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
Q85X07 UniProt NPD GO	CYB6_PINKO	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P41628 UniProt NPD GO	CYB6_PINTH	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P51341 UniProt NPD GO	CYB6_PORPU	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q8WHZ3 UniProt NPD GO	CYB6_PSINU	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q6ENT4 UniProt NPD GO	CYB6_SACOF	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
O96801 UniProt NPD GO	CYB6_SKECO	Cytochrome b6	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q71KP4 UniProt NPD GO	CYB6_SPIMX	Cytochrome b6	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P00165 UniProt NPD GO	CYB6_SPIOL	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P06247 UniProt NPD GO	CYB6_TOBAC	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P60162 UniProt NPD GO	CYB6_WHEAT	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
O47043 UniProt NPD GO	CYB6_PICAB	Cytochrome b6 (Fragment)	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				204
P08980 UniProt NPD GO	UCRIA_SPIOL	Cytochrome b6-f complex iron-sulfur subunit, chloroplast precursor (EC 1.10.99.1) (Rieske iron-sulfu ...	0.00	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein. The transmembran ...			1RFS	230
Q3V503 UniProt NPD GO	PETD_ACOCL	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q85FJ2 UniProt NPD GO	PETD_ADICA	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				159
Q70XX7 UniProt NPD GO	PETD_AMBTC	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q9MTQ3 UniProt NPD GO	PETD_AMPOP	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				157
Q85AY5 UniProt NPD GO	PETD_ANTFO	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
P56774 UniProt NPD GO	PETD_ARATH	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q7FNS2 UniProt NPD GO	PETD_ATRBE	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q7YJU7 UniProt NPD GO	PETD_CALFE	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				167
Q8M9Z5 UniProt NPD GO	PETD_CHAGL	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
P11093 UniProt NPD GO	PETD_CHLEU	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
P13348 UniProt NPD GO	PETD_CHLPR	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
P23230 UniProt NPD GO	PETD_CHLRE	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein			1Q90	160
P56322 UniProt NPD GO	PETD_CHLVU	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q71KQ5 UniProt NPD GO	PETD_COLOB	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q4VZK4 UniProt NPD GO	PETD_CUCSA	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q9TLZ8 UniProt NPD GO	PETD_CYACA	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				161
Q85G15 UniProt NPD GO	PETD_CYAME	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
P48122 UniProt NPD GO	PETD_CYAPA	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; cyanelle; cyanelle thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q4G3F7 UniProt NPD GO	PETD_EMIHU	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q49KW7 UniProt NPD GO	PETD_EUCGG	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q6B904 UniProt NPD GO	PETD_GRATL	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
O78415 UniProt NPD GO	PETD_GUITH	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q5SD24 UniProt NPD GO	PETD_HUPLU	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q332U6 UniProt NPD GO	PETD_LACSA	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q9BBQ5 UniProt NPD GO	PETD_LOTJA	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
P05643 UniProt NPD GO	PETD_MAIZE	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
P06250 UniProt NPD GO	PETD_MARPO	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q9MUV2 UniProt NPD GO	PETD_MESVI	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q9TL32 UniProt NPD GO	PETD_NEPOL	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q3C1M4 UniProt NPD GO	PETD_NICSY	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q33C01 UniProt NPD GO	PETD_NICTO	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q6EW21 UniProt NPD GO	PETD_NYMAL	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				170
P49489 UniProt NPD GO	PETD_ODOSI	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q9MTJ4 UniProt NPD GO	PETD_OENHO	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q6ENE3 UniProt NPD GO	PETD_ORYNI	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
P12118 UniProt NPD GO	PETD_ORYSA	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
Q68RX6 UniProt NPD GO	PETD_PANGI	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160
P06527 UniProt NPD GO	PETD_PEA	Cytochrome b6-f complex subunit 4 (17 kDa polypeptide)	0.00	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				160

You are viewing entries 93901 to 93950 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.