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
Q42968 UniProt NPD GO	SSG1_ORYGL	Granule-bound starch synthase 1, chloroplast precursor (EC 2.4.1.242) (Granule-bound starch synthase ...	0.05	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound				609
P19395 UniProt NPD GO	SSG1_ORYSA	Granule-bound starch synthase 1, chloroplast precursor (EC 2.4.1.242) (Granule-bound starch synthase ...	0.05	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound	amyloplast [IMP]			609
P12544 UniProt NPD GO	GRAA_HUMAN	Granzyme A precursor (EC 3.4.21.78) (Cytotoxic T-lymphocyte proteinase 1) (Hanukkah factor) (H facto ...	0.05	-	mit	0	Secreted protein; cytoplasmic granule	immunological synapse [TAS] nucleus [TAS]	140050	1ORF	262
P49863 UniProt NPD GO	GRAK_HUMAN	Granzyme K precursor (EC 3.4.21.-) (Granzyme-3) (NK-tryptase-2) (NK-TRYP-2) (Fragmentin-3)	0.05	-	mit	1 *	Secreted protein; cytoplasmic granule		600784	1MZD	264
P51124 UniProt NPD GO	GRAM_HUMAN	Granzyme M precursor (EC 3.4.21.-) (Met-ase) (Natural killer cell granular protease) (HU-Met-1) (Met ...	0.05	-	nuc	1 *	Granules of large granular lymphocytes		600311	1LZP	257
Q9NZK7 UniProt NPD GO	PA2GE_HUMAN	Group IIE secretory phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase GII ...	0.05	-	exc	1 *	Secreted protein	extracellular region [TAS]			142
Q5R4J7 UniProt NPD GO	GRB2_PONPY	Growth factor receptor-bound protein 2 (Adapter protein GRB2) (SH2/SH3 adapter GRB2)	0.05	-	cyt	0					217
P62993 UniProt NPD GO	GRB2_HUMAN	Growth factor receptor-bound protein 2 (Adapter protein GRB2) (SH2/SH3 adapter GRB2) (Protein Ash)	0.05	-	cyt	0		cytosol [TAS]	108355	2H46	217
P62994 UniProt NPD GO	GRB2_RAT	Growth factor receptor-bound protein 2 (Adapter protein GRB2) (SH2/SH3 adapter GRB2) (Protein Ash)	0.05	-	cyt	0					217
Q02644 UniProt NPD GO	GHRHR_RAT	Growth hormone-releasing hormone receptor precursor (GHRH receptor) (GRF receptor) (GRFR)	0.05	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			464
P22800 UniProt NPD GO	GBP_APAKA	Growth-blocking peptide (GBP) (Juvenile hormone esterase activity repressive peptide)	0.05	-	nuc	0					25
P14095 UniProt NPD GO	GROA_RAT	Growth-regulated alpha protein precursor (CXCL1) (Cytokine-induced neutrophil chemoattractant) (CINC ...	0.05	-	exc	0	Secreted protein				96
P47854 UniProt NPD GO	GRO2_RABIT	Growth-regulated protein homolog precursor (GRO homolog)	0.05	-	mit	0	Secreted protein				104
Q2TBQ3 UniProt NPD GO	GAMT_BOVIN	Guanidinoacetate N-methyltransferase (EC 2.1.1.2)	0.05	-	cyt	0					236
P10868 UniProt NPD GO	GAMT_RAT	Guanidinoacetate N-methyltransferase (EC 2.1.1.2)	0.05	-	cyt	0				1XCL	235
P43425 UniProt NPD GO	GBG7_RAT	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-7 subunit precursor	0.05	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	heterotrimeric G-protein complex [NAS]			68
Q21215 UniProt NPD GO	GBLP_CAEEL	Guanine nucleotide-binding protein subunit beta 2-like 1	0.05	-	cyt	0					324
Q4R7Y4 UniProt NPD GO	GBLP_MACFA	Guanine nucleotide-binding protein subunit beta 2-like 1	0.05	-	cyt	0					316
P63247 UniProt NPD GO	GBLP_CHICK	Guanine nucleotide-binding protein subunit beta 2-like 1 (Guanine nucleotide-binding protein subunit ...	0.05	-	cyt	0					317
P63244 UniProt NPD GO	GBLP_HUMAN	Guanine nucleotide-binding protein subunit beta 2-like 1 (Guanine nucleotide-binding protein subunit ...	0.05	-	cyt	0			176981		316
P63243 UniProt NPD GO	GBLP_BOVIN	Guanine nucleotide-binding protein subunit beta 2-like 1 (Receptor of activated protein kinase C 1) ...	0.05	-	cyt	0					316
P63246 UniProt NPD GO	GBLP_PIG	Guanine nucleotide-binding protein subunit beta 2-like 1 (Receptor of activated protein kinase C 1) ...	0.05	-	cyt	0					316
P63245 UniProt NPD GO	GBLP_RAT	Guanine nucleotide-binding protein subunit beta 2-like 1 (Receptor of activated protein kinase C 1) ...	0.05	-	cyt	0					316
P68040 UniProt NPD GO	GBLP_MOUSE	Guanine nucleotide-binding protein subunit beta 2-like 1 (Receptor of activated protein kinase C 1) ...	0.05	-	cyt	0		cell soma [IDA] cytoplasm [IDA]			316
