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
Q85FH2 UniProt NPD GO	NU6C_ADICA	NAD(P)H-quinone oxidoreductase chain 6, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 6) (N ...	0.01	-	end	5 *	Plastid; chloroplast				197
O98693 UniProt NPD GO	NU6C_HORVU	NAD(P)H-quinone oxidoreductase chain 6, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 6) (N ...	0.01	-	end	5 *	Plastid; chloroplast				176
P46621 UniProt NPD GO	NU6C_MAIZE	NAD(P)H-quinone oxidoreductase chain 6, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 6) (N ...	0.01	-	end	5 *	Plastid; chloroplast				176
Q9MUL3 UniProt NPD GO	NU6C_MESVI	NAD(P)H-quinone oxidoreductase chain 6, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 6) (N ...	0.01	-	end	5 *	Plastid; chloroplast				189
Q6ENA4 UniProt NPD GO	NU6C_ORYNI	NAD(P)H-quinone oxidoreductase chain 6, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 6) (N ...	0.01	-	end	5 *	Plastid; chloroplast				176
P12130 UniProt NPD GO	NU6C_ORYSA	NAD(P)H-quinone oxidoreductase chain 6, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 6) (N ...	0.01	-	end	5 *	Plastid; chloroplast				176
Q6L3D7 UniProt NPD GO	NU6C_SACHY	NAD(P)H-quinone oxidoreductase chain 6, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 6) (N ...	0.01	-	end	5 *	Plastid; chloroplast				176
Q6ENP4 UniProt NPD GO	NU6C_SACOF	NAD(P)H-quinone oxidoreductase chain 6, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 6) (N ...	0.01	-	end	5 *	Plastid; chloroplast				176
Q32722 UniProt NPD GO	NU6C_TOBAC	NAD(P)H-quinone oxidoreductase chain 6, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 6) (N ...	0.01	-	end	5 *	Plastid; chloroplast				176
Q95H44 UniProt NPD GO	NU6C_WHEAT	NAD(P)H-quinone oxidoreductase chain 6, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 6) (N ...	0.01	-	end	5 *	Plastid; chloroplast				176
Q9MUR1 UniProt NPD GO	NUGC_MESVI	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.01	-	cyt	0	Plastid; chloroplast				174
Q85FH0 UniProt NPD GO	NU1C_ADICA	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				371
Q2L952 UniProt NPD GO	NU1C_GOSHI	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q1KXQ8 UniProt NPD GO	NU1C_HELAN	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q5SCZ2 UniProt NPD GO	NU1C_HUPLU	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				369
Q332S2 UniProt NPD GO	NU1C_LACSA	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q2MI45 UniProt NPD GO	NU1C_LYCES	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
P25706 UniProt NPD GO	NU1C_MAIZE	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				362
Q9MUL1 UniProt NPD GO	NU1C_MESVI	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				367
Q33BW7 UniProt NPD GO	NU1C_NICTO	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q68RV1 UniProt NPD GO	NU1C_PANGI	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q6YXP8 UniProt NPD GO	NU1C_PHYPA	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				368
Q8WHX4 UniProt NPD GO	NU1C_PSINU	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				371
Q2MID2 UniProt NPD GO	NU1C_SOLBU	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q2VEC6 UniProt NPD GO	NU1C_SOLTU	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
P06254 UniProt NPD GO	NU1C_TOBAC	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				367
Q86Y39 UniProt NPD GO	NDUAB_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqu ...	0.01	-	nuc	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...	mitochondrion [ISS]			140
Q80W89 UniProt NPD GO	NDUAB_RAT	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqu ...	0.01	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...	mitochondrion [ISS]			141
Q9CQ91 UniProt NPD GO	NDUA3_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.01	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA]			84
O00483 UniProt NPD GO	NDUA4_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.01	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; matrix side		603833		81
Q9CQZ6 UniProt NPD GO	NDUB3_MOUSE	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			104
P80729 UniProt NPD GO	NUO6_SOLTU	NADH-ubiquinone oxidoreductase 11 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-11KD) (CI-11KD) ...	0.01	-		0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				19
P15602 UniProt NPD GO	NUKM_PARTE	NADH-ubiquinone oxidoreductase 20 kDa subunit (EC 1.6.5.3)	0.01	-	cyt	0					156
P49820 UniProt NPD GO	NUHM_CANFA	NADH-ubiquinone oxidoreductase 24 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Fragment)	0.01	-		0	Mitochondrion; mitochondrial inner membrane				11
P80262 UniProt NPD GO	NUO5_SOLTU	NADH-ubiquinone oxidoreductase 29 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-29KD) (CI-29KD) ...	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				23
P33502 UniProt NPD GO	NU1M_ANOQU	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				314
P69234 UniProt NPD GO	NU1M_BRAFL	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				313
P69235 UniProt NPD GO	NU1M_BRALA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				313
O78679 UniProt NPD GO	NU1M_CARAU	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
P24969 UniProt NPD GO	NU1M_CYPCA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
P07710 UniProt NPD GO	NU1M_DROYA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
Q37556 UniProt NPD GO	NU1M_METSE	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				334
P48174 UniProt NPD GO	NU1M_ONCMY	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				323
P12772 UniProt NPD GO	NU1M_PARLI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				323
Q37603 UniProt NPD GO	NU1M_PETMA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				321
Q37676 UniProt NPD GO	NU1M_SALSA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
O78714 UniProt NPD GO	NU1M_TACAC	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
O48358 UniProt NPD GO	NU1M_THYAR	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
O78708 UniProt NPD GO	NU1M_VOMUR	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q70Y24 UniProt NPD GO	NU1M_ZAEPI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.01	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318

You are viewing entries 89701 to 89750 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.