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
P81399 UniProt NPD GO	FABP1_AMBME	Fatty acid-binding protein 1, liver (L-FABP)	0.02	-	cyt	0	Cytoplasm				126
O01814 UniProt NPD GO	FABP5_CAEEL	Fatty acid-binding protein homolog 5	0.02	-	cyt	0					136
P55776 UniProt NPD GO	FABH_ASCSU	Fatty acid-binding protein homolog precursor (AS-P18)	0.02	-	end	0				1AS1	163
Q99P61 UniProt NPD GO	FABPH_SPETR	Fatty acid-binding protein, heart (H-FABP) (Heart-type fatty acid-binding protein)	0.02	-	cyt	0	Cytoplasm (By similarity)				132
P11404 UniProt NPD GO	FABPH_MOUSE	Fatty acid-binding protein, heart (H-FABP) (Heart-type fatty acid-binding protein) (Mammary-derived ...	0.02	-	cyt	0	Cytoplasm				132
Q9ES43 UniProt NPD GO	FLVC1_MUSDU	Feline leukemia virus subgroup C receptor-related protein 1	0.02	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				560
P16464 UniProt NPD GO	F802_SCHMA	Female-specific protein 800 (FS800)	0.02	-	end	1 *					132
O78510 UniProt NPD GO	FER_GUITH	Ferredoxin	0.02	-	nuc	0	Plastid; chloroplast				96
P10770 UniProt NPD GO	FER_PERBI	Ferredoxin	0.02	-	nuc	0	Plastid; chloroplast				93
P21149 UniProt NPD GO	FER_TRIVA	Ferredoxin precursor	0.02	-	cyt	0	Hydrogenosome			1L5P	100
O04166 UniProt NPD GO	FER_PHYPA	Ferredoxin, chloroplast precursor	0.02	-	mit	0	Plastid; chloroplast				145
P17007 UniProt NPD GO	FER1_CYAPA	Ferredoxin-1 (Ferredoxin I)	0.02	-	nuc	0	Plastid; cyanelle				98
P00239 UniProt NPD GO	FER1_DUNSA	Ferredoxin-1 (Ferredoxin I)	0.02	-	nuc	0	Plastid; chloroplast				95
P81372 UniProt NPD GO	FERA_ALOMA	Ferredoxin-A (Fd A)	0.02	-	cyt	0	Plastid; chloroplast				97
Q08905 UniProt NPD GO	FRE3_YEAST	Ferric reductase transmembrane component 3 precursor (EC 1.16.1.7) (Ferric-chelate reductase 3)	0.02	+	end	7 *	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA]			711
Q39101 UniProt NPD GO	FRI1_ARATH	Ferritin-1, chloroplast precursor (EC 1.16.3.1) (AtFer1)	0.02	-	nuc	0	Plastid; chloroplast				255
P29036 UniProt NPD GO	FRI1_MAIZE	Ferritin-1, chloroplast precursor (EC 1.16.3.1) (ZmFer1)	0.02	-	nuc	0	Plastid; chloroplast. Plastid				254
P29390 UniProt NPD GO	FRI2_MAIZE	Ferritin-2, chloroplast precursor (EC 1.16.3.1) (ZmFer2)	0.02	-	mit	0	Plastid; chloroplast. Plastid				252
Q8CEK7 UniProt NPD GO	FATE1_MOUSE	Fetal and adult testis-expressed transcript protein homolog	0.02	-	nuc	1					99
P14440 UniProt NPD GO	FIBA_ANTAM	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.02	-		0	Secreted protein				19
P14535 UniProt NPD GO	FIBA_CERSI	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.02	-		0	Secreted protein				16
P14449 UniProt NPD GO	FIBA_EQUAS	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.02	-		0	Secreted protein				16
P14455 UniProt NPD GO	FIBA_MANLE	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.02	-		0	Secreted protein				16
P68117 UniProt NPD GO	FIBB_CAPHI	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.02	-		0	Secreted protein				20
P19346 UniProt NPD GO	FIBB_ERYPA	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.02	-		0	Secreted protein				9
P68116 UniProt NPD GO	FIBB_SHEEP	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.02	-		0	Secreted protein				20
P14481 UniProt NPD GO	FIBB_SYNCA	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.02	-	nuc	0	Secreted protein				21
P48803 UniProt NPD GO	FGF4_BOVIN	Fibroblast growth factor 4 precursor (FGF-4) (Heparin secretory-transforming protein) (HST) (HBGF-4) ...	0.02	-	mit	0					206
