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
P20137 UniProt NPD GO	GST5_CHICK	Glutathione S-transferase 5 (EC 2.5.1.18) (GST-CL5) (GST class-sigma) (Fragment)	0.04	-	cyt	0	Cytoplasm				28
Q96266 UniProt NPD GO	GSTF6_ARATH	Glutathione S-transferase 6 (EC 2.5.1.18) (GST class phi)	0.04	-	cyt	0	Cytoplasm (Probable)				215
Q9VG96 UniProt NPD GO	GSTT4_DROME	Glutathione S-transferase D4 (EC 2.5.1.18) (DmGST23)	0.04	-	cyt	0					215
P04904 UniProt NPD GO	GSTA3_RAT	Glutathione S-transferase alpha-3 (EC 2.5.1.18) (Glutathione S-transferase Yc-1) (GST Yc1) (GST 2-2) ...	0.04	-	cyt	0	Cytoplasm				220
O59858 UniProt NPD GO	GPX1_SCHPO	Glutathione peroxidase (EC 1.11.1.9)	0.04	-	cyt	0					158
P36014 UniProt NPD GO	GPX1_YEAST	Glutathione peroxidase 1 (EC 1.11.1.9)	0.04	-	cyt	0					167
P38143 UniProt NPD GO	GPX2_YEAST	Glutathione peroxidase 2 (EC 1.11.1.9)	0.04	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			162
P37141 UniProt NPD GO	GPX3_BOVIN	Glutathione peroxidase 3 precursor (EC 1.11.1.9) (GSHPx-3) (GPx-3) (Plasma glutathione peroxidase) ( ...	0.04	-	exc	0	Secreted protein	extracellular space [ISS]			226
Q4AEH5 UniProt NPD GO	GPX3_HYLLA	Glutathione peroxidase 3 precursor (EC 1.11.1.9) (GSHPx-3) (GPx-3) (Plasma glutathione peroxidase) ( ...	0.04	-	end	0	Secreted protein (By similarity)	extracellular space [ISS]			226
Q4AEH4 UniProt NPD GO	GPX3_MACFU	Glutathione peroxidase 3 precursor (EC 1.11.1.9) (GSHPx-3) (GPx-3) (Plasma glutathione peroxidase) ( ...	0.04	-	end	0	Secreted protein (By similarity)	extracellular space [ISS]			226
P46412 UniProt NPD GO	GPX3_MOUSE	Glutathione peroxidase 3 precursor (EC 1.11.1.9) (GSHPx-3) (GPx-3) (Plasma glutathione peroxidase) ( ...	0.04	-	exc	0	Secreted protein	extracellular space [ISS]			226
P55071 UniProt NPD GO	G3P_AMAMU	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH) (Fragment)	0.04	-	cyt	0	Cytoplasm				289
P19866 UniProt NPD GO	G3PA_SPIOL	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glyc ...	0.04	-	cyt	0	Plastid; chloroplast			1RM5	401
P09043 UniProt NPD GO	G3PA_TOBAC	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glyc ...	0.04	-	cyt	0	Plastid; chloroplast				392
P52425 UniProt NPD GO	GPDA_CUPLA	Glycerol-3-phosphate dehydrogenase [NAD+] (EC 1.1.1.8)	0.04	-	cyt	0	Cytoplasm (By similarity)				372
Q7ZA45 UniProt NPD GO	GPD_KLUTH	Glycerol-3-phosphate dehydrogenase [NAD+] (EC 1.1.1.8)	0.04	-	mit	0					411
Q6FN96 UniProt NPD GO	GPD1_CANGA	Glycerol-3-phosphate dehydrogenase [NAD+] 1 (EC 1.1.1.8)	0.04	-	cyt	0					400
Q9HGY2 UniProt NPD GO	GPD1_ZYGRO	Glycerol-3-phosphate dehydrogenase [NAD+] 1 (EC 1.1.1.8)	0.04	-	cyt	0	Cytoplasm (Potential)				401
Q29555 UniProt NPD GO	GNMT_PIG	Glycine N-methyltransferase (EC 2.1.1.20) (Fragment)	0.04	-	cyt	0	Cytoplasm				292
P93255 UniProt NPD GO	GCSH_MESCR	Glycine cleavage system H protein, mitochondrial precursor	0.04	-	mit	0	Mitochondrion				163
Q91WK5 UniProt NPD GO	GCSH_MOUSE	Glycine cleavage system H protein, mitochondrial precursor	0.04	-	mit	0	Mitochondrion (By similarity)				170
Q9N121 UniProt NPD GO	GCSH_RABIT	Glycine cleavage system H protein, mitochondrial precursor	0.04	-	mit	0	Mitochondrion (By similarity)				173
Q9SVM8 UniProt NPD GO	GRP2_ARATH	Glycine-rich RNA-binding protein 2, mitochondrial precursor (AtGRP2)	0.04	-	mit	0	Mitochondrion				158
P37703 UniProt NPD GO	GRP9_DAUCA	Glycine-rich protein DC9.1	0.04	-	exc	0					144
P11898 UniProt NPD GO	GRP1_CHERU	Glycine-rich protein HC1	0.04	-	exc	0					144
P02725 UniProt NPD GO	GLP_PIG	Glycophorin	0.04	-	nuc	1	Membrane; single-pass type I membrane protein				133
P04921 UniProt NPD GO	GLPC_HUMAN	Glycophorin C (PAS-2') (Glycoprotein beta) (GLPC) (Glycoconnectin) (Sialoglycoprotein D) (Glycophori ...	0.04	-	nuc	1	Cell membrane; single-pass type III membrane protein. Linked to the membrane via Band 4.1	integral to plasma membrane [TAS] plasma membrane [NAS]	110750		128
