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
Q9GR88 UniProt NPD GO	ERF1_POLMI	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.06	-	cyt	0	Cytoplasm (By similarity)				435
O81481 UniProt NPD GO	IF4E1_MAIZE	Eukaryotic translation initiation factor 4E-1 (eIF4E-1) (eIF-4E-1) (mRNA cap-binding protein) (eIF-4 ...	0.06	-	cyt	0					218
O81482 UniProt NPD GO	IF4E2_MAIZE	Eukaryotic translation initiation factor 4E-2 (eIF4E-2) (eIF-4E-2) (mRNA cap-binding protein) (eIF-( ...	0.06	-	cyt	0					216
P48600 UniProt NPD GO	IF4E2_ORYSA	Eukaryotic translation initiation factor 4E-2 (eIF4E-2) (eIF-4E-2) (mRNA cap-binding protein) (eIF-( ...	0.06	-	cyt	0					206
Q09121 UniProt NPD GO	IF5A1_CHICK	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1) (eIF-5A1) (Eukaryotic initiation factor 5A ...	0.06	-	cyt	0					143
Q12522 UniProt NPD GO	IF6_YEAST	Eukaryotic translation initiation factor 6 (eIF-6)	0.06	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]		1G62	245
Q00548 UniProt NPD GO	GUX1_CRYPA	Exoglucanase 1 precursor (EC 3.2.1.91) (Exoglucanase I) (Exocellobiohydrolase I) (1,4-beta-cellobioh ...	0.06	-	exc	0					452
P24548 UniProt NPD GO	PGLR_OENOR	Exopolygalacturonase (EC 3.2.1.67) (ExoPG) (Pectinase) (Galacturan 1,4-alpha-galacturonidase) (Fragm ...	0.06	-	nuc	0					362
Q08285 UniProt NPD GO	RRP40_YEAST	Exosome complex exonuclease RRP40 (EC 3.1.13.-) (Ribosomal RNA-processing protein 40)	0.06	-	cyt	0	Cytoplasm. Nucleus; nucleolus	cytoplasmic exosome (RNase complex) [IDA] nuclear exosome (RNase complex) [IDA]			240
Q9D753 UniProt NPD GO	EXOS8_MOUSE	Exosome complex exonuclease RRP43 (EC 3.1.13.-) (Ribosomal RNA-processing protein 43) (Exosome compo ...	0.06	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				276
Q96B26 UniProt NPD GO	EXOS8_HUMAN	Exosome complex exonuclease RRP43 (EC 3.1.13.-) (Ribosomal RNA-processing protein 43) (Exosome compo ...	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)		606019		276
P02218 UniProt NPD GO	GLB2_LUMTE	Extracellular globin-2 (Globin II) (Erythrocruorin) (Globin AIII) (Globin B)	0.06	-	cyt	0				1X9F	145
P13579 UniProt NPD GO	GLB4_LUMTE	Extracellular globin-4 (Globin IV) (Erythrocruorin) (Globin A)	0.06	-	cyt	0				1X9F	151
P16411 UniProt NPD GO	RNF1_GIBBA	Extracellular guanyl-specific ribonuclease Fl1 (EC 3.1.27.3) (RNase Fl1)	0.06	-	nuc	0					105
P41963 UniProt NPD GO	SODE_BRUPA	Extracellular superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1) (EC-SOD)	0.06	-	nuc	0	Secreted protein; extracellular space				199
P41974 UniProt NPD GO	SODE_DIRIM	Extracellular superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1) (EC-SOD)	0.06	-	nuc	0	Secreted protein; extracellular space				195
P13022 UniProt NPD GO	CAPZA_DICDI	F-actin capping protein subunit alpha (CAP34)	0.06	-	nuc	0					281
Q9GKV7 UniProt NPD GO	FBX15_MACFA	F-box only protein 15	0.06	-	cyt	0					434
Q6FJ69 UniProt NPD GO	YFAS1_CANGA	FAS1 domain-containing protein CAGL0M08734g precursor	0.06	-	cyt	0	Vacuole (By similarity)				253
Q4WHX4 UniProt NPD GO	FKBP2_ASPFU	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.06	-	exc	0	Endoplasmic reticulum (By similarity)				134
Q5ATN7 UniProt NPD GO	FKBP2_EMENI	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.06	-	end	0	Endoplasmic reticulum (By similarity)				135
Q4IN00 UniProt NPD GO	FKBP2_GIBZE	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.06	-	exc	0	Endoplasmic reticulum (By similarity)				195
P32472 UniProt NPD GO	FKBP2_YEAST	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.06	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Is not secreted ...	endoplasmic reticulum membrane [IEP]			135
P49349 UniProt NPD GO	FPPS_KLULA	Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes ...	0.06	-	mit	1	Cytoplasm				349
P08524 UniProt NPD GO	FPPS_YEAST	Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes ...	0.06	-	mit	0	Cytoplasm				352
