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
P28251 UniProt NPD GO	PSAI_ANGLY	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P56768 UniProt NPD GO	PSAI_ARATH	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
Q7FNS8 UniProt NPD GO	PSAI_ATRBE	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q31909 UniProt NPD GO	PSAI_BRAOL	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q7YJW3 UniProt NPD GO	PSAI_CALFE	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q6QBN9 UniProt NPD GO	PSAI_CASSA	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
P58214 UniProt NPD GO	PSAI_CHLVU	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q6B8K8 UniProt NPD GO	PSAI_GRATL	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q5SCW1 UniProt NPD GO	PSAI_HUPLU	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P12185 UniProt NPD GO	PSAI_MARPO	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q6EW69 UniProt NPD GO	PSAI_NYMAL	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P49484 UniProt NPD GO	PSAI_ODOSI	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P17227 UniProt NPD GO	PSAI_PEA	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
Q8WI10 UniProt NPD GO	PSAI_PSINU	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
O96813 UniProt NPD GO	PSAI_SKECO	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P49159 UniProt NPD GO	PSAI_SOYBN	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
P12187 UniProt NPD GO	PSAI_TOBAC	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
O78469 UniProt NPD GO	PSAL_GUITH	Photosystem I reaction center subunit XI (PSI-L) (PSI subunit V)	0.01	-	mit	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				152
Q5ENP6 UniProt NPD GO	PSAL_ISOGA	Photosystem I reaction center subunit XI (PSI-L) (PSI subunit V)	0.01	-	mit	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				147
P51222 UniProt NPD GO	PSAL_PORPU	Photosystem I reaction center subunit XI (PSI-L) (PSI subunit V)	0.01	-	end	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				153
P23993 UniProt NPD GO	PSAL_HORVU	Photosystem I reaction center subunit XI, chloroplast precursor (PSI-L) (PSI subunit V)	0.01	-	mit	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				209
P31479 UniProt NPD GO	PSAM_EUGGR	Photosystem I reaction center subunit XII (PSI-M)	0.01	-	nuc	1 *	Plastid; chloroplast				31
P17226 UniProt NPD GO	PSAK_PEA	Photosystem I reaction center subunit psaK, chloroplast (Photosystem I subunit X) (PSI-K) (Light-har ...	0.01	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				20
Q40070 UniProt NPD GO	PSBR_HORVU	Photosystem II 10 kDa polypeptide, chloroplast precursor	0.01	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				138
P10690 UniProt NPD GO	PSBR_SPIOL	Photosystem II 10 kDa polypeptide, chloroplast precursor	0.01	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				140
P54773 UniProt NPD GO	PSBS_LYCES	Photosystem II 22 kDa protein, chloroplast precursor (CP22)	0.01	-	end	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				276
Q9SMB4 UniProt NPD GO	PSBS_TOBAC	Photosystem II 22 kDa protein, chloroplast precursor (CP22)	0.01	-	end	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				274
P48187 UniProt NPD GO	PSBC_MAIZE	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
Q85FM2 UniProt NPD GO	PSBD_ADICA	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q85AC9 UniProt NPD GO	PSBD_ANTFO	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P31557 UniProt NPD GO	PSBD_EUGGR	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
O78427 UniProt NPD GO	PSBD_GUITH	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				351
P06404 UniProt NPD GO	PSBD_MARPO	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q85FJ7 UniProt NPD GO	PSBB_ADICA	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.01	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
P37255 UniProt NPD GO	PSBB_CHLRE	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
Q9MUV7 UniProt NPD GO	PSBB_MESVI	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
Q9TKW4 UniProt NPD GO	PSBB_NEPOL	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
Q6B935 UniProt NPD GO	PSBY_GRATL	Photosystem II protein Y	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q9BAC7 UniProt NPD GO	PSBY_FUCVE	Photosystem II protein Y (Fragment)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				27
Q8M9Z3 UniProt NPD GO	PSBH_CHAGL	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				73
P31555 UniProt NPD GO	PSBH_EUGGR	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				70
Q71KN4 UniProt NPD GO	PSBH_KLEBI	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				78
P69552 UniProt NPD GO	PSBH_OENAR	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
P69553 UniProt NPD GO	PSBH_OENHO	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
Q6ENE5 UniProt NPD GO	PSBH_ORYNI	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
P09449 UniProt NPD GO	PSBH_ORYSA	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
Q68RX8 UniProt NPD GO	PSBH_PANGI	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
P05146 UniProt NPD GO	PSBH_SPIOL	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				72
Q70Y13 UniProt NPD GO	PSBI_AMBTC	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P59762 UniProt NPD GO	PSBI_ATRBE	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36

You are viewing entries 90401 to 90450 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.