISS]			227
Q95W85 UniProt NPD GO	NFCP_RADMA	GFP-like non-fluorescent chromoprotein (hcCP) (HcRed)	0.15	-	cyt	0		host [ISS]		1YZW	227
Q6BZ57 UniProt NPD GO	GPI7_DEBHA	GPI ethanolamine phosphate transferase 2 (EC 2.-.-.-) (Glycosylphosphatidylinositol-anchor biosynthe ...	0.15	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				877
Q6FWN4 UniProt NPD GO	GPI18_CANGA	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.15	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				433
P20791 UniProt NPD GO	SAS2_DICDI	GTP-binding protein SAS2	0.15	-	mit	0					203
P51996 UniProt NPD GO	YPT32_YEAST	GTP-binding protein YPT32/YPT11 (Rab GTPase YPT32)	0.15	-	nuc	0	Golgi apparatus; Golgi membrane; lipid-anchor	endosome [IDA] Golgi apparatus [IDA] mitochondrial outer membrane [IDA]			221
P16976 UniProt NPD GO	YPTM1_MAIZE	GTP-binding protein YPTM1	0.15	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				208
Q7Z444 UniProt NPD GO	RASE_HUMAN	GTPase ERas precursor (E-Ras) (Embryonic stem cell-expressed Ras)	0.15	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity)		300437		233
P08642 UniProt NPD GO	RASH_CHICK	GTPase HRas precursor (Transforming protein p21) (p21ras) (H-Ras-1) (c-H-ras)	0.15	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Golgi apparatus; Golgi membrane; lipi ...				189
P01112 UniProt NPD GO	RASH_HUMAN	GTPase HRas precursor (Transforming protein p21) (p21ras) (H-Ras-1) (c-H-ras)	0.15	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side. Golgi apparatus; Golgi membrane; lipid-anchor. Shuttl ...	cytoplasm [TAS] plasma membrane [TAS]	109800	821P	189
Q61411 UniProt NPD GO	RASH_MOUSE	GTPase HRas precursor (Transforming protein p21) (p21ras) (H-Ras-1) (c-H-ras)	0.15	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Golgi apparatus; Golgi membrane; lipi ...				189
Q99JY3 UniProt NPD GO	GIMA4_MOUSE	GTPase, IMAP family member 4 (Immunity-associated protein 4) (Immunity-associated nucleotide 1 prote ...	0.15	-	cyt	0					219
Q01745 UniProt NPD GO	GAOA_DACDE	Galactose oxidase precursor (EC 1.1.3.9) (GAO)	0.15	-	exc	0	Secreted protein			1GOH	680
Q9PSN0 UniProt NPD GO	LECG_BITAR	Galactose-specific lectin (PAL)	0.15	-	cyt	0	Secreted protein	extracellular region [NAS]			135
P07480 UniProt NPD GO	GALA_PIG	Galanin precursor [Contains: Galanin; Galanin message-associated peptide (GMAP)]	0.15	-	exc	0	Secreted protein				123
Q62805 UniProt NPD GO	GALR1_RAT	Galanin receptor type 1 (GAL1-R) (GALR1)	0.15	+	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]			346
P38486 UniProt NPD GO	LEG3_CANFA	Galectin-3 (Galactose-specific lectin 3) (Mac-2 antigen) (IgE-binding protein) (35 kDa lectin) (Carb ...	0.15	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). May be secreted by a non-classical secretory pat ...				295
P08219 UniProt NPD GO	GBRA1_BOVIN	Gamma-aminobutyric-acid receptor alpha-1 subunit precursor (GABA(A) receptor)	0.15	-	end	4	Membrane; multi-pass membrane protein				456
P51914 UniProt NPD GO	CX41_XENLA	Gap junction Cx41 protein (Connexin-41)	0.15	-	end	4 *	Membrane; multi-pass membrane protein				351

You are viewing entries 56901 to 56950 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.