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
Q5CC93 UniProt NPD GO	UCRIA_CYAPA	Cytochrome b6-f complex iron-sulfur subunit 1, cyanelle precursor (EC 1.10.99.1) (Rieske iron-sulfur ...	0.05	-	cyt	1	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity). The tr ...				239
Q02585 UniProt NPD GO	UCRIB_TOBAC	Cytochrome b6-f complex iron-sulfur subunit 2, chloroplast precursor (EC 1.10.99.1) (Rieske iron-sul ...	0.05	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein. The transmembran ...				228
P49728 UniProt NPD GO	UCRIA_CHLRE	Cytochrome b6-f complex iron-sulfur subunit, chloroplast precursor (EC 1.10.99.1) (Rieske iron-sulfu ...	0.05	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein. The transmembran ...			1Q90	206
P83688 UniProt NPD GO	CC12_EUGGR	Cytochrome b6/f complex 12.6 kDa peptide (Fragment)	0.05	-	nuc	0	Plastid; chloroplast	chloroplast [IDA]			30
P00064 UniProt NPD GO	CYC_ALLPO	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				111
P62894 UniProt NPD GO	CYC_BOVIN	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix			2B4Z	104
P68099 UniProt NPD GO	CYC_CAMDR	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P00011 UniProt NPD GO	CYC_CANFA	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]			104
P68517 UniProt NPD GO	CYC_CROAD	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P68518 UniProt NPD GO	CYC_CROAT	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P68519 UniProt NPD GO	CYC_CROVV	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P00075 UniProt NPD GO	CYC_ENTIN	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				111
P68100 UniProt NPD GO	CYC_ESCGI	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P00072 UniProt NPD GO	CYC_FAGES	Cytochrome c	0.05	-	nuc	0	Mitochondrion; mitochondrial matrix				111
P00070 UniProt NPD GO	CYC_HELAN	Cytochrome c	0.05	-	nuc	0	Mitochondrion; mitochondrial matrix				111
P68098 UniProt NPD GO	CYC_LAMGU	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P00060 UniProt NPD GO	CYC_LYCES	Cytochrome c	0.05	-	nuc	0	Mitochondrion; mitochondrial matrix				111
P00014 UniProt NPD GO	CYC_MACGI	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]			104
P00012 UniProt NPD GO	CYC_MIRLE	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]			104
Q6QLW4 UniProt NPD GO	CYC_PECGU	Cytochrome c	0.05	-	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)				109
P62895 UniProt NPD GO	CYC_PIG	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P00008 UniProt NPD GO	CYC_RABIT	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]			104
P00057 UniProt NPD GO	CYC_RICCO	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				111
P62896 UniProt NPD GO	CYC_SHEEP	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P00061 UniProt NPD GO	CYC_SOLTU	Cytochrome c	0.05	-	nuc	0	Mitochondrion; mitochondrial matrix				111
P00073 UniProt NPD GO	CYC_SPIOL	Cytochrome c	0.05	-	nuc	0	Mitochondrion; mitochondrial matrix				111
Q52V09 UniProt NPD GO	CYC_TARBA	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				104
P00049 UniProt NPD GO	CYC_USTSP	Cytochrome c	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				107
P49523 UniProt NPD GO	CCSA_ODOSI	Cytochrome c biogenesis protein ccsA	0.05	-	end	8 *	Plastid; chloroplast				312
Q14061 UniProt NPD GO	COX17_HUMAN	Cytochrome c oxidase copper chaperone	0.05	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)	cytoplasm [TAS]	604813		62
P26310 UniProt NPD GO	COX6_DICDI	Cytochrome c oxidase polypeptide 6 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide VI)	0.05	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				92
P04037 UniProt NPD GO	COX4_YEAST	Cytochrome c oxidase polypeptide IV, mitochondrial precursor (EC 1.9.3.1)	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane	respiratory chain complex IV (sensu Eukaryota) [IPI]		1HR8	155
Q863G6 UniProt NPD GO	COX82_ATEBE	Cytochrome c oxidase polypeptide VIII-liver, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.05	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				69
Q863G1 UniProt NPD GO	COX82_EULFU	Cytochrome c oxidase polypeptide VIII-liver, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.05	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				69
Q863G3 UniProt NPD GO	COX82_GALCR	Cytochrome c oxidase polypeptide VIII-liver, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.05	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				69
Q1W0Y2 UniProt NPD GO	COX7C_PIG	Cytochrome c oxidase polypeptide VIIc, mitochondrial precursor (EC 1.9.3.1)	0.05	-	mit	1 *					63
P00430 UniProt NPD GO	COX7C_BOVIN	Cytochrome c oxidase polypeptide VIIc, mitochondrial precursor (EC 1.9.3.1) (VIIIA)	0.05	-	mit	1 *	Mitochondrion; mitochondrial inner membrane			2OCC	63
P32799 UniProt NPD GO	COX13_YEAST	Cytochrome c oxidase polypeptide VIa, mitochondrial precursor (EC 1.9.3.1)	0.05	-	mit	1	Mitochondrion; mitochondrial inner membrane	respiratory chain complex IV (sensu Eukaryota) [IPI]			129
Q01519 UniProt NPD GO	COX12_YEAST	Cytochrome c oxidase polypeptide VIb (EC 1.9.3.1) (AED)	0.05	-	cyt	0		respiratory chain complex IV (sensu Eukaryota) [IPI]			82
P11240 UniProt NPD GO	COX5A_RAT	Cytochrome c oxidase polypeptide Va, mitochondrial precursor (EC 1.9.3.1)	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane				146
P00428 UniProt NPD GO	COX5B_BOVIN	Cytochrome c oxidase polypeptide Vb, mitochondrial precursor (EC 1.9.3.1) (VI)	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane			2OCC	129
P24893 UniProt NPD GO	COX1_CAEEL	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.05	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [NAS]			525
O79548 UniProt NPD GO	COX1_DINSE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.05	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				533
Q07434 UniProt NPD GO	COX1_PHYPO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.05	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				594
Q37370 UniProt NPD GO	COX1_ACACA	Cytochrome c oxidase subunit 1+2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I+II)	0.05	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				873
P50672 UniProt NPD GO	COX2_ACOWI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47870 UniProt NPD GO	COX2_ALLMI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P24882 UniProt NPD GO	COX2_ASCSU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				232
Q7J6G4 UniProt NPD GO	COX2_ATEMI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				227
P41294 UniProt NPD GO	COX2_BALMU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.05	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227

You are viewing entries 74201 to 74250 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.