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
P47967 UniProt NPD GO	LEG5_RAT	Galectin-5 (RL-18)	0.03	-	cyt	0					144
O54974 UniProt NPD GO	LEG7_MOUSE	Galectin-7 (Gal-7)	0.03	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity). Secreted protein (By similarity). May be secrete ...				135
P47929 UniProt NPD GO	LEG7_HUMAN	Galectin-7 (Gal-7) (HKL-14) (PI7) (p53-induced protein 1)	0.03	-	cyt	0	Cytoplasm. Nucleus. Secreted protein (Potential). May be secreted by a non-classical secretory pathw ...	extracellular space [TAS]	600615	5GAL	135
Q62665 UniProt NPD GO	LEG8_RAT	Galectin-8 (30 kDa S-type lectin) (RL-30)	0.03	-	cyt	0	Cytoplasm				316
O00214 UniProt NPD GO	LEG8_HUMAN	Galectin-8 (Gal-8) (Prostate carcinoma tumor antigen 1) (PCTA-1) (Po66 carbohydrate-binding protein) ...	0.03	-	cyt	0	Cytoplasm (Probable)	extracellular space [TAS]	606099		316
Q9DG58 UniProt NPD GO	GLL3_CHICK	Gallinacin-3 precursor (Gal-3)	0.03	-	end	0	Secreted protein				80
Q8JHE9 UniProt NPD GO	APH1B_BRARE	Gamma-secretase subunit Aph-1b (Anterior-pharynx-defective protein 1b)	0.03	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				258
O24115 UniProt NPD GO	THG1_NICPA	Gamma-thionin 1 precursor	0.03	-	exc	1 *					106
Q60648 UniProt NPD GO	SAP3_MOUSE	Ganglioside GM2 activator precursor (GM2-AP) (Cerebroside sulfate activator protein) (Shingolipid ac ...	0.03	-	end	0	Lysosome	mitochondrion [IDA]		2AGC	193
P17900 UniProt NPD GO	SAP3_HUMAN	Ganglioside GM2 activator precursor (GM2-AP) (Cerebroside sulfate activator protein) (Shingolipid ac ...	0.03	-	end	0	Lysosome	lysosome [NAS]	272750	2AG9	193
P09680 UniProt NPD GO	GIP_BOVIN	Gastric inhibitory polypeptide (GIP) (Glucose-dependent insulinotropic polypeptide)	0.03	-	cyt	0	Secreted protein				42
P52787 UniProt NPD GO	IF_MOUSE	Gastric intrinsic factor precursor (Intrinsic factor) (IF) (INF)	0.03	-	exc	0	Secreted protein				417
Q64411 UniProt NPD GO	PEPC_CAVPO	Gastricsin precursor (EC 3.4.23.3) (Pepsinogen C)	0.03	-	vac	0	Secreted protein				394
P06885 UniProt NPD GO	GAST_CAVPO	Gastrin precursor [Contains: Big gastrin (Gastrin 33) (G33); Gastrin]	0.03	-	cyt	0	Secreted protein				33
P10034 UniProt NPD GO	GAST_CHIBR	Gastrin precursor [Contains: Big gastrin (Gastrin 33) (G33); Gastrin]	0.03	-	cyt	0	Secreted protein				33
P01295 UniProt NPD GO	GRP_CHICK	Gastrin-releasing peptide (GRP) (Proventricular peptide) [Contains: Neuromedin C (GRP-10)]	0.03	-	cyt	0	Secreted protein				27
P63152 UniProt NPD GO	GRP_CAVPO	Gastrin-releasing peptide (GRP) [Contains: Neuromedin C (GRP-10)]	0.03	-	nuc	0	Secreted protein				27
P63153 UniProt NPD GO	GRP_PIG	Gastrin-releasing peptide (GRP) [Contains: Neuromedin C (GRP-10)]	0.03	-	nuc	0	Secreted protein				27
P14885 UniProt NPD GO	GELS_XENLA	Gelsolin (Actin-depolymerizing factor) (ADF) (Brevin) (Fragment)	0.03	-	cyt	0					417
Q8WXD5 UniProt NPD GO	GEMI6_HUMAN	Gem-associated protein 6 (Gemin-6) (SIP2)	0.03	-	nuc	0	Nucleus. Found both in the nucleoplasm and in nuclear bodies called gems (Gemini of Cajal bodies) th ...	cytoplasm [IDA] nuclear body [IDA] nucleoplasm [IDA]	607006	1Y96	167
P25376 UniProt NPD GO	AGP1_YEAST	General amino acid permease AGP1 (Asparagine/glutamine permease)	0.03	-	end	12	Membrane; multi-pass membrane protein (Probable)				595
P19145 UniProt NPD GO	GAP1_YEAST	General amino-acid permease GAP1	0.03	-	end	12	Membrane; multi-pass membrane protein	endosome [IDA] ER to Golgi transport vesicle [IDA] integral to plasma membrane [IDA] multivesicular body [IMP] plasma membrane [IDA] vacuolar lumen (sensu Fungi) [IDA]			602
P34171 UniProt NPD GO	OBP2_BOMMO	General odorant-binding protein 2 precursor (GOBP2) (GOBP1)	0.03	-	cyt	0					164
O04046 UniProt NPD GO	GGPP2_ARATH	Geranylgeranyl pyrophosphate synthetase 2 precursor (GGPP synthetase 2) (GGPS2) [Includes: Dimethyla ...	0.03	-	nuc	1 *	Endoplasmic reticulum				376
P48368 UniProt NPD GO	CRTE_CYAPA	Geranylgeranyl pyrophosphate synthetase homolog (EC 2.5.1.29) (GGPP synthetase) (Farnesyltranstransf ...	0.03	-	cyt	0	Plastid; cyanelle				300
