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
P79756 UniProt NPD GO	OPSD_GAMAF	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
Q9YGZ2 UniProt NPD GO	OPSD_GOBNI	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				352
P22671 UniProt NPD GO	OPSD_LAMJA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
Q9YH00 UniProt NPD GO	OPSD_LITMO	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
Q9YGZ6 UniProt NPD GO	OPSD_LIZAU	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
Q9YGZ7 UniProt NPD GO	OPSD_LIZSA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
Q68J47 UniProt NPD GO	OPSD_LOXAF	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
O62793 UniProt NPD GO	OPSD_MESBI	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
P15409 UniProt NPD GO	OPSD_MOUSE	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein	photoreceptor outer segment [IDA]			348
Q9YGZ9 UniProt NPD GO	OPSD_MUGCE	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
Q9YH01 UniProt NPD GO	OPSD_MULSU	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
P79812 UniProt NPD GO	OPSD_NEOSA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				351
Q98980 UniProt NPD GO	OPSD_PETMA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
O62795 UniProt NPD GO	OPSD_PHOGR	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
O62794 UniProt NPD GO	OPSD_PHOVI	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
P79848 UniProt NPD GO	OPSD_POERE	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
P35403 UniProt NPD GO	OPSD_POMMI	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				352
P49912 UniProt NPD GO	OPSD_RABIT	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
P51470 UniProt NPD GO	OPSD_RANCA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
P31355 UniProt NPD GO	OPSD_RANPI	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
Q9YGZ3 UniProt NPD GO	OPSD_SALPV	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
P79898 UniProt NPD GO	OPSD_SARDI	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				351
Q9YH03 UniProt NPD GO	OPSD_SARSL	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
P02700 UniProt NPD GO	OPSD_SHEEP	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
Q9YH02 UniProt NPD GO	OPSD_SPAAU	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
Q9DGG4 UniProt NPD GO	OPSD_TETNG	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
O62796 UniProt NPD GO	OPSD_TRIMA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
P29403 UniProt NPD GO	OPSD_XENLA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
O42604 UniProt NPD GO	OPSD_ZEUFA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
Q9YGY9 UniProt NPD GO	OPSD_ZOSOP	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				352
O42294 UniProt NPD GO	OPSD_ABYKO	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				289
O42300 UniProt NPD GO	OPSD_BATMU	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				289
O42301 UniProt NPD GO	OPSD_BATNI	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				289
O18312 UniProt NPD GO	OPSD_CAMHU	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				301
O16017 UniProt NPD GO	OPSD_CAMLU	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				301
O18315 UniProt NPD GO	OPSD_CAMMA	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				300
O42327 UniProt NPD GO	OPSD_COMDY	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				289
O42307 UniProt NPD GO	OPSD_COTBO	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				289
O42330 UniProt NPD GO	OPSD_COTIN	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				289
Q90373 UniProt NPD GO	OPSD_COTKE	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				289
O42268 UniProt NPD GO	OPSD_ICTPU	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				304
O42427 UniProt NPD GO	OPSD_LIMBE	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				289
O42431 UniProt NPD GO	OPSD_LIMPA	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				289
P79798 UniProt NPD GO	OPSD_MYRBE	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				349
P79807 UniProt NPD GO	OPSD_MYRVI	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				349
P79808 UniProt NPD GO	OPSD_NEOAR	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
P79809 UniProt NPD GO	OPSD_NEOAU	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				347
O18481 UniProt NPD GO	OPSD_ORCAU	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				301
O16019 UniProt NPD GO	OPSD_ORCVI	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				301
O42452 UniProt NPD GO	OPSD_PARKN	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				289

You are viewing entries 97601 to 97650 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.