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
P34191 UniProt NPD GO	ATP6_CROLA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.00	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P24946 UniProt NPD GO	ATP6_CYPCA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.00	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P26853 UniProt NPD GO	ATP6_MARPO	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.00	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				252
O47494 UniProt NPD GO	ATP6_METSE	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.00	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P05500 UniProt NPD GO	ATP6_OENBE	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.00	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				281
Q37601 UniProt NPD GO	ATP6_PYLLI	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.00	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				248
Q31721 UniProt NPD GO	ATP6_BRATO	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6) (Fragment)	0.00	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				58
Q8HEC5 UniProt NPD GO	ATP6_CAEBR	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6) (Fragment)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				86
Q85Q99 UniProt NPD GO	ATP6_CANGA	ATP synthase a chain precursor (EC 3.6.3.14) (ATPase protein 6) (ATP synthase subunit 6)	0.00	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				260
Q6DN61 UniProt NPD GO	ATP6_KLULA	ATP synthase a chain precursor (EC 3.6.3.14) (ATPase protein 6) (ATP synthase subunit 6)	0.00	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				256
P92547 UniProt NPD GO	ATP62_ARATH	ATP synthase a chain precursor 2 (EC 3.6.3.14) (ATPase protein 6) (P6-2)	0.00	-	end	7	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				349
P17604 UniProt NPD GO	ATPO_PEA	ATP synthase delta chain, mitochondrial (EC 3.6.3.14) (Oligomycin sensitivity conferral protein) (OS ...	0.00	-	cyt	1 *	Mitochondrion				38
P80085 UniProt NPD GO	ATP4_SPIOL	ATP synthase delta' chain, mitochondrial (EC 3.6.3.14) (Fragment)	0.00	-		0	Mitochondrion				20
P07891 UniProt NPD GO	ATPE_CHLRE	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				140
P48083 UniProt NPD GO	ATPE_CYAPA	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.00	-	cyt	0	Plastid; cyanelle; cyanelle thylakoid membrane; peripheral membrane protein (By similarity)				132
P26534 UniProt NPD GO	ATPE_PYLLI	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				132
Q41898 UniProt NPD GO	ATP5E_MAIZE	ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14)	0.00	-	nuc	0	Mitochondrion				70
Q28851 UniProt NPD GO	ATPK_BOVIN	ATP synthase f chain, mitochondrial (EC 3.6.3.14)	0.00	-	cyt	1					87
Q95339 UniProt NPD GO	ATPK_PIG	ATP synthase f chain, mitochondrial (EC 3.6.3.14)	0.00	-	cyt	1					87
P17345 UniProt NPD GO	ATP8_CANPA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.00	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				48
P21536 UniProt NPD GO	ATP8_SCHPO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.00	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				48
Q37377 UniProt NPD GO	ATP9_ACACA	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				79
P60112 UniProt NPD GO	ATP9_ARATH	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	cyt	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
P14571 UniProt NPD GO	ATP9_BETVU	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	nuc	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				88
P60113 UniProt NPD GO	ATP9_BRANA	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	cyt	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
P48880 UniProt NPD GO	ATP9_CHOCR	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				76
Q37315 UniProt NPD GO	ATP9_DICDI	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				88
P17254 UniProt NPD GO	ATP9_HELAN	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	nuc	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				83
P92811 UniProt NPD GO	ATP9_KLULA	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				76
P60117 UniProt NPD GO	ATP9_LYCES	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	cyt	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
P00840 UniProt NPD GO	ATP9_MAIZE	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
Q37550 UniProt NPD GO	ATP9_MALDO	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	nuc	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				82
P26855 UniProt NPD GO	ATP9_MARPO	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
P60115 UniProt NPD GO	ATP9_OENBI	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	cyt	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
P14863 UniProt NPD GO	ATP9_ORYSA	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
P16001 UniProt NPD GO	ATP9_PARTE	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	exc	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				75
P69420 UniProt NPD GO	ATP9_PEA	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	mit	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
P60118 UniProt NPD GO	ATP9_PETHY	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	cyt	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
Q07060 UniProt NPD GO	ATP9_PETSP	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	cyt	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				77
P48881 UniProt NPD GO	ATP9_PICCA	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				76
P61828 UniProt NPD GO	ATP9_SACDO	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				76
P21537 UniProt NPD GO	ATP9_SCHPO	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
P60114 UniProt NPD GO	ATP9_SOLTU	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	cyt	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
P69421 UniProt NPD GO	ATP9_SOYBN	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	mit	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
P60116 UniProt NPD GO	ATP9_TOBAC	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	cyt	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
Q01554 UniProt NPD GO	ATP9_TRIRU	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
P69422 UniProt NPD GO	ATP9_VICFA	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	mit	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
P13547 UniProt NPD GO	ATP9_WHEAT	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				74
Q36852 UniProt NPD GO	ATP9_WILMR	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				76
Q37695 UniProt NPD GO	ATP9_YARLI	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				76

You are viewing entries 92351 to 92400 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.