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
P52884 UniProt NPD GO	SAR2_LYCES	GTP-binding protein SAR2	0.00	-	cyt	0					193
O94363 UniProt NPD GO	RHB1_SCHPO	GTP-binding protein rhb1 (GTP-binding protein Rheb homolog)	0.00	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				185
Q9P4C8 UniProt NPD GO	SAR1_PICPA	GTP-binding protein sar1	0.00	-	cyt	0					190
P80400 UniProt NPD GO	GGN6_RANRU	Gaegurin-6	0.00	-	nuc	0	Secreted protein				24
O42821 UniProt NPD GO	GAL1_CANPA	Galactokinase (EC 2.7.1.6) (Galactose kinase)	0.00	-	cyt	0					504
Q10984 UniProt NPD GO	FUT2_RAT	Galactoside 2-alpha-L-fucosyltransferase 2 (EC 2.4.1.69) (Secretor blood group alpha-2-fucosyltransf ...	0.00	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				354
P56217 UniProt NPD GO	LEG1_BUFAR	Galectin-1	0.00	-	cyt	0				1GAN	134
P11116 UniProt NPD GO	LEG1_BOVIN	Galectin-1 (Lectin galactoside-binding soluble 1) (Beta-galactoside-binding lectin L-14-I) (Lactose- ...	0.00	-	cyt	0				1SLT	134
Q5R7M1 UniProt NPD GO	LEG1_PONPY	Galectin-1 (Lectin galactoside-binding soluble 1) (Beta-galactoside-binding lectin L-14-I) (Lactose- ...	0.00	-	cyt	0					134
P09382 UniProt NPD GO	LEG1_HUMAN	Galectin-1 (Lectin galactoside-binding soluble 1) (Beta-galactoside-binding lectin L-14-I) (Lactose- ...	0.00	-	cyt	0		cytoplasm [TAS]	150570	1W6Q	134
Q29373 UniProt NPD GO	LEG2_PIG	Galectin-2 (Fragment)	0.00	-	cyt	0					123
P54885 UniProt NPD GO	PROA_YEAST	Gamma-glutamyl phosphate reductase (GPR) (EC 1.2.1.41) (Glutamate-5-semialdehyde dehydrogenase) (Glu ...	0.00	-	nuc	0		cytoplasm [IDA] nucleus [IDA]		1VLU	456
Q8C7N7 UniProt NPD GO	APH1B_MOUSE	Gamma-secretase subunit APH-1B (APH-1b) (Aph-1beta)	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				257
Q9VQG2 UniProt NPD GO	APH1_DROME	Gamma-secretase subunit Aph-1 (Presenilin-stabilization factor)	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [NAS]			238
Q921C1 UniProt NPD GO	CXE1_MOUSE	Gap junction epsilon-1 protein (Connexin-29) (Cx29)	0.00	-	end	3 *	Membrane; multi-pass membrane protein				258
P01358 UniProt NPD GO	GAJU_HUMAN	Gastric juice peptide 1 [Contains: Gastric juice peptide 2]	0.00	-		0			137220		10
Q9CPP7 UniProt NPD GO	LIPG_MOUSE	Gastric triacylglycerol lipase precursor (EC 3.1.1.3) (Gastric lipase) (GL)	0.00	-	vac	0	Secreted protein (By similarity)				395
P04634 UniProt NPD GO	LIPG_RAT	Gastric triacylglycerol lipase precursor (EC 3.1.1.3) (Gastric lipase) (GL) (Lingual lipase)	0.00	-	mit	0	Secreted protein	mitochondrion [IDA]			395
Q9PS30 UniProt NPD GO	GRP_ONCMY	Gastrin-releasing peptide (GRP)	0.00	-	cyt	0	Secreted protein				23
P24816 UniProt NPD GO	D1_NEPNO	Gastrin/cholecystokinin-like peptide D1	0.00	-		0	Secreted protein				9
Q8HYA9 UniProt NPD GO	GKN1_PIG	Gastrokine-1 precursor (18 kDa antrum mucosa protein) (AMP-18)	0.00	-	exc	0	Secreted protein (By similarity)				185
P50119 UniProt NPD GO	ILBP_RABIT	Gastrotropin (GT) (Ileal lipid-binding protein) (ILBP)	0.00	-	cyt	0	Cytoplasm				127
P34169 UniProt NPD GO	OBP_ANTPO	General odorant-binding protein (GOBP) (Fragment)	0.00	-	cyt	0					24
Q95VP3 UniProt NPD GO	GOBP1_EPIPO	General odorant-binding protein 1 precursor (GOBP 1)	0.00	-	vac	0					166
Q27288 UniProt NPD GO	OBP2_HELVI	General odorant-binding protein 2 precursor (GOBP 2)	0.00	-	exc	1 *					162
P31419 UniProt NPD GO	OBP2_MANSE	General odorant-binding protein 2 precursor (GOBP 2)	0.00	-	cyt	0					161
