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
Q678S9 UniProt NPD GO	CYB_LOBCR	Cytochrome b	0.02	-	end	9 *					379
Q34952 UniProt NPD GO	CYB_LORTA	Cytochrome b	0.02	-	end	9 *					379
O48100 UniProt NPD GO	CYB_LOXBI	Cytochrome b	0.02	-	end	10 *					371
Q34945 UniProt NPD GO	CYB_LUMTE	Cytochrome b	0.02	-	end	9 *					379
O03473 UniProt NPD GO	CYB_MACGI	Cytochrome b	0.02	-	end	9 *					381
O03474 UniProt NPD GO	CYB_MACRU	Cytochrome b	0.02	-	end	9 *					381
Q9TEB4 UniProt NPD GO	CYB_MARFA	Cytochrome b	0.02	-	end	9 *					379
Q8WGL0 UniProt NPD GO	CYB_MELME	Cytochrome b	0.02	-	end	9 *					379
Q36922 UniProt NPD GO	CYB_MICAR	Cytochrome b	0.02	-	end	9 *					380
Q35019 UniProt NPD GO	CYB_MIRLE	Cytochrome b	0.02	-	end	9 *					379
Q678S3 UniProt NPD GO	CYB_MONMN	Cytochrome b	0.02	-	end	9 *					379
Q35078 UniProt NPD GO	CYB_MURRO	Cytochrome b	0.02	-	end	9 *					381
P92651 UniProt NPD GO	CYB_MUSAV	Cytochrome b	0.02	-	end	9 *					379
Q957A4 UniProt NPD GO	CYB_MYOMO	Cytochrome b	0.02	-	end	9 *					379
Q9G2W6 UniProt NPD GO	CYB_MYXGL	Cytochrome b	0.02	-	end	8 *					385
P34872 UniProt NPD GO	CYB_NEGBR	Cytochrome b	0.02	-	end	9 *					381
Q35172 UniProt NPD GO	CYB_NINRI	Cytochrome b	0.02	-	end	9 *					381
O20435 UniProt NPD GO	CYB_NINTI	Cytochrome b	0.02	-	end	9 *					381
Q35196 UniProt NPD GO	CYB_NINYV	Cytochrome b	0.02	-	end	9 *					381
O03538 UniProt NPD GO	CYB_NOTPE	Cytochrome b	0.02	-	end	9 *					381
O03478 UniProt NPD GO	CYB_NOTTY	Cytochrome b	0.02	-	end	9 *					381
Q9TDM3 UniProt NPD GO	CYB_ORCBR	Cytochrome b	0.02	-	end	9 *					379
Q94SA4 UniProt NPD GO	CYB_PAGMA	Cytochrome b	0.02	-	end	9 *					380
Q9G250 UniProt NPD GO	CYB_PANBA	Cytochrome b	0.02	-	end	8 *					372
Q35380 UniProt NPD GO	CYB_PARBI	Cytochrome b	0.02	-	end	9 *					381
O79219 UniProt NPD GO	CYB_PELGE	Cytochrome b	0.02	-	end	9 *					380
O79220 UniProt NPD GO	CYB_PELMG	Cytochrome b	0.02	-	end	9 *					380
O79221 UniProt NPD GO	CYB_PELUR	Cytochrome b	0.02	-	end	9 *					380
Q94T21 UniProt NPD GO	CYB_PERTA	Cytochrome b	0.02	-	end	9 *					380
Q35534 UniProt NPD GO	CYB_PETMA	Cytochrome b	0.02	-	end	9 *					396
Q35409 UniProt NPD GO	CYB_PHACL	Cytochrome b	0.02	-	end	9 *					381
Q35673 UniProt NPD GO	CYB_PHATA	Cytochrome b	0.02	-	end	9 *					381
O03811 UniProt NPD GO	CYB_PHOPH	Cytochrome b	0.02	-	end	9 *					379
P48877 UniProt NPD GO	CYB_PICCA	Cytochrome b	0.02	-	end	10 *					386
Q36507 UniProt NPD GO	CYB_PICPJ	Cytochrome b	0.02	-	end	10 *					386
O99253 UniProt NPD GO	CYB_PLABE	Cytochrome b	0.02	-	end	10 *					376
Q35459 UniProt NPD GO	CYB_PLAGI	Cytochrome b	0.02	-	end	9 *					381
Q35533 UniProt NPD GO	CYB_PLAMS	Cytochrome b	0.02	-	end	9 *					381
Q35532 UniProt NPD GO	CYB_PLAMU	Cytochrome b	0.02	-	end	9 *					381
Q35675 UniProt NPD GO	CYB_PLATE	Cytochrome b	0.02	-	end	9 *					381
Q95920 UniProt NPD GO	CYB_POLOR	Cytochrome b	0.02	-	end	9 *					380
Q9MG84 UniProt NPD GO	CYB_PONBL	Cytochrome b	0.02	-	end	9 *					379
P34873 UniProt NPD GO	CYB_PRIGL	Cytochrome b	0.02	-	end	9 *					381
Q9G2U4 UniProt NPD GO	CYB_PROCU	Cytochrome b	0.02	-	end	9 *					379
Q9ZY49 UniProt NPD GO	CYB_PSECU	Cytochrome b	0.02	-	end	9 *					379
O03543 UniProt NPD GO	CYB_PSEMD	Cytochrome b	0.02	-	end	9 *					381
Q35553 UniProt NPD GO	CYB_PSENI	Cytochrome b	0.02	-	end	8 *					381
Q35695 UniProt NPD GO	CYB_PSEWO	Cytochrome b	0.02	-	end	9 *					381
Q5UVI5 UniProt NPD GO	CYB_PUDPU	Cytochrome b	0.02	-	end	9 *					379
O48106 UniProt NPD GO	CYB_PYTMO	Cytochrome b	0.02	-	end	10 *					371

You are viewing entries 83001 to 83050 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.