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
Q13003 UniProt NPD GO	GRIK3_HUMAN	Glutamate receptor, ionotropic kainate 3 precursor (Glutamate receptor 7) (GluR-7) (GluR7) (Excitato ...	0.12	-	end	3	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	138243		919
Q5XI13 UniProt NPD GO	GRWD1_RAT	Glutamate-rich WD repeat-containing protein 1	0.12	-	cyt	0	Nucleus; nucleolus (By similarity)				445
P46425 UniProt NPD GO	GSTP2_MOUSE	Glutathione S-transferase P 2 (EC 2.5.1.18) (GST YF-YF) (GST-piA) (GST class-pi) (Gst P2)	0.12	-	cyt	0					209
Q08862 UniProt NPD GO	GSTA_RABIT	Glutathione S-transferase Yc (EC 2.5.1.18) (Alpha II) (GST class-alpha)	0.12	-	cyt	0	Cytoplasm				220
Q9Y2Q3 UniProt NPD GO	GSTK1_HUMAN	Glutathione S-transferase kappa 1 (EC 2.5.1.18) (GST 13-13) (Glutathione S-transferase subunit 13) ( ...	0.12	-	cyt	0	Peroxisome		602321	1YZX	225
P11352 UniProt NPD GO	GPX1_MOUSE	Glutathione peroxidase 1 (EC 1.11.1.9) (GSHPx-1) (GPx-1) (Cellular glutathione peroxidase)	0.12	-	mit	0	Cytoplasm	mitochondrion [IDA]			201
Q99LJ6 UniProt NPD GO	GPX7_MOUSE	Glutathione peroxidase 7 precursor (EC 1.11.1.9)	0.12	-	exc	0	Secreted protein (Potential)				186
Q6AXV9 UniProt NPD GO	GSTO2_RAT	Glutathione transferase omega-2 (EC 2.5.1.18)	0.12	-	cyt	0					248
P02862 UniProt NPD GO	GLT2_WHEAT	Glutenin, high molecular weight subunit PC237 (Fragment)	0.12	-	nuc	0					39
Q05966 UniProt NPD GO	GRP10_BRANA	Glycine-rich RNA-binding protein 10	0.12	+	cyt	0					169
P13230 UniProt NPD GO	GRP33_ARTSA	Glycine-rich protein GRP33	0.12	-	nuc	0					308
P14221 UniProt NPD GO	GLP_MACFU	Glycophorin MK	0.12	-	nuc	1	Membrane; single-pass type I membrane protein				144
Q9WTK3 UniProt NPD GO	GPAA1_MOUSE	Glycosylphosphatidylinositol anchor attachment 1 protein (GPI anchor attachment protein 1) (GAA1 pro ...	0.12	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	GPI-anchor transamidase complex [ISS]			620
Q8ILW6 UniProt NPD GO	NMT_PLAF7	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.12	-	cyt	0	Cytoplasm (Potential)				410
O75487 UniProt NPD GO	GPC4_HUMAN	Glypican-4 precursor (K-glypican)	0.12	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	integral to plasma membrane [TAS]	300168		556
Q9R064 UniProt NPD GO	GORS2_RAT	Golgi reassembly-stacking protein 2 (GRS2) (Golgi reassembly-stacking protein of 55 kDa) (GRASP55)	0.12	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; lipid-anchor. Intermediate Golgi, membrane-assoc ...	Golgi apparatus [IDA]			453
P53543 UniProt NPD GO	GTHB2_CLAGA	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta)	0.12	-	exc	0	Secreted protein				138
Q8CH60 UniProt NPD GO	GNRHR_CAVPO	Gonadotropin-releasing hormone receptor (GnRH receptor) (GnRH-R)	0.12	-	mit	7 *	Membrane; multi-pass membrane protein				328
P49922 UniProt NPD GO	GNRHR_PIG	Gonadotropin-releasing hormone receptor (GnRH receptor) (GnRH-R) (Luteinizing hormone-releasing horm ...	0.12	+	nuc	7 *	Membrane; multi-pass membrane protein				328
Q8LL05 UniProt NPD GO	SSG1B_HORVU	Granule-bound starch synthase 1b, chloroplast precursor (EC 2.4.1.242) (Granule-bound starch synthas ...	0.12	-	nuc	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound (By similarity)				565
O62757 UniProt NPD GO	CSF2_FELCA	Granulocyte-macrophage colony-stimulating factor precursor (GM-CSF) (Colony-stimulating factor) (CSF ...	0.12	-	nuc	0	Secreted protein				144
P16260 UniProt NPD GO	GDC_HUMAN	Grave disease carrier protein (GDC) (Grave disease autoantigen) (GDA) (Mitochondrial solute carrier ...	0.12	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [NAS]	139080		332
Q09553 UniProt NPD GO	GAS1_CAEEL	Growth-arrest-specific protein 1 homolog precursor (Pharynx-associated gas1 homolog)	0.12	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Localized on the muscle cell plasma membrane	anchored to plasma membrane [IDA]			228
Q61592 UniProt NPD GO	GAS6_MOUSE	Growth-arrest-specific protein 6 precursor (GAS-6)	0.12	-	cyt	0	Secreted protein (By similarity)				674
