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
P48422 UniProt NPD GO	C86A1_ARATH	Cytochrome P450 86A1 (EC 1.14.-.-) (CYPLXXXVI) (P450-dependent fatty acid omega-hydroxylase)	0.04	-	mit	1 *					513
Q9MLL5 UniProt NPD GO	CYB_ACAAN	Cytochrome b	0.04	-	end	8 *					372
P29663 UniProt NPD GO	CYB_AMICA	Cytochrome b	0.04	-	end	9 *					379
Q8HLR2 UniProt NPD GO	CYB_ANOCO	Cytochrome b	0.04	-	end	9 *					384
Q85IN5 UniProt NPD GO	CYB_ARCCL	Cytochrome b	0.04	-	end	9 *					379
Q9MLL4 UniProt NPD GO	CYB_ASPMU	Cytochrome b	0.04	-	end	9 *					372
Q9MLK0 UniProt NPD GO	CYB_ASPSC	Cytochrome b	0.04	-	end	8 *					372
Q33818 UniProt NPD GO	CYB_ASTPE	Cytochrome b	0.04	-	end	9 *					379
Q539Z1 UniProt NPD GO	CYB_CHECR	Cytochrome b	0.04	-	end	9 *					379
Q34169 UniProt NPD GO	CYB_CHEMA	Cytochrome b	0.04	-	end	9 *					379
Q5VJ55 UniProt NPD GO	CYB_CHEME	Cytochrome b	0.04	-	end	9 *					379
Q9TEC1 UniProt NPD GO	CYB_CHEMY	Cytochrome b	0.04	-	end	9 *					381
O47885 UniProt NPD GO	CYB_ELEMA	Cytochrome b	0.04	-	end	9 *					378
Q8SJL2 UniProt NPD GO	CYB_EMYOR	Cytochrome b	0.04	-	end	9 *					379
O48047 UniProt NPD GO	CYB_EPIEX	Cytochrome b	0.04	-	end	10 *					370
O48049 UniProt NPD GO	CYB_EPIFO	Cytochrome b	0.04	-	end	10 *					370
O48060 UniProt NPD GO	CYB_EPISF	Cytochrome b	0.04	-	end	10 *					370
O48055 UniProt NPD GO	CYB_EPISM	Cytochrome b	0.04	-	end	10 *					370
O48057 UniProt NPD GO	CYB_EPISS	Cytochrome b	0.04	-	end	10 *					370
O48053 UniProt NPD GO	CYB_EPIST	Cytochrome b	0.04	-	end	10 *					370
O48062 UniProt NPD GO	CYB_EPISU	Cytochrome b	0.04	-	end	10 *					370
O48066 UniProt NPD GO	CYB_ERYCC	Cytochrome b	0.04	-	end	10 *					371
O48067 UniProt NPD GO	CYB_ERYCL	Cytochrome b	0.04	-	end	10 *					371
O99800 UniProt NPD GO	CYB_EULRU	Cytochrome b	0.04	-	end	9 *					379
O48063 UniProt NPD GO	CYB_EUNMU	Cytochrome b	0.04	-	end	10 *					370
O21163 UniProt NPD GO	CYB_FALFE	Cytochrome b	0.04	-	end	9 *					380
Q9XKC0 UniProt NPD GO	CYB_GALLA	Cytochrome b	0.04	-	end	9 *					380
Q9ZZT5 UniProt NPD GO	CYB_GRAMU	Cytochrome b	0.04	-	end	9 *					379
Q34683 UniProt NPD GO	CYB_GRUVI	Cytochrome b	0.04	-	end	9 *					380
O79520 UniProt NPD GO	CYB_HARDI	Cytochrome b	0.04	-	end	9 *					380
Q9B9F6 UniProt NPD GO	CYB_HEMDE	Cytochrome b	0.04	-	end	9 *					379
Q9MLJ5 UniProt NPD GO	CYB_HOMLA	Cytochrome b	0.04	-	end	11 *					371
Q04910 UniProt NPD GO	CYB_HYSAF	Cytochrome b	0.04	-	end	9 *					384
Q5VJ49 UniProt NPD GO	CYB_LEPDO	Cytochrome b	0.04	-	end	9 *					379
O48093 UniProt NPD GO	CYB_LIAMA	Cytochrome b	0.04	-	end	10 *					371
O48098 UniProt NPD GO	CYB_LIAPA	Cytochrome b	0.04	-	end	10 *					371
Q34889 UniProt NPD GO	CYB_LOPGA	Cytochrome b	0.04	-	end	9 *					380
P24958 UniProt NPD GO	CYB_LOXAF	Cytochrome b	0.04	-	end	9 *					378
Q35000 UniProt NPD GO	CYB_MESHI	Cytochrome b	0.04	-	end	9 *					379
Q9G273 UniProt NPD GO	CYB_MICBE	Cytochrome b	0.04	-	end	9 *					379
Q9MLI9 UniProt NPD GO	CYB_MICFL	Cytochrome b	0.04	-	end	8 *					371
O48101 UniProt NPD GO	CYB_MICFM	Cytochrome b	0.04	-	end	8 *					371
Q9MLK2 UniProt NPD GO	CYB_MICIK	Cytochrome b	0.04	-	end	8 *					370
O48102 UniProt NPD GO	CYB_MORAE	Cytochrome b	0.04	-	end	10 *					371
Q9MLJ3 UniProt NPD GO	CYB_NAJKA	Cytochrome b	0.04	-	end	8 *					372
Q8LZ88 UniProt NPD GO	CYB_NANAN	Cytochrome b	0.04	-	end	9 *					378
Q8HLB9 UniProt NPD GO	CYB_NEORH	Cytochrome b	0.04	-	end	9 *					380
Q9MLJ1 UniProt NPD GO	CYB_PARMU	Cytochrome b	0.04	-	end	8 *					372
O20645 UniProt NPD GO	CYB_PAVMU	Cytochrome b	0.04	-	end	9 *					380
Q9TDN2 UniProt NPD GO	CYB_PHOSS	Cytochrome b	0.04	-	end	9 *					379

You are viewing entries 76651 to 76700 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.