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
P48892 UniProt NPD GO	COX3_FELCA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
P55777 UniProt NPD GO	COX3_GADMO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
P68531 UniProt NPD GO	COX3_GAZBE	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
O47708 UniProt NPD GO	COX3_GAZCU	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
O48374 UniProt NPD GO	COX3_GAZDA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
P68299 UniProt NPD GO	COX3_GAZDO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
P68532 UniProt NPD GO	COX3_GAZGA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
P68088 UniProt NPD GO	COX3_GAZGR	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
O47709 UniProt NPD GO	COX3_GAZLE	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
O47705 UniProt NPD GO	COX3_GAZRU	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
O47710 UniProt NPD GO	COX3_GAZSA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
P68089 UniProt NPD GO	COX3_GAZSO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
P68300 UniProt NPD GO	COX3_GAZSP	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
O48316 UniProt NPD GO	COX3_GAZSU	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
O47706 UniProt NPD GO	COX3_GAZTH	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
Q9T9Y6 UniProt NPD GO	COX3_GORGO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
P32808 UniProt NPD GO	COX3_HELAN	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	5 *					265
Q9ZZY5 UniProt NPD GO	COX3_HIPAM	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
P00414 UniProt NPD GO	COX3_HUMAN	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *			535000		261
Q95707 UniProt NPD GO	COX3_HYLLA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	5 *					261
Q9XLW9 UniProt NPD GO	COX3_KLULA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					269
O03170 UniProt NPD GO	COX3_LATCH	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
O47700 UniProt NPD GO	COX3_LITWA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
P14574 UniProt NPD GO	COX3_LOCMI	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					263
O47475 UniProt NPD GO	COX3_LOLBL	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					259
P92665 UniProt NPD GO	COX3_MACRO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
O47699 UniProt NPD GO	COX3_MADGU	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
Q95840 UniProt NPD GO	COX3_MAGGR	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					269
P26858 UniProt NPD GO	COX3_MARPO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					265
O47491 UniProt NPD GO	COX3_METSE	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					262
P41775 UniProt NPD GO	COX3_MYTED	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					265
O47698 UniProt NPD GO	COX3_NEOMO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
P00422 UniProt NPD GO	COX3_NEUCR	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					269
P08745 UniProt NPD GO	COX3_OENBE	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					265
P20684 UniProt NPD GO	COX3_ONCCL	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
P69217 UniProt NPD GO	COX3_ONCMA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
P48172 UniProt NPD GO	COX3_ONCMY	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
P69218 UniProt NPD GO	COX3_ONCNE	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
Q36455 UniProt NPD GO	COX3_ORNAN	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
O47695 UniProt NPD GO	COX3_OUROU	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
Q9T9W8 UniProt NPD GO	COX3_PANPA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	mit	6 *					261
Q9T9V9 UniProt NPD GO	COX3_PANTR	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	mit	6 *					261
P12702 UniProt NPD GO	COX3_PARLI	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
Q35539 UniProt NPD GO	COX3_PETMA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
P48874 UniProt NPD GO	COX3_PICCA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					269
Q35916 UniProt NPD GO	COX3_PIG	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
Q02654 UniProt NPD GO	COX3_PODAN	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					269
P92696 UniProt NPD GO	COX3_PONPA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
Q9T9X6 UniProt NPD GO	COX3_PONPY	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
Q37620 UniProt NPD GO	COX3_PROWI	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					262

You are viewing entries 94151 to 94200 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.