P01221 UniProt NPD GO	GLHA1_CYPCA	Glycoprotein hormones alpha chain 1 precursor (Gonadotropin alpha chain 1) (GTH-alpha)	0.04	-	mit	0	Secreted protein				118
P18857 UniProt NPD GO	GLHA2_CYPCA	Glycoprotein hormones alpha chain 2 precursor (Gonadotropin alpha chain 2) (GTH-alpha)	0.04	-	exc	1 *	Secreted protein				118
Q9BDI8 UniProt NPD GO	GLHA_PANTA	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.04	-	exc	1 *	Secreted protein				120
P30970 UniProt NPD GO	GLHA_ACALA	Glycoprotein hormones alpha chain precursor (Gonadotropin alpha chain) (GTH-alpha)	0.04	-	exc	0	Secreted protein				117
Q99445 UniProt NPD GO	GML_HUMAN	Glycosyl-phosphatidylinositol-anchored molecule-like protein precursor	0.04	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	extrinsic to membrane [TAS] plasma membrane [TAS]	602370		158
Q9H4G4 UniProt NPD GO	GAPR1_HUMAN	Golgi-associated plant pathogenesis-related protein 1 (Golgi-associated PR-1 protein) (GAPR-1) (Glio ...	0.04	-	nuc	0	Golgi apparatus; Golgi membrane; lipid-anchor. Binds lipid-enriched microdomains of Golgi membranes ...		607141	1SMB	153
P10257 UniProt NPD GO	GTHB1_ONCKE	Gonadotropin beta-1 subunit precursor (Gonadotropin beta-I chain) (GTH-I-beta)	0.04	-	exc	0	Secreted protein				137
Q9PW98 UniProt NPD GO	GTHB2_TRITC	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta)	0.04	-	mit	1 *	Secreted protein				146
P69835 UniProt NPD GO	GRAF_GRASX	Grammistin Gs F (Gs 1)	0.04	-	nuc	0	Secreted protein				25
O82627 UniProt NPD GO	SSG1_ANTMA	Granule-bound starch synthase 1, chloroplast precursor (EC 2.4.1.21) (Granule-bound starch synthase ...	0.04	-	nuc	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound				608
P40754 UniProt NPD GO	GRAR_RANRU	Granuliberin-R	0.04	-		0	Secreted protein				12
P81013 UniProt NPD GO	GRN1_CYPCA	Granulin-1	0.04	-	nuc	0	Secreted protein			1QGM	57
Q99P27 UniProt NPD GO	PG12B_MOUSE	Group XIIB secretory phospholipase A2-like protein precursor (Group XIII secretory phospholipase A2- ...	0.04	-	exc	0	Secreted protein				195
Q02643 UniProt NPD GO	GHRHR_HUMAN	Growth hormone-releasing hormone receptor precursor (GHRH receptor) (GRF receptor) (GRFR)	0.04	-	end	5	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	262400		423
P29829 UniProt NPD GO	GBB2_DROME	Guanine nucleotide-binding protein subunit beta 2	0.04	-	cyt	0		cytoplasm [IDA] heterotrimeric G-protein complex [IDA] rhabdomere [IDA]			346
P81762 UniProt NPD GO	RNPO_PLEOS	Guanyl-specific ribonuclease Po1 (EC 3.1.27.3) (RNase Po1)	0.04	-	cyt	0					101
Q39524 UniProt NPD GO	HUP2_CHLKE	H(+)/hexose cotransporter 2 (Galactose-H+ symporter)	0.04	-	end	11 *	Membrane; multi-pass membrane protein				540
P14435 UniProt NPD GO	HA2F_MOUSE	H-2 class II histocompatibility antigen, A-F alpha chain	0.04	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)	external side of plasma membrane [IDA] lysosome [IDA] MHC class II protein complex [IDA] plasma membrane [IDA]			233
P14436 UniProt NPD GO	HA2R_MOUSE	H-2 class II histocompatibility antigen, A-R alpha chain	0.04	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				233
P01904 UniProt NPD GO	HA21_MOUSE	H-2 class II histocompatibility antigen, E-D alpha chain precursor (H2-IE-alpha)	0.04	-	end	1	Membrane; single-pass type I membrane protein (Potential)	external side of plasma membrane [IDA]		1KTD	255
P04224 UniProt NPD GO	HA22_MOUSE	H-2 class II histocompatibility antigen, E-K alpha chain precursor	0.04	-	end	1	Membrane; single-pass type I membrane protein (Potential)	external side of plasma membrane [IDA]		1R5W	255
Q6NTV9 UniProt NPD GO	NOLA2_XENLA	H/ACA ribonucleoprotein complex subunit 2-like protein	0.04	-	nuc	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			149
Q6P8C4 UniProt NPD GO	NOLA2_XENTR	H/ACA ribonucleoprotein complex subunit 2-like protein	0.04	-	nuc	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			149

You are viewing entries 77151 to 77200 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.