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
Q9LPV8 UniProt NPD GO	ERF1Y_ARATH	Eukaryotic peptide chain release factor subunit 1-2 (eRF1-2) (Eukaryotic release factor 1-2) (Omnipo ...	0.20	-	cyt	0	Cytoplasm				434
Q3T0V3 UniProt NPD GO	IF3C_BOVIN	Eukaryotic translation initiation factor 3 subunit 12 (eIF-3 p25) (eIF3k)	0.20	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				218
O02195 UniProt NPD GO	IF32_DROME	Eukaryotic translation initiation factor 3 subunit 2 (eIF-3 beta) (eIF3i) (TRIP-1 homolog)	0.20	-	cyt	0					326
Q06886 UniProt NPD GO	GUX1_PENJA	Exoglucanase 1 precursor (EC 3.2.1.91) (Exoglucanase I) (Exocellobiohydrolase I) (1,4-beta-cellobioh ...	0.20	-	exc	0	Secreted protein				537
P28316 UniProt NPD GO	GLB_ASCSU	Extracellular globin precursor	0.20	-	mit	0	Secreted protein; extracellular space			1ASH	338
P38248 UniProt NPD GO	ECM33_YEAST	Extracellular matrix protein 33 precursor	0.20	-	mit	2	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA] mitochondrion [IDA] plasma membrane [IDA]			469
Q2QLH5 UniProt NPD GO	CAZA2_OTOGA	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.20	-	nuc	0					285
P26885 UniProt NPD GO	FKBP2_HUMAN	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.20	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Probable)	endoplasmic reticulum [TAS]	186946		142
Q00688 UniProt NPD GO	FKBP3_HUMAN	FK506-binding protein 3 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (25 k ...	0.20	-	cyt	0	Nucleus		186947	1PBK	224
Q9Z247 UniProt NPD GO	FKBP9_MOUSE	FK506-binding protein 9 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.20	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [IDA]			570
O18282 UniProt NPD GO	FRG1_CAEEL	FRG1 protein homolog	0.20	-	nuc	0	Nucleus; nucleoplasm; Cajal body (By similarity). Nucleus; nucleoplasm; nuclear speckle (By similari ...				274
P01403 UniProt NPD GO	TXF7_DENAN	Fasciculin-1/2 (Fasciculin-I/II) (FAS-I/FAS-II) (Acetylcholinesterase toxin F-VII) (Toxin TA1)	0.20	-	nuc	0	Secreted protein			1MAH	61
Q9TUI8 UniProt NPD GO	FAAH_PIG	Fatty-acid amide hydrolase (EC 3.1.-.-) (Oleamide hydrolase) (Anandamide amidohydrolase)	0.20	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Golgi apparatus ...				579
P25320 UniProt NPD GO	FRIH2_SCHMA	Ferritin-2 heavy chain (EC 1.16.3.1)	0.20	-	cyt	0					172
P14465 UniProt NPD GO	FIBB_ANTAM	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.20	-	nuc	0	Secreted protein				21
P02679 UniProt NPD GO	FIBG_HUMAN	Fibrinogen gamma chain precursor	0.20	-	exc	1 *	Secreted protein	fibrinogen complex [TAS]	134850	3FIB	453
P04148 UniProt NPD GO	SI25_BOMMO	Fibrohexamerin precursor (25 kDa silk glycoprotein) (p25)	0.20	-	mit	0	Secreted protein				220
Q8VHX6 UniProt NPD GO	FLNC_MOUSE	Filamin-C (Gamma-filamin) (Filamin-2) (FLN-C) (Actin-binding-like protein) (ABP-L) (ABP-280-like pro ...	0.20	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). A small amount loc ...	actin cytoskeleton [TAS]			1144
Q7G188 UniProt NPD GO	FIMB1_ARATH	Fimbrin 1 (AtFIM1)	0.20	-	cyt	0	Cytoplasm			1PXY	687
Q60634 UniProt NPD GO	FLOT2_MOUSE	Flotillin-2 (Epidermal surface antigen) (ESA)	0.20	-	cyt	0	Cell membrane; caveola; peripheral membrane protein. Membrane-associated protein of caveolae	lipid raft [IDA]		1WIN	379
Q22931 UniProt NPD GO	FOLT2_CAEEL	Folate-like transporter 2	0.20	+	end	7 *	Membrane; multi-pass membrane protein (Probable)				535
P31515 UniProt NPD GO	FST_XENLA	Follistatin precursor (FS) (Activin-binding protein) (XFS-319)	0.20	-	nuc	0	Secreted protein				341
O74831 UniProt NPD GO	FRDA_SCHPO	Frataxin homolog, mitochondrial precursor	0.20	-	mit	0	Mitochondrion (By similarity)				158
Q9W385 UniProt NPD GO	FRDA_DROME	Frataxin homolog, mitochondrial precursor (Dfh)	0.20	-	mit	0	Mitochondrion (By similarity)				190
Q9ULW2 UniProt NPD GO	FZD10_HUMAN	Frizzled-10 precursor (Fz-10) (hFz10) (FzE7)	0.20	+	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	606147		581
