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
P41344 UniProt NPD GO	FENR1_ORYSA	Ferredoxin--NADP reductase, leaf isozyme, chloroplast precursor (EC 1.18.1.2) (FNR)	0.04	-	mit	0	Plastid; chloroplast; chloroplast stroma. Stromal side of the thylakoid membrane in the vicinity of ...				362
O04977 UniProt NPD GO	FENR1_TOBAC	Ferredoxin--NADP reductase, leaf-type isozyme, chloroplast precursor (EC 1.18.1.2) (FNR)	0.04	-	mit	0	Plastid; chloroplast; chloroplast stroma. Stromal side of the thylakoid membrane in the vicinity of ...				362
Q7M258 UniProt NPD GO	FER2_PEA	Ferredoxin-2 (Ferredoxin II) (Fragment)	0.04	-	nuc	0	Plastid; chloroplast				40
P27789 UniProt NPD GO	FER5_MAIZE	Ferredoxin-5, chloroplast precursor (Ferredoxin V) (Fd V)	0.04	-	mit	0	Plastid; chloroplast				135
P38365 UniProt NPD GO	FTRV_SPIOL	Ferredoxin-thioredoxin reductase, variable chain, chloroplast precursor (FTR-V) (Ferredoxin-thioredo ...	0.04	-	mit	0	Plastid; chloroplast				174
Q94FY2 UniProt NPD GO	FRI_MALXI	Ferritin, chloroplast precursor (EC 1.16.3.1) (Apf1)	0.04	-	nuc	0	Plastid; chloroplast (By similarity)				250
Q9S756 UniProt NPD GO	FRI4_ARATH	Ferritin-4, chloroplast precursor (EC 1.16.3.1)	0.04	-	mit	0	Plastid; chloroplast (By similarity)				259
Q948P5 UniProt NPD GO	FRI4_SOYBN	Ferritin-4, chloroplast precursor (EC 1.16.3.1) (SFerH-4)	0.04	-	mit	0	Plastid; chloroplast (By similarity)				247
Q9P979 UniProt NPD GO	FAEA_ASPAW	Feruloyl esterase A precursor (EC 3.1.1.73) (Ferulic acid esterase A) (FAEA) (Feruloylesterase)	0.04	-	mit	0	Secreted protein (By similarity)	extracellular region [ISS]			281
Q8WZI8 UniProt NPD GO	FAEB_ASPNG	Feruloyl esterase B precursor (EC 3.1.1.73) (Ferulic acid esterase B) (FAEB) (FAE-I) (Cinnamoyl este ...	0.04	-	vac	0	Secreted protein	extracellular region [IDA]			521
P81070 UniProt NPD GO	FIBR_PACLE	Fibrinogen (VHDL) (Fragment)	0.04	-		0	Secreted protein; extracellular space				20
P14537 UniProt NPD GO	FIBB_CERSI	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.04	-		0	Secreted protein				10
P14538 UniProt NPD GO	FIBB_ELEMA	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.04	-		0	Secreted protein				20
P14476 UniProt NPD GO	FIBB_ODOHE	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.04	-	cyt	0	Secreted protein				21
P19343 UniProt NPD GO	FIBB_PAPHA	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.04	-		0	Secreted protein				9
P14477 UniProt NPD GO	FIBB_PIG	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.04	-		0	Secreted protein				19
P19342 UniProt NPD GO	FIBB_THEGE	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.04	-		0	Secreted protein				9
Q99050 UniProt NPD GO	FIBH_BOMMA	Fibroin heavy chain precursor (Fib-H) (H-fibroin) (Fragment)	0.04	-	exc	0					178
P49013 UniProt NPD GO	FBP3_STRPU	Fibropellin C precursor (Epidermal growth factor-related protein 3) (EGF III) (Fibropellin III)	0.04	-	exc	0	Secreted protein; extracellular space				570
P10079 UniProt NPD GO	FBP1_STRPU	Fibropellin-1 precursor (Fibropellin-I) (Epidermal growth factor-related protein 1) (UEGF-1)	0.04	-	exc	0	Secreted protein; extracellular space. Cytoplasmic vesicle. Secreted protein; extracellular space; h ...				1064
O00602 UniProt NPD GO	FCN1_HUMAN	Ficolin-1 precursor (Collagen/fibrinogen domain-containing protein 1) (Ficolin-A) (Ficolin A) (M-Fic ...	0.04	-	mit	0	Secreted protein. Found on the monocyte surface		601252		326
Q26678 UniProt NPD GO	FCA3_TRYBB	Flagellar calcium-binding protein TB-44A (44 kDa calflagin) (44 kDa calcimedin)	0.04	-	nuc	0	Flagellum				407
Q01657 UniProt NPD GO	RSP6_CHLRE	Flagellar radial spoke protein 6	0.04	-	cyt	0	Radial spoke				459
P39676 UniProt NPD GO	FHP_YEAST	Flavohemoprotein (Hemoglobin-like protein) (Flavohemoglobin) (Nitric oxide dioxygenase) (EC 1.14.12. ...	0.04	-	nuc	0		cytoplasm [IDA] cytosol [IDA] mitochondrial matrix [IDA] mitochondrion [IDA]			399