P12850 UniProt NPD GO	GROA_MOUSE	Growth-regulated alpha protein precursor (CXCL1) (Platelet-derived growth factor-inducible protein K ...	0.12	-	exc	0	Secreted protein				96
P50290 UniProt NPD GO	BB1_HUMAN	Growth-regulating protein BB1	0.12	-	cyt	0					57
P63217 UniProt NPD GO	GBG5_BOVIN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-5 subunit precursor	0.12	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	heterotrimeric G-protein complex [ISS]			68
P63218 UniProt NPD GO	GBG5_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-5 subunit precursor	0.12	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	heterotrimeric G-protein complex [NAS]	600874		67
Q80SZ7 UniProt NPD GO	GBG5_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-5 subunit precursor	0.12	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	heterotrimeric G-protein complex [ISS]			68
Q5REH7 UniProt NPD GO	GBG5_PONPY	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-5 subunit precursor	0.12	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				67
P63219 UniProt NPD GO	GBG5_RAT	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-5 subunit precursor	0.12	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	heterotrimeric G-protein complex [ISS]			68
Q9Y3K8 UniProt NPD GO	GBG5L_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-5-like subunit	0.12	-	nuc	0		extracellular region [NAS]			68
P52287 UniProt NPD GO	GBB3_RAT	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 3 (Transducin beta chain 3)	0.12	-	cyt	0					340
Q60397 UniProt NPD GO	GNAI3_CRIGR	Guanine nucleotide-binding protein G(k) subunit alpha (G(i) alpha-3) (Fragment)	0.12	-	cyt	0					63
Q39336 UniProt NPD GO	GBLP_BRANA	Guanine nucleotide-binding protein subunit beta-like protein	0.12	-	cyt	0					327
P93340 UniProt NPD GO	GBLP_NICPL	Guanine nucleotide-binding protein subunit beta-like protein	0.12	-	cyt	0					326
Q4VT26 UniProt NPD GO	GBG_CAEBR	Guanine nucleotide-binding protein subunit gamma precursor	0.12	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				62
P36915 UniProt NPD GO	GNL1_HUMAN	Guanine nucleotide-binding protein-like 1 (GTP-binding protein HSR1)	0.12	-	nuc	0			143024		430
Q64520 UniProt NPD GO	KGUA_MOUSE	Guanylate kinase (EC 2.7.4.8) (GMP kinase)	0.12	-	cyt	0				1LVG	197
Q9VTN0 UniProt NPD GO	GR68A_DROME	Gustatory receptor 68a	0.12	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			389
Q6AYA1 UniProt NPD GO	NOLA1_RAT	H/ACA ribonucleoprotein complex subunit 1 (Nucleolar protein family A member 1)	0.12	+	cyt	0	Nucleus; nucleolus (By similarity). Also localized to Cajal bodies (coiled bodies) (By similarity)				226
Q9NY12 UniProt NPD GO	NOLA1_HUMAN	H/ACA ribonucleoprotein complex subunit 1 (Nucleolar protein family A member 1) (snoRNP protein GAR1 ...	0.12	+	cyt	0	Nucleus; nucleolus. Nucleus; nucleoplasm; Cajal body. Also localized to Cajal bodies (coiled bodies) ...		606468		217
Q9CY66 UniProt NPD GO	NOLA1_MOUSE	H/ACA ribonucleoprotein complex subunit 1 (Nucleolar protein family A member 1) (snoRNP protein GAR1 ...	0.12	+	cyt	0	Nucleus; nucleolus (By similarity). Also localized to Cajal bodies (coiled bodies) (By similarity)				231
Q99074 UniProt NPD GO	HA34_BRELC	HAM34 protein	0.12	-	exc	0					173
Q9P298 UniProt NPD GO	HIG1B_HUMAN	HIG1 domain family member 1B (Protein CLST 11240)	0.12	-	cyt	2 *	Membrane; multi-pass membrane protein (Potential)				99
P81176 UniProt NPD GO	VSP1_AGKHA	Halystase (EC 3.4.21.-)	0.12	-	nuc	0	Secreted protein				238
P27541 UniProt NPD GO	HSP70_BRUMA	Heat shock 70 kDa protein	0.12	-	cyt	0					644
P26791 UniProt NPD GO	HSP70_DAUCA	Heat shock 70 kDa protein	0.12	-	cyt	0					655
P29844 UniProt NPD GO	HSP7C_DROME	Heat shock 70 kDa protein cognate 3 precursor (78 kDa glucose-regulated protein homolog) (GRP 78) (H ...	0.12	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [NAS]			656
Q875P5 UniProt NPD GO	HSP7F_SACKL	Heat shock protein homolog SSE1	0.12	-	cyt	0	Cytoplasm (By similarity)				693

You are viewing entries 61201 to 61250 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.