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
Q5R5S1 UniProt NPD GO	FBX21_PONPY	F-box only protein 21	0.22	-	cyt	0					621
Q9H4M3 UniProt NPD GO	FBX44_HUMAN	F-box only protein 44 (F-box protein FBX30) (F-box/G-domain protein 3)	0.22	-	cyt	0			609111		255
P26884 UniProt NPD GO	FKBP3_BOVIN	FK506-binding protein 3 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (25 k ...	0.22	-	nuc	0	Nucleus				224
O46638 UniProt NPD GO	FKBP3_RABIT	FK506-binding protein 3 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (25 k ...	0.22	-	cyt	0	Nucleus				223
O14926 UniProt NPD GO	FSCN2_HUMAN	Fascin-2 (Retinal fascin)	0.22	-	cyt	0		actin cytoskeleton [TAS]	607921		492
Q12473 UniProt NPD GO	FRE6_YEAST	Ferric reductase transmembrane component 6 precursor (EC 1.16.1.7) (Ferric-chelate reductase 6)	0.22	-	end	7	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			712
P49947 UniProt NPD GO	FRIM_SALSA	Ferritin, middle subunit (EC 1.16.3.1) (Ferritin M)	0.22	-	nuc	0					176
Q8TC84 UniProt NPD GO	FANK1_HUMAN	Fibronectin type 3 and ankyrin repeat domains protein 1	0.22	-	cyt	0					345
Q9ZQ95 UniProt NPD GO	FOGT1_ARATH	Flavonol-3-O-glycoside-7-O-glucosyltransferase 1 (EC 2.4.1.-)	0.22	-	cyt	0					495
Q8BFR2 UniProt NPD GO	FSTL5_MOUSE	Follistatin-related protein 5 precursor (Follistatin-like 5) (m-D/Bsp120I 1-2)	0.22	-	exc	0	Secreted protein (Probable)				847
P19112 UniProt NPD GO	F16P1_RAT	Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase 1) (FBPa ...	0.22	-	cyt	0					362
P24862 UniProt NPD GO	CCNB_PATVU	G2/mitotic-specific cyclin-B	0.22	-	nuc	0					408
Q8VHI3 UniProt NPD GO	OFUT2_MOUSE	GDP-fucose protein O-fucosyltransferase 2 precursor (EC 2.4.1.221) (Peptide-O-fucosyltransferase) (O ...	0.22	-	end	0	Endoplasmic reticulum (By similarity)				429
P38211 UniProt NPD GO	GPI18_YEAST	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.22	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				433
Q8BXQ2 UniProt NPD GO	PIGT_MOUSE	GPI transamidase component PIG-T precursor (Phosphatidylinositol-glycan biosynthesis class T protein ...	0.22	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	GPI-anchor transamidase complex [IDA]			582
P41915 UniProt NPD GO	RAN_TETTH	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.22	-	cyt	0	Nucleus (By similarity)				225
P41916 UniProt NPD GO	RAN1_ARATH	GTP-binding nuclear protein Ran-1	0.22	-	cyt	0	Nucleus (By similarity)				221
P41917 UniProt NPD GO	RAN2_ARATH	GTP-binding nuclear protein Ran-2	0.22	-	cyt	0	Nucleus (By similarity)				221
Q8H156 UniProt NPD GO	RAN3_ARATH	GTP-binding nuclear protein Ran-3	0.22	-	cyt	0	Nucleus (By similarity)				221
P63032 UniProt NPD GO	RHES_MOUSE	GTP-binding protein Rhes (Ras homolog enriched in striatum)	0.22	-	mit	0	Membrane; lipid-anchor (Potential)				266
P63033 UniProt NPD GO	RHES_RAT	GTP-binding protein Rhes (Ras homolog enriched in striatum) (SE6C)	0.22	-	mit	0	Membrane; lipid-anchor (Potential)				266
Q8NHV1 UniProt NPD GO	GIMA7_HUMAN	GTPase, IMAP family member 7 (Immunity-associated nucleotide 7 protein)	0.22	-	mit	0					300
Q9VTG7 UniProt NPD GO	B3G2P_DROME	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase P (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.22	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	Golgi apparatus [NAS]			479
O60755 UniProt NPD GO	GALR3_HUMAN	Galanin receptor type 3 (GAL3-R) (GALR3)	0.22	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	603692		368
P34903 UniProt NPD GO	GBRA3_HUMAN	Gamma-aminobutyric-acid receptor alpha-3 subunit precursor (GABA(A) receptor)	0.22	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	305660		492
P19019 UniProt NPD GO	GBRB3_CHICK	Gamma-aminobutyric-acid receptor beta-3 subunit precursor (GABA(A) receptor)	0.22	-	end	4	Membrane; multi-pass membrane protein				476
