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
Q41575 UniProt NPD GO	H2B6_WHEAT	Histone H2B.6 (H2B123)	0.14	-	nuc	0	Nucleus (By similarity)				120
Q75C99 UniProt NPD GO	HAT2_ASHGO	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.14	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				423
Q6P3E7 UniProt NPD GO	HDA10_MOUSE	Histone deacetylase 10 (HD10)	0.14	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Excluded from the nucleoli (By similarity)				666
Q86X55 UniProt NPD GO	CARM1_HUMAN	Histone-arginine methyltransferase CARM1 (EC 2.1.1.125) (EC 2.1.1.-) (Protein arginine N-methyltrans ...	0.14	-	cyt	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]	603934		585
P82959 UniProt NPD GO	TXH21_ORNHU	Huwentoxin-2 form 1 precursor (Huwentoxin-II) (HwTx-II)	0.14	-	vac	0	Secreted protein			1I25	85
P68421 UniProt NPD GO	TXH7_ORNHU	Huwentoxin-7 precursor (Huwentoxin-VII) (HwTx-VII)	0.14	-	exc	0	Secreted protein				84
P55252 UniProt NPD GO	HPLN1_BOVIN	Hyaluronan and proteoglycan link protein 1 precursor (Proteoglycan link protein) (Cartilage link pro ...	0.14	-	vac	0					354
O97711 UniProt NPD GO	HAS2_BOVIN	Hyaluronan synthase 2 (EC 2.4.1.212) (Hyaluronate synthase 2) (Hyaluronic acid synthase 2) (HA synth ...	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				552
P70312 UniProt NPD GO	HAS2_MOUSE	Hyaluronan synthase 2 (EC 2.4.1.212) (Hyaluronate synthase 2) (Hyaluronic acid synthase 2) (HA synth ...	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				552
O35776 UniProt NPD GO	HAS2_RAT	Hyaluronan synthase 2 (EC 2.4.1.212) (Hyaluronate synthase 2) (Hyaluronic acid synthase 2) (HA synth ...	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				552
P54870 UniProt NPD GO	HMCS2_BLAGE	Hydroxymethylglutaryl-CoA synthase 2 (EC 2.3.3.10) (HMG-CoA synthase 2) (3-hydroxy-3-methylglutaryl ...	0.14	-	nuc	0					455
P22369 UniProt NPD GO	YPC4_CLAPU	Hypothetical 11.6 kDa protein (ORF4)	0.14	-	nuc	0					106
P40503 UniProt NPD GO	YII6_YEAST	Hypothetical 11.6 kDa protein in SGA1-KTR7 intergenic region	0.14	-	nuc	0					102
P40575 UniProt NPD GO	YIU0_YEAST	Hypothetical 11.7 kDa protein in MAL5-MRS1 intergenic region	0.14	-	exc	1 *					100
P40097 UniProt NPD GO	YE11_YEAST	Hypothetical 12.5 kDa protein in ISC10 3'region	0.14	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				107
P05720 UniProt NPD GO	YCX1_CHLPY	Hypothetical 12.7 kDa protein in 16S-23S DNA spacer	0.14	-	nuc	0	Plastid; chloroplast				110
Q04201 UniProt NPD GO	YMK1_YEAST	Hypothetical 12.9 kDa protein in CAC2-TSL1 intergenic region	0.14	-	nuc	1 *		cytoplasm [IDA] endoplasmic reticulum [IDA]			117
P40520 UniProt NPD GO	YIF9_YEAST	Hypothetical 13.0 kDa protein in SNP1-GPP1 intergenic region	0.14	-	cyt	0					121
P53827 UniProt NPD GO	YN43_YEAST	Hypothetical 13.6 kDa protein in MCK1-RPS19B intergenic region	0.14	-	cyt	1 *					115
P53268 UniProt NPD GO	YG2Z_YEAST	Hypothetical 15.4 kDa protein in SHY1-SPT6 intergenic region	0.14	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				129
P32616 UniProt NPD GO	YEF5_YEAST	Hypothetical 16.5 kDa protein in GLY1-GDA1 intergenic region	0.14	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				141
P38457 UniProt NPD GO	YMF13_MARPO	Hypothetical 17.9 kDa protein in NAD1-COB intergenic region (ORF 154)	0.14	-	nuc	0					154