P55052 UniProt NPD GO	FABPE_BOVIN	Fatty acid-binding protein, epidermal (E-FABP) (Differentiation-associated lipid-binding protein LP2 ...	0.06	-	cyt	0	Cytoplasm				134
P02693 UniProt NPD GO	FABPI_RAT	Fatty acid-binding protein, intestinal (I-FABP) (FABPI)	0.06	-	cyt	0	Cytoplasm	plasma membrane [IDA]		2IFB	131
P47740 UniProt NPD GO	AL3A2_MOUSE	Fatty aldehyde dehydrogenase (EC 1.2.1.3) (Aldehyde dehydrogenase, microsomal) (Aldehyde dehydrogena ...	0.06	-	gol	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein; cytoplasmic sid ...	mitochondrial inner membrane [IDA]			484
P02450 UniProt NPD GO	KRFC_CHICK	Feather keratin I (Keratin gene C protein) (F-ker)	0.06	-	nuc	0					97
Q9TLW0 UniProt NPD GO	FER1_CYACA	Ferredoxin	0.06	-	nuc	0	Plastid; chloroplast				98
P41347 UniProt NPD GO	FTRC_MAIZE	Ferredoxin-thioredoxin reductase catalytic chain, chloroplast precursor (EC 1.18.-.-) (FTR-C) (Ferre ...	0.06	-	pox	0	Plastid; chloroplast				152
P19976 UniProt NPD GO	FRI1_SOYBN	Ferritin-1, chloroplast precursor (EC 1.16.3.1) (SOF-35) (SFerH-1)	0.06	-	nuc	0	Plastid; chloroplast. Plastid				250
O22101 UniProt NPD GO	HEMH_ORYSA	Ferrochelatase-2, chloroplast precursor (EC 4.99.1.1) (Ferrochelatase II) (Protoheme ferro-lyase 2) ...	0.06	-	nuc	0	Plastid; chloroplast				526
O42815 UniProt NPD GO	FAEA_ASPTU	Feruloyl esterase A precursor (EC 3.1.1.73) (Ferulic acid esterase A)	0.06	-	exc	0	Secreted protein	extracellular region [ISS]			280
P12801 UniProt NPD GO	FIBA_ANAPL	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.06	-		0	Secreted protein				15
P10767 UniProt NPD GO	FGF6_HUMAN	Fibroblast growth factor 6 precursor (FGF-6) (HBGF-6) (HST-2)	0.06	-	mit	1 *	Secreted protein; extracellular space	extracellular region [TAS]	134921		208
P21658 UniProt NPD GO	FGF6_MOUSE	Fibroblast growth factor 6 precursor (FGF-6) (HBGF-6) (HST-2)	0.06	-	mit	1 *	Secreted protein; extracellular space				208
P22607 UniProt NPD GO	FGFR3_HUMAN	Fibroblast growth factor receptor 3 precursor (EC 2.7.10.1) (FGFR-3) (CD333 antigen)	0.06	-	end	2	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	100800	1RY7	806
P83255 UniProt NPD GO	FIBR_VIPLE	Fibrolase (EC 3.4.24.72) (VlF) (Fibrinolytic proteinase) (Non-hemorrhagic fibrinolytic metalloprotei ...	0.06	-	cyt	0	Secreted protein				202
O04790 UniProt NPD GO	C75A7_EUSGR	Flavonoid 3',5'-hydroxylase (EC 1.14.13.88) (F3'5'H) (Cytochrome P450 75A7)	0.06	-	nuc	1 *					510
Q96330 UniProt NPD GO	FLS1_ARATH	Flavonol synthase/flavanone 3-hydroxylase (EC 1.14.11.23) (EC 1.14.11.9) (FLS 1)	0.06	-	cyt	0	Cytoplasm				336
Q9XHG2 UniProt NPD GO	FLS_MALDO	Flavonol synthase/flavanone 3-hydroxylase (EC 1.14.11.23) (EC 1.14.11.9) (FLS)	0.06	-	cyt	0	Cytoplasm (By similarity)				337
Q07512 UniProt NPD GO	FLS_PETHY	Flavonol synthase/flavanone 3-hydroxylase (EC 1.14.11.23) (EC 1.14.11.9) (FLS)	0.06	-	cyt	0	Cytoplasm				348
Q9JK69 UniProt NPD GO	FSHB_CAVPO	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.06	-	end	0	Secreted protein				129
Q60687 UniProt NPD GO	FSHB_MOUSE	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.06	-	exc	0	Secreted protein				130
Q9QYB0 UniProt NPD GO	FSHB_PHOSU	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B) (Fra ...	0.06	-	nuc	0	Secreted protein				126
Q12676 UniProt NPD GO	FOLD_YEAST	Folylpolyglutamate synthase (EC 6.3.2.17) (Folylpoly-gamma-glutamate synthetase) (FPGS) (Tetrahydrof ...	0.06	-	cyt	0		cytoplasm [IDA]			427
Q61091 UniProt NPD GO	FZD8_MOUSE	Frizzled-8 precursor (Fz-8) (mFz8)	0.06	-	end	7	Membrane; multi-pass membrane protein			1IJY	685
P46267 UniProt NPD GO	F16P2_BRANA	Fructose-1,6-bisphosphatase, cytosolic (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase ...	0.06	-	nuc	0	Cytoplasm				339
P09972 UniProt NPD GO	ALDOC_HUMAN	Fructose-bisphosphate aldolase C (EC 4.1.2.13) (Brain-type aldolase)	0.06	-	cyt	0			103870	1XFB	363

You are viewing entries 72051 to 72100 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.