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
O48277 UniProt NPD GO	CYB_PYTRE	Cytochrome b	0.02	-	end	10 *					371
Q8WE97 UniProt NPD GO	CYB_RIVMA	Cytochrome b	0.02	-	end	9 *					391
Q36549 UniProt NPD GO	CYB_SARSA	Cytochrome b	0.02	-	end	9 *					380
Q9XP88 UniProt NPD GO	CYB_SMIAR	Cytochrome b	0.02	-	end	9 *					381
Q35810 UniProt NPD GO	CYB_SMICR	Cytochrome b	0.02	-	end	9 *					381
Q9XP83 UniProt NPD GO	CYB_SMIGA	Cytochrome b	0.02	-	end	9 *					381
O20433 UniProt NPD GO	CYB_SMIMA	Cytochrome b	0.02	-	end	9 *					381
O79445 UniProt NPD GO	CYB_SORAR	Cytochrome b	0.02	-	end	9 *					379
O79450 UniProt NPD GO	CYB_SORCA	Cytochrome b	0.02	-	end	9 *					379
Q8SE77 UniProt NPD GO	CYB_SORCM	Cytochrome b	0.02	-	end	9 *					379
O79448 UniProt NPD GO	CYB_SORCO	Cytochrome b	0.02	-	end	9 *					379
O79996 UniProt NPD GO	CYB_SORGA	Cytochrome b	0.02	-	end	9 *					379
Q8SEL4 UniProt NPD GO	CYB_SORHD	Cytochrome b	0.02	-	end	9 *					379
Q8SFK7 UniProt NPD GO	CYB_SORLO	Cytochrome b	0.02	-	end	9 *					379
Q7HFG0 UniProt NPD GO	CYB_SORPO	Cytochrome b	0.02	-	end	9 *					379
O79462 UniProt NPD GO	CYB_SORRA	Cytochrome b	0.02	-	end	9 *					379
O79463 UniProt NPD GO	CYB_SORSH	Cytochrome b	0.02	-	end	9 *					379
O79464 UniProt NPD GO	CYB_SORTU	Cytochrome b	0.02	-	end	9 *					379
Q7HFF9 UniProt NPD GO	CYB_SORUG	Cytochrome b	0.02	-	end	9 *					379
O79468 UniProt NPD GO	CYB_SORUN	Cytochrome b	0.02	-	end	9 *					379
Q9TF89 UniProt NPD GO	CYB_SPEAN	Cytochrome b	0.02	-	end	9 *					379
Q9TF31 UniProt NPD GO	CYB_SPEMO	Cytochrome b	0.02	-	end	9 *					379
Q9TDK9 UniProt NPD GO	CYB_STEBR	Cytochrome b	0.02	-	end	9 *					379
O03548 UniProt NPD GO	CYB_STRCA	Cytochrome b	0.02	-	end	9 *					379
O79659 UniProt NPD GO	CYB_SYRRE	Cytochrome b	0.02	-	end	9 *					380
Q8LWN0 UniProt NPD GO	CYB_TAMTE	Cytochrome b	0.02	-	end	9 *					379
Q36099 UniProt NPD GO	CYB_THEPA	Cytochrome b	0.02	-	end	8 *					363
O79660 UniProt NPD GO	CYB_TRATE	Cytochrome b	0.02	-	end	9 *					380
O03503 UniProt NPD GO	CYB_TRIVU	Cytochrome b	0.02	-	end	9 *					381
O79524 UniProt NPD GO	CYB_TROCU	Cytochrome b	0.02	-	end	9 *					380
Q9TDK1 UniProt NPD GO	CYB_TURAD	Cytochrome b	0.02	-	end	9 *					379
Q33695 UniProt NPD GO	CYB_ARTFU	Cytochrome b (Fragment)	0.02	-	end	3 *					134
P87421 UniProt NPD GO	CYB_ATRMI	Cytochrome b (Fragment)	0.02	-	end	5 *					214
P92847 UniProt NPD GO	CYB_BOTBI	Cytochrome b (Fragment)	0.02	-	end	5 *					214
P49390 UniProt NPD GO	CYB_BRANA	Cytochrome b (Fragment)	0.02	-	mit	1 *					89
Q33377 UniProt NPD GO	CYB_CANSI	Cytochrome b (Fragment)	0.02	-	end	3 *					132
Q34253 UniProt NPD GO	CYB_CENSE	Cytochrome b (Fragment)	0.02	-	mit	3 *					134
P87419 UniProt NPD GO	CYB_CERCE	Cytochrome b (Fragment)	0.02	-	mit	5 *					214
P16364 UniProt NPD GO	CYB_CORME	Cytochrome b (Fragment)	0.02	-	cyt	1 *					79
Q34462 UniProt NPD GO	CYB_EUMGL	Cytochrome b (Fragment)	0.02	-	end	4 *					176
Q33537 UniProt NPD GO	CYB_IDIPH	Cytochrome b (Fragment)	0.02	-	end	4 *					176
P92853 UniProt NPD GO	CYB_LACMU	Cytochrome b (Fragment)	0.02	-	mit	5 *					214
Q33607 UniProt NPD GO	CYB_LASNO	Cytochrome b (Fragment)	0.02	-	end	3 *					176
Q36294 UniProt NPD GO	CYB_MYOLE	Cytochrome b (Fragment)	0.02	-	mit	3 *					176
P29639 UniProt NPD GO	CYB_PITSO	Cytochrome b (Fragment)	0.02	-	end	8 *					308
Q35467 UniProt NPD GO	CYB_PLAHE	Cytochrome b (Fragment)	0.02	-	end	3 *					134
Q36659 UniProt NPD GO	CYB_PROCE	Cytochrome b (Fragment)	0.02	-	end	4 *					176
O99468 UniProt NPD GO	CYB_RHIHI	Cytochrome b (Fragment)	0.02	-	end	3 *					134
Q35805 UniProt NPD GO	CYB_SCICA	Cytochrome b (Fragment)	0.02	-	end	3 *					176
O21411 UniProt NPD GO	CYB_SORDA	Cytochrome b (Fragment)	0.02	-	end	3 *					134

You are viewing entries 83051 to 83100 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.