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
Q9M3I8 UniProt NPD GO	NU6C_SPIOL	NAD(P)H-quinone oxidoreductase chain 6, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 6) (N ...	0.00	-	end	5 *	Plastid; chloroplast				176
Q85BI5 UniProt NPD GO	NU1C_ANTFO	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				366
Q8M9T6 UniProt NPD GO	NU1C_CHAGL	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
P06255 UniProt NPD GO	NU1C_MARPO	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				368
Q32S02 UniProt NPD GO	NU1C_STAPU	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				372
Q32RK2 UniProt NPD GO	NU1C_ZYGCR	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
P20016 UniProt NPD GO	DHE2_THUTH	NAD-specific glutamate dehydrogenase (EC 1.4.1.2) (NAD-GDH) (Fragment)	0.00	-		0					16
P54713 UniProt NPD GO	NDUAA_CANFA	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqu ...	0.00	-		0	Mitochondrion; mitochondrial matrix				12
O95167 UniProt NPD GO	NDUA3_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.00	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein		603832		84
Q4R542 UniProt NPD GO	NDUA4_MACFA	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4 (EC 1.6.5.3) (EC 1.6.99.3)	0.00	-	end	1 *	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				81
Q3YAJ5 UniProt NPD GO	NDUA4_MACMU	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.00	-	end	1 *	Mitochondrion; mitochondrial inner membrane; matrix side				81
P80730 UniProt NPD GO	NUO7_SOLTU	NADH-ubiquinone oxidoreductase 16 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-16KD) (CI-16KD) ...	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				22
P80268 UniProt NPD GO	NUO2_SOLTU	NADH-ubiquinone oxidoreductase 18 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-18KD) (CI-18KD) ...	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				30
P80263 UniProt NPD GO	NUO3_SOLTU	NADH-ubiquinone oxidoreductase 20 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-20KD) (CI-20KD) ...	0.00	-		0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				15
Q02854 UniProt NPD GO	NUXM_NEUCR	NADH-ubiquinone oxidoreductase 21 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-21KD) (CI-21KD)	0.00	-	cyt	1	Mitochondrion; mitochondrial inner membrane				189
P19968 UniProt NPD GO	NUZM_NEUCR	NADH-ubiquinone oxidoreductase 21.3 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3)	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane. Importation into mitochondrion is membrane potential de ...				201
P80266 UniProt NPD GO	NDUA5_SOLTU	NADH-ubiquinone oxidoreductase 22.5 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-22.5Kd) (CI-22 ...	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side				37
P21301 UniProt NPD GO	NUCM_TRYBB	NADH-ubiquinone oxidoreductase 49 kDa subunit homolog (EC 1.6.5.3) (NADH dehydrogenase subunit 7 hom ...	0.00	-	end	6 *	Mitochondrion				386
P34846 UniProt NPD GO	NU1M_ANOGA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.00	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				314
Q9MIZ0 UniProt NPD GO	NU1M_BRARE	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.00	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
P11658 UniProt NPD GO	NU1M_CHLRE	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.00	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				292
P18929 UniProt NPD GO	NU1M_DROME	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.00	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				312
P51937 UniProt NPD GO	NU1M_DROSU	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.00	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				312
P15576 UniProt NPD GO	NU1M_LEITA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.00	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				313
O47479 UniProt NPD GO	NU1M_LOLBL	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.00	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				313
Q00860 UniProt NPD GO	NU1M_MYTED	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.00	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				305
P05513 UniProt NPD GO	NU1M_PARTE	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.00	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				261
Q96186 UniProt NPD GO	NU1M_PECMA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.00	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				354
Q33756 UniProt NPD GO	NU1M_ARBLI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragment)	0.00	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				125
P50659 UniProt NPD GO	NU1M_SIMVI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragment)	0.00	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				27
P51926 UniProt NPD GO	NU1M_DROAI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P84301 UniProt NPD GO	NU1M_DROAL	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P84303 UniProt NPD GO	NU1M_DROAM	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P84300 UniProt NPD GO	NU1M_DROAZ	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P51930 UniProt NPD GO	NU1M_DROBF	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P51931 UniProt NPD GO	NU1M_DROGU	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P51932 UniProt NPD GO	NU1M_DROMD	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P84305 UniProt NPD GO	NU1M_DROMI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P84304 UniProt NPD GO	NU1M_DROOB	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P84295 UniProt NPD GO	NU1M_DROPB	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P84294 UniProt NPD GO	NU1M_DROPE	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P51938 UniProt NPD GO	NU1M_DROSS	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P84302 UniProt NPD GO	NU1M_DROTR	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				163
P08740 UniProt NPD GO	NU2M_CHLRE	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.00	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				382
P26846 UniProt NPD GO	NU2M_MARPO	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.00	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				489
P48907 UniProt NPD GO	NU3M_ALBCO	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					117
P24883 UniProt NPD GO	NU3M_ASCSU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					111
P11991 UniProt NPD GO	NU3M_ASTPE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					116
O21540 UniProt NPD GO	NU3M_BOLLA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					115
P69236 UniProt NPD GO	NU3M_BRAFL	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.00	-	end	3 *					117

You are viewing entries 95801 to 95850 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.