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
Q85QA4 UniProt NPD GO	CYB_CANGA	Cytochrome b	0.01	-	end	9 *					385
Q6ED58 UniProt NPD GO	CYB_CANST	Cytochrome b	0.01	-	end	10 *					384
O47923 UniProt NPD GO	CYB_CAPCA	Cytochrome b	0.01	-	end	9 *					379
O78785 UniProt NPD GO	CYB_CAPIB	Cytochrome b	0.01	-	end	9 *					379
P34865 UniProt NPD GO	CYB_CARCH	Cytochrome b	0.01	-	end	9 *					381
P29634 UniProt NPD GO	CYB_CATGU	Cytochrome b	0.01	-	end	9 *					380
Q8LX87 UniProt NPD GO	CYB_CEPGR	Cytochrome b	0.01	-	end	9 *					380
Q9G3R1 UniProt NPD GO	CYB_CHATU	Cytochrome b	0.01	-	end	9 *					379
Q85AV3 UniProt NPD GO	CYB_CHIHI	Cytochrome b	0.01	-	end	9 *					379
Q9G1R4 UniProt NPD GO	CYB_CLEGA	Cytochrome b	0.01	-	end	9 *					380
Q8SJK5 UniProt NPD GO	CYB_CLEMU	Cytochrome b	0.01	-	end	9 *					379
Q9G4Q1 UniProt NPD GO	CYB_CLERU	Cytochrome b	0.01	-	end	9 *					380
Q85AG5 UniProt NPD GO	CYB_CONCR	Cytochrome b	0.01	-	end	9 *					379
Q9ZZD4 UniProt NPD GO	CYB_CORCU	Cytochrome b	0.01	-	end	9 *					380
O48039 UniProt NPD GO	CYB_COREN	Cytochrome b	0.01	-	end	10 *					370
O79386 UniProt NPD GO	CYB_CORFR	Cytochrome b	0.01	-	end	9 *					380
Q8WFX3 UniProt NPD GO	CYB_CRECR	Cytochrome b	0.01	-	end	8 *					379
O79652 UniProt NPD GO	CYB_CROCS	Cytochrome b	0.01	-	end	9 *					380
Q8SE89 UniProt NPD GO	CYB_CRODS	Cytochrome b	0.01	-	end	9 *					379
Q94QP2 UniProt NPD GO	CYB_CROKU	Cytochrome b	0.01	-	end	9 *					379
Q8SJX5 UniProt NPD GO	CYB_CROLS	Cytochrome b	0.01	-	end	9 *					379
Q8SET9 UniProt NPD GO	CYB_CROSB	Cytochrome b	0.01	-	end	9 *					379
Q8SJX4 UniProt NPD GO	CYB_CROWA	Cytochrome b	0.01	-	end	9 *					379
O21795 UniProt NPD GO	CYB_CRYDA	Cytochrome b	0.01	-	end	9 *					379
Q9TF27 UniProt NPD GO	CYB_CYNGU	Cytochrome b	0.01	-	end	9 *					379
Q9TFA0 UniProt NPD GO	CYB_CYNLE	Cytochrome b	0.01	-	end	9 *					379
Q9TF91 UniProt NPD GO	CYB_CYNME	Cytochrome b	0.01	-	end	9 *					379
Q34070 UniProt NPD GO	CYB_CYSCR	Cytochrome b	0.01	-	end	9 *					379
Q94SD0 UniProt NPD GO	CYB_DACPE	Cytochrome b	0.01	-	end	9 *					380
O47716 UniProt NPD GO	CYB_DAMLU	Cytochrome b	0.01	-	end	9 *					379
O79197 UniProt NPD GO	CYB_DAPCA	Cytochrome b	0.01	-	end	9 *					380
Q34289 UniProt NPD GO	CYB_DASAL	Cytochrome b	0.01	-	end	8 *					381
O20604 UniProt NPD GO	CYB_DASGE	Cytochrome b	0.01	-	end	9 *					381
Q34321 UniProt NPD GO	CYB_DASHA	Cytochrome b	0.01	-	end	9 *					381
Q34376 UniProt NPD GO	CYB_DASRO	Cytochrome b	0.01	-	end	9 *					381
Q34382 UniProt NPD GO	CYB_DASSP	Cytochrome b	0.01	-	end	9 *					381
Q34399 UniProt NPD GO	CYB_DASVI	Cytochrome b	0.01	-	end	9 *					381
Q34279 UniProt NPD GO	CYB_DIDAL	Cytochrome b	0.01	-	end	8 *					382
P41303 UniProt NPD GO	CYB_DIDMA	Cytochrome b	0.01	-	end	9 *					382
Q953K8 UniProt NPD GO	CYB_ECHGY	Cytochrome b	0.01	-	end	9 *					380
Q9ZZT7 UniProt NPD GO	CYB_ELIQU	Cytochrome b	0.01	-	end	9 *					379
O48043 UniProt NPD GO	CYB_EPICE	Cytochrome b	0.01	-	end	10 *					370
Q3ZEG3 UniProt NPD GO	CYB_EPIFL	Cytochrome b	0.01	-	end	8 *					400
P92487 UniProt NPD GO	CYB_EQUAS	Cytochrome b	0.01	-	end	9 *					379
P24956 UniProt NPD GO	CYB_EQUGR	Cytochrome b	0.01	-	end	9 *					379
Q34409 UniProt NPD GO	CYB_ERIBA	Cytochrome b	0.01	-	end	9 *					379
P41288 UniProt NPD GO	CYB_ESCGI	Cytochrome b	0.01	-	end	9 *					379
Q598V2 UniProt NPD GO	CYB_EUBAS	Cytochrome b	0.01	-	end	9 *					379
Q4FBI3 UniProt NPD GO	CYB_EUBGL	Cytochrome b	0.01	-	end	9 *					379
Q598T9 UniProt NPD GO	CYB_EUBJA	Cytochrome b	0.01	-	end	9 *					379

You are viewing entries 87351 to 87400 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.