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
P91907 UniProt NPD GO	GPA15_CAEEL	Guanine nucleotide-binding protein alpha-15 subunit	0.42	-	nuc	0					356
Q4VT35 UniProt NPD GO	GPA2_CAEBR	Guanine nucleotide-binding protein alpha-2 subunit	0.42	-	cyt	0					356
O14438 UniProt NPD GO	GPA3_USTHO	Guanine nucleotide-binding protein alpha-3 subunit	0.42	-	mit	0					354
Q6JZK2 UniProt NPD GO	NOLA3_TRYCR	H/ACA ribonucleoprotein complex subunit 3-like protein (Ribosome biogenesis protein Nop10)	0.42	-	nuc	0	Nucleus; nucleolus (By similarity)				63
Q9I8F9 UniProt NPD GO	HSP71_ORYLA	Heat shock 70 kDa protein 1 (HSP70-1)	0.42	-	cyt	0					639
P36181 UniProt NPD GO	HSP80_LYCES	Heat shock cognate protein 80	0.42	+	cyt	0	Cytoplasm (Potential)				699
Q6F2Y7 UniProt NPD GO	HS101_ORYSA	Heat shock protein 101	0.42	+	cyt	0					912
P17156 UniProt NPD GO	HSP72_MOUSE	Heat shock-related 70 kDa protein 2 (Heat shock protein 70.2)	0.42	-	cyt	0		mitochondrion [IDA]			633
Q9Y278 UniProt NPD GO	OST2_HUMAN	Heparan sulfate glucosamine 3-O-sulfotransferase 2 (EC 2.8.2.29) (Heparan sulfate D-glucosaminyl 3-O ...	0.42	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	integral to membrane [TAS]	604056		367
Q9Y662 UniProt NPD GO	OST3B_HUMAN	Heparan sulfate glucosamine 3-O-sulfotransferase 3B1 (EC 2.8.2.30) (Heparan sulfate D-glucosaminyl 3 ...	0.42	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	integral to plasma membrane [TAS]	604058	1T8U	390
Q6QNF4 UniProt NPD GO	HGFA_CANFA	Hepatocyte growth factor activator precursor (EC 3.4.21.-) (HGF activator) (HGFA) [Contains: Hepatoc ...	0.42	-	exc	1 *	Secreted protein. Secreted as an inactive single-chain precursor and is then activated to a heterodi ...				654
P17130 UniProt NPD GO	ROA1_XENLA	Heterogeneous nuclear ribonucleoproteins A1 homolog (hnRNP A1) (Helix-destabilizing protein) (Single ...	0.42	+	cyt	0					365
Q2YDK4 UniProt NPD GO	HMGN4_BOVIN	High-mobility group nucleosome-binding domain-containing protein 4	0.42	-	nuc	0	Nucleus (By similarity)				89
P08284 UniProt NPD GO	H101_CHICK	Histone H1.01	0.42	+	nuc	0	Nucleus				218
P15865 UniProt NPD GO	H12_RAT	Histone H1.2 (H1d)	0.42	+	nuc	0	Nucleus				218
P02294 UniProt NPD GO	H2B2_YEAST	Histone H2B.2	0.42	-	nuc	0	Nucleus	nuclear nucleosome [TAS]		2FSB	130
P08903 UniProt NPD GO	H3_ENCAL	Histone H3	0.42	-	nuc	0	Nucleus (By similarity)				135
P69149 UniProt NPD GO	H31_TETPY	Histone H3.1	0.42	-	nuc	0	Nucleus (By similarity)				135
P69150 UniProt NPD GO	H31_TETTH	Histone H3.1	0.42	-	nuc	0	Nucleus (By similarity)				135
P41353 UniProt NPD GO	H33_TETTH	Histone H3.3 (HV2)	0.42	-	nuc	0	Nucleus (By similarity)				135
Q9C5P4 UniProt NPD GO	SUVH3_ARATH	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH3 (EC 2.1.1.43) (Histone H3-K9 methyltr ...	0.42	-	nuc	0	Nucleus. Associates with centromeric constitutive heterochromatin				669
Q8SWA6 UniProt NPD GO	HD11_ENCCU	Homeobox protein HD-11 (EcHD-11)	0.42	-	nuc	0	Nucleus				167
P31247 UniProt NPD GO	HXB3_XENLA	Homeobox protein Hox-B3 (XlHox-2.7) (Fragment)	0.42	+	nuc	0	Nucleus				60
Q2VL80 UniProt NPD GO	MSX1_PERPO	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.42	+	nuc	0	Nucleus (By similarity)				297
