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
O21764 UniProt NPD GO	CYB_CTECO	Cytochrome b	0.03	-	end	9 *					379
P24951 UniProt NPD GO	CYB_CYPCA	Cytochrome b	0.03	-	end	9 *					381
O99655 UniProt NPD GO	CYB_CYRMO	Cytochrome b	0.03	-	end	9 *					380
Q9TDK4 UniProt NPD GO	CYB_DELCA	Cytochrome b	0.03	-	end	9 *					379
Q9T4B2 UniProt NPD GO	CYB_DELDE	Cytochrome b	0.03	-	end	9 *					379
O79558 UniProt NPD GO	CYB_DINSE	Cytochrome b	0.03	-	end	8 *					372
Q9G964 UniProt NPD GO	CYB_ELAVU	Cytochrome b	0.03	-	end	9 *					372
Q37006 UniProt NPD GO	CYB_ENHLU	Cytochrome b	0.03	-	end	9 *					379
O48052 UniProt NPD GO	CYB_EPIMO	Cytochrome b	0.03	-	end	10 *					371
O48073 UniProt NPD GO	CYB_ERYEL	Cytochrome b	0.03	-	end	10 *					371
O48079 UniProt NPD GO	CYB_ERYMI	Cytochrome b	0.03	-	end	10 *					371
O48080 UniProt NPD GO	CYB_ERYMN	Cytochrome b	0.03	-	end	10 *					371
O48085 UniProt NPD GO	CYB_ERYTA	Cytochrome b	0.03	-	end	8 *					371
Q34459 UniProt NPD GO	CYB_EULFC	Cytochrome b	0.03	-	end	9 *					379
O99798 UniProt NPD GO	CYB_EULMF	Cytochrome b	0.03	-	end	9 *					379
O99797 UniProt NPD GO	CYB_EULMM	Cytochrome b	0.03	-	end	9 *					379
O21166 UniProt NPD GO	CYB_FALPE	Cytochrome b	0.03	-	end	9 *					380
O48087 UniProt NPD GO	CYB_FARAB	Cytochrome b	0.03	-	end	8 *					371
Q9TDN1 UniProt NPD GO	CYB_FERAT	Cytochrome b	0.03	-	end	9 *					379
Q37080 UniProt NPD GO	CYB_GADMO	Cytochrome b	0.03	-	end	9 *					380
P34868 UniProt NPD GO	CYB_GALCU	Cytochrome b	0.03	-	end	9 *					381
Q9BA02 UniProt NPD GO	CYB_GONGR	Cytochrome b	0.03	-	end	9 *					382
Q34724 UniProt NPD GO	CYB_HAPGR	Cytochrome b	0.03	-	end	9 *					379
Q9MLK7 UniProt NPD GO	CYB_HEMHA	Cytochrome b	0.03	-	end	8 *					372
Q9MLI8 UniProt NPD GO	CYB_HETSI	Cytochrome b	0.03	-	end	10 *					372
Q9G7U1 UniProt NPD GO	CYB_INIGE	Cytochrome b	0.03	-	end	9 *					379
Q9TDL6 UniProt NPD GO	CYB_LAGAU	Cytochrome b	0.03	-	end	9 *					379
Q9TDL7 UniProt NPD GO	CYB_LAGCR	Cytochrome b	0.03	-	end	9 *					379
Q9TDL9 UniProt NPD GO	CYB_LAGOB	Cytochrome b	0.03	-	end	9 *					379
Q9TA00 UniProt NPD GO	CYB_LAMFL	Cytochrome b	0.03	-	end	9 *					396
Q34876 UniProt NPD GO	CYB_LEMCA	Cytochrome b	0.03	-	end	9 *					379
Q5VJ50 UniProt NPD GO	CYB_LEPRU	Cytochrome b	0.03	-	end	9 *					379
P29664 UniProt NPD GO	CYB_LEPSP	Cytochrome b	0.03	-	end	9 *					380
Q9TDM1 UniProt NPD GO	CYB_LISBO	Cytochrome b	0.03	-	end	9 *					379
Q9TDM0 UniProt NPD GO	CYB_LISPE	Cytochrome b	0.03	-	end	9 *					379
Q34900 UniProt NPD GO	CYB_LUTLU	Cytochrome b	0.03	-	end	9 *					379
Q9MLK5 UniProt NPD GO	CYB_MICEU	Cytochrome b	0.03	-	end	8 *					371
Q9MI35 UniProt NPD GO	CYB_MICFO	Cytochrome b	0.03	-	end	9 *					380
Q3YLA8 UniProt NPD GO	CYB_MICLH	Cytochrome b	0.03	-	end	9 *					379
P56731 UniProt NPD GO	CYB_MICLO	Cytochrome b	0.03	-	end	9 *					380
Q9MI32 UniProt NPD GO	CYB_MICME	Cytochrome b	0.03	-	end	9 *					380
Q9T7M0 UniProt NPD GO	CYB_MICOE	Cytochrome b	0.03	-	end	9 *					380
Q9G1Z0 UniProt NPD GO	CYB_MICRF	Cytochrome b	0.03	-	end	9 *					379
Q34972 UniProt NPD GO	CYB_MIRCO	Cytochrome b	0.03	-	end	9 *					379
P92657 UniProt NPD GO	CYB_MONMO	Cytochrome b	0.03	-	end	9 *					379
O79512 UniProt NPD GO	CYB_MYCAM	Cytochrome b	0.03	-	end	9 *					380
O20603 UniProt NPD GO	CYB_MYOWA	Cytochrome b	0.03	-	end	9 *					381
Q9B7V7 UniProt NPD GO	CYB_NEOPH	Cytochrome b	0.03	-	end	9 *					379
Q35160 UniProt NPD GO	CYB_NUMME	Cytochrome b	0.03	-	end	9 *					380
Q678S8 UniProt NPD GO	CYB_OMMRO	Cytochrome b	0.03	-	end	9 *					379

You are viewing entries 79551 to 79600 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.