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
O21575 UniProt NPD GO	NU3M_NEOLE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					115
O21587 UniProt NPD GO	NU3M_OCHNU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					115
O21560 UniProt NPD GO	NU3M_ORYPA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					115
Q9T9W7 UniProt NPD GO	NU3M_PANPA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					115
Q35540 UniProt NPD GO	NU3M_PETMA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					116
Q00541 UniProt NPD GO	NU3M_PHOVI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					115
O79880 UniProt NPD GO	NU3M_PIG	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					115
O21616 UniProt NPD GO	NU3M_PODFL	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					115
O99978 UniProt NPD GO	NU3M_PORPU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					121
O21592 UniProt NPD GO	NU3M_REIFU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					115
Q96066 UniProt NPD GO	NU3M_RHIUN	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					115
O21581 UniProt NPD GO	NU3M_SCOTE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					115
P15550 UniProt NPD GO	NU3M_STRPU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.02	-	end	3 *					116
P34852 UniProt NPD GO	NU4M_ANOGA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.02	-	end	13 *					447
P93313 UniProt NPD GO	NU4M_ARATH	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				495
O78687 UniProt NPD GO	NU4M_CARAU	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.02	-	end	12 *					460
P07707 UniProt NPD GO	NU4M_DROYA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.02	-	end	12 *					446
P26848 UniProt NPD GO	NU4M_MARPO	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.02	-	end	13 *					495
P27572 UniProt NPD GO	NU4M_WHEAT	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.02	-	end	13 *					495
P19046 UniProt NPD GO	NU4M_ARTSA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.02	-	end	2 *					71
P48928 UniProt NPD GO	NU4LM_ALBCO	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					99
P03902 UniProt NPD GO	NU4LM_BOVIN	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
Q9ZZ59 UniProt NPD GO	NU4LM_CANFA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
P34193 UniProt NPD GO	NU4LM_CROLA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
Q8HHD3 UniProt NPD GO	NU4LM_CRYPA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					89
P48931 UniProt NPD GO	NU4LM_FELCA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
P68309 UniProt NPD GO	NU4LM_HALGR	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
Q9XL66 UniProt NPD GO	NU4LM_MACBR	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	2 *					98
Q9XJY3 UniProt NPD GO	NU4LM_MACMR	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
Q9XL62 UniProt NPD GO	NU4LM_MACOC	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
Q7J3B5 UniProt NPD GO	NU4LM_MACPG	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
P03903 UniProt NPD GO	NU4LM_MOUSE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					97
P05509 UniProt NPD GO	NU4LM_NEUCR	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					89
P69306 UniProt NPD GO	NU4LM_ONCCL	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
P69303 UniProt NPD GO	NU4LM_ONCGO	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
P69304 UniProt NPD GO	NU4LM_ONCKI	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
P69302 UniProt NPD GO	NU4LM_ONCMY	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
P69305 UniProt NPD GO	NU4LM_ONCNE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
P69307 UniProt NPD GO	NU4LM_ONCTS	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
P68310 UniProt NPD GO	NU4LM_PHOVI	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
P20680 UniProt NPD GO	NU4LM_PODAN	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					89
P61795 UniProt NPD GO	NU4LM_PONPA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
P61796 UniProt NPD GO	NU4LM_PONPY	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
P05507 UniProt NPD GO	NU4LM_RAT	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	2 *					98
Q9ZZM5 UniProt NPD GO	NU4LM_SALSA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					98
Q8SHP8 UniProt NPD GO	NU4LM_TRIRE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.02	-	end	3 *					89
Q6QU67 UniProt NPD GO	NU5M_ASPNG	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3)	0.02	-	end	17 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				656
Q8SHP7 UniProt NPD GO	NU5M_TRIRE	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3)	0.02	-	end	17 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				692
Q5DUY0 UniProt NPD GO	NU5H_NYCOV	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.02	-	end	41	Hydrogenosome; hydrogenosomal membrane; multi-pass membrane protein (Potential)				1849
Q37372 UniProt NPD GO	NU5M_ACACA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.02	-	end	18 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				675

You are viewing entries 84501 to 84550 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.)

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