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
P54281 UniProt NPD GO	ECLC_BOVIN	Epithelial chloride channel protein (Calcium-activated chloride channel)	0.44	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				903
O24473 UniProt NPD GO	IF2B_WHEAT	Eukaryotic translation initiation factor 2 subunit beta (eIF-2-beta) (P38)	0.44	+	cyt	0					270
P32844 UniProt NPD GO	SEC6_YEAST	Exocyst complex component SEC6	0.44	-	cyt	0	Cytoplasm	bud tip [IPI] exocyst [IPI]		2FJI	805
Q5U2X1 UniProt NPD GO	FBX9_RAT	F-box only protein 9	0.44	-	cyt	0					435
Q8VBV4 UniProt NPD GO	FBXW7_MOUSE	F-box/WD repeat protein 7 (F-box and WD-40 domain protein 7) (F-box protein FBW7) (F-box protein Fbx ...	0.44	-	exc	1 *	Nucleus	cytoplasm [TAS] endoplasmic reticulum [IDA] Golgi apparatus [IDA] nucleus [TAS]			629
Q5XUX1 UniProt NPD GO	FBXW9_HUMAN	F-box/WD repeat protein 9 (F-box and WD-40 domain protein 9)	0.44	-	cyt	0			609074		478
P0C1J6 UniProt NPD GO	FKBP4_RHIOR	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.44	-	nuc	0	Nucleus; nucleolus (By similarity)				382
O35870 UniProt NPD GO	FANCC_RAT	Fanconi anemia group C protein homolog (Protein FACC)	0.44	-	nuc	0	Nucleus (By similarity). Major form. Cytoplasm (By similarity). Minor form				557
Q02020 UniProt NPD GO	FIBB_CHICK	Fibrinogen beta chain precursor [Contains: Fibrinopeptide B] (Fragment)	0.44	-	nuc	0	Secreted protein			1M1J	463
P53848 UniProt NPD GO	FAS_YEAST	Folic acid synthesis protein FOL1 [Includes: Dihydroneopterin aldolase (EC 4.1.2.25) (DHNA) (FASA) ( ...	0.44	-	cyt	0	Mitochondrion; mitochondrial membrane	cytoplasm [IDA] mitochondrial envelope [IDA] mitochondrion [IDA]		2BMB	824
P24871 UniProt NPD GO	CG24_YEAST	G2/mitotic-specific cyclin-4	0.44	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			460
Q9CX99 UniProt NPD GO	GRAP_MOUSE	GRB2-related adapter protein	0.44	-	cyt	0					217
Q00582 UniProt NPD GO	GTR1_YEAST	GTP-binding protein GTR1	0.44	-	nuc	0		cytoplasm [IDA] nucleus [IDA] vacuolar membrane [IDA]			310
P09580 UniProt NPD GO	GAL7_KLULA	Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (Gal-1-P uridylyltransferase) (UDP-glucose-- ...	0.44	+	cyt	0					370
Q5E9W5 UniProt NPD GO	G3ST4_BOVIN	Galactose-3-O-sulfotransferase 4 (EC 2.8.2.-) (Galbeta1-3GalNAc 3'-sulfotransferase) (Beta-galactose ...	0.44	-	nuc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)				483
Q5J2D6 UniProt NPD GO	GGNB1_RAT	Gametogenetin-binding protein 1	0.44	-	mit	0	Cytoplasm. Membrane; peripheral membrane protein. Golgi apparatus (By similarity)				373
P04345 UniProt NPD GO	CRGA_MOUSE	Gamma crystallin A (Gamma crystallin 4)	0.44	-	nuc	0					173
Q28088 UniProt NPD GO	CRGE_BOVIN	Gamma crystallin E (Gamma crystallin IIIA) (Gamma-C-crystallin)	0.44	-	nuc	0					173
Q92696 UniProt NPD GO	PGTA_HUMAN	Geranylgeranyl transferase type-2 alpha subunit (EC 2.5.1.60) (Geranylgeranyl transferase type II al ...	0.44	-	nuc	0			601905		567
O12956 UniProt NPD GO	GLUC_HELSU	Glucagon precursor [Contains: Glicentin-related polypeptide (GRPP); Glucagon; Glucagon-like peptide ...	0.44	-	exc	0	Secreted protein				204
Q91971 UniProt NPD GO	GLUC1_ONCMY	Glucagon-1 precursor (Glucagon I) [Contains: Glicentin-related polypeptide 1 (GRPP 1); Glucagon-1; G ...	0.44	-	nuc	0	Secreted protein				178
Q4WBL2 UniProt NPD GO	GNT1_ASPFU	Glucose N-acetyltransferase 1 (EC 2.4.1.-) (N-acetylglucosaminyltransferase)	0.44	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity). Vacuole; vacu ...				384
P40208 UniProt NPD GO	GID8_YEAST	Glucose-induced degradation protein 8 (Dosage-dependent cell cycle regulator 1)	0.44	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			455
Q7XJL2 UniProt NPD GO	GLR31_ARATH	Glutamate receptor 3.1 precursor (Ligand-gated ion channel 3.1) (AtGLR2)	0.44	-	end	3	Membrane; multi-pass membrane protein				921
Q5IS46 UniProt NPD GO	GRIK4_PANTR	Glutamate receptor, ionotropic kainate 4 precursor	0.44	-	end	4	Membrane; multi-pass membrane protein (By similarity)				956
Q16099 UniProt NPD GO	GRIK4_HUMAN	Glutamate receptor, ionotropic kainate 4 precursor (Glutamate receptor KA-1) (KA1) (Excitatory amino ...	0.44	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600282		956
