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
Q01556 UniProt NPD GO	COX2_TRIRU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				237
P04372 UniProt NPD GO	COX2_TRYBB	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				210
O03889 UniProt NPD GO	COX2_APTAU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II) (Fragment)	0.01	-	end	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				199
O03890 UniProt NPD GO	COX2_CASBE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II) (Fragment)	0.01	-	end	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				199
O03891 UniProt NPD GO	COX2_DRONO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II) (Fragment)	0.01	-	end	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				199
P29660 UniProt NPD GO	COX2_MEGAT	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II) (Fragment)	0.01	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				74
P80498 UniProt NPD GO	COX2_SOLTU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II) (Fragment)	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				26
P43377 UniProt NPD GO	COX2_SACEX	Cytochrome c oxidase subunit 2 precursor (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				249
Q9XLW8 UniProt NPD GO	COX2_SACKL	Cytochrome c oxidase subunit 2 precursor (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				251
P48891 UniProt NPD GO	COX3_ALBCO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					259
Q75G34 UniProt NPD GO	COX3_ASHGO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					269
Q33824 UniProt NPD GO	COX3_ASTPE	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					260
P41295 UniProt NPD GO	COX3_BALMU	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					261
P24989 UniProt NPD GO	COX3_BALPH	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					261
P69216 UniProt NPD GO	COX3_BRAFL	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	6 *					262
P69215 UniProt NPD GO	COX3_BRALA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	6 *					262
P18945 UniProt NPD GO	COX3_CHICK	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *				1LLK	261
O21331 UniProt NPD GO	COX3_DASNO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					261
Q2I3G8 UniProt NPD GO	COX3_ELEMA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					261
P00421 UniProt NPD GO	COX3_EMENI	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *				2PHV	269
P92481 UniProt NPD GO	COX3_EQUAS	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					261
P38597 UniProt NPD GO	COX3_HALGR	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	6 *					261
P48661 UniProt NPD GO	COX3_HORSE	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					261
Q2I3F5 UniProt NPD GO	COX3_LOXAF	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	mit	6 *					261
Q34943 UniProt NPD GO	COX3_LUMTE	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					259
Q38PR6 UniProt NPD GO	COX3_MAMPR	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	cyt	6 *					261
P00416 UniProt NPD GO	COX3_MOUSE	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					261
O63915 UniProt NPD GO	COX3_MYXGL	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					261
Q9ZXX8 UniProt NPD GO	COX3_PAPHA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					261
O47692 UniProt NPD GO	COX3_PELCP	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	6 *					261
O79676 UniProt NPD GO	COX3_PELSU	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	6 *					261
Q00529 UniProt NPD GO	COX3_PHOVI	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	6 *					261
P25003 UniProt NPD GO	COX3_PISOC	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					260
Q95914 UniProt NPD GO	COX3_POLOR	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	6 *					261
O99822 UniProt NPD GO	COX3_RHISA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	6 *					257
P14575 UniProt NPD GO	COX3_SCHPO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					269
O79407 UniProt NPD GO	COX3_SCYCA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					261
Q36837 UniProt NPD GO	COX3_TRIRU	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *					269
Q37355 UniProt NPD GO	COX3_TRYBO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	8 *					286
P15953 UniProt NPD GO	COX3_WHEAT	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	6 *					265
P00420 UniProt NPD GO	COX3_YEAST	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.01	-	end	7 *		respiratory chain complex IV (sensu Eukaryota) [IPI]			269
Q85Q96 UniProt NPD GO	COX3_CANGA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III) (Cytochrome oxida ...	0.01	-	end	7 *					269
Q34214 UniProt NPD GO	COX3_CANPA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III) (Cytochrome oxida ...	0.01	-	end	7 *					269
P50657 UniProt NPD GO	COX3_ANAPL	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III) (Fragment)	0.01	-	nuc	2 *					86
Q33752 UniProt NPD GO	COX3_ARBLI	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III) (Fragment)	0.01	-	mit	3 *					109
Q33845 UniProt NPD GO	COX3_ARTSA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III) (Fragment)	0.01	-	end	2 *					115
P50271 UniProt NPD GO	COX3_DROSI	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III) (Fragment)	0.01	-	cyt	2 *					74
P92504 UniProt NPD GO	CYC1_ASCSU	Cytochrome c type-1	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix				111
P00109 UniProt NPD GO	CYC6_ALAES	Cytochrome c6 (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				86
P22343 UniProt NPD GO	CYC6_EUGVI	Cytochrome c6 (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				87

You are viewing entries 87951 to 88000 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.