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
Q9CXY9 UniProt NPD GO	GPI8_MOUSE	GPI-anchor transamidase precursor (EC 3.-.-.-) (GPI transamidase) (Phosphatidylinositol-glycan biosy ...	0.30	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	GPI-anchor transamidase complex [ISS]			395
Q8K025 UniProt NPD GO	FRAT2_MOUSE	GSK-3-binding protein FRAT2 (Frat-2)	0.30	-	nuc	0					231
P38066 UniProt NPD GO	GCH2_YEAST	GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)	0.30	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			345
Q11126 UniProt NPD GO	FUT3_BOVIN	Galactoside 3(4)-L-fucosyltransferase (EC 2.4.1.65) (Blood group Lewis alpha-4-fucosyltransferase) ( ...	0.30	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				365
P08209 UniProt NPD GO	CRGD_BOVIN	Gamma crystallin D (Gamma crystallin IIIB)	0.30	-	nuc	0				1ELP	173
P36382 UniProt NPD GO	CXA5_HUMAN	Gap junction alpha-5 protein (Connexin-40) (Cx40)	0.30	-	end	3 *	Membrane; multi-pass membrane protein	gap junction [TAS]	121013		357
Q12051 UniProt NPD GO	GGPPS_YEAST	Geranylgeranyl pyrophosphate synthetase (GGPP synthetase) (GGPPSase) (Geranylgeranyl diphosphate syn ...	0.30	-	nuc	0	Cytoplasm (By similarity)	mitochondrion [IDA]		2DH4	335
Q5EAD5 UniProt NPD GO	PGT1_BOVIN	Geranylgeranyl transferase type-1 subunit beta (EC 2.5.1.59) (Geranylgeranyl transferase type I subu ...	0.30	-	nuc	0					377
Q8BUY9 UniProt NPD GO	PGT1_MOUSE	Geranylgeranyl transferase type-1 subunit beta (EC 2.5.1.59) (Geranylgeranyl transferase type I subu ...	0.30	-	cyt	0					377
Q2HJ87 UniProt NPD GO	GMEB1_BOVIN	Glucocorticoid modulatory element-binding protein 1 (GMEB-1)	0.30	-	cyt	0	Nucleus. Cytoplasm. May be also cytoplasmic (By similarity)				563
Q04409 UniProt NPD GO	EMI2_YEAST	Glucokinase EMI2 (EC 2.7.1.2) (Glucose kinase) (GLK) (Early meiotic induction protein 2)	0.30	-	nuc	0	Cytoplasm	cytoplasm [IDA]			500
P47856 UniProt NPD GO	GFPT1_MOUSE	Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (EC 2.6.1.16) (Hexosephosphate am ...	0.30	-	nuc	0					696
P82808 UniProt NPD GO	GFPT1_RAT	Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (EC 2.6.1.16) (Hexosephosphate am ...	0.30	-	nuc	0					680
Q68Y21 UniProt NPD GO	GRID2_BRARE	Glutamate receptor delta-2 subunit precursor (GluR delta-2)	0.30	-	end	3	Membrane; multi-pass membrane protein (By similarity)	plasma membrane [ISS]			1009
Q61625 UniProt NPD GO	GRID2_MOUSE	Glutamate receptor delta-2 subunit precursor (GluR delta-2)	0.30	-	end	3	Membrane; multi-pass membrane protein (By similarity)	synaptosome [IDA]			1007
Q95334 UniProt NPD GO	AMPE_PIG	Glutamyl aminopeptidase (EC 3.4.11.7) (EAP) (Aminopeptidase A) (APA)	0.30	-	gol	1 *	Membrane; single-pass type II membrane protein				942
Q9Z339 UniProt NPD GO	GSTO1_RAT	Glutathione transferase omega-1 (EC 2.5.1.18) (GSTO 1-1) (Glutathione-dependent dehydroascorbate red ...	0.30	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [NAS]			241
P04706 UniProt NPD GO	GLU2_MAIZE	Glutelin-2 precursor (Zein-gamma) (27 kDa zein) (Alcohol-soluble reduced glutelin) (ASG) (Zein ZC2)	0.30	-	nuc	0	Protein body; protein body membrane. Border of the inner part of the membrane of endosperm protein b ...				223
Q43869 UniProt NPD GO	PLSB_SPIOL	Glycerol-3-phosphate acyltransferase, chloroplast precursor (EC 2.3.1.15) (GPAT)	0.30	-	nuc	0	Plastid; chloroplast; chloroplast stroma				472
P43304 UniProt NPD GO	GPDM_HUMAN	Glycerol-3-phosphate dehydrogenase, mitochondrial precursor (EC 1.1.99.5) (GPD-M) (GPDH-M) (mtGPD)	0.30	-	cyt	1 *	Mitochondrion		138430		727
P11216 UniProt NPD GO	PYGB_HUMAN	Glycogen phosphorylase, brain form (EC 2.4.1.1)	0.30	-	nuc	0			138550		842
Q5R5M6 UniProt NPD GO	PYGB_PONPY	Glycogen phosphorylase, brain form (EC 2.4.1.1)	0.30	-	nuc	0					842
Q66PG2 UniProt NPD GO	LARGE_BRARE	Glycosyltransferase-like protein LARGE1 (EC 2.4.-.-) (Acetylglucosaminyltransferase-like 1A)	0.30	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				757