Q10281 UniProt NPD GO	GBLP_SCHPO	Guanine nucleotide-binding protein subunit beta-like protein (Receptor of activated protein kinase C ...	0.05	-	cyt	0	Membrane. Associated with particulate fractions				314
Q25189 UniProt NPD GO	GBLP_HYDAT	Guanine nucleotide-binding protein subunit beta-like protein (Receptor of activated protein kinase C ...	0.05	-	cyt	0					317
P15454 UniProt NPD GO	KGUA_YEAST	Guanylate kinase (EC 2.7.4.8) (GMP kinase)	0.05	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		1GKY	186
P33680 UniProt NPD GO	GUC2A_MOUSE	Guanylin precursor (Guanylate cyclase activator 2A)	0.05	-	exc	1 *	Secreted protein				116
P28902 UniProt NPD GO	GUC2A_RAT	Guanylin precursor (Guanylate cyclase activator 2A)	0.05	-	exc	1 *	Secreted protein				115
Q04457 UniProt NPD GO	EST1_CAEEL	Gut esterase 1 precursor (EC 3.1.1.1) (Non-specific carboxylesterase)	0.05	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				562
P25807 UniProt NPD GO	CPR1_CAEEL	Gut-specific cysteine proteinase precursor (EC 3.4.22.-)	0.05	-	end	0					329
P63123 UniProt NPD GO	VPK7_HUMAN	HERV-K_1q23.3 provirus ancestral Pro protein (EC 3.4.23.-) (HERV-K18 Pro protein) (HERV-K110 Pro pro ...	0.05	-	cyt	0					156
Q8VH49 UniProt NPD GO	HIG1A_RAT	HIG1 domain family member 1A (Hypoxia-inducible gene 1 protein)	0.05	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				93
Q76I25 UniProt NPD GO	HIG1C_MOUSE	HIG1 domain family member 1C	0.05	-	cyt	2 *	Membrane; multi-pass membrane protein (Potential)				96
Q9UMS0 UniProt NPD GO	HIRP5_HUMAN	HIRA-interacting protein 5	0.05	-	cyt	0			608100		196
P01903 UniProt NPD GO	2DRA_HUMAN	HLA class II histocompatibility antigen, DR alpha chain precursor (MHC class II antigen DRA)	0.05	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS] lysosome [IDA] plasma membrane [IDA]	142860	2SEB	254
P01912 UniProt NPD GO	HB2B_HUMAN	HLA class II histocompatibility antigen, DR-1 beta chain precursor (Clone P2-beta-3)	0.05	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)			1A6A	266
P20039 UniProt NPD GO	2B1B_HUMAN	HLA class II histocompatibility antigen, DRB1-11 beta chain precursor (MHC class I antigen DRB1*11) ...	0.05	-	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	609532		266
P13761 UniProt NPD GO	2B17_HUMAN	HLA class II histocompatibility antigen, DRB1-7 beta chain precursor (MHC class I antigen DRB1*7) (D ...	0.05	-	end	1 *	Membrane; single-pass type I membrane protein	membrane [NAS]	609532		266
Q9QZU4 UniProt NPD GO	HRSL1_MOUSE	HRAS-like suppressor (A-C1)	0.05	-	cyt	1	Cytoplasm	cytoplasm [IDA] nuclear envelope lumen [IDA]			167
P53817 UniProt NPD GO	HRSL3_RAT	HRAS-like suppressor 3 (H-rev 107 protein)	0.05	-	nuc	1	Cytoplasm. Membrane; single-pass membrane protein	cytoplasm [IMP] plasma membrane [IMP]			160
Q9S7V4 UniProt NPD GO	HA22A_ARATH	HVA22-like protein a (AtHVA22a)	0.05	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				177
P82656 UniProt NPD GO	HADR_HADAZ	Hadrurin	0.05	-	cyt	0	Secreted protein				41
P83471 UniProt NPD GO	TXHA4_SELHA	Hainantoxin-4 (Hainantoxin-IV) (HnTx-IV)	0.05	-	nuc	0	Secreted protein			1RYV	35
O14558 UniProt NPD GO	HSPB6_HUMAN	Heat-shock protein beta-6 (HspB6) (Heat-shock 20 kDa-like protein p20)	0.05	-	cyt	0					160
Q9EPX0 UniProt NPD GO	HSPB8_RAT	Heat-shock protein beta-8 (HspB8) (Alpha crystallin C chain) (Small stress protein-like protein HSP2 ...	0.05	-	nuc	0					196
P36078 UniProt NPD GO	HOT13_YEAST	Helper of Tim protein 13	0.05	-	nuc	0	Mitochondrion; mitochondrial intermembrane space. Mitochondrion; mitochondrial membrane; peripheral ...	mitochondrial intermembrane space [IDA]			116
P02246 UniProt NPD GO	HEMT_THEDY	Hemerythrin	0.05	-	nuc	0				2HMZ	113
P02245 UniProt NPD GO	HEMT_THEZO	Hemerythrin	0.05	-	cyt	0					113
P80476 UniProt NPD GO	HCY6_ANDAU	Hemocyanin AA6 chain	0.05	-	nuc	0	Secreted protein; extracellular space	extracellular space [ISS]			626

You are viewing entries 74551 to 74600 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.