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
Q9MTK6 UniProt NPD GO	PSBL_OENHO	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q6YXL7 UniProt NPD GO	PSBL_PHYPA	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P41617 UniProt NPD GO	PSBL_PINTH	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				38
P51389 UniProt NPD GO	PSBL_PORPU	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60152 UniProt NPD GO	PSBL_PSINU	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P60136 UniProt NPD GO	PSBL_SAUCE	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q67HD2 UniProt NPD GO	PSBL_SISMO	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q67HJ6 UniProt NPD GO	PSBL_TYPAN	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q6YLT3 UniProt NPD GO	PSBL_WELMI	Photosystem II reaction center L protein (PSII-L) (PSII 5 kDa protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q70Y09 UniProt NPD GO	PSBM_AMBTC	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q85BK0 UniProt NPD GO	PSBM_ANTFO	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q7YNV4 UniProt NPD GO	PSBM_ARAEL	Photosystem II reaction center M protein (PSII-M)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P62109 UniProt NPD GO	PSBM_ARATH	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q7FNT0 UniProt NPD GO	PSBM_ATRBE	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q7HKX9 UniProt NPD GO	PSBM_CALFE	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q8MA15 UniProt NPD GO	PSBM_CHAGL	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
P92277 UniProt NPD GO	PSBM_CHLRE	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q5SCY3 UniProt NPD GO	PSBM_HUPLU	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q56P14 UniProt NPD GO	PSBM_LACSA	Photosystem II reaction center M protein (PSII-M)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
P69528 UniProt NPD GO	PSBM_LOTJA	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
P48189 UniProt NPD GO	PSBM_MAIZE	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
P12168 UniProt NPD GO	PSBM_MARPO	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q9MUQ7 UniProt NPD GO	PSBM_MESVI	Photosystem II reaction center M protein (PSII-M)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q9TL37 UniProt NPD GO	PSBM_NEPOL	Photosystem II reaction center M protein (PSII-M)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q6EW54 UniProt NPD GO	PSBM_NYMAL	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q9MTM8 UniProt NPD GO	PSBM_OENHO	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q6ENI6 UniProt NPD GO	PSBM_ORYNI	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
P62110 UniProt NPD GO	PSBM_ORYSA	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q7YNW2 UniProt NPD GO	PSBM_PANGI	Photosystem II reaction center M protein (PSII-M)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q7Y7G0 UniProt NPD GO	PSBM_PANQU	Photosystem II reaction center M protein (PSII-M)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P69529 UniProt NPD GO	PSBM_PEA	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q672I5 UniProt NPD GO	PSBM_PENAM	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q6YXR8 UniProt NPD GO	PSBM_PHYPA	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q85X47 UniProt NPD GO	PSBM_PINKO	Photosystem II reaction center M protein (PSII-M)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
P41608 UniProt NPD GO	PSBM_PINTH	Photosystem II reaction center M protein (PSII-M)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
Q5IBK3 UniProt NPD GO	PSBM_PLALA	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q8WI22 UniProt NPD GO	PSBM_PSINU	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q6L3A9 UniProt NPD GO	PSBM_SACHY	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q6ENX5 UniProt NPD GO	PSBM_SACOF	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
P62112 UniProt NPD GO	PSBM_SPIOL	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
P62111 UniProt NPD GO	PSBM_TOBAC	Photosystem II reaction center M protein (PSII-M)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q9XPS6 UniProt NPD GO	PSBM_WHEAT	Photosystem II reaction center M protein (PSII-M)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q7J199 UniProt NPD GO	PSBN_ACOCL	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7GZA7 UniProt NPD GO	PSBN_ALLOC	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q67HV8 UniProt NPD GO	PSBN_ALLTE	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q9G2I2 UniProt NPD GO	PSBN_AMBTC	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q67I70 UniProt NPD GO	PSBN_ANACO	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q85BG2 UniProt NPD GO	PSBN_ANTFO	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P62113 UniProt NPD GO	PSBN_ARATH	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EYL4 UniProt NPD GO	PSBN_ARIMA	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43

You are viewing entries 96651 to 96700 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.