Q42698 UniProt NPD GO	GGPPS_CATRO	Geranylgeranyl pyrophosphate synthetase, chloroplast precursor (GGPP synthetase) (GGPS) [Includes: D ...	0.03	-	mit	0	Plastid; chloroplast				357
Q5E9B3 UniProt NPD GO	PGTB_BOVIN	Geranylgeranyl transferase type-2 subunit beta (EC 2.5.1.60) (Geranylgeranyl transferase type II sub ...	0.03	-	cyt	0					331
P53612 UniProt NPD GO	PGTB_MOUSE	Geranylgeranyl transferase type-2 subunit beta (EC 2.5.1.60) (Geranylgeranyl transferase type II sub ...	0.03	-	nuc	0					339
Q9C971 UniProt NPD GO	G3OX4_ARATH	Gibberellin 3-beta-dioxygenase 4 (EC 1.14.11.15) (Gibberellin 3 beta-hydroxylase 4) (GA 3-oxidase 4) ...	0.03	-	mit	0					355
P15947 UniProt NPD GO	KLK1_MOUSE	Glandular kallikrein K1 precursor (EC 3.4.21.35) (Tissue kallikrein-6) (mGK-6) (Renal kallikrein) (K ...	0.03	-	exc	0					261
P36375 UniProt NPD GO	KLK10_RAT	Glandular kallikrein-10 precursor (EC 3.4.21.35) (Tissue kallikrein) (T-kininogenase) (K10) (Protein ...	0.03	-	cyt	0					244
O77003 UniProt NPD GO	GLB_BIOGL	Globin (Myoglobin)	0.03	-	cyt	0					150
P80722 UniProt NPD GO	GLB_ISOHY	Globin (Myoglobin)	0.03	-	cyt	0					148
P51536 UniProt NPD GO	GLBC_NIPBR	Globin, cuticular isoform precursor	0.03	-	vac	0	Secreted protein; extracellular space (By similarity)				173
P23216 UniProt NPD GO	GLBP1_GLYDI	Globin, major polymeric component P1	0.03	-	cyt	0					147
P32301 UniProt NPD GO	GLP1R_RAT	Glucagon-like peptide 1 receptor precursor (GLP-1 receptor) (GLP-1-R) (GLP-1R)	0.03	-	end	7	Membrane; multi-pass membrane protein				463
P43070 UniProt NPD GO	BGL2_CANAL	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.03	-	end	0	Cell wall. Tightly bound to cell wall				308
P29717 UniProt NPD GO	EXG_CANAL	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.03	-	mit	0	Secreted protein			1EQP	438
Q8NKF9 UniProt NPD GO	EXG_CANOL	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.03	-	cyt	0	Secreted protein				425
P52400 UniProt NPD GO	E131_SOLTU	Glucan endo-1,3-beta-glucosidase, basic isoform 1 precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohy ...	0.03	-	cyt	0	Vacuole (By similarity)				337
P52408 UniProt NPD GO	E13B_PRUPE	Glucan endo-1,3-beta-glucosidase, basic isoform precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydr ...	0.03	-	vac	1 *					350
Q96EK6 UniProt NPD GO	GNA1_HUMAN	Glucosamine 6-phosphate N-acetyltransferase (EC 2.3.1.4) (Phosphoglucosamine transacetylase) (Phosph ...	0.03	-	cyt	0	Golgi apparatus; Golgi membrane; peripheral membrane protein. Endosome; endosomal membrane; peripher ...				184
Q5RAL9 UniProt NPD GO	GNA1_PONPY	Glucosamine 6-phosphate N-acetyltransferase (EC 2.3.1.4) (Phosphoglucosamine transacetylase) (Phosph ...	0.03	-	cyt	0	Golgi apparatus; Golgi membrane; peripheral membrane protein. Endosome; endosomal membrane; peripher ...				184
Q9JK38 UniProt NPD GO	GNA1_MOUSE	Glucosamine 6-phosphate N-acetyltransferase (EC 2.3.1.4) (Phosphoglucosamine transacetylase) (Phosph ...	0.03	-	cyt	0	Golgi apparatus; Golgi membrane; peripheral membrane protein. Endosome; endosomal membrane; peripher ...	ER-Golgi intermediate compartment [IDA] Golgi apparatus [IDA] late endosome [IDA]			184
O97439 UniProt NPD GO	GNP1_GIALA	Glucosamine-6-phosphate isomerase 1 (EC 3.5.99.6) (Glucosamine-6-phosphate deaminase 1) (GNPDA 1) (G ...	0.03	-	nuc	0					266
O97440 UniProt NPD GO	GNP2_GIALA	Glucosamine-6-phosphate isomerase 2 (EC 3.5.99.6) (Glucosamine-6-phosphate deaminase 2) (GNPDA 2) (G ...	0.03	-	nuc	0					263
Q27115 UniProt NPD GO	HT1_TRYVI	Glucose transporter HT1	0.03	-	end	11 *	Membrane; multi-pass membrane protein				543
P55235 UniProt NPD GO	GLGS_SPIOL	Glucose-1-phosphate adenylyltransferase small subunit (EC 2.7.7.27) (ADP-glucose synthase) (ADP-gluc ...	0.03	-		0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				14
O19133 UniProt NPD GO	G6PT_CANFA	Glucose-6-phosphatase (EC 3.1.3.9) (G6Pase) (G-6-Pase)	0.03	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				357
P35575 UniProt NPD GO	G6PT_HUMAN	Glucose-6-phosphatase (EC 3.1.3.9) (G6Pase) (G-6-Pase)	0.03	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein		232200		357

You are viewing entries 80001 to 80050 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.