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
Q6BHI9 UniProt NPD GO	GPI14_DEBHA	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Glycosylphosphatidyli ...	0.07	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				414
Q6CU99 UniProt NPD GO	SMP3_KLULA	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV)	0.07	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				505
P99025 UniProt NPD GO	GFRP_MOUSE	GTP cyclohydrolase 1 feedback regulatory protein (GTP cyclohydrolase I feedback regulatory protein) ...	0.07	-	cyt	0					83
P38543 UniProt NPD GO	RAN_GIALA	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.07	-	cyt	0	Nucleus				226
P17610 UniProt NPD GO	YPT3_SCHPO	GTP-binding protein ypt3 (RAB)	0.07	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	cytoplasm [IDA]			214
Q9HDU5 UniProt NPD GO	GAL7_SCHPO	Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (Gal-1-P uridylyltransferase) (UDP-glucose-- ...	0.07	-	nuc	0					369
Q866E1 UniProt NPD GO	FUT1_ALOBE	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.07	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				366
Q28113 UniProt NPD GO	FUT2_BOVIN	Galactoside 2-alpha-L-fucosyltransferase 2 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.07	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				344
Q9UBC7 UniProt NPD GO	GALP_HUMAN	Galanin-like peptide precursor	0.07	-	exc	0	Secreted protein				116
Q9TT95 UniProt NPD GO	GALP_PIG	Galanin-like peptide precursor	0.07	-	vac	0	Secreted protein				120
P08699 UniProt NPD GO	LEG3_RAT	Galectin-3 (Galactose-specific lectin 3) (Mac-2 antigen) (IgE-binding protein) (35 kDa lectin) (Carb ...	0.07	-	nuc	0	Nucleus (By similarity). Cytoplasmic in adenomas and carcinomas. May be secreted by a non-classical ...				261
P20159 UniProt NPD GO	THG2_WHEAT	Gamma-2 purothionin	0.07	-	nuc	0					47
P19865 UniProt NPD GO	CRG2_SCOWA	Gamma-II crystallin (Fragment)	0.07	-	nuc	0				2GS1	30
P93164 UniProt NPD GO	GGH_SOYBN	Gamma-glutamyl hydrolase precursor (EC 3.4.19.9) (Gamma-Glu-X carboxypeptidase) (Conjugase) (GH)	0.07	-	mit	0	Secreted protein; extracellular space. Cell wall. Extracellular or cell-wall bound				342
Q9Z2A9 UniProt NPD GO	GGT5_MOUSE	Gamma-glutamyltransferase 5 precursor (EC 2.3.2.2) (Gamma-glutamyltransferase-like activity 1) (Gamm ...	0.07	-	end	1 *	Membrane; single-pass type II membrane protein (By similarity)	plasma membrane [IDA]			573
Q9BX51 UniProt NPD GO	GGTL6_HUMAN	Gamma-glutamyltransferase-like protein 6 (Gamma-glutamyltransferase-like activity 4)	0.07	-	cyt	0					225
P60591 UniProt NPD GO	PIG1_LACMU	Gamma-phospholipase A2 inhibitor LNF1 precursor	0.07	-	nuc	0	Secreted protein				200
Q96BI3 UniProt NPD GO	APH1A_HUMAN	Gamma-secretase subunit APH-1A (APH-1a) (Aph-1alpha) (Presenilin-stabilization factor)	0.07	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [IDA] Golgi apparatus [IDA] integral to plasma membrane [IDA]	607629		265
P81009 UniProt NPD GO	THZ2_MAIZE	Gamma-zeathionin-2	0.07	-	nuc	0					47
P03955 UniProt NPD GO	PEPC_MACFU	Gastricsin precursor (EC 3.4.23.3) (Pepsinogen C) (Fragment)	0.07	-	cyt	0	Secreted protein				377
Q7M3P2 UniProt NPD GO	GAMP_PROCL	Gastrolith matrix protein (Fragment)	0.07	-	nuc	0	Secreted protein				96
P20305 UniProt NPD GO	GELS_PIG	Gelsolin precursor (Actin-depolymerizing factor) (ADF) (Brevin) (Fragment)	0.07	-	exc	0	Isoform 2: Cytoplasm. Isoform 1: Secreted protein	actin cytoskeleton [ISS] cytosol [IDA] extracellular region [IDA]			772
Q94B08 UniProt NPD GO	GCP1_ARATH	Germination-specific cysteine protease 1 precursor (EC 3.4.22.-)	0.07	-	exc	0					376
P36373 UniProt NPD GO	KLK7_RAT	Glandular kallikrein-7, submandibular/renal precursor (EC 3.4.21.35) (Tissue kallikrein) (RGK-7) (RS ...	0.07	-	mit	0					261
P14393 UniProt NPD GO	GLB_APLJU	Globin (Myoglobin)	0.07	-	mit	0					144
P68956 UniProt NPD GO	GLUC_PLAFE	Glucagon	0.07	-	nuc	0	Secreted protein				29