Q17075 UniProt NPD GO	OBP2_ANTPE	General odorant-binding protein 2 precursor (GOBP 2) (Pheromone-binding protein 10) (APR-10)	0.00	-	mit	0					160
Q9V8Y2 UniProt NPD GO	OB56A_DROME	General odorant-binding protein 56a precursor	0.00	-	exc	1 *	Secreted protein (By similarity)	extracellular region [ISS]			139
Q9VAI6 UniProt NPD GO	OB99B_DROME	General odorant-binding protein 99b precursor	0.00	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			149
P58844 UniProt NPD GO	CXST_CONGE	Geographus scratcher peptide	0.00	-	cyt	0	Secreted protein				29
P28525 UniProt NPD GO	GER1_HORVU	Germin GS1 (Fragment)	0.00	-		0	Cytoplasm; cytosol. Microsome. Cell wall. Soluble, microsomal and cell wall fractions				13
P28526 UniProt NPD GO	GER2_HORVU	Germin GS2 (Fragment)	0.00	-		0	Cytoplasm; cytosol. Microsome. Cell wall. Soluble, microsomal and cell wall fractions				13
P45854 UniProt NPD GO	GLP1_SINAL	Germin-like protein 1 precursor	0.00	-	end	0	Cell wall				211
P45853 UniProt NPD GO	GLP1_IPONI	Germin-like protein precursor	0.00	-	mit	0	Secreted protein; extracellular space; apoplast (By similarity)				214
P45852 UniProt NPD GO	GLP1_MESCR	Germin-like protein precursor	0.00	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				233
Q9FMA9 UniProt NPD GO	GL110_ARATH	Germin-like protein subfamily 1 member 10 precursor	0.00	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				223
Q9M8X3 UniProt NPD GO	GL13_ARATH	Germin-like protein subfamily 1 member 3 precursor	0.00	-	exc	0	Secreted protein; extracellular space; apoplast (By similarity)				227
Q9M8X4 UniProt NPD GO	GL14_ARATH	Germin-like protein subfamily 1 member 4 precursor	0.00	-	exc	0	Secreted protein; extracellular space; apoplast (By similarity)				222
Q9M8X5 UniProt NPD GO	GL15_ARATH	Germin-like protein subfamily 1 member 5 precursor	0.00	-	exc	0	Secreted protein; extracellular space; apoplast (By similarity)				222
P94014 UniProt NPD GO	GL21_ARATH	Germin-like protein subfamily 2 member 1 precursor	0.00	-	exc	1	Secreted protein; extracellular space; apoplast (By similarity)				207
Q9FZ27 UniProt NPD GO	GL22_ARATH	Germin-like protein subfamily 2 member 2 precursor	0.00	-	mit	0	Secreted protein; extracellular space; apoplast (By similarity)				219
P93000 UniProt NPD GO	GL23_ARATH	Germin-like protein subfamily 2 member 3 precursor	0.00	-	exc	0	Secreted protein; extracellular space; apoplast (By similarity)				219
Q9M263 UniProt NPD GO	GL24_ARATH	Germin-like protein subfamily 2 member 4 precursor	0.00	-	mit	0	Secreted protein; extracellular space; apoplast (By similarity)				220
P94040 UniProt NPD GO	GL31_ARATH	Germin-like protein subfamily 3 member 1 precursor (AtGER1) (At-GERM1) (AtGLP1)	0.00	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				208
P94072 UniProt NPD GO	GL33_ARATH	Germin-like protein subfamily 3 member 3 precursor (AtGER3) (AtGLP2)	0.00	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				211
Q76CA3 UniProt NPD GO	GIG2_STIGI	Gigantoxin-2 precursor (Gigantoxin II) (Gigt II)	0.00	-	exc	0	Secreted protein. Found in nematocyst				74
P02211 UniProt NPD GO	GLB_APLKU	Globin (Myoglobin)	0.00	-	cyt	0					144
P02210 UniProt NPD GO	GLB_APLLI	Globin (Myoglobin)	0.00	-	cyt	0				5MBA	146
P29287 UniProt NPD GO	GLB_BURLE	Globin (Myoglobin)	0.00	-	mit	0					146
P56532 UniProt NPD GO	GLB_DICDE	Globin (Myoglobin) (Fragments)	0.00	-	cyt	0					108

You are viewing entries 94651 to 94700 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.