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
P27442 UniProt NPD GO	GMPR_ASCSU	GMP reductase (EC 1.7.1.7) (Guanosine 5'-monophosphate oxidoreductase) (Guanosine monophosphate redu ...	0.16	-	cyt	0					356
P38625 UniProt NPD GO	GUAA_YEAST	GMP synthase [glutamine-hydrolyzing] (EC 6.3.5.2) (Glutamine amidotransferase) (GMP synthetase)	0.16	-	cyt	0	Cytoplasm (By similarity)				524
Q2U0S9 UniProt NPD GO	MCD4_ASPOR	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-)	0.16	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				1022
O95427 UniProt NPD GO	PIGN_HUMAN	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-) (Phosphatidylinositol-glycan biosynthesis clas ...	0.16	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)		606097		931
Q758B8 UniProt NPD GO	GPI7_ASHGO	GPI ethanolamine phosphate transferase 2 (EC 2.-.-.-) (Glycosylphosphatidylinositol-anchor biosynthe ...	0.16	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				806
P47088 UniProt NPD GO	GPI14_YEAST	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Glycosylphosphatidyli ...	0.16	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				403
Q6PD26 UniProt NPD GO	PIGS_MOUSE	GPI transamidase component PIG-S (Phosphatidylinositol-glycan biosynthesis class S protein)	0.16	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	GPI-anchor transamidase complex [ISS]			554
Q2HCW8 UniProt NPD GO	GWT1_CHAGB	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.16	+	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				512
P51601 UniProt NPD GO	GCH1_YEAST	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I)	0.16	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			243
P54766 UniProt NPD GO	RAN1B_LOTJA	GTP-binding nuclear protein Ran1B (Fragment)	0.16	-	cyt	0	Nucleus (By similarity)				209
P32235 UniProt NPD GO	GTP1_SCHPO	GTP-binding protein 1	0.16	-	cyt	0					364
O81004 UniProt NPD GO	Y2287_ARATH	GTP-binding protein At2g22870	0.16	-	mit	0					300
P01116 UniProt NPD GO	RASK_HUMAN	GTPase KRas (K-Ras 2) (Ki-Ras) (c-K-ras) (c-Ki-ras)	0.16	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side		115150	1D8E	189
Q8K3L6 UniProt NPD GO	GIMA5_RAT	GTPase, IMAP family member 5 (Immunity-associated nucleotide 4-like 1 protein) (Immunity-associated ...	0.16	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				326
Q9R0N0 UniProt NPD GO	GALK1_MOUSE	Galactokinase (EC 2.7.1.6) (Galactose kinase)	0.16	-	cyt	0					391
P47211 UniProt NPD GO	GALR1_HUMAN	Galanin receptor type 1 (GAL1-R) (GALR1)	0.16	+	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	600377		349
O43603 UniProt NPD GO	GALR2_HUMAN	Galanin receptor type 2 (GAL2-R) (GALR2)	0.16	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	603691		387
P14867 UniProt NPD GO	GBRA1_HUMAN	Gamma-aminobutyric-acid receptor alpha-1 subunit precursor (GABA(A) receptor)	0.16	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	606904		456
P62812 UniProt NPD GO	GBRA1_MOUSE	Gamma-aminobutyric-acid receptor alpha-1 subunit precursor (GABA(A) receptor)	0.16	-	end	4	Membrane; multi-pass membrane protein				455
P62813 UniProt NPD GO	GBRA1_RAT	Gamma-aminobutyric-acid receptor alpha-1 subunit precursor (GABA(A) receptor)	0.16	-	end	4	Membrane; multi-pass membrane protein				455
O75936 UniProt NPD GO	BODG_HUMAN	Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine,2-oxoglutarate dioxygenase) (Gam ...	0.16	-	cyt	0	Cytoplasm		603312		387
Q05902 UniProt NPD GO	ECM38_YEAST	Gamma-glutamyltransferase precursor (EC 2.3.2.2) (Gamma-glutamyltranspeptidase) (Gamma-GT) (Extracel ...	0.16	-	mit	1 *	Vacuole; vacuolar membrane; single-pass type II membrane protein	intracellular [TAS]			660
P14154 UniProt NPD GO	CXA1_CHICK	Gap junction alpha-1 protein (Connexin-43) (Cx43)	0.16	-	end	4 *	Membrane; multi-pass membrane protein				380
Q8NFK1 UniProt NPD GO	CXE1_HUMAN	Gap junction epsilon-1 protein (Connexin-31.3) (Cx31.3)	0.16	-	end	3 *	Membrane; multi-pass membrane protein				279
