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
O35118 UniProt NPD GO	GFRA3_MOUSE	GDNF family receptor alpha-3 precursor (GFR-alpha-3)	0.69	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	external side of plasma membrane [IDA]			397
P57773 UniProt NPD GO	CXA10_HUMAN	Gap junction alpha-10 protein (Connexin-59) (Cx59) (Connexin-58) (Cx58)	0.69	-	nuc	2 *	Membrane; multi-pass membrane protein				515
Q9ULK0 UniProt NPD GO	GRID1_HUMAN	Glutamate receptor delta-1 subunit precursor (GluR delta-1)	0.69	-	end	3	Membrane; multi-pass membrane protein (By similarity)				1009
Q9VUL9 UniProt NPD GO	FUCTA_DROME	Glycoprotein 3-alpha-L-fucosyltransferase A (EC 2.4.1.214) (Core alpha-(1,3)-fucosyltransferase)	0.69	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				503
Q2TBU3 UniProt NPD GO	GOSR1_BOVIN	Golgi SNAP receptor complex member 1	0.69	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity). Enriched on v ...				250
P40223 UniProt NPD GO	CSF3R_MOUSE	Granulocyte colony-stimulating factor receptor precursor (G-CSF-R) (CD114 antigen)	0.69	-	exc	1	Membrane; single-pass type I membrane protein			1PGR	837
Q96NM4 UniProt NPD GO	GCX1_HUMAN	Granulosa cell HMG box protein 1 (GCX-1)	0.69	-	nuc	0	Nucleus (By similarity)				488
Q07105 UniProt NPD GO	GDF9_MOUSE	Growth/differentiation factor 9 precursor (GDF-9)	0.69	-	exc	0	Secreted protein (By similarity)				441
P91950 UniProt NPD GO	GNAQ_HOMAM	Guanine nucleotide-binding protein G(q) subunit alpha (Guanine nucleotide-binding protein alpha-q)	0.69	-	cyt	0					353
P38412 UniProt NPD GO	GNAQ_LOLFO	Guanine nucleotide-binding protein G(q) subunit alpha (Guanine nucleotide-binding protein alpha-q)	0.69	-	cyt	0					354
P19687 UniProt NPD GO	GCYA1_BOVIN	Guanylate cyclase soluble subunit alpha-1 (EC 4.6.1.2) (GCS-alpha-1) (Soluble guanylate cyclase larg ...	0.69	-	cyt	0	Cytoplasm			1AWN	691
Q01886 UniProt NPD GO	HTS1_COCCA	HC-toxin synthetase (EC 6.3.2.-) (HTS)	0.69	-	end	0					5218
Q8BQM4 UniProt NPD GO	HEAT3_MOUSE	HEAT repeat-containing protein 3	0.69	-	nuc	0					679
P57102 UniProt NPD GO	HAND2_BRARE	Heart- and neural crest derivatives-expressed protein 2 (Deciduum, heart, autonomic nervous system a ...	0.69	-	nuc	0					208
P15489 UniProt NPD GO	HS60_GIALA	Heat shock protein 60	0.69	-	nuc	0					529
Q9JMG7 UniProt NPD GO	HDGR3_MOUSE	Hepatoma-derived growth factor-related protein 3 (HRP-3)	0.69	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]		1N27	202
Q00839 UniProt NPD GO	HNRPU_HUMAN	Heterogeneous nuclear ribonucleoprotein U (hnRNP U) (Scaffold attachment factor A) (SAF-A) (p120) (p ...	0.69	-	nuc	0	Nucleus. Component of ribonucleosomes. Cell surface. Also found associated with the cell surface	heterogeneous nuclear ribonucleoprotein com... [TAS]	602869	1ZRJ	823
P52927 UniProt NPD GO	HMGA2_MOUSE	High mobility group protein HMGI-C (High mobility group AT-hook protein 2)	0.69	+	nuc	0	Nucleus	nuclear chromosome [IDA]			108
O82768 UniProt NPD GO	HIS2_ARATH	Histidine biosynthesis bifunctional protein hisIE, chloroplast precursor [Includes: Phosphoribosyl-A ...	0.69	-	nuc	0	Plastid; chloroplast (Potential)				281
P06180 UniProt NPD GO	HIBN_XENLA	Histone-binding protein N1/N2	0.69	-	nuc	0	Nucleus			1PJN	589
P43241 UniProt NPD GO	CDX2_MOUSE	Homeobox protein CDX-2 (Caudal-type homeobox protein 2)	0.69	+	nuc	0	Nucleus	condensed nuclear chromosome [IDA]			311
Q08727 UniProt NPD GO	HXA2_CHICK	Homeobox protein Hox-A2	0.69	+	nuc	0	Nucleus				375