Q26680 UniProt NPD GO	FCA2_TRYBB	Flagellar calcium-binding protein TB-24 (24 kDa calflagin) (24 kDa calcimedin)	0.02	-	cyt	0	Flagellum				218
Q01656 UniProt NPD GO	RSP4_CHLRE	Flagellar radial spoke protein 4	0.02	-	cyt	0	Radial spoke	cilium [IDA]			465
O04773 UniProt NPD GO	C75A6_CAMME	Flavonoid 3',5'-hydroxylase (EC 1.14.13.88) (F3'5'H) (Cytochrome P450 75A6)	0.02	-	cyt	1 *					523
P48419 UniProt NPD GO	C75A3_PETHY	Flavonoid 3',5'-hydroxylase 2 (EC 1.14.13.88) (F3'5'H) (Cytochrome P450 75A3) (CYPLXXVA3)	0.02	-	nuc	3 *	Microsome (Potential)				508
Q8WN19 UniProt NPD GO	FSHB_AILME	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.02	-	exc	0	Secreted protein				129
Q6U830 UniProt NPD GO	FSHB_MERUN	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.02	-	exc	0	Secreted protein				129
O46430 UniProt NPD GO	FSHB_TRIVU	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.02	-	vac	0	Secreted protein				129
P37836 UniProt NPD GO	PFL_CHLRE	Formate acetyltransferase (EC 2.3.1.54) (Pyruvate formate-lyase) (Fragment)	0.02	-	cyt	0	Cytoplasm (By similarity)				195
Q9I9M5 UniProt NPD GO	FZD1_XENLA	Frizzled-1 precursor (Fz-1) (Xfz1)	0.02	-	end	7	Membrane; multi-pass membrane protein				559
Q9PUU6 UniProt NPD GO	FZD2_XENLA	Frizzled-2 precursor (Fz-2) (Xfz2)	0.02	-	end	7	Membrane; multi-pass membrane protein				551
P58421 UniProt NPD GO	FZD5_XENLA	Frizzled-5 precursor (Fz-5) (Xfz5)	0.02	-	end	6 *	Membrane; multi-pass membrane protein				559
O00144 UniProt NPD GO	FZD9_HUMAN	Frizzled-9 precursor (Fz-9) (hFz9) (FzE6)	0.02	-	end	7	Cell membrane; multi-pass membrane protein (By similarity)	integral to membrane [TAS] plasma membrane [TAS]	601766		591
Q9R216 UniProt NPD GO	FZD9_MOUSE	Frizzled-9 precursor (Fz-9) (mFz9) (mFz3)	0.02	-	end	7	Cell membrane; multi-pass membrane protein				592
P09201 UniProt NPD GO	F16P_YEAST	Fructose-1,6-bisphosphatase (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase) (FBPase)	0.02	-	cyt	0		cytosol [IDA]			347
P97323 UniProt NPD GO	F16P3_MOUSE	Fructose-1,6-bisphosphatase isozyme 3 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.02	-	end	1 *					94
Q42649 UniProt NPD GO	F16P2_BETVU	Fructose-1,6-bisphosphatase, cytosolic (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.02	-	nuc	0	Cytoplasm				341
Q9SDL8 UniProt NPD GO	F16P2_ORYCO	Fructose-1,6-bisphosphatase, cytosolic (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.02	-	nuc	0	Cytoplasm (By similarity)				344
O64421 UniProt NPD GO	F16P2_ORYSA	Fructose-1,6-bisphosphatase, cytosolic (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.02	-	nuc	0	Cytoplasm				339
Q8RW99 UniProt NPD GO	F16P2_PEA	Fructose-1,6-bisphosphatase, cytosolic (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.02	-	nuc	0	Cytoplasm (By similarity)				341
Q43139 UniProt NPD GO	F16P2_SACHY	Fructose-1,6-bisphosphatase, cytosolic (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.02	-	nuc	0	Cytoplasm				343
P14766 UniProt NPD GO	F16P2_SPIOL	Fructose-1,6-bisphosphatase, cytosolic (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.02	-	nuc	0	Cytoplasm				341
P46276 UniProt NPD GO	F16P2_SOLTU	Fructose-1,6-bisphosphatase, cytosolic (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.02	-	nuc	0	Cytoplasm				340

You are viewing entries 83501 to 83550 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.