Q9Y625 UniProt NPD GO	GPC6_HUMAN	Glypican-6 precursor	0.30	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	integral to plasma membrane [TAS]	604404		555
O15976 UniProt NPD GO	GNAO_PATYE	Guanine nucleotide-binding protein G(o) subunit alpha	0.30	-	cyt	0					356
P18872 UniProt NPD GO	GNAO1_MOUSE	Guanine nucleotide-binding protein G(o) subunit alpha 1	0.30	-	cyt	0		heterotrimeric G-protein complex [TAS] membrane fraction [TAS]			353
Q86FX7 UniProt NPD GO	GPA17_CAEBR	Guanine nucleotide-binding protein alpha-17 subunit (Odorant response abnormal protein 3)	0.30	-	cyt	0					356
Q18434 UniProt NPD GO	GPA17_CAEEL	Guanine nucleotide-binding protein alpha-17 subunit (Odorant response abnormal protein 3)	0.30	-	cyt	0					356
P18851 UniProt NPD GO	GBB_YEAST	Guanine nucleotide-binding protein subunit beta	0.30	-	nuc	0		heterotrimeric G-protein complex [IDA] mating projection [IDA] plasma membrane [IDA]		1SCG	423
Q61ZF6 UniProt NPD GO	GBB1_CAEBR	Guanine nucleotide-binding protein subunit beta 1	0.30	-	cyt	0					340
P17343 UniProt NPD GO	GBB1_CAEEL	Guanine nucleotide-binding protein subunit beta 1	0.30	-	cyt	0					340
Q6FJ50 UniProt NPD GO	GBG_CANGA	Guanine nucleotide-binding protein subunit gamma	0.30	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				88
Q6BQP3 UniProt NPD GO	NOP10_DEBHA	H/ACA ribonucleoprotein complex subunit 3 (Nucleolar protein family A member 3) (snoRNP protein NOP1 ...	0.30	-	nuc	0	Nucleus; nucleolus (By similarity)				58
Q2KHZ2 UniProt NPD GO	HBS1L_BOVIN	HBS1-like protein	0.30	-	cyt	0					686
Q9UQF0 UniProt NPD GO	ENW1_HUMAN	HERV-W_7q21.2 provirus ancestral Env polyprotein precursor (Envelope polyprotein gPr73) (HERV-7q Env ...	0.30	-	end	1	TM: Cell membrane; single-pass type I membrane protein. SU: Cell membrane; peripheral membrane prote ...		604659		538
Q07437 UniProt NPD GO	HSP70_LEIAM	Heat shock 70 kDa protein	0.30	-	cyt	0					652
P14834 UniProt NPD GO	HSP70_LEIMA	Heat shock 70 kDa protein (Fragment)	0.30	-	cyt	0					516
Q05746 UniProt NPD GO	HSP70_PLACB	Heat shock 70 kDa protein (HSP70) (Cytoplasmic antigen) (74.6 kDa protein)	0.30	-	cyt	0					686
P34931 UniProt NPD GO	HS70L_HUMAN	Heat shock 70 kDa protein 1L (Heat shock 70 kDa protein 1-like) (Heat shock 70 kDa protein 1-Hom) (H ...	0.30	-	cyt	0			140559		641
Q24789 UniProt NPD GO	HSP70_ECHGR	Heat shock cognate 70 kDa protein (HSP70)	0.30	-	cyt	0					665
Q9T0D3 UniProt NPD GO	HSF7_ARATH	Heat shock factor protein 7 (HSF 7) (Heat shock transcription factor 7) (HSTF 7)	0.30	-	cyt	0	Nucleus (By similarity)				377
Q6AXU6 UniProt NPD GO	HN1_RAT	Hematological and neurological expressed 1 protein	0.30	-	nuc	0	Nucleus (By similarity)				148
O19998 UniProt NPD GO	HO_RHOVL	Heme oxygenase (EC 1.14.99.3)	0.30	-	cyt	0	Plastid; chloroplast				235
P14791 UniProt NPD GO	HMOX1_CHICK	Heme oxygenase 1 (EC 1.14.99.3) (HO-1)	0.30	-	nuc	1	Microsome				296
Q6ZVN8 UniProt NPD GO	RGMC_HUMAN	Hemojuvelin precursor (Hemochromatosis type 2 protein) (RGM domain family member C)	0.30	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (By similarity)		608374		426
P25722 UniProt NPD GO	HS2ST_DROME	Heparin sulfate O-sulfotransferase (EC 2.8.2.-)	0.30	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				349
Q9GL41 UniProt NPD GO	HFE_RHIUN	Hereditary hemochromatosis protein homolog precursor	0.30	-	end	1	Membrane; single-pass type I membrane protein				348
Q62826 UniProt NPD GO	HNRPM_RAT	Heterogeneous nuclear ribonucleoprotein M (hnRNP M) (M4 protein)	0.30	-	cyt	0	Nucleus; nucleoplasm; nuclear matrix				689
P70612 UniProt NPD GO	CXCR1_RAT	High affinity interleukin-8 receptor A (IL-8R A) (CXCR-1) (CD181 antigen)	0.30	-	end	6 *	Membrane; multi-pass membrane protein				349
O70628 UniProt NPD GO	PDE9A_MOUSE	High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35)	0.30	-	mit	0					534

You are viewing entries 40351 to 40400 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.