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
P47063 UniProt NPD GO	YJC7_YEAST	Hypothetical 15.7 kDa protein in MAD2-RNR2 intergenic region	0.15	-	mit	0					138
P38461 UniProt NPD GO	YMF18_MARPO	Hypothetical 18.6 kDa protein in RPS1-NAD4L intergenic region (ORF 155)	0.15	-	mit	3 *					155
P29065 UniProt NPD GO	YAGL_CANTS	Hypothetical 18.6 kDa protein in alpha-glucosidase 3'region (ORF2)	0.15	-	nuc	0					170
P36087 UniProt NPD GO	YKH0_YEAST	Hypothetical 19.8 kDa protein in STB6-NUP100 intergenic region	0.15	+	cyt	0		mitochondrion [IDA]			169
P17962 UniProt NPD GO	YALD_TRYBB	Hypothetical 21 kDa protein in aldolase locus (ORFD)	0.15	-	nuc	0					186
P56739 UniProt NPD GO	Y212_BOTCI	Hypothetical 21.2 kDa protein	0.15	-	cyt	0					183
P46993 UniProt NPD GO	YJR0_YEAST	Hypothetical 22.0 kDa protein in CPS1-FPP1 intergenic region	0.15	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA]			183
P53288 UniProt NPD GO	YG3R_YEAST	Hypothetical 22.2 kDa protein in NSR1-TIF4631 intergenic region	0.15	-	cyt	1					203
Q9MUQ5 UniProt NPD GO	YCX1_MESVI	Hypothetical 26.1 kDa protein in ndhB-psaI intergenic region	0.15	-	end	4 *	Plastid; chloroplast				223
P40586 UniProt NPD GO	YIW2_YEAST	Hypothetical 27.4 kDa protein in HYR1 3'region	0.15	-	cyt	0					236
P40364 UniProt NPD GO	YJG6_YEAST	Hypothetical 28.5 kDa protein in SMC3-MRPL8 intergenic region	0.15	-	nuc	0		membrane fraction [IDA] mitochondrion [IDA]			252
O20143 UniProt NPD GO	YCX6_CHLVU	Hypothetical 43.6 kDa protein in ycf4-trnK intergenic region (ORF390)	0.15	-	mit	1 *	Plastid; chloroplast				390
P15564 UniProt NPD GO	YMN4_PODAN	Hypothetical 50.9 kDa protein in ND4 intron 1	0.15	-	end	5 *					449
O19900 UniProt NPD GO	YCF18_CYACA	Hypothetical 6.6 kDa protein ycf18	0.15	-	nuc	0	Plastid; chloroplast				54
O14155 UniProt NPD GO	YE72_SCHPO	Hypothetical UPF0047 protein C4A8.02c in chromosome I	0.15	-	mit	0					142
Q9M8T3 UniProt NPD GO	U131_ARATH	Hypothetical UPF0131 protein At3g02910	0.15	-	cyt	0					182
Q17963 UniProt NPD GO	YKY4_CAEEL	Hypothetical WD repeat protein C14B1.4	0.15	-	nuc	0					376
P93290 UniProt NPD GO	M240_ARATH	Hypothetical mitochondrial protein AtMg00240 (ORF111a)	0.15	-	mit	0	Mitochondrion (Potential)				111
P92535 UniProt NPD GO	M1010_ARATH	Hypothetical mitochondrial protein AtMg01010 (ORF118)	0.15	-	cyt	0	Mitochondrion (Potential)				118
P92551 UniProt NPD GO	M1210_ARATH	Hypothetical mitochondrial protein AtMg01210 (ORF101b)	0.15	-	cyt	0	Mitochondrion (Potential)				101
Q09216 UniProt NPD GO	YP67_CAEEL	Hypothetical protein B0495.7	0.15	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				895
Q11106 UniProt NPD GO	YPB3_CAEEL	Hypothetical protein C03B8.3	0.15	-	mit	0					128
Q9URV6 UniProt NPD GO	YBL5_SCHPO	Hypothetical protein C106.05c in chromosome II	0.15	-	nuc	0					96
