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
P02727 UniProt NPD GO	GLP_CANFA	Glycophorin (Fragment)	0.16	-	nuc	0	Membrane; single-pass type I membrane protein				52
O61613 UniProt NPD GO	NMT_DROME	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.16	-	cyt	0	Membrane; peripheral membrane protein	membrane fraction [IDA]			472
Q99JX3 UniProt NPD GO	GORS2_MOUSE	Golgi reassembly-stacking protein 2 (GRS2) (Golgi reassembly-stacking protein of 55 kDa) (GRASP55)	0.16	-	nuc	0	Golgi apparatus; Golgi membrane; lipid-anchor				450
Q8BH60 UniProt NPD GO	GOPC_MOUSE	Golgi-associated PDZ and coiled-coil motif-containing protein (PDZ protein interacting specifically ...	0.16	-	cyt	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein. Golgi apparatus; trans-Golg ...	cytoplasm [ISS] Golgi apparatus [ISS] plasma membrane [ISS] synaptosome [IDA]			463
Q6Y290 UniProt NPD GO	GOLI_RAT	Goliath homolog precursor (RING finger protein 130) (R-goliath)	0.16	-	mit	2	Membrane; single-pass type I membrane protein (Potential). Mitochondrion (Probable). May be mitochon ...	integral to membrane [ISS]			419
Q5RAI6 UniProt NPD GO	GRAN_PONPY	Grancalcin	0.16	-	cyt	0	Cytoplasm (By similarity). Membrane (By similarity). Attached to membranes and granules (By similari ...				218
P48750 UniProt NPD GO	CSF2_RAT	Granulocyte-macrophage colony-stimulating factor (GM-CSF) (Colony-stimulating factor) (CSF)	0.16	-	nuc	0	Secreted protein				127
Q95254 UniProt NPD GO	GHSR_PIG	Growth hormone secretagogue receptor type 1 (GHS-R) (GH-releasing peptide receptor) (GHRP) (Ghrelin ...	0.16	-	end	7 *	Membrane; multi-pass membrane protein				366
Q18421 UniProt NPD GO	GRPE_CAEEL	GrpE protein homolog, mitochondrial precursor	0.16	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				237
P61952 UniProt NPD GO	GBG11_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-11 subunit precursor	0.16	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		604390		73
P61953 UniProt NPD GO	GBG11_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-11 subunit precursor	0.16	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				73
P61954 UniProt NPD GO	GBG11_RAT	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-11 subunit precursor	0.16	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				73
P18873 UniProt NPD GO	GNAO2_MOUSE	Guanine nucleotide-binding protein G(o) subunit alpha 2	0.16	-	cyt	0		heterotrimeric G-protein complex [TAS] membrane fraction [TAS]			353
P04696 UniProt NPD GO	GNAT2_BOVIN	Guanine nucleotide-binding protein G(t), alpha-2 subunit (Transducin alpha-2 chain)	0.16	-	gol	0					353
Q9NFZ3 UniProt NPD GO	GBGE_DROME	Guanine nucleotide-binding protein gamma-e subunit precursor (Ggamma(e))	0.16	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	cytoplasm [IDA] heterotrimeric G-protein complex [IPI] rhabdomere [IDA]			72
P23232 UniProt NPD GO	GBB_LOLFO	Guanine nucleotide-binding protein subunit beta	0.16	-	cyt	0					341
Q39836 UniProt NPD GO	GBLP_SOYBN	Guanine nucleotide-binding protein subunit beta-like protein	0.16	-	cyt	0					325
Q9EQ15 UniProt NPD GO	GNB1L_MOUSE	Guanine nucleotide-binding protein subunit beta-like protein 1 (G protein subunit beta-like protein ...	0.16	-	mit	0		internal side of plasma membrane [ISS]			326
O94309 UniProt NPD GO	GBG_SCHPO	Guanine nucleotide-binding protein subunit gamma	0.16	-	nuc	0	Membrane; peripheral membrane protein (By similarity)	heterotrimeric G-protein complex [TAS]			72
P46195 UniProt NPD GO	KGUA_BOVIN	Guanylate kinase (EC 2.7.4.8) (GMP kinase)	0.16	-	cyt	0					197
P79881 UniProt NPD GO	GUC1B_CHICK	Guanylyl cyclase-activating protein 2 (GCAP 2) (Guanylate cyclase activator 1B)	0.16	-	cyt	0					197
P01921 UniProt NPD GO	HB2D_MOUSE	H-2 class II histocompatibility antigen, A-D beta chain precursor	0.16	-	end	1	Membrane; single-pass type I membrane protein (Potential)	early endosome [IDA] external side of plasma membrane [IDA] Golgi apparatus [IDA] integral to membrane [IDA] intracellular [IDA] MHC class II protein complex [IDA] multivesicular body [IDA] plasma membrane [IDA]			265
