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
P81706 UniProt NPD GO	GSTA1_CAVPO	Glutathione S-transferase A (EC 2.5.1.18) (GST A) (Class-alpha) (GGST A1-1)	0.07	-	cyt	0	Cytoplasm				218
P46409 UniProt NPD GO	GSTMU_RABIT	Glutathione S-transferase Mu 1 (EC 2.5.1.18) (GST Mu I) (GST class-mu)	0.07	-	cyt	0	Cytoplasm				217
P09211 UniProt NPD GO	GSTP1_HUMAN	Glutathione S-transferase P (EC 2.5.1.18) (GST class-pi) (GSTP1-1)	0.07	-	cyt	0		cytoplasm [TAS]	134660	9GSS	209
Q28035 UniProt NPD GO	GSTA1_BOVIN	Glutathione S-transferase alpha-1 (EC 2.5.1.18) (GST class-alpha)	0.07	-	nuc	0	Cytoplasm (By similarity)				221
Q9DCM2 UniProt NPD GO	GSTK1_MOUSE	Glutathione S-transferase kappa 1 (EC 2.5.1.18) (GST 13-13) (Glutathione S-transferase subunit 13) ( ...	0.07	-	cyt	0	Mitochondrion	mitochondrial inner membrane [IDA] mitochondrion [IDA]			225
P57108 UniProt NPD GO	GSTZ_EUPES	Glutathione S-transferase zeta class (EC 2.5.1.18)	0.07	-	cyt	0	Cytoplasm (By similarity)				225
Q4AEI1 UniProt NPD GO	GPX1_CEBAP	Glutathione peroxidase 1 (EC 1.11.1.9) (GSHPx-1) (GPx-1) (Cellular glutathione peroxidase)	0.07	-	mit	0	Cytoplasm (By similarity)				201
P07203 UniProt NPD GO	GPX1_HUMAN	Glutathione peroxidase 1 (EC 1.11.1.9) (GSHPx-1) (GPx-1) (Cellular glutathione peroxidase)	0.07	-	mit	0	Cytoplasm		138320	2F8A	201
Q4AEH3 UniProt NPD GO	GPX3_CEBAP	Glutathione peroxidase 3 precursor (EC 1.11.1.9) (GSHPx-3) (GPx-3) (Plasma glutathione peroxidase) ( ...	0.07	-	end	0	Secreted protein (By similarity)	extracellular space [ISS]			226
Q95003 UniProt NPD GO	GPX3_CAEEL	Glutathione peroxidase precursor (EC 1.11.1.9)	0.07	-	vac	0	Secreted protein; extracellular space (By similarity)				224
P42770 UniProt NPD GO	GSHRP_ARATH	Glutathione reductase, chloroplast precursor (EC 1.8.1.7) (GR) (GRase)	0.07	-	mit	0	Plastid; chloroplast (Potential)				565
P27456 UniProt NPD GO	GSHRP_PEA	Glutathione reductase, chloroplast/mitochondrial precursor (EC 1.8.1.7) (GR) (GRase) (GOR1)	0.07	-	mit	0	Plastid; chloroplast. Mainly. Mitochondrion. The majority of the protein is found in chloroplast, wi ...				552
P47791 UniProt NPD GO	GSHR_MOUSE	Glutathione reductase, mitochondrial precursor (EC 1.8.1.7) (GR) (GRase)	0.07	-	nuc	0	Mitochondrion. Cytoplasm				500
P90518 UniProt NPD GO	GSP_CRIFA	Glutathionylspermidine synthase (EC 6.3.1.8)	0.07	-	cyt	0					719
Q64467 UniProt NPD GO	G3PT_MOUSE	Glyceraldehyde-3-phosphate dehydrogenase, testis-specific (EC 1.2.1.12) (Spermatogenic cell-specific ...	0.07	-	mit	0	Cytoplasm (By similarity)	flagellum (sensu Eukaryota) [IDA]			440
Q5G5B9 UniProt NPD GO	GPD_MAGGR	Glycerol-3-phosphate dehydrogenase [NAD+] (EC 1.1.1.8)	0.07	-	cyt	0					433
P90593 UniProt NPD GO	GPDA_TRYBB	Glycerol-3-phosphate dehydrogenase [NAD+], glycosomal (EC 1.1.1.8)	0.07	-	end	0	Glycosome				354
Q26756 UniProt NPD GO	GPDA_TRYBR	Glycerol-3-phosphate dehydrogenase [NAD+], glycosomal (EC 1.1.1.8)	0.07	-	end	0	Glycosome				354
Q9QXF8 UniProt NPD GO	GNMT_MOUSE	Glycine N-methyltransferase (EC 2.1.1.20)	0.07	-	cyt	0	Cytoplasm (By similarity)			1R8Y	292
P10496 UniProt NPD GO	GRP2_PHAVU	Glycine-rich cell wall structural protein 1.8 precursor (GRP 1.8)	0.07	-	exc	1 *	Cell wall (Potential)				465
P51137 UniProt NPD GO	MSK1_MEDSA	Glycogen synthase kinase-3 homolog MsK-1 (EC 2.7.11.1)	0.07	-	cyt	0					411
P51139 UniProt NPD GO	MSK3_MEDSA	Glycogen synthase kinase-3 homolog MsK-3 (EC 2.7.11.1)	0.07	-	cyt	0					411
P51499 UniProt NPD GO	GLHA_CALJA	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.07	-	exc	1 *	Secreted protein				120
Q9CYL5 UniProt NPD GO	GAPR1_MOUSE	Golgi-associated plant pathogenesis-related protein 1 (Golgi-associated PR-1 protein) (GAPR-1) (Glio ...	0.07	-	nuc	0	Golgi apparatus; Golgi membrane; lipid-anchor. Binds lipid-enriched microdomains of Golgi membranes ...				153
Q9DG81 UniProt NPD GO	GTHB1_ICTPU	Gonadotropin beta-1 subunit precursor (Gonadotropin beta-I chain) (GTH-I-beta) (GTH beta-1)	0.07	-	exc	0	Secreted protein				132
