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
P48239 UniProt NPD GO	YG3P_YEAST	Hypothetical 41.3 kDa protein in RSR1-CYS4 intergenic region	0.04	-	cyt	0					356
Q9TM07 UniProt NPD GO	YCF17_CYACA	Hypothetical 5.1 kDa protein ycf17	0.04	-	mit	1 *	Plastid; chloroplast				43
Q34806 UniProt NPD GO	YVAR1_PICCA	Hypothetical 6.8 kDa protein in VAR1 3' region	0.04	-	cyt	0					58
P35006 UniProt NPD GO	YCX4_CHLRE	Hypothetical 7.3 kDa protein in petA 5'region (ORF62)	0.04	-	cyt	0	Plastid; chloroplast				62
P38467 UniProt NPD GO	YMF25_MARPO	Hypothetical 7.5 kDa protein in NAD5 5'region (ORF64)	0.04	-	cyt	0					64
O96808 UniProt NPD GO	YCF33_SKECO	Hypothetical 7.7 kDa protein ycf33	0.04	-	end	2 *	Plastid; chloroplast				64
P53835 UniProt NPD GO	YN19_YEAST	Hypothetical 73.4 kDa protein in ERG24-MET2 intragenic region	0.04	-	end	3	Membrane; multi-pass membrane protein (Potential)	mating projection tip [IDA]			661
P34779 UniProt NPD GO	YCX5_ASTLO	Hypothetical 8.7 kDa protein in rpl22-rpl23 intergenic region (ORF70)	0.04	-	mit	2 *	Plastid				70
Q6B0R7 UniProt NPD GO	YM9D_YEAST	Hypothetical UPF0320 protein YMR326C	0.04	-	cyt	0					102
Q751T2 UniProt NPD GO	U327_ASHGO	Hypothetical UPF0327 protein AFR743W	0.04	-	mit	1 *					82
Q7RYI0 UniProt NPD GO	U327_NEUCR	Hypothetical UPF0327 protein NCU06495	0.04	-	nuc	1 *					93
P93277 UniProt NPD GO	M050_ARATH	Hypothetical mitochondrial protein AtMg00050 (ORF131)	0.04	-	cyt	0	Mitochondrion (Potential)				131
O13991 UniProt NPD GO	YEG9_SCHPO	Hypothetical oxidoreductase C26H5.09c (EC 1.-.-.-)	0.04	-	cyt	0					369
Q11189 UniProt NPD GO	YPDA_CAEEL	Hypothetical protein C05D11.10	0.04	-	cyt	0					160
Q10080 UniProt NPD GO	YAO1_SCHPO	Hypothetical protein C11D3.01c in chromosome I	0.04	-	nuc	0					79
Q10089 UniProt NPD GO	YAOA_SCHPO	Hypothetical protein C11D3.10 in chromosome I	0.04	-	cyt	0					434
O74419 UniProt NPD GO	YQ52_SCHPO	Hypothetical protein C162.02c in chromosome III	0.04	-	nuc	0					981
Q10474 UniProt NPD GO	YDF2_SCHPO	Hypothetical protein C17C9.02c in chromosome I	0.04	-	mit	0					258
Q9P7K7 UniProt NPD GO	YOSH_SCHPO	Hypothetical protein C21C3.17c precursor	0.04	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				186
O14345 UniProt NPD GO	YB3F_SCHPO	Hypothetical protein C2F12.15c in chromosome II	0.04	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				329
O59791 UniProt NPD GO	YCNE_SCHPO	Hypothetical protein C320.14 in chromosome III	0.04	-	cyt	0				1WTC	323
P34362 UniProt NPD GO	YLH8_CAEEL	Hypothetical protein C48B4.8	0.04	-	end	4 *					196
O14169 UniProt NPD GO	YE52_SCHPO	Hypothetical protein C4D7.02c in chromosome I	0.04	-	cyt	0					319
Q8STB3 UniProt NPD GO	Y112_ENCCU	Hypothetical protein ECU01_0120/ECU01_1490/ECU08_0050	0.04	-	cyt	0					199
Q8STY8 UniProt NPD GO	Y902_ENCCU	Hypothetical protein ECU09_0020	0.04	-	end	7 *					271