Q06975 UniProt NPD GO	GAR1_SCHPO	H/ACA ribonucleoprotein complex subunit 1 (snoRNP protein GAR1)	0.16	-	cyt	0	Nucleus; nucleolus (By similarity)	nucleolus [IDA] small nucleolar ribonucleoprotein complex [IGI]			194
Q8I7X7 UniProt NPD GO	NOLA2_BRABE	H/ACA ribonucleoprotein complex subunit 2-like protein	0.16	-	nuc	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			159
P40620 UniProt NPD GO	HMGL_VICFA	HMG1/2-like protein	0.16	-	nuc	0	Nucleus (Potential)				149
P27894 UniProt NPD GO	HSP70_LEIBR	Heat shock 70 kDa protein (HSP 70) (Fragment)	0.16	-	nuc	0					228
P22774 UniProt NPD GO	HSP7M_SCHPO	Heat shock 70 kDa protein, mitochondrial precursor	0.16	-	mit	0	Mitochondrion. Nucleus (Probable). Probably found also in the nucleus	presequence translocase-associated import m... [IDA]			674
O16068 UniProt NPD GO	HSP83_DROPB	Heat shock protein 83 (HSP 82) (Fragment)	0.16	-	cyt	0	Cytoplasm	centrosome [ISS]			269
P50519 UniProt NPD GO	HSP9_SCHPO	Heat shock protein hsp9	0.16	-	nuc	0					68
P23711 UniProt NPD GO	HMOX2_RAT	Heme oxygenase 2 (EC 1.14.99.3) (HO-2)	0.16	-	nuc	1	Microsome				315
Q9WU63 UniProt NPD GO	HEBP2_MOUSE	Heme-binding protein 2 (Protein SOUL)	0.16	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA]			205
P82303 UniProt NPD GO	HCY2_MAISQ	Hemocyanin subunit 2 (Fragment)	0.16	-	nuc	0	Secreted protein; extracellular space				31
P30403 UniProt NPD GO	DISR_AGKRH	Hemorrhagic protein-rhodostomin precursor (EC 3.4.24.-) (RHO) [Contains: Disintegrin rhodostomin (Di ...	0.16	-	nuc	0	Secreted protein			1XAZ	478
P48798 UniProt NPD GO	FGF2_MONDO	Heparin-binding growth factor 2 precursor (HBGF-2) (Basic fibroblast growth factor) (BFGF) (Prostatr ...	0.16	-	cyt	0					156
Q8LH82 UniProt NPD GO	HXK1_ORYSA	Hexokinase-1 (EC 2.7.1.1)	0.16	-	cyt	0					498
P27881 UniProt NPD GO	HXK2_RAT	Hexokinase-2 (EC 2.7.1.1) (Hexokinase type II) (HK II)	0.16	-	cyt	0		mitochondrial outer membrane [TAS]			917
P14895 UniProt NPD GO	ELI5_HORVU	High molecular mass early light-inducible protein HV58, chloroplast precursor (ELIP)	0.16	-	mit	2	Plastid; chloroplast. Associated with both photosystems I and II				231
Q9D0S9 UniProt NPD GO	HINT2_MOUSE	Histidine triad nucleotide-binding protein 2 (EC 3.-.-.-) (HINT-2) (HINT-3)	0.16	-	cyt	0		mitochondrion [IDA]			163
P49590 UniProt NPD GO	SYHH_HUMAN	Histidyl-tRNA synthetase homolog (EC 6.1.1.21) (Histidine--tRNA ligase homolog) (HisRS)	0.16	-	mit	0		cytoplasm [NAS]	600783		506
P13630 UniProt NPD GO	H2A_PARLI	Histone H2A	0.16	-	nuc	0	Nucleus				123
Q07135 UniProt NPD GO	H2AO_CHITH	Histone H2A, orphon	0.16	-	nuc	0	Nucleus				124
Q43215 UniProt NPD GO	H2B4_WHEAT	Histone H2B.4 (H2B153)	0.16	+	nuc	0	Nucleus (By similarity)				134
P18638 UniProt NPD GO	H5_COTJA	Histone H5 (Fragment)	0.16	-		0	Nucleus				16
Q91WA3 UniProt NPD GO	HDA11_MOUSE	Histone deacetylase 11 (HD11)	0.16	-	cyt	0	Nucleus (By similarity)	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]			347
Q25451 UniProt NPD GO	UBX_MUSDO	Homeotic protein ultrabithorax (Fragment)	0.16	-	nuc	0	Nucleus				248
Q4P521 UniProt NPD GO	LYS4_USTMA	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.16	-	mit	0	Mitochondrion (By similarity)				698
Q28381 UniProt NPD GO	HPLN1_HORSE	Hyaluronan and proteoglycan link protein 1 precursor (Proteoglycan link protein) (Cartilage link pro ...	0.16	-	vac	0					354
Q92819 UniProt NPD GO	HAS2_HUMAN	Hyaluronan synthase 2 (EC 2.4.1.212) (Hyaluronate synthase 2) (Hyaluronic acid synthase 2) (HA synth ...	0.16	-	end	6 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS]	601636		552
Q9NYQ3 UniProt NPD GO	HAOX2_HUMAN	Hydroxyacid oxidase 2 (EC 1.1.3.15) (HAOX2) ((S)-2-hydroxy-acid oxidase, peroxisomal) (Long chain al ...	0.16	-	cyt	0	Peroxisome	peroxisome [TAS]	605176		351
P48232 UniProt NPD GO	YNI6_YEAST	Hypothetical 11.5 kDa protein in TOP2-MKT1 intergenic region	0.16	-	nuc	0		endosome [IDA]			102

You are viewing entries 55701 to 55750 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.