P07728 UniProt NPD GO	GLUA1_ORYSA	Glutelin type-A 1 precursor (Glutelin type I) [Contains: Glutelin type-A 1 acidic chain; Glutelin ty ...	0.44	-	mit	1 *					499
P08488 UniProt NPD GO	GLT3_WHEAT	Glutenin, high molecular weight subunit 12 precursor	0.44	-	exc	0					660
Q08929 UniProt NPD GO	GUP2_YEAST	Glycerol uptake protein 2	0.44	-	end	10	Membrane; multi-pass membrane protein (Potential)				609
P54859 UniProt NPD GO	GYS3_MOUSE	Glycogen [starch] synthase, brain (EC 2.4.1.11)	0.44	-	nuc	0					737
Q8N3Y3 UniProt NPD GO	LARG2_HUMAN	Glycosyltransferase-like protein LARGE2 (EC 2.4.-.-) (Glycosyltransferase-like 1B)	0.44	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to Golgi membrane [ISS]	609709		721
P30419 UniProt NPD GO	NMT1_HUMAN	Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) (Peptide N-myristoyltransferase 1) (Myristo ...	0.44	+	cyt	0	Cytoplasm		160993	1RXT	496
P10144 UniProt NPD GO	GRAB_HUMAN	Granzyme B precursor (EC 3.4.21.79) (T-cell serine protease 1-3E) (Cytotoxic T-lymphocyte proteinase ...	0.44	-	exc	0	Cytoplasmic granule. Cytoplasmic granules of cytolytic T-lymphocytes and natural killer cells	immunological synapse [TAS] nucleus [TAS]	123910	1IAU	247
Q95ML5 UniProt NPD GO	GHR_SAIBB	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.44	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				632
Q9BDW8 UniProt NPD GO	GDF7_CERAE	Growth/differentiation factor 7 precursor (GDF-7)	0.44	+	nuc	0	Secreted protein (By similarity)				447
Q8UWD7 UniProt NPD GO	GDF8_COTCH	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.44	+	nuc	0	Secreted protein (By similarity)				375
P38406 UniProt NPD GO	GNAL_RAT	Guanine nucleotide-binding protein G(olf) subunit alpha (Adenylate cyclase-stimulating G alpha prote ...	0.44	-	nuc	0		heterotrimeric G-protein complex [TAS]			381
P30669 UniProt NPD GO	GNAS_SCHMA	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.44	-	cyt	0					379
Q60W52 UniProt NPD GO	GPA3_CAEBR	Guanine nucleotide-binding protein alpha-3 subunit	0.44	-	cyt	0					354
P28052 UniProt NPD GO	GPA3_CAEEL	Guanine nucleotide-binding protein alpha-3 subunit	0.44	-	cyt	0					354
P30443 UniProt NPD GO	1A01_HUMAN	HLA class I histocompatibility antigen, A-1 alpha chain precursor (MHC class I antigen A*1)	0.44	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142800	1W72	365
P30455 UniProt NPD GO	1A36_HUMAN	HLA class I histocompatibility antigen, A-36 alpha chain precursor (MHC class I antigen A*36) (Aw-36 ...	0.44	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142800		365
P30483 UniProt NPD GO	1B45_HUMAN	HLA class I histocompatibility antigen, B-45 alpha chain precursor (MHC class I antigen B*45) (Bw-45 ...	0.44	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
P30488 UniProt NPD GO	1B50_HUMAN	HLA class I histocompatibility antigen, B-50 alpha chain precursor (MHC class I antigen B*50) (Bw-50 ...	0.44	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
P41827 UniProt NPD GO	HSP74_ANOAL	Heat shock protein 70 B2	0.44	-	cyt	0					640
O44314 UniProt NPD GO	ALLP_HELAM	Helicostatins precursor [Contains: Helicostatin I; Helicostatin IIa; Helicostatin IIb; Helicostatin ...	0.44	-	exc	0	Secreted protein				225
P98092 UniProt NPD GO	HMCT_BOMMO	Hemocytin precursor (Humoral lectin)	0.44	-	nuc	0					3133
Q04756 UniProt NPD GO	HGFA_HUMAN	Hepatocyte growth factor activator precursor (EC 3.4.21.-) (HGF activator) (HGFA) [Contains: Hepatoc ...	0.44	+	exc	1 *	Secreted protein. Secreted as an inactive single-chain precursor and is then activated to a heterodi ...	extracellular region [NAS]	604552	1YC0	655
P04256 UniProt NPD GO	ROA1_RAT	Heterogeneous nuclear ribonucleoprotein A1 (Helix-destabilizing protein) (Single-strand RNA-binding ...	0.44	+	cyt	0	Nucleus. Cytoplasm. Shuttles continuously between the nucleus and the cytoplasm along with mRNA. Com ...	spliceosome complex [ISS]			319
Q28521 UniProt NPD GO	ROA1_MACMU	Heterogeneous nuclear ribonucleoprotein A1 (Helix-destabilizing protein) (Single-strand-binding prot ...	0.44	+	cyt	0	Nucleus. Cytoplasm. Shuttles continuously between the nucleus and the cytoplasm along with mRNA. Com ...				319

You are viewing entries 28951 to 29000 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.