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
Q9TDM5 UniProt NPD GO	CYB_ORCOR	Cytochrome b	0.03	-	end	9 *					379
Q8WBV2 UniProt NPD GO	CYB_OSTNU	Cytochrome b	0.03	-	end	9 *					381
Q9G210 UniProt NPD GO	CYB_PANOS	Cytochrome b	0.03	-	end	9 *					372
P41290 UniProt NPD GO	CYB_PHYCA	Cytochrome b	0.03	-	end	9 *					379
O99256 UniProt NPD GO	CYB_PLACH	Cytochrome b	0.03	-	end	10 *					376
Q35485 UniProt NPD GO	CYB_PLAIN	Cytochrome b	0.03	-	end	9 *					381
O63696 UniProt NPD GO	CYB_PLAVS	Cytochrome b	0.03	-	end	10 *					382
Q9MLK4 UniProt NPD GO	CYB_PSEAU	Cytochrome b	0.03	-	end	8 *					372
Q9TDM6 UniProt NPD GO	CYB_PSECS	Cytochrome b	0.03	-	end	9 *					379
Q9T6R2 UniProt NPD GO	CYB_RANAM	Cytochrome b	0.03	-	end	9 *					380
Q9T6R8 UniProt NPD GO	CYB_RANPL	Cytochrome b	0.03	-	end	9 *					380
O03545 UniProt NPD GO	CYB_RHEAM	Cytochrome b	0.03	-	end	9 *					379
Q9G2R8 UniProt NPD GO	CYB_RHISO	Cytochrome b	0.03	-	end	9 *					379
Q8M0K7 UniProt NPD GO	CYB_SAMCR	Cytochrome b	0.03	-	end	9 *					382
O48114 UniProt NPD GO	CYB_SANME	Cytochrome b	0.03	-	end	10 *					372
Q85DF5 UniProt NPD GO	CYB_SCALA	Cytochrome b	0.03	-	end	9 *					379
Q35886 UniProt NPD GO	CYB_SMIMU	Cytochrome b	0.03	-	end	9 *					381
Q9XP77 UniProt NPD GO	CYB_SMIOO	Cytochrome b	0.03	-	end	8 *					381
Q9TDK6 UniProt NPD GO	CYB_SOUCH	Cytochrome b	0.03	-	end	9 *					379
Q9T4P2 UniProt NPD GO	CYB_SPECI	Cytochrome b	0.03	-	end	9 *					379
Q9ZZ42 UniProt NPD GO	CYB_SQUAC	Cytochrome b	0.03	-	end	9 *					381
P24962 UniProt NPD GO	CYB_STELO	Cytochrome b	0.03	-	end	9 *					379
Q8HL81 UniProt NPD GO	CYB_SYNMA	Cytochrome b	0.03	-	end	8 *					393
O79229 UniProt NPD GO	CYB_THAIM	Cytochrome b	0.03	-	end	9 *					380
Q36012 UniProt NPD GO	CYB_THYCY	Cytochrome b	0.03	-	end	8 *					381
O03553 UniProt NPD GO	CYB_TINMA	Cytochrome b	0.03	-	end	9 *					379
Q94SJ5 UniProt NPD GO	CYB_ZENNE	Cytochrome b	0.03	-	end	9 *					380
Q94SK8 UniProt NPD GO	CYB_ZEUFA	Cytochrome b	0.03	-	end	9 *					380
Q94T42 UniProt NPD GO	CYB_ZUCRI	Cytochrome b	0.03	-	end	9 *					380
P48520 UniProt NPD GO	CYB_AKOOL	Cytochrome b (Fragment)	0.03	-	end	6 *					267
Q33452 UniProt NPD GO	CYB_EUMPE	Cytochrome b (Fragment)	0.03	-	end	4 *					176
O47558 UniProt NPD GO	CYB_LEPAL	Cytochrome b (Fragment)	0.03	-	end	5 *					234
O47555 UniProt NPD GO	CYB_LEPAR	Cytochrome b (Fragment)	0.03	-	end	5 *					234
O48350 UniProt NPD GO	CYB_LEPCO	Cytochrome b (Fragment)	0.03	-	end	5 *					234
O47556 UniProt NPD GO	CYB_LEPOT	Cytochrome b (Fragment)	0.03	-	end	5 *					234
Q36644 UniProt NPD GO	CYB_PLERA	Cytochrome b (Fragment)	0.03	-	end	3 *					176
O21804 UniProt NPD GO	CYB_SORGR	Cytochrome b (Fragment)	0.03	-	end	3 *					134
O21425 UniProt NPD GO	CYB_SORSA	Cytochrome b (Fragment)	0.03	-	end	3 *					134
Q95L74 UniProt NPD GO	CY24B_BISBI	Cytochrome b-245 heavy chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 91 kDa polypeptid ...	0.03	-	end	4 *	Membrane; multi-pass membrane protein				570
O46522 UniProt NPD GO	CY24B_BOVIN	Cytochrome b-245 heavy chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 91 kDa polypeptid ...	0.03	-	end	4 *	Membrane; multi-pass membrane protein				570
Q3V518 UniProt NPD GO	PSBE_ACOCL	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q7YJV8 UniProt NPD GO	PSBE_CALFE	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P36442 UniProt NPD GO	PSBE_MESCR	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P49473 UniProt NPD GO	PSBE_ODOSI	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q9MTK5 UniProt NPD GO	PSBE_OENHO	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.03	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q3BAM3 UniProt NPD GO	PSBE_PHAAO	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q32RX7 UniProt NPD GO	PSBE_STAPU	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
P46305 UniProt NPD GO	PSBF_CHLEU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
Q4G381 UniProt NPD GO	PSBF_EMIHU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
O78465 UniProt NPD GO	PSBF_GUITH	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42

You are viewing entries 79601 to 79650 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.