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
Q9T469 UniProt NPD GO	CYB_SPEBE	Cytochrome b	0.00	-	end	9 *					379
Q9TF57 UniProt NPD GO	CYB_SPEFR	Cytochrome b	0.00	-	end	9 *					379
Q9TF55 UniProt NPD GO	CYB_SPEPA	Cytochrome b	0.00	-	end	9 *					379
P49341 UniProt NPD GO	CYB_SPERI	Cytochrome b	0.00	-	end	9 *					379
O79274 UniProt NPD GO	CYB_SPHVA	Cytochrome b	0.00	-	end	9 *					380
Q950S3 UniProt NPD GO	CYB_SPIPN	Cytochrome b	0.00	-	end	9 *					396
Q9T3Q2 UniProt NPD GO	CYB_STEPA	Cytochrome b	0.00	-	end	9 *					380
P15547 UniProt NPD GO	CYB_STRPU	Cytochrome b	0.00	-	end	9 *					380
Q36551 UniProt NPD GO	CYB_STRTC	Cytochrome b	0.00	-	end	8 *					389
Q35873 UniProt NPD GO	CYB_STULI	Cytochrome b	0.00	-	end	9 *					379
Q6ELV8 UniProt NPD GO	CYB_SYLAQ	Cytochrome b	0.00	-	end	9 *					379
Q6ELW2 UniProt NPD GO	CYB_SYLAU	Cytochrome b	0.00	-	end	9 *					379
O47415 UniProt NPD GO	CYB_SYLFL	Cytochrome b	0.00	-	end	9 *					379
Q9B5Q1 UniProt NPD GO	CYB_SYLGR	Cytochrome b	0.00	-	end	9 *					379
Q6ELW1 UniProt NPD GO	CYB_SYLNU	Cytochrome b	0.00	-	end	8					379
Q6ELV9 UniProt NPD GO	CYB_SYLOB	Cytochrome b	0.00	-	end	9 *					379
Q6ELV7 UniProt NPD GO	CYB_SYLPA	Cytochrome b	0.00	-	end	9 *					379
Q9MQY5 UniProt NPD GO	CYB_TALAL	Cytochrome b	0.00	-	end	9 *					379
Q9MQY6 UniProt NPD GO	CYB_TALEU	Cytochrome b	0.00	-	end	9 *					379
Q94Y66 UniProt NPD GO	CYB_TAMDR	Cytochrome b	0.00	-	end	9 *					379
Q94Y62 UniProt NPD GO	CYB_TAMMI	Cytochrome b	0.00	-	end	9 *					379
Q94Y56 UniProt NPD GO	CYB_TAMOB	Cytochrome b	0.00	-	end	9 *					379
Q94Q38 UniProt NPD GO	CYB_TAMQU	Cytochrome b	0.00	-	end	9 *					379
Q94Y51 UniProt NPD GO	CYB_TAMRU	Cytochrome b	0.00	-	end	9 *					379
Q94Y47 UniProt NPD GO	CYB_TAMSE	Cytochrome b	0.00	-	end	9 *					379
O99343 UniProt NPD GO	CYB_TAUDE	Cytochrome b	0.00	-	end	9 *					379
Q5J1T0 UniProt NPD GO	CYB_TAYPE	Cytochrome b	0.00	-	end	9 *					379
P24966 UniProt NPD GO	CYB_TAYTA	Cytochrome b	0.00	-	end	9 *					379
Q9B506 UniProt NPD GO	CYB_TETBI	Cytochrome b	0.00	-	end	9 *					377
Q4UJ67 UniProt NPD GO	CYB_THEAN	Cytochrome b	0.00	-	end	9 *					363
Q8WEK7 UniProt NPD GO	CYB_THOMA	Cytochrome b	0.00	-	end	9 *					379
Q8WEK2 UniProt NPD GO	CYB_THOMO	Cytochrome b	0.00	-	end	9 *					379
O48001 UniProt NPD GO	CYB_THOTA	Cytochrome b	0.00	-	end	9 *					379
P16360 UniProt NPD GO	CYB_THOTO	Cytochrome b	0.00	-	end	9 *					379
O47993 UniProt NPD GO	CYB_THOUM	Cytochrome b	0.00	-	end	9 *					379
Q9B6F0 UniProt NPD GO	CYB_THRSW	Cytochrome b	0.00	-	end	9 *					379
O20672 UniProt NPD GO	CYB_TOXGO	Cytochrome b	0.00	-	end	8 *					368
Q9TG16 UniProt NPD GO	CYB_TRAAN	Cytochrome b	0.00	-	end	9 *					379
O20964 UniProt NPD GO	CYB_TRAEU	Cytochrome b	0.00	-	end	9 *					379
O20965 UniProt NPD GO	CYB_TRAIM	Cytochrome b	0.00	-	end	9 *					379
Q36058 UniProt NPD GO	CYB_TRAJA	Cytochrome b	0.00	-	end	9 *					379
Q9T9B6 UniProt NPD GO	CYB_TRAOR	Cytochrome b	0.00	-	end	9 *					379
O20968 UniProt NPD GO	CYB_TRASP	Cytochrome b	0.00	-	end	9 *					379
Q9T9B7 UniProt NPD GO	CYB_TRASR	Cytochrome b	0.00	-	end	9 *					379
Q36089 UniProt NPD GO	CYB_TREOR	Cytochrome b	0.00	-	end	9 *					379
Q9ZZ40 UniProt NPD GO	CYB_TRIRU	Cytochrome b	0.00	-	end	8 *					386
Q36201 UniProt NPD GO	CYB_UROBI	Cytochrome b	0.00	-	end	9 *					379
Q6Y8J7 UniProt NPD GO	CYB_UROMA	Cytochrome b	0.00	-	end	9 *					379
Q36194 UniProt NPD GO	CYB_URSAM	Cytochrome b	0.00	-	end	9 *					379
Q36192 UniProt NPD GO	CYB_URSAR	Cytochrome b	0.00	-	end	9 *					379

You are viewing entries 93751 to 93800 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.