Q19408 UniProt NPD GO	YSMK_CAEEL	Hypothetical protein F13E9.3, mitochondrial precursor	0.04	-	vac	0	Mitochondrion (Potential)				298
P46500 UniProt NPD GO	YLX4_CAEEL	Hypothetical protein F23F12.4	0.04	-	cyt	0					345
P52880 UniProt NPD GO	YAF1_CAEEL	Hypothetical protein F46C5.1	0.04	-	exc	1 *					121
P52879 UniProt NPD GO	YAF8_CAEEL	Hypothetical protein F46C5.8 in chromosome II	0.04	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				191
Q09389 UniProt NPD GO	YR43_CAEEL	Hypothetical protein F47D12.3	0.04	-	cyt	0					140
P34452 UniProt NPD GO	YMA7_CAEEL	Hypothetical protein F54F2.7	0.04	-	cyt	0					157
P34457 UniProt NPD GO	YMD3_CAEEL	Hypothetical protein F54H12.3	0.04	-	nuc	1					286
Q09571 UniProt NPD GO	YRD1_CAEEL	Hypothetical protein K02A2.1	0.04	-	cyt	0	Membrane; multi-pass membrane protein (Potential)				158
P34526 UniProt NPD GO	YM65_CAEEL	Hypothetical protein K12H4.5	0.04	-	mit	1 *					97
P78833 UniProt NPD GO	YHZ8_SCHPO	Hypothetical protein SPBC21B10.08c in chromosome II	0.04	-	cyt	0					198
Q9XUC4 UniProt NPD GO	YGJK_CAEEL	Hypothetical protein T28F3.3	0.04	-	end	7	Membrane; multi-pass membrane protein (Probable)				393
Q23280 UniProt NPD GO	YOCA_CAEEL	Hypothetical protein ZC395.10 in chromosome III	0.04	-	cyt	0					175
Q09375 UniProt NPD GO	YS49_CAEEL	Hypothetical protein ZK177.9	0.04	-	cyt	0					121
P34677 UniProt NPD GO	YO27_CAEEL	Hypothetical protein ZK688.7	0.04	-	cyt	2					243
Q09621 UniProt NPD GO	YS81_CAEEL	Hypothetical protein ZK945.1	0.04	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				473
O74487 UniProt NPD GO	WTF20_SCHPO	Hypothetical protein wtf20	0.04	-	end	2	Membrane; multi-pass membrane protein (Potential)				258
Q33301 UniProt NPD GO	YCF70_MAIZE	Hypothetical protein ycf70 (ORF69)	0.04	-	mit	2 *	Plastid; chloroplast				69
P36172 UniProt NPD GO	YK85_YEAST	Hypothetical transport protein YKR105C	0.04	-	end	14 *	Membrane; multi-pass membrane protein (Probable)				582
Q27541 UniProt NPD GO	HPRT_CRIFA	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase)	0.04	-	pox	0	Cytoplasm				208
P00494 UniProt NPD GO	HPRT_CRIGR	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase)	0.04	-	cyt	0	Cytoplasm				217
Q7Z0A6 UniProt NPD GO	CXI1_CONRA	I-superfamily conotoxin R11.1	0.04	-	nuc	0	Secreted protein				42
Q7Z0A5 UniProt NPD GO	CXI10_CONRA	I-superfamily conotoxin R11.10 (Fragment)	0.04	-	nuc	0	Secreted protein				45
Q7Z0A2 UniProt NPD GO	CXI15_CONRA	I-superfamily conotoxin R11.15	0.04	-	nuc	0	Secreted protein				42
Q7Z0A1 UniProt NPD GO	CXI16_CONRA	I-superfamily conotoxin R11.16	0.04	-	nuc	0	Secreted protein				42
P01753 UniProt NPD GO	HV09_MOUSE	Ig heavy chain V region 186-1 precursor	0.04	-	vac	0					117

You are viewing entries 77301 to 77350 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.