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
Q5SD42 UniProt NPD GO	PSBF_HUPLU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7HIV0 UniProt NPD GO	PSBF_HYDCA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6EYS3 UniProt NPD GO	PSBF_HYDMC	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7J1A9 UniProt NPD GO	PSBF_ILLPA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7H8J8 UniProt NPD GO	PSBF_IPOAL	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7H8K9 UniProt NPD GO	PSBF_IPOAQ	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7H8K0 UniProt NPD GO	PSBF_IPOBA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7H8L6 UniProt NPD GO	PSBF_IPOCC	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7H8I8 UniProt NPD GO	PSBF_IPOOB	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7H8L3 UniProt NPD GO	PSBF_IPOQU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7H8K7 UniProt NPD GO	PSBF_IPOSE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7H8L1 UniProt NPD GO	PSBF_IPOWR	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7J1A7 UniProt NPD GO	PSBF_LACFR	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q332W2 UniProt NPD GO	PSBF_LACSA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7HIU8 UniProt NPD GO	PSBF_LILSU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7J1A5 UniProt NPD GO	PSBF_LIRTU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q9BBR6 UniProt NPD GO	PSBF_LOTJA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q3SC83 UniProt NPD GO	PSBF_LYCES	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7HIU6 UniProt NPD GO	PSBF_MAGST	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q67HA1 UniProt NPD GO	PSBF_MAIRA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P69523 UniProt NPD GO	PSBF_MAIZE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P06853 UniProt NPD GO	PSBF_MARPO	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P69524 UniProt NPD GO	PSBF_MESCR	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q71L59 UniProt NPD GO	PSBF_METGY	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7H828 UniProt NPD GO	PSBF_MONCA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q67H97 UniProt NPD GO	PSBF_MUIMA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q67H93 UniProt NPD GO	PSBF_MUSCM	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q67H89 UniProt NPD GO	PSBF_NAREL	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6EYS0 UniProt NPD GO	PSBF_NELLU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q9TKY2 UniProt NPD GO	PSBF_NEPOL	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				41
Q2UVD8 UniProt NPD GO	PSBF_NICGU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7HML6 UniProt NPD GO	PSBF_NICSY	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7HML5 UniProt NPD GO	PSBF_NICTO	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6EW37 UniProt NPD GO	PSBF_NYMAL	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q7IW40 UniProt NPD GO	PSBF_NYMOD	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P62097 UniProt NPD GO	PSBF_OENBE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P62098 UniProt NPD GO	PSBF_OENHO	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6ENF7 UniProt NPD GO	PSBF_ORYNI	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P69522 UniProt NPD GO	PSBF_ORYSA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q68RZ0 UniProt NPD GO	PSBF_PANGI	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P62096 UniProt NPD GO	PSBF_PEA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q3BAM4 UniProt NPD GO	PSBF_PHAAO	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q67HD7 UniProt NPD GO	PSBF_PHOTN	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6EYR0 UniProt NPD GO	PSBF_PHYAM	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6YXL8 UniProt NPD GO	PSBF_PHYPA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q85X32 UniProt NPD GO	PSBF_PINKO	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P41616 UniProt NPD GO	PSBF_PINTH	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
P62099 UniProt NPD GO	PSBF_POPDE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q8WI05 UniProt NPD GO	PSBF_PSINU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6L384 UniProt NPD GO	PSBF_SACHY	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39

You are viewing entries 87701 to 87750 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.