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
O65355 UniProt NPD GO	GGH_ARATH	Gamma-glutamyl hydrolase precursor (EC 3.4.19.9) (Gamma-Glu-X carboxypeptidase) (Conjugase) (GH)	0.01	-	cyt	0	Secreted protein; extracellular space (By similarity). Cell wall (By similarity). Extracellular or c ...				347
Q5RDM3 UniProt NPD GO	APH1B_PONPY	Gamma-secretase subunit APH-1B (APH-1b) (Aph-1beta)	0.01	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				257
Q8WW43 UniProt NPD GO	APH1B_HUMAN	Gamma-secretase subunit APH-1B (APH-1b) (Aph-1beta) (Presenilin-stabilization factor-like)	0.01	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [IDA]	607630		257
O45876 UniProt NPD GO	APH1_CAEEL	Gamma-secretase subunit aph-1 (Anterior-pharynx-defective protein 1) (Presenilin enhancer protein 1) ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				308
Q9Z0F7 UniProt NPD GO	SYUG_MOUSE	Gamma-synuclein (Persyn)	0.01	-	cyt	0	Cytoplasm; perinuclear region (By similarity). Centrosome (By similarity). Spindle (By similarity). ...	axon [IDA] cell soma [IDA] cytoplasm [IDA]			123
O76070 UniProt NPD GO	SYUG_HUMAN	Gamma-synuclein (Persyn) (Breast cancer-specific gene 1 protein) (Synoretin) (SR)	0.01	-	cyt	0	Cytoplasm; perinuclear region. Centrosome. Spindle. Associated with centrosomes in several interphas ...		602998		127
Q9NZ50 UniProt NPD GO	SYUG_BOVIN	Gamma-synuclein (Synoretin) (SR)	0.01	-	cyt	0	Cytoplasm; perinuclear region. Centrosome. Spindle. Associated with centrosomes in several interphas ...				127
Q8HXX6 UniProt NPD GO	SAP3_MACFA	Ganglioside GM2 activator precursor (GM2-AP) (Cerebroside sulfate activator protein) (Shingolipid ac ...	0.01	-	end	0	Lysosome (By similarity)				190
P07098 UniProt NPD GO	LIPG_HUMAN	Gastric triacylglycerol lipase precursor (EC 3.1.1.3) (Gastric lipase) (GL)	0.01	-	mit	0	Secreted protein		601980	1HLG	398
P33714 UniProt NPD GO	GAST_MACMU	Gastrin	0.01	-		0	Secreted protein				17
P04564 UniProt NPD GO	GAST_CAPHI	Gastrin precursor [Contains: Big gastrin (Gastrin 34) (G34); Gastrin]	0.01	-	cyt	0	Secreted protein				34
P09472 UniProt NPD GO	GRP_SCYCA	Gastrin-releasing peptide (GRP)	0.01	-	cyt	0	Secreted protein				25
Q9CR36 UniProt NPD GO	GKN1_MOUSE	Gastrokine-1 precursor (18 kDa antrum mucosa protein) (AMP-18) (CA11 protein homolog)	0.01	-	exc	0	Secreted protein	secretory granule [IDA]			184
Q9NS71 UniProt NPD GO	GKN1_HUMAN	Gastrokine-1 precursor (18 kDa antrum mucosa protein) (AMP-18) (CA11 protein)	0.01	-	exc	1 *	Secreted protein (By similarity)		606402		185
P51161 UniProt NPD GO	ILBP_HUMAN	Gastrotropin (GT) (Ileal lipid-binding protein) (ILBP) (Intestinal 15 kDa protein) (I-15P) (Intestin ...	0.01	-	cyt	0	Cytoplasm	cytoplasm [TAS]	600422	1O1V	127
P10289 UniProt NPD GO	ILBP_PIG	Gastrotropin (GT) (Ileal lipid-binding protein) (ILBP) (Porcine ileal peptide) (PIP)	0.01	-	cyt	0	Cytoplasm			1EIO	127
P34172 UniProt NPD GO	OBP_HYACE	General odorant-binding protein (GOBP) (Fragment)	0.01	-		0					18
P34173 UniProt NPD GO	OBP_LYMDI	General odorant-binding protein (GOBP) (Fragment)	0.01	-		0					18
P34170 UniProt NPD GO	OBP1_BOMMO	General odorant-binding protein 1 precursor (GOBP1) (GOBP2)	0.01	-	end	0					160
Q95VP2 UniProt NPD GO	GOBP2_EPIPO	General odorant-binding protein 2 precursor (GOBP 2)	0.01	-	mit	0					161
Q8SY61 UniProt NPD GO	OB56D_DROME	General odorant-binding protein 56d precursor	0.01	-	end	0	Secreted protein (By similarity)	extracellular region [ISS]			131
Q9V938 UniProt NPD GO	OB57E_DROME	General odorant-binding protein 57e precursor	0.01	-	cyt	0					136
Q9VAJ4 UniProt NPD GO	OB99A_DROME	General odorant-binding protein 99a precursor	0.01	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			142