P53279 UniProt NPD GO	YG3B_YEAST	Hypothetical 19.2 kDa protein in ASN2-PHB1 intergenic region	0.14	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				174
P47056 UniProt NPD GO	YJD7_YEAST	Hypothetical 24.8 kDa protein in NSP1-TAD2 intergenic region	0.14	-	exc	1	Membrane; multi-pass membrane protein (Potential)				224
P46314 UniProt NPD GO	YCF23_ANTSP	Hypothetical 30.3 kDa protein ycf23 (ORF 277)	0.14	-	nuc	0	Plastid; chloroplast				277
P53242 UniProt NPD GO	YG29_YEAST	Hypothetical 34.0 kDa protein in VHT1-ROM1 intergenic region	0.14	-	nuc	0					292
P53748 UniProt NPD GO	YN91_YEAST	Hypothetical 35.7 kDa protein in BIO3-HXT17 intergenic region	0.14	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				327
P51238 UniProt NPD GO	YCF39_PORPU	Hypothetical 35.7 kDa protein ycf39 (ORF319)	0.14	-	mit	0	Plastid; chloroplast				319
P47172 UniProt NPD GO	YJ9I_YEAST	Hypothetical 39.9 kDa protein in HOM6-PMT4 intergenic region	0.14	-	nuc	0					347
P49539 UniProt NPD GO	YCF44_ODOSI	Hypothetical 43.8 kDa protein ycf44 (ORF382)	0.14	-	end	3 *	Plastid; chloroplast				382
P39997 UniProt NPD GO	YEB6_YEAST	Hypothetical 57.4 kDa protein in PMP2-VAC8 intergenic region	0.14	-	cyt	0					493
P48447 UniProt NPD GO	YCF18_GALSU	Hypothetical 7.5 kDa protein ycf18	0.14	-	nuc	0	Plastid; chloroplast				62
P53918 UniProt NPD GO	YNM5_YEAST	Hypothetical 73.8 kDa protein in SPC98-TOM70 intergenic region	0.14	-	end	11	Membrane; multi-pass membrane protein (Probable)	mitochondrion [IDA]			673
P48274 UniProt NPD GO	YCF34_CYAPA	Hypothetical 8.9 kDa protein ycf34	0.14	-	cyt	0	Plastid; cyanelle				77
Q22306 UniProt NPD GO	YW12_CAEEL	Hypothetical UPF0046 protein T07D4.2 in chromosome II	0.14	-	cyt	0					254
P36030 UniProt NPD GO	YKW5_YEAST	Hypothetical UPF0320 protein YKL225W	0.14	-	nuc	1					115
P93291 UniProt NPD GO	M260_ARATH	Hypothetical mitochondrial protein AtMg00260 (ORF101a)	0.14	-	cyt	0	Mitochondrion (Potential)				101
P93309 UniProt NPD GO	M540_ARATH	Hypothetical mitochondrial protein AtMg00540 (ORF102b)	0.14	-	nuc	0	Mitochondrion (Potential)				122
P92513 UniProt NPD GO	M720_ARATH	Hypothetical mitochondrial protein AtMg00720 (ORF107d)	0.14	-	cyt	0	Mitochondrion (Potential)				107
Q11084 UniProt NPD GO	YT68_CAEEL	Hypothetical protein B0563.8	0.14	-	mit	0					66
Q11123 UniProt NPD GO	YX12_CAEEL	Hypothetical protein C03F11.2	0.14	-	cyt	0					362
Q9URV4 UniProt NPD GO	YBL7_SCHPO	Hypothetical protein C106.07c in chromosome II	0.14	-	nuc	1					167
O60127 UniProt NPD GO	YH7D_SCHPO	Hypothetical protein C16G5.13 in chromosome II	0.14	-	nuc	0					126
O13948 UniProt NPD GO	YEH5_SCHPO	Hypothetical protein C23H4.05c precursor	0.14	-	mit	0					97
Q10253 UniProt NPD GO	YD25_SCHPO	Hypothetical protein C56F8.05c in chromosome I	0.14	-	mit	0					295
Q9P802 UniProt NPD GO	YCZC_SCHPO	Hypothetical protein C970.12 in chromosome III	0.14	-	cyt	0		Mis6-Sim4 complex [TAS]			155
Q8STE8 UniProt NPD GO	Y303_ENCCU	Hypothetical protein ECU03_0030/ECU05_0040/ECU06_0010/ECU06_1710/ ECU11_0010	0.14	-	cyt	0					118
Q8SW83 UniProt NPD GO	Y304_ENCCU	Hypothetical protein ECU03_0040	0.14	-	end	7 *					268
Q8SVY5 UniProt NPD GO	Y411_ENCCU	Hypothetical protein ECU04_0110	0.14	-	nuc	0					213
Q8SVN9 UniProt NPD GO	Y505_ENCCU	Hypothetical protein ECU05_0050	0.14	-	end	7 *					275

You are viewing entries 58451 to 58500 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.