Q9PT62 UniProt NPD GO	FZD4_XENLA	Frizzled-4 precursor (Fz-4) (Xfz4)	0.20	-	end	8 *	Membrane; multi-pass membrane protein				523
P09467 UniProt NPD GO	F16P1_HUMAN	Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase 1) (FBPa ...	0.20	-	cyt	0			229700	2FIX	337
P54216 UniProt NPD GO	ALF1_CAEEL	Fructose-bisphosphate aldolase 1 (EC 4.1.2.13) (Aldolase CE-1) (CE1)	0.20	-	nuc	0					366
P00884 UniProt NPD GO	ALDOB_RAT	Fructose-bisphosphate aldolase B (EC 4.1.2.13) (Liver-type aldolase)	0.20	-	nuc	0				1N30	363
Q60HG0 UniProt NPD GO	FCMD_MACFA	Fukutin (EC 2.-.-.-)	0.20	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				461
Q80T02 UniProt NPD GO	GPBAR_RAT	G-protein coupled bile acid receptor 1 (Membrane-type receptor for bile acids) (M-BAR)	0.20	-	end	7 *	Cell membrane; multi-pass membrane protein (By similarity)				329
Q04827 UniProt NPD GO	CCND2_RAT	G1/S-specific cyclin-D2 (Vin-1 proto-oncogene)	0.20	-	cyt	0					288
Q91ZW2 UniProt NPD GO	OFUT1_MOUSE	GDP-fucose protein O-fucosyltransferase 1 precursor (EC 2.4.1.221) (Peptide-O-fucosyltransferase) (O ...	0.20	-	exc	0	Endoplasmic reticulum (By similarity)	integral to Golgi membrane [ISS]			393
Q873N1 UniProt NPD GO	GWT1_ASPFU	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.20	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				501
Q5BF53 UniProt NPD GO	GWT1_EMENI	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.20	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				474
P30047 UniProt NPD GO	GFRP_HUMAN	GTP cyclohydrolase 1 feedback regulatory protein (GTP cyclohydrolase I feedback regulatory protein) ...	0.20	-	cyt	0			602437		83
P41914 UniProt NPD GO	RAN_TETPY	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.20	-	cyt	0	Nucleus (By similarity)				223
P41918 UniProt NPD GO	RANA1_TOBAC	GTP-binding nuclear protein Ran-A1	0.20	-	cyt	0	Nucleus (By similarity)				221
P38546 UniProt NPD GO	RAN1_LYCES	GTP-binding nuclear protein Ran1	0.20	-	cyt	0	Nucleus (By similarity)				221
Q96D21 UniProt NPD GO	RHES_HUMAN	GTP-binding protein Rhes (Ras homolog enriched in striatum) (Tumor endothelial marker 2)	0.20	-	mit	0	Membrane; lipid-anchor (Potential)				266
Q9UTE7 UniProt NPD GO	MSS1_SCHPO	GTPase mss1, mitochondrial precursor	0.20	-	mit	0	Mitochondrion				496
O88853 UniProt NPD GO	GALR3_MOUSE	Galanin receptor type 3 (GAL3-R) (GALR3)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				370
Q08380 UniProt NPD GO	LG3BP_HUMAN	Galectin-3-binding protein precursor (Lectin galactoside-binding soluble 3-binding protein) (Mac-2-b ...	0.20	-	exc	0	Secreted protein. Secreted protein; extracellular space; extracellular matrix	extracellular space [TAS]	600626	1BY2	585
P20735 UniProt NPD GO	GGT1_PIG	Gamma-glutamyltranspeptidase 1 precursor (EC 2.3.2.2) (Gamma-glutamyltransferase 1) (GGT 1) (CD224 a ...	0.20	-	end	2 *	Membrane; single-pass type II membrane protein (By similarity)				568
P55885 UniProt NPD GO	GAST_HORSE	Gastrin precursor [Contains: Big gastrin (Gastrin 34) (G34); Gastrin]	0.20	-	exc	0	Secreted protein				107
P21729 UniProt NPD GO	GRPR_MOUSE	Gastrin-releasing peptide receptor (GRP-R) (GRP-preferring bombesin receptor)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				384
P30552 UniProt NPD GO	GASR_CANFA	Gastrin/cholecystokinin type B receptor (CCK-B receptor) (CCK-BR) (Cholecystokinin-2 receptor) (CCK2 ...	0.20	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS] plasma membrane [ISS]			453
P09859 UniProt NPD GO	ANTR_CHICK	Gastrin/cholecystokinin-like peptide precursor (Antral peptide)	0.20	-	vac	0					105
Q8BMQ2 UniProt NPD GO	TF3C4_MOUSE	General transcription factor 3C polypeptide 4 (EC 2.3.1.48) (Transcription factor IIIC subunit delta ...	0.20	-	cyt	0	Nucleus (By similarity)				817
P56966 UniProt NPD GO	GGPPS_BOVIN	Geranylgeranyl pyrophosphate synthetase (GGPP synthetase) (GGPPSase) (Geranylgeranyl diphosphate syn ...	0.20	-	cyt	0	Cytoplasm (Potential)	soluble fraction [ISS]			294

You are viewing entries 50601 to 50650 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.