Q9SD85 UniProt NPD GO	F3PH_ARATH	Flavonoid 3'-monooxygenase (EC 1.14.13.21) (Flavonoid 3'-hydroxylase) (AtF3'H) (Cytochrome P450 75B1 ...	0.04	-	mit	1 *	Membrane; single-pass type III membrane protein (Potential)				513
Q9M547 UniProt NPD GO	FLS_EUSGR	Flavonol synthase/flavanone 3-hydroxylase (EC 1.14.11.23) (EC 1.14.11.9) (FLS)	0.04	-	cyt	0	Cytoplasm (By similarity)				334
Q41452 UniProt NPD GO	FLS_SOLTU	Flavonol synthase/flavanone 3-hydroxylase (EC 1.14.11.23) (EC 1.14.11.9) (FLS)	0.04	-	cyt	0	Cytoplasm				349
Q8GTM0 UniProt NPD GO	DEF_NICAL	Flower-specific defensin precursor (NaD1)	0.04	-	exc	1 *	Vacuole			1MR4	105
Q17766 UniProt NPD GO	FOLT1_CAEEL	Folate-like transporter 1	0.04	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				360
P80663 UniProt NPD GO	FSHB_STRCA	Follitropin beta chain (Follicle-stimulating hormone subunit beta) (FSH-beta) (FSH-B)	0.04	-	cyt	0	Secreted protein				106
P04837 UniProt NPD GO	FSHB_BOVIN	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.04	-	mit	0	Secreted protein				129
P01227 UniProt NPD GO	FSHB_SHEEP	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.04	-	exc	0	Secreted protein				129
Q6EV79 UniProt NPD GO	FSHB_MACFA	Follitropin beta chain precursor (Follicle-stimulating hormone subunit beta) (FSH-beta) (FSH-B)	0.04	-	exc	0	Secreted protein (By similarity)				129
Q08911 UniProt NPD GO	FDH1_YEAST	Formate dehydrogenase 1 (EC 1.2.1.2) (NAD-dependent formate dehydrogenase 1)	0.04	-	nuc	0	Cytoplasm	cytosol [IDA]			376
Q08987 UniProt NPD GO	FDH2_YEAST	Formate dehydrogenase 2 (EC 1.2.1.2) (NAD-dependent formate dehydrogenase 2)	0.04	-	nuc	0	Cytoplasm				376
O35943 UniProt NPD GO	FRDA_MOUSE	Frataxin, mitochondrial precursor (Fxn)	0.04	-	mit	0	Mitochondrion. Mitochondrial and extramitochondrial (By similarity)	mitochondrion [IDA]			207
O70421 UniProt NPD GO	FZD1_MOUSE	Frizzled-1 precursor (Fz-1) (mFz1)	0.04	-	end	7	Membrane; multi-pass membrane protein				642
Q08463 UniProt NPD GO	FZD1_RAT	Frizzled-1 precursor (Fz-1) (rFz1)	0.04	-	end	7	Membrane; multi-pass membrane protein				641
Q8CHL0 UniProt NPD GO	FZD5_RAT	Frizzled-5 precursor (Fz-5)	0.04	-	end	7	Cell membrane; multi-pass membrane protein (By similarity). Golgi apparatus; Golgi membrane; multi-p ...				585
Q05079 UniProt NPD GO	F16P_KLULA	Fructose-1,6-bisphosphatase (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase) (FBPase)	0.04	-	cyt	0					354
Q07204 UniProt NPD GO	F16P1_BRANA	Fructose-1,6-bisphosphatase, chloroplast precursor (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phos ...	0.04	-	end	0	Plastid; chloroplast; chloroplast stroma				411
Q9HGY9 UniProt NPD GO	ALF_ASPOR	Fructose-bisphosphate aldolase (EC 4.1.2.13)	0.04	-	cyt	0					362
P36580 UniProt NPD GO	ALF_SCHPO	Fructose-bisphosphate aldolase (EC 4.1.2.13)	0.04	-	cyt	0					358
P46563 UniProt NPD GO	ALF2_CAEEL	Fructose-bisphosphate aldolase 2 (EC 4.1.2.13) (Aldolase CE-2) (CE2)	0.04	-	cyt	0					366
P17784 UniProt NPD GO	ALF_ORYSA	Fructose-bisphosphate aldolase cytoplasmic isozyme (EC 4.1.2.13) (Gravity-specific protein GSC 233)	0.04	-	cyt	0	Cytoplasm				358
Q40677 UniProt NPD GO	ALFC_ORYSA	Fructose-bisphosphate aldolase, chloroplast precursor (EC 4.1.2.13) (ALDP)	0.04	-	cyt	0	Plastid; chloroplast				388
P22197 UniProt NPD GO	ALF_ARATH	Fructose-bisphosphate aldolase, cytoplasmic isozyme (EC 4.1.2.13)	0.04	-	cyt	0	Cytoplasm				358
P53445 UniProt NPD GO	ALF1_LAMJA	Fructose-bisphosphate aldolase, muscle type (EC 4.1.2.13)	0.04	-	cyt	0					363
P14903 UniProt NPD GO	FSPM_LYCES	Fruit-specific protein	0.04	-	nuc	1 *					96
Q40299 UniProt NPD GO	FCPC_MACPY	Fucoxanthin-chlorophyll a-c binding protein C, chloroplast precursor	0.04	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. FCPs are probably ...				216

You are viewing entries 77001 to 77050 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.