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
P48914 UniProt NPD GO	NU4M_ALBCO	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.01	-	end	12 *					437
P24880 UniProt NPD GO	NU4M_ASCSU	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.01	-	end	13 *					409
O47423 UniProt NPD GO	NU4M_BRAFL	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.01	-	end	13 *					452
O79421 UniProt NPD GO	NU4M_BRALA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.01	-	end	13 *					452
Q34048 UniProt NPD GO	NU4M_CERCA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.01	-	end	13 *					446
P15581 UniProt NPD GO	NU4M_PARTE	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.01	-	end	12 *					474
Q37617 UniProt NPD GO	NU4M_PROWI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.01	-	end	14 *					523
P34859 UniProt NPD GO	NU4LM_APILI	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	2 *					87
Q04614 UniProt NPD GO	NU4LM_ARATH	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				100
P24874 UniProt NPD GO	NU4LM_ASCSU	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	2 *					77
P24976 UniProt NPD GO	NU4LM_BALPH	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	2 *					98
Q8HEB9 UniProt NPD GO	NU4LM_CAEBR	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	2 *					76
P24886 UniProt NPD GO	NU4LM_CAEEL	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	2 *					77
O03203 UniProt NPD GO	NU4LM_CERSI	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
P18942 UniProt NPD GO	NU4LM_CHICK	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	mit	3 *					98
Q6U7Y2 UniProt NPD GO	NU4LM_CRIPE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	exc	3 *					87
Q9B987 UniProt NPD GO	NU4LM_ELACE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
Q8LX40 UniProt NPD GO	NU4LM_EUMJU	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
Q34572 UniProt NPD GO	NU4LM_GORGO	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
P92667 UniProt NPD GO	NU4LM_MACRO	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
P26851 UniProt NPD GO	NU4LM_MARPO	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					100
Q7IVV3 UniProt NPD GO	NU4LM_MUNFE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
Q7IVV2 UniProt NPD GO	NU4LM_MUNGO	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
Q9B996 UniProt NPD GO	NU4LM_MUNVU	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
Q9G2X0 UniProt NPD GO	NU4LM_MYXGL	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	2 *					96
Q35588 UniProt NPD GO	NU4LM_PANPA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
Q37809 UniProt NPD GO	NU4LM_PANTR	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
Q9ZXX6 UniProt NPD GO	NU4LM_PAPHA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
Q6V9E0 UniProt NPD GO	NU4LM_PENMA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					89
Q36903 UniProt NPD GO	NU4LM_PICCA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					93
Q37627 UniProt NPD GO	NU4LM_PROWI	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					100
Q9G3S8 UniProt NPD GO	NU4LM_PTESA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
O99826 UniProt NPD GO	NU4LM_RHISA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					91
O78754 UniProt NPD GO	NU4LM_SHEEP	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
O21567 UniProt NPD GO	NU4LM_SIGHI	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					98
Q36832 UniProt NPD GO	NU4LM_TRIPI	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	2 *					88
Q01562 UniProt NPD GO	NU4LM_TRIRU	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.01	-	end	3 *					89
P11628 UniProt NPD GO	NU5M_EMENI	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.01	-	end	18 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				657
P04540 UniProt NPD GO	NU5M_TRYBB	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.01	-	end	18 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				590
Q31696 UniProt NPD GO	NU5M_ANOQN	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.01	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				265
Q33753 UniProt NPD GO	NU5M_ARBLI	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.01	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				190
Q34313 UniProt NPD GO	NU5M_DICDI	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.01	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				232
P15583 UniProt NPD GO	NU5M_LEITA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.01	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				101
Q35639 UniProt NPD GO	NU5M_PEA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.01	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				183
Q37371 UniProt NPD GO	NU6M_ACACA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	6 *					260
P43190 UniProt NPD GO	NU6M_AETPU	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					173
P41300 UniProt NPD GO	NU6M_BALMU	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
P24980 UniProt NPD GO	NU6M_BALPH	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
P03924 UniProt NPD GO	NU6M_BOVIN	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
O03206 UniProt NPD GO	NU6M_CERSI	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	6 *					175

You are viewing entries 89801 to 89850 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.