Q8C7E7 UniProt NPD GO	GET1_MOUSE	Genethonin-1	0.01	-	end	1 *	Membrane; single-pass type III membrane protein. Distributed in the transverse tubules and/or near t ...				338
Q9SLG2 UniProt NPD GO	GGPP4_ARATH	Geranylgeranyl pyrophosphate synthetase 4 precursor (GGPP synthetase 4) (GGPS4) [Includes: Dimethyla ...	0.01	-	nuc	1 *	Endoplasmic reticulum				372
P53611 UniProt NPD GO	PGTB_HUMAN	Geranylgeranyl transferase type-2 subunit beta (EC 2.5.1.60) (Geranylgeranyl transferase type II sub ...	0.01	-	cyt	0			179080		331
Q08603 UniProt NPD GO	PGTB_RAT	Geranylgeranyl transferase type-2 subunit beta (EC 2.5.1.60) (Geranylgeranyl transferase type II sub ...	0.01	-	cyt	0				1LTX	331
P46271 UniProt NPD GO	GLP1_BRANA	Germin-like protein 1 precursor	0.01	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				207
Q9FMA8 UniProt NPD GO	GL111_ARATH	Germin-like protein subfamily 1 member 11 precursor	0.01	-	end	1 *	Secreted protein; extracellular space; apoplast (By similarity)				223
P92997 UniProt NPD GO	GL113_ARATH	Germin-like protein subfamily 1 member 13 precursor	0.01	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				222
Q9FID0 UniProt NPD GO	GL114_ARATH	Germin-like protein subfamily 1 member 14 precursor	0.01	-	mit	0	Secreted protein; extracellular space; apoplast (By similarity)				222
Q9FIC9 UniProt NPD GO	GL115_ARATH	Germin-like protein subfamily 1 member 15 precursor	0.01	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				221
Q9FIC8 UniProt NPD GO	GL116_ARATH	Germin-like protein subfamily 1 member 16 precursor	0.01	-	exc	0	Secreted protein; extracellular space; apoplast (By similarity)				222
P92999 UniProt NPD GO	GL118_ARATH	Germin-like protein subfamily 1 member 18 precursor (GLP2a copy 1)	0.01	-	exc	0	Secreted protein; extracellular space; apoplast (By similarity)				222
P92996 UniProt NPD GO	GL120_ARATH	Germin-like protein subfamily 1 member 20 precursor (GLP2a copy 2) (Germin type 2) (GLP2b) (At-GERM2 ...	0.01	-	exc	0	Secreted protein; extracellular space; apoplast (By similarity)				222
Q9LEA7 UniProt NPD GO	GL18_ARATH	Germin-like protein subfamily 1 member 8 precursor	0.01	-	end	1 *	Secreted protein; extracellular space; apoplast (By similarity)				222
P92995 UniProt NPD GO	GLT1_ARATH	Germin-like protein subfamily T member 1 precursor	0.01	-	exc	0	Secreted protein; extracellular space; apoplast (By similarity)				220
Q9LMC9 UniProt NPD GO	GLT2_ARATH	Germin-like protein subfamily T member 2 precursor	0.01	-	exc	0	Secreted protein; extracellular space; apoplast (By similarity)				220
P20412 UniProt NPD GO	GLB1_LAMSP	Giant hemoglobin AI chain (Fragment)	0.01	-	cyt	0					41
Q76CA1 UniProt NPD GO	GIG1_STIGI	Gigantoxin-1 precursor (Gigantoxin I) (Gigt I) (EGF-like peptide toxin)	0.01	-	exc	1 *	Secreted protein. Found in nematocyst				86
P43685 UniProt NPD GO	GILX_HELHO	Gilatoxin (EC 3.4.21.-)	0.01	-	cyt	0	Secreted protein				245
P12322 UniProt NPD GO	KLK1_CAVPO	Glandular kallikrein, submandibular (EC 3.4.21.35) (Tissue kallikrein) (Fragment)	0.01	-	cyt	0					31
P36376 UniProt NPD GO	KLK12_RAT	Glandular kallikrein-12, submandibular/renal precursor (EC 3.4.21.35) (Tissue kallikrein) (RSKG-3)	0.01	-	exc	0					259
P02207 UniProt NPD GO	GLB_LAMFL	Globin	0.01	-	cyt	0				1UC3	149
Q7M424 UniProt NPD GO	GLB_BUCUU	Globin (Myoglobin)	0.01	-	mit	0					146
P09965 UniProt NPD GO	GLB_DOLAU	Globin (Myoglobin)	0.01	-	cyt	0					146
P31331 UniProt NPD GO	GLB_NASMU	Globin (Myoglobin)	0.01	-	cyt	0					147
P18202 UniProt NPD GO	GLB_TUBTU	Globin, extracellular monomeric	0.01	-	cyt	0	Secreted protein				141
P02217 UniProt NPD GO	GLB2_GLYDI	Globin, minor monomeric component (Fragment)	0.01	-	cyt	0					45
P09967 UniProt NPD GO	GLB1_PETMA	Globin-1 (Globin I)	0.01	-	mit	0					149

You are viewing entries 88401 to 88450 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.