P70178 UniProt NPD GO	SIX5_MOUSE	Homeobox protein SIX5 (DM locus-associated homeodomain protein homolog)	0.42	-	nuc	0	Nucleus (By similarity)				719
Q08169 UniProt NPD GO	HUGA_APIME	Hyalurononglucosaminidase precursor (EC 3.2.1.35) (Hyaluronidase) (Hya) (Allergen Api m 2) (Api m II ...	0.42	-	exc	1 *				1FCV	382
P53921 UniProt NPD GO	YNM2_YEAST	Hypothetical 13.2 kDa protein in SPC98-TOM70 intergenic region	0.42	-	mit	0		mitochondrion [IDA]			115
Q04210 UniProt NPD GO	YMT0_YEAST	Hypothetical 19.2 kDa protein in SUB1-ARGR1 intergenic region	0.42	+	end	3 *	Membrane; multi-pass membrane protein (Potential)				160
P43578 UniProt NPD GO	YFB5_YEAST	Hypothetical 19.3 kDa protein in MDJ1-HSP12 intergenic region	0.42	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				164
P40058 UniProt NPD GO	YER5_YEAST	Hypothetical 20.5 kDa protein in SER3-ILV1 intergenic region	0.42	-	nuc	0					173
P47148 UniProt NPD GO	YJ81_YEAST	Hypothetical 32.2 kDa protein in CPA2-NNF1 intergenic region	0.42	-	mit	0		mitochondrion [IDA]			283
P53923 UniProt NPD GO	YNL9_YEAST	Hypothetical 56.5 kDa protein in TOM70-PSU1 intergenic region	0.42	-	nuc	0		cytoplasm [IDA]			493
Q9M3J5 UniProt NPD GO	YCF1_SPIOL	Hypothetical 56.9 kDa protein ycf1	0.42	-	end	6 *	Plastid; chloroplast				481
Q03722 UniProt NPD GO	YMC0_YEAST	Hypothetical 76.1 kDa protein in UNG1-OST6 intergenic region	0.42	-	nuc	0					664
P47014 UniProt NPD GO	YJN2_YEAST	Hypothetical 84.5 kDa protein in MRS3-URA2 intergenic region	0.42	-	mit	1 *	Membrane; multi-pass membrane protein (Potential)	membrane fraction [IDA]			750
Q9TLX2 UniProt NPD GO	YCF24_CYACA	Hypothetical UPF0051 protein ycf24	0.42	-	nuc	0	Plastid; chloroplast				483
P93297 UniProt NPD GO	M400_ARATH	Hypothetical mitochondrial protein AtMg00400 (ORF157)	0.42	-	cyt	0	Mitochondrion (Potential)				157
P34276 UniProt NPD GO	YKJ2_CAEEL	Hypothetical protein C02D5.2	0.42	-	nuc	3 *					323
Q10340 UniProt NPD GO	YBLJ_SCHPO	Hypothetical protein C106.19 in chromosome II	0.42	-	mit	0					515
O94249 UniProt NPD GO	YCM2_SCHPO	Hypothetical protein C13B11.02c in chromosome III	0.42	-	cyt	0					138
O13804 UniProt NPD GO	YE07_SCHPO	Hypothetical protein C17H9.07 in chromosome I	0.42	+	nuc	0					120
Q9UU86 UniProt NPD GO	YQL7_SCHPO	Hypothetical protein C1827.07c in chromosome III	0.42	-	end	8	Membrane; multi-pass membrane protein (Potential)				682
Q10414 UniProt NPD GO	YD89_SCHPO	Hypothetical protein C1F3.09 in chromosome I	0.42	-	nuc	0					561
Q9HE11 UniProt NPD GO	YK91_SCHPO	Hypothetical protein C20H4.01 in chromosome I	0.42	-	nuc	0					666
O14015 UniProt NPD GO	YDPC_SCHPO	Hypothetical protein C29A4.12c in chromosome I	0.42	+	nuc	0					150
Q09272 UniProt NPD GO	YQG1_CAEEL	Hypothetical protein C41C4.1	0.42	-	mit	1 *					329
P87052 UniProt NPD GO	YDJ4_SCHPO	Hypothetical protein C57A10.04 in chromosome I	0.42	-	mit	0					338
P34399 UniProt NPD GO	YLU5_CAEEL	Hypothetical protein F10E9.5	0.42	-	nuc	0					171
P55326 UniProt NPD GO	YZG1_CAEEL	Hypothetical protein F13E6.1 in chromosome X	0.42	-	nuc	0					195
P34449 UniProt NPD GO	YM2B_CAEEL	Hypothetical protein F54F2.2, isoform b	0.42	-	nuc	1 *					211

You are viewing entries 30401 to 30450 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.