P28472 UniProt NPD GO	GBRB3_HUMAN	Gamma-aminobutyric-acid receptor beta-3 subunit precursor (GABA(A) receptor)	0.22	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	137192		473
P63080 UniProt NPD GO	GBRB3_MOUSE	Gamma-aminobutyric-acid receptor beta-3 subunit precursor (GABA(A) receptor)	0.22	-	end	4	Membrane; multi-pass membrane protein (By similarity)				473
P63079 UniProt NPD GO	GBRB3_RAT	Gamma-aminobutyric-acid receptor subunit beta-3 precursor (GABA(A) receptor)	0.22	-	end	4	Membrane; multi-pass membrane protein				473
Q9HBI0 UniProt NPD GO	PARVG_HUMAN	Gamma-parvin	0.22	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side (By similarity). Constituent o ...	cytoskeleton [TAS]	608122		331
P81008 UniProt NPD GO	THG1_MAIZE	Gamma-zeathionin-1	0.22	-	mit	0					47
Q80XF7 UniProt NPD GO	CXA12_RAT	Gap junction alpha-12 protein (Connexin-47) (Cx47)	0.22	-	end	4 *	Membrane; multi-pass membrane protein				440
Q06145 UniProt NPD GO	GIP_RAT	Gastric inhibitory polypeptide precursor (GIP) (Glucose-dependent insulinotropic polypeptide)	0.22	-	vac	0	Secreted protein				144
P48546 UniProt NPD GO	GIPR_HUMAN	Gastric inhibitory polypeptide receptor precursor (GIP-R) (Glucose-dependent insulinotropic polypept ...	0.22	-	end	5	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	137241		466
Q07235 UniProt NPD GO	GDN_MOUSE	Glia-derived nexin precursor (GDN) (Protease nexin I) (PN-1) (Serine protease-inhibitor 4)	0.22	-	end	0	Secreted protein; extracellular space				397
P41534 UniProt NPD GO	PACA_CHICK	Glucagon family neuropeptides precursor [Contains: Growth hormone-releasing factor 1-46 (GRF) (Growt ...	0.22	-	cyt	0	Secreted protein				175
Q10444 UniProt NPD GO	EXG2_SCHPO	Glucan 1,3-beta-glucosidase 2 precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.22	-	cyt	1 *	Secreted protein (By similarity)				570
P49236 UniProt NPD GO	E13B_BRACM	Glucan endo-1,3-beta-glucosidase precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase) ((1->3)- ...	0.22	-	exc	0	Vacuole. In intact tissues				342
Q07346 UniProt NPD GO	DCE_PETHY	Glutamate decarboxylase (EC 4.1.1.15) (GAD)	0.22	-	mit	0				1NWD	500
P54767 UniProt NPD GO	DCE_LYCES	Glutamate decarboxylase (EC 4.1.1.15) (GAD) (ERT D1)	0.22	-	cyt	0					502
P14748 UniProt NPD GO	DCE1_FELCA	Glutamate decarboxylase 1 (EC 4.1.1.15) (Glutamate decarboxylase, 67 kDa isoform) (GAD-67) (67 kDa g ...	0.22	-	cyt	0					594
P18088 UniProt NPD GO	DCE1_RAT	Glutamate decarboxylase 1 (EC 4.1.1.15) (Glutamate decarboxylase, 67 kDa isoform) (GAD-67) (67 kDa g ...	0.22	-	cyt	0					593
Q9BQ67 UniProt NPD GO	GRWD1_HUMAN	Glutamate-rich WD repeat-containing protein 1	0.22	-	cyt	0	Nucleus; nucleolus				446
O48674 UniProt NPD GO	HEM1_ORYSA	Glutamyl-tRNA reductase, chloroplast precursor (EC 1.2.1.70) (GluTR)	0.22	-	mit	0	Plastid; chloroplast				537
P35754 UniProt NPD GO	GLRX1_HUMAN	Glutaredoxin-1 (Thioltransferase-1) (TTase-1)	0.22	-	cyt	0	Cytoplasm		600443	1JHB	105
Q9ESH6 UniProt NPD GO	GLRX1_RAT	Glutaredoxin-1 (Thioltransferase-1) (TTase-1)	0.22	-	cyt	0	Cytoplasm				106
P13745 UniProt NPD GO	GSTA1_MOUSE	Glutathione S-transferase Ya chain (EC 2.5.1.18) (GST class-alpha) (Ya1)	0.22	-	cyt	0				1F3B	222
Q9JHC0 UniProt NPD GO	GPX2_MOUSE	Glutathione peroxidase 2 (EC 1.11.1.9) (GSHPx-2) (GPx-2) (Glutathione peroxidase-gastrointestinal) ( ...	0.22	-	cyt	0	Cytoplasm (By similarity)	cytosol [TAS]			190
O60760 UniProt NPD GO	PTGD2_HUMAN	Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) (Glutathione-dependent PGD synthetase) ...	0.22	-	cyt	0	Cytoplasm	cytoplasm [TAS]	602598	2CVD	198
O14400 UniProt NPD GO	GPDM_SCHPO	Glycerol-3-phosphate dehydrogenase, mitochondrial precursor (EC 1.1.99.5) (GPD-M) (GPDH-M)	0.22	-	mit	0	Mitochondrion (By similarity)				649

You are viewing entries 48401 to 48450 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.