P30553 UniProt NPD GO	GASR_RAT	Gastrin/cholecystokinin type B receptor (CCK-B receptor) (CCK-BR) (Cholecystokinin-2 receptor) (CCK2 ...	0.16	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS] plasma membrane [ISS]			452
Q27226 UniProt NPD GO	OBP1_HELVI	General odorant-binding protein 1 precursor (GOBP 1)	0.16	-	vac	0					164
Q8MMF9 UniProt NPD GO	OB57D_DROME	General odorant-binding protein 57d precursor	0.16	-	mit	0					136
Q03555 UniProt NPD GO	GEPH_RAT	Gephyrin (Putative glycine receptor-tubulin linker protein)	0.16	-	nuc	0	Cytoplasmic face of glycinergic postsynaptic membranes			2FU3	768
P80018 UniProt NPD GO	GLBC_CAUAR	Globin C, coelomic	0.16	-	cyt	0				1HLB	158
P81880 UniProt NPD GO	GLUC_PIAME	Glucagon precursor [Contains: Glucagon; Glucagon-like peptide] (Fragment)	0.16	-	cyt	0	Secreted protein				71
O93983 UniProt NPD GO	EXG2_HANAN	Glucan 1,3-beta-glucosidase 2 precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase 2)	0.16	-	exc	0	Secreted protein (Potential)				427
P04065 UniProt NPD GO	AMYH_SACDI	Glucoamylase S1 precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohydro ...	0.16	-	exc	1 *					767
P29760 UniProt NPD GO	AMYI_SACDI	Glucoamylase S2 precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohydro ...	0.16	-	exc	1 *					768
P17709 UniProt NPD GO	HXKG_YEAST	Glucokinase GLK1 (EC 2.7.1.2) (Glucose kinase) (GLK)	0.16	-	cyt	0					500
Q01098 UniProt NPD GO	NMDE3_MOUSE	Glutamate [NMDA] receptor subunit epsilon 3 precursor (N-methyl D-aspartate receptor subtype 2C) (NR ...	0.16	-	end	4	Membrane; multi-pass membrane protein				1239
Q00961 UniProt NPD GO	NMDE3_RAT	Glutamate [NMDA] receptor subunit epsilon 3 precursor (N-methyl D-aspartate receptor subtype 2C) (NR ...	0.16	-	end	4	Membrane; multi-pass membrane protein				1237
P70627 UniProt NPD GO	FOLH1_RAT	Glutamate carboxypeptidase 2 (EC 3.4.17.21) (Glutamate carboxypeptidase II) (Membrane glutamate carb ...	0.16	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity)				752
O81078 UniProt NPD GO	GLR29_ARATH	Glutamate receptor 2.9 precursor (Ligand-gated ion channel 2.9)	0.16	-	end	4 *	Membrane; multi-pass membrane protein				940
Q42624 UniProt NPD GO	GLNAC_BRANA	Glutamine synthetase, chloroplast precursor (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS2)	0.16	-	mit	0	Plastid; chloroplast				428
O65796 UniProt NPD GO	HEM13_HORVU	Glutamyl-tRNA reductase 3, chloroplast precursor (EC 1.2.1.70) (GluTR)	0.16	-	mit	0	Plastid; chloroplast				535
Q60759 UniProt NPD GO	GCDH_MOUSE	Glutaryl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.7) (GCD)	0.16	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			438
Q9VG98 UniProt NPD GO	GSTT2_DROME	Glutathione S-transferase D2 (EC 2.5.1.18) (DmGST21)	0.16	-	cyt	0					215
P15626 UniProt NPD GO	GSTM2_MOUSE	Glutathione S-transferase Mu 2 (EC 2.5.1.18) (GST class-mu 2) (Glutathione S-transferase pmGT2) (GST ...	0.16	-	cyt	0	Cytoplasm				217
Q5R8E8 UniProt NPD GO	GSTM2_PONPY	Glutathione S-transferase Mu 2 (EC 2.5.1.18) (GSTM2-2) (GST class-mu 2)	0.16	-	cyt	0	Cytoplasm (By similarity)				217
P00502 UniProt NPD GO	GSTA1_RAT	Glutathione S-transferase alpha-1 (EC 2.5.1.18) (Glutathione S-transferase Ya-1) (GST Ya1) (Ligandin ...	0.16	-	nuc	0	Cytoplasm			1EV9	221
O18879 UniProt NPD GO	GSTA2_BOVIN	Glutathione S-transferase alpha-2 (EC 2.5.1.18) (GST class-alpha)	0.16	-	nuc	0	Cytoplasm (By similarity)				221
Q4AEI0 UniProt NPD GO	GPX2_PONPY	Glutathione peroxidase 2 (EC 1.11.1.9) (GSHPx-2) (GPx-2) (Glutathione peroxidase-gastrointestinal) ( ...	0.16	-	cyt	0	Cytoplasm (By similarity)				190
Q6FRV2 UniProt NPD GO	GSHR_CANGA	Glutathione reductase (EC 1.8.1.7) (GR) (GRase)	0.16	-	mit	0	Cytoplasm (By similarity)				476
Q6HA23 UniProt NPD GO	GSHR_KLULA	Glutathione reductase (EC 1.8.1.7) (GR) (GRase)	0.16	-	nuc	0	Cytoplasm (By similarity)				484
P13280 UniProt NPD GO	GLYG_RABIT	Glycogenin-1 (EC 2.4.1.186)	0.16	-	cyt	0				1ZDG	332

You are viewing entries 55651 to 55700 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.