P68957 UniProt NPD GO	GLUC_THUOB	Glucagon	0.07	-	nuc	0	Secreted protein				29
P07449 UniProt NPD GO	GLUC_ONCKI	Glucagon precursor [Contains: Glucagon; Glucagon-like peptide] (Fragment)	0.07	-	cyt	0	Secreted protein				68
P23432 UniProt NPD GO	E13C_TOBAC	Glucan endo-1,3-beta-glucosidase precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase) ((1->3)- ...	0.07	-	cyt	1 *	Stylar secretory matrix				351
P23433 UniProt NPD GO	E13D_TOBAC	Glucan endo-1,3-beta-glucosidase precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase) ((1->3)- ...	0.07	-	exc	1 *	Stylar secretory matrix				351
P36401 UniProt NPD GO	E13H_TOBAC	Glucan endo-1,3-beta-glucosidase, acidic isoform PR-Q' precursor (EC 3.2.1.39) ((1->3)-beta-glucan e ...	0.07	-	exc	0	Secreted protein; extracellular space				339
O74254 UniProt NPD GO	AMYG_CANAL	Glucoamylase 1 precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohydrol ...	0.07	-	exc	0	Cell wall; peripheral membrane protein				946
P22861 UniProt NPD GO	AMYG_DEBOC	Glucoamylase 1 precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohydrol ...	0.07	-	exc	0					958
Q9GTW9 UniProt NPD GO	GLK1_TRIVA	Glucokinase 1 (EC 2.7.1.2) (Glucose kinase 1) (Hexokinase 1)	0.07	-	cyt	0					375
P11410 UniProt NPD GO	G6PD_PICJA	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD)	0.07	-	cyt	0					495
P54234 UniProt NPD GO	G6PI1_CLAAR	Glucose-6-phosphate isomerase, cytosolic 1 (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phos ...	0.07	-	cyt	0	Cytoplasm (By similarity)				568
P54237 UniProt NPD GO	G6PI1_CLAMI	Glucose-6-phosphate isomerase, cytosolic 1 (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phos ...	0.07	-	cyt	0	Cytoplasm (By similarity)				568
P54242 UniProt NPD GO	G6PI2_CLAXA	Glucose-6-phosphate isomerase, cytosolic 2 (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phos ...	0.07	-	cyt	0	Cytoplasm (By similarity)				569
P29333 UniProt NPD GO	G6PI2_CLALE	Glucose-6-phosphate isomerase, cytosolic 2A (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Pho ...	0.07	-	cyt	0	Cytoplasm				569
Q94B38 UniProt NPD GO	GPT2_ARATH	Glucose-6-phosphate/phosphate translocator 2, chloroplast precursor	0.07	-	end	7	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				388
O35409 UniProt NPD GO	FOLH1_MOUSE	Glutamate carboxypeptidase 2 (EC 3.4.17.21) (Glutamate carboxypeptidase II) (Membrane glutamate carb ...	0.07	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity)	integral to plasma membrane [IDA]			752
P10860 UniProt NPD GO	DHE3_RAT	Glutamate dehydrogenase 1, mitochondrial precursor (EC 1.4.1.3) (GDH) (Memory-related protein 2) (MR ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix				558
Q85WB7 UniProt NPD GO	GSA_BRANA	Glutamate-1-semialdehyde 2,1-aminomutase, chloroplast precursor (EC 5.4.3.8) (GSA) (Glutamate-1-semi ...	0.07	-	mit	0	Plastid; chloroplast				473
Q04831 UniProt NPD GO	GLNA_PANAR	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase)	0.07	-	nuc	0	Cytoplasm				361
Q75BT9 UniProt NPD GO	GLNA_ASHGO	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.07	-	cyt	0	Cytoplasm				369
Q6FMT6 UniProt NPD GO	GLNA_CANGA	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.07	-	cyt	0	Cytoplasm				372
P04078 UniProt NPD GO	GLNA1_MEDSA	Glutamine synthetase cytosolic isozyme (EC 6.3.1.2) (Glutamate--ammonia ligase)	0.07	-	cyt	0	Cytoplasm				356
P14636 UniProt NPD GO	GLNA3_LUPAN	Glutamine synthetase nodule isozyme (EC 6.3.1.2) (Glutamate--ammonia ligase) (Fragment)	0.07	-	cyt	0	Cytoplasm				315
P38559 UniProt NPD GO	GLNA1_MAIZE	Glutamine synthetase root isozyme 1 (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS122)	0.07	-	cyt	0	Cytoplasm				357
P30111 UniProt NPD GO	GSTF2_WHEAT	Glutathione S-transferase 2 (EC 2.5.1.18) (GST class-phi)	0.07	-	end	0					291

You are viewing entries 70051 to 70100 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.