Q28600 UniProt NPD GO	HXA7_SHEEP	Homeobox protein Hox-A7 (Fragment)	0.69	+	nuc	0	Nucleus				71
Q92826 UniProt NPD GO	HXB13_HUMAN	Homeobox protein Hox-B13	0.69	+	nuc	0	Nucleus		604607	2CRA	284
P09023 UniProt NPD GO	HXB6_MOUSE	Homeobox protein Hox-B6 (Hox-2.2) (MH-22A)	0.69	+	nuc	0	Nucleus				224
P17509 UniProt NPD GO	HXB6_HUMAN	Homeobox protein Hox-B6 (Hox-2B) (Hox-2.2) (HU-2)	0.69	+	nuc	0	Nucleus	nucleus [NAS]	142961		224
Q00444 UniProt NPD GO	HXC5_HUMAN	Homeobox protein Hox-C5 (Hox-3D) (CP11)	0.69	+	nuc	0	Nucleus		142973		222
Q9IA17 UniProt NPD GO	HXD13_HETFR	Homeobox protein Hox-D13	0.69	+	nuc	0	Nucleus (By similarity)				284
P97334 UniProt NPD GO	NKX23_MOUSE	Homeobox protein Nkx-2.3 (Homeobox protein NK-2 homolog C) (Nkx2-C) (Homeobox protein NK-2 homolog 3 ...	0.69	+	nuc	0	Nucleus (Probable)				362
P46609 UniProt NPD GO	OSH1_ORYSA	Homeobox protein OSH1	0.69	-	nuc	0	Nucleus (Probable)	nucleus [IGI]			361
P17488 UniProt NPD GO	HM13_CAEEL	Homeobox protein ceh-13	0.69	+	nuc	0	Nucleus (Probable)	cytoplasm [IDA] nucleus [IDA]			202
Q9TTD8 UniProt NPD GO	PROP1_CANFA	Homeobox protein prophet of Pit-1 (PROP-1) (Pituitary-specific homeodomain factor)	0.69	+	nuc	0	Nucleus (By similarity)				226
P22810 UniProt NPD GO	HMOC_DROME	Homeotic protein ocelliless (Protein orthodenticle)	0.69	-	nuc	0	Nucleus (Probable)				671
Q16543 UniProt NPD GO	CDC37_HUMAN	Hsp90 co-chaperone Cdc37 (Hsp90 chaperone protein kinase-targeting subunit) (p50Cdc37)	0.69	-	cyt	0	Cytoplasm		605065	1US7	378
P53138 UniProt NPD GO	YGK9_YEAST	Hypothetical 12.4 kDa protein in TAF60-MLC1 intergenic region	0.69	-	nuc	0					107
Q04978 UniProt NPD GO	YMF3_YEAST	Hypothetical 23.9 kDa protein in CYB2-SUR7 intergenic region	0.69	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			212
P36169 UniProt NPD GO	YK80_YEAST	Hypothetical 27.0 kDa protein in BAS1-SIR1 intergenic region	0.69	-	nuc	1 *		bud tip [IDA] incipient bud site [IDA]			241
P40167 UniProt NPD GO	YNT6_YEAST	Hypothetical 34.3 kDa protein in WHI3-CHS1 intergenic region	0.69	+	nuc	0					298
P40214 UniProt NPD GO	YM22_YEAST	Hypothetical 38.6 kDa protein in RPS16A-TIF34 intergenic region	0.69	-	nuc	0		nucleus [IDA]			342
P47101 UniProt NPD GO	YJ00_YEAST	Hypothetical 84.3 kDa protein in BNA1-GEA1 intergenic region	0.69	-	nuc	0					745
Q9LQX4 UniProt NPD GO	DOF13_ARATH	Hypothetical Dof zinc finger protein DOF1.3 (AtDOF1.3)	0.69	-	nuc	0	Nucleus (Probable)				366
P93314 UniProt NPD GO	M590_ARATH	Hypothetical mitochondrial cytochrome b-like protein AtMg00590 (ORF313)	0.69	-	end	3 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				313
P92539 UniProt NPD GO	M1050_ARATH	Hypothetical mitochondrial protein AtMg01050 (ORF159)	0.69	-	nuc	0	Mitochondrion (Potential)				159
Q11193 UniProt NPD GO	YX22_CAEEL	Hypothetical protein C04E7.2	0.69	-	cyt	0					552
Q09784 UniProt NPD GO	YA95_SCHPO	Hypothetical protein C13G6.05c in chromosome I	0.69	-	nuc	0					245
Q09259 UniProt NPD GO	YQB6_CAEEL	Hypothetical protein C30G12.6	0.69	-	cyt	0					1100
P87055 UniProt NPD GO	YDJ7_SCHPO	Hypothetical protein C57A10.07 in chromosome I	0.69	-	mit	1 *	Membrane; multi-pass membrane protein (Potential)				311
Q10126 UniProt NPD GO	YSM6_CAEEL	Hypothetical protein F52C9.6	0.69	-	nuc	0					279
P34469 UniProt NPD GO	YMH2_CAEEL	Hypothetical protein F58A4.2	0.69	-	nuc	0					159
P34484 UniProt NPD GO	YMJ9_CAEEL	Hypothetical protein F59B2.9	0.69	-	cyt	0					425

You are viewing entries 14251 to 14300 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.