Q10083 UniProt NPD GO	YAO4_SCHPO	Hypothetical protein C11D3.04c in chromosome I	0.15	-	cyt	0					130
Q9P378 UniProt NPD GO	YLM2_SCHPO	Hypothetical protein C19B12.02c precursor	0.15	-	exc	0					542
Q92344 UniProt NPD GO	YDI6_SCHPO	Hypothetical protein C1F8.06 in chromosome I	0.15	-	exc	0					385
O14359 UniProt NPD GO	YB4E_SCHPO	Hypothetical protein C30D10.14 in chromosome II	0.15	-	mit	0					249
O94485 UniProt NPD GO	YC74_SCHPO	Hypothetical protein C417.04 in chromosome III	0.15	-	mit	0					180
P87138 UniProt NPD GO	YDM7_SCHPO	Hypothetical protein C57A7.07c in chromosome I	0.15	-	nuc	0					308
Q10333 UniProt NPD GO	YBM9_SCHPO	Hypothetical protein C582.09 in chromosome II	0.15	-	mit	0					238
Q10311 UniProt NPD GO	YD58_SCHPO	Hypothetical protein C6C3.08 in chromosome I	0.15	-	nuc	0					234
Q9UT31 UniProt NPD GO	YKG5_SCHPO	Hypothetical protein C8F11.05c precursor	0.15	-	cyt	0					241
Q8STF1 UniProt NPD GO	Y5G4_ENCCU	Hypothetical protein ECU05_1640/ECU11_0090	0.15	-	end	7 *					268
Q8SVF5 UniProt NPD GO	Y607_ENCCU	Hypothetical protein ECU06_0070	0.15	-	end	6 *					267
Q8STJ1 UniProt NPD GO	Y7I7_ENCCU	Hypothetical protein ECU07_1870/ECU10_0030	0.15	-	end	7 *					260
P52883 UniProt NPD GO	YAF7_CAEEL	Hypothetical protein F46C5.7	0.15	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				199
Q09399 UniProt NPD GO	YRB2_CAEEL	Hypothetical protein F58F12.2	0.15	-	cyt	1 *					125
Q09410 UniProt NPD GO	YRJ4_CAEEL	Hypothetical protein K10D2.4	0.15	-	nuc	0					81
Q21890 UniProt NPD GO	YF64_CAEEL	Hypothetical protein R102.4 in chromosome IV	0.15	-	mit	0					433
P82636 UniProt NPD GO	SCR17_ARATH	Hypothetical protein SCRL17 precursor	0.15	-	mit	1 *					98
Q09336 UniProt NPD GO	YOF9_CAEEL	Hypothetical protein ZK1290.9	0.15	-	cyt	0					360
Q09365 UniProt NPD GO	YS23_CAEEL	Hypothetical protein ZK1320.3	0.15	-	exc	0					208
Q09384 UniProt NPD GO	YS88_CAEEL	Hypothetical protein ZK945.8	0.15	-	nuc	0					109
Q37082 UniProt NPD GO	YCF72_MAIZE	Hypothetical protein ycf72 (ORF137)	0.15	-	nuc	0	Plastid; chloroplast				137
Q6ENC9 UniProt NPD GO	YCF72_ORYNI	Hypothetical protein ycf72 (ORF137)	0.15	-	nuc	0	Plastid; chloroplast				137
Q36996 UniProt NPD GO	YCF72_ORYSA	Hypothetical protein ycf72 (ORF137)	0.15	-	nuc	0	Plastid; chloroplast				137
Q6L3B8 UniProt NPD GO	YCF72_SACHY	Hypothetical protein ycf72 (ORF137)	0.15	-	nuc	0	Plastid; chloroplast				137
Q6ENS0 UniProt NPD GO	YCF72_SACOF	Hypothetical protein ycf72 (ORF137)	0.15	-	nuc	0	Plastid; chloroplast				137
P01868 UniProt NPD GO	IGHG1_MOUSE	Ig gamma-1 chain C region secreted form	0.15	-	nuc	0	Secreted protein	immunoglobulin complex, circulating [IDA]		2B2X	324
P01866 UniProt NPD GO	GCB_MOUSE	Ig gamma-2B chain C region secreted form	0.15	-	nuc	0	Secreted protein (Potential)				336

You are viewing entries 57051 to 57100 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.