P37206 UniProt NPD GO	GTHB2_THUOB	Gonadotropin beta-2 subunit (Gonadotropin beta-II chain) (GTH-II-beta)	0.07	-	nuc	0	Secreted protein				115
Q90225 UniProt NPD GO	GTHB2_ACALA	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta)	0.07	-	exc	0	Secreted protein				137
Q91121 UniProt NPD GO	GTHB2_MORSA	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta)	0.07	-	cyt	0	Secreted protein				139
Q9MZI6 UniProt NPD GO	GNRHR_CANFA	Gonadotropin-releasing hormone receptor (GnRH receptor) (GnRH-R)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				327
O18821 UniProt NPD GO	GNRHR_HORSE	Gonadotropin-releasing hormone receptor (GnRH receptor) (GnRH-R)	0.07	-	nuc	7 *	Membrane; multi-pass membrane protein				328
P30968 UniProt NPD GO	GNRHR_HUMAN	Gonadotropin-releasing hormone receptor (GnRH receptor) (GnRH-R)	0.07	-	nuc	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane [TAS]	228300		328
Q9VVR4 UniProt NPD GO	BGBP2_DROME	Gram-negative bacteria-binding protein 2 precursor	0.07	-	mit	0	Secreted protein (By similarity)	extracellular region [ISS]			461
P11032 UniProt NPD GO	GRAA_MOUSE	Granzyme A precursor (EC 3.4.21.78) (T cell-specific serine protease 1) (TSP-1) (CTLA-3) (Fragmentin ...	0.07	-	exc	0	Secreted protein; cytoplasmic granule. Cytoplasmic granules of cytolytic T-lymphocytes	immunological synapse [ISS] nucleus [ISS]			260
Q9BX93 UniProt NPD GO	PG12B_HUMAN	Group XIIB secretory phospholipase A2-like protein precursor (Group XIII secretory phospholipase A2- ...	0.07	-	exc	0	Secreted protein				195
P22339 UniProt NPD GO	GA45B_MOUSE	Growth arrest and DNA-damage-inducible protein GADD45 beta (Negative growth-regulatory protein MyD11 ...	0.07	-	cyt	0		nucleus [TAS]			160
Q60631 UniProt NPD GO	GRB2_MOUSE	Growth factor receptor-bound protein 2 (Adapter protein GRB2) (SH2/SH3 adapter GRB2)	0.07	-	cyt	0		cytoplasm [IDA] vesicle membrane [IDA]		4GBQ	217
Q66II3 UniProt NPD GO	GRB2_XENTR	Growth factor receptor-bound protein 2 (Adapter protein GRB2) (SH2/SH3 adapter GRB2)	0.07	-	cyt	0		cytosol [ISS]			229
P87379 UniProt NPD GO	GRB2A_XENLA	Growth factor receptor-bound protein 2-A (Adapter protein GRB2-A) (SH2/SH3 adapter GRB2-A)	0.07	-	cyt	0		cytosol [ISS]			229
Q99P50 UniProt NPD GO	GHSR_MOUSE	Growth hormone secretagogue receptor type 1 (GHS-R) (GH-releasing peptide receptor) (GHRP) (Ghrelin ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein	cell surface [ISS]			364
O46675 UniProt NPD GO	GROG_BOVIN	Growth-regulated protein homolog gamma precursor (GRO-gamma)	0.07	-	mit	0	Secreted protein				98
P47224 UniProt NPD GO	MSS4_HUMAN	Guanine nucleotide exchange factor MSS4 (Rab-interacting factor)	0.07	-	cyt	0			603417	2FU5	123
Q91X96 UniProt NPD GO	MSS4_MOUSE	Guanine nucleotide exchange factor MSS4 (Rab-interacting factor)	0.07	-	cyt	0					123
Q9VLP3 UniProt NPD GO	MSS4_DROME	Guanine nucleotide exchange factor MSS4 homolog	0.07	-	cyt	0					122
O60262 UniProt NPD GO	GBG7_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-7 subunit precursor	0.07	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		604430		68
P36408 UniProt NPD GO	GBB_DICDI	Guanine nucleotide-binding protein subunit beta	0.07	-	cyt	0					347
Q25306 UniProt NPD GO	GBLP_LEIMA	Guanine nucleotide-binding protein subunit beta-like protein (Antigen LACK)	0.07	-	cyt	0					312
Q9HEM6 UniProt NPD GO	GDA1_KLULA	Guanosine-diphosphatase (EC 3.6.1.42) (GDPase)	0.07	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				522
P04228 UniProt NPD GO	HA2D_MOUSE	H-2 class II histocompatibility antigen, A-D alpha chain precursor	0.07	-	end	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]		1F3J	256
P18469 UniProt NPD GO	HB2J_MOUSE	H-2 class II histocompatibility antigen, I-E beta chain precursor	0.07	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				264
P32495 UniProt NPD GO	NHP2_YEAST	H/ACA ribonucleoprotein complex subunit 2 (H/ACA snoRNP protein NHP2) (High mobility group-like nucl ...	0.07	-	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IDA]			156

You are viewing entries 70101 to 70150 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.