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
P46979 UniProt NPD GO	MY14_EISFO	Myoactive tetradecapeptide (ETP)	0.02	-		0					14
P02200 UniProt NPD GO	MYG_ALLMI	Myoglobin	0.02	-	cyt	0					154
P02201 UniProt NPD GO	MYG_GRAGE	Myoglobin	0.02	-	cyt	0					153
P68081 UniProt NPD GO	MYG_HALGR	Myoglobin	0.02	-	cyt	0					153
P02206 UniProt NPD GO	MYG_HETPO	Myoglobin	0.02	-	cyt	0					148
P02184 UniProt NPD GO	MYG_KOGSI	Myoglobin	0.02	-	cyt	0					153
P11343 UniProt NPD GO	MYG_LUTLU	Myoglobin	0.02	-	cyt	0					153
P02167 UniProt NPD GO	MYG_NYCCO	Myoglobin	0.02	-	cyt	0					153
P02166 UniProt NPD GO	MYG_PERPO	Myoglobin	0.02	-	cyt	0					153
P68080 UniProt NPD GO	MYG_PHOVI	Myoglobin	0.02	-	cyt	0				1MBS	153
P02185 UniProt NPD GO	MYG_PHYCA	Myoglobin	0.02	-	mit	0				5MBN	153
P02161 UniProt NPD GO	MYG_ZALCA	Myoglobin	0.02	-	cyt	0					153
Q9GYZ9 UniProt NPD GO	HEMTM_THETS	Myohemerythrin (MHR)	0.02	-	cyt	0	Cytoplasm (Potential)				120
P02247 UniProt NPD GO	HEMTM_THEZO	Myohemerythrin (MHR)	0.02	-	cyt	0				2MHR	118
P27686 UniProt NPD GO	HEMT1_PHAGO	Myohemerythrin-1 (MHR 1)	0.02	-	cyt	0					119
P14649 UniProt NPD GO	MLEY_HUMAN	Myosin light chain 1, slow-twitch muscle A isoform (MLC1sa) (Alkali)	0.02	-	cyt	0		muscle myosin [TAS] unconventional myosin [IEP]	609930	1W7J	208
P06741 UniProt NPD GO	MLE3_HUMAN	Myosin light chain 3, skeletal muscle isoform (A2 catalytic) (Alkali myosin light chain 3) (MLC3F)	0.02	-	cyt	0		muscle myosin [NAS]	160780		149
O44107 UniProt NPD GO	MLC1_DROSU	Myosin light chain alkali (Fragment)	0.02	-	cyt	0		muscle myosin [ISS]			86
P09402 UniProt NPD GO	MLE_DICDI	Myosin, essential light chain (Myosin light chain alkali) (EMLC)	0.02	-	cyt	0					150
O80950 UniProt NPD GO	MB22_ARATH	Myrosinase-binding protein-like At2g39310	0.02	-	cyt	0					458
Q9SDM9 UniProt NPD GO	MB33_ARATH	Myrosinase-binding protein-like At3g16400	0.02	-	cyt	0					470
O04312 UniProt NPD GO	MB32_ARATH	Myrosinase-binding protein-like At3g16440	0.02	-	cyt	0					300
P82102 UniProt NPD GO	MYNB_MYTGA	Myticin-B precursor	0.02	-	exc	0	Secreted protein				96
Q9D7V9 UniProt NPD GO	ASAHL_MOUSE	N-acylethanolamine-hydrolyzing acid amidase precursor (EC 3.5.1.-) (N-acylsphingosine amidohydrolase ...	0.02	-	exc	1 *	Lysosome (By similarity)				362
Q8M9T9 UniProt NPD GO	NU4LC_CHAGL	NAD(P)H-quinone oxidoreductase chain 4L, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4L) ...	0.02	-	end	3 *	Plastid; chloroplast				100
Q8S8U5 UniProt NPD GO	NU1C_ATRBE	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q7YJS9 UniProt NPD GO	NU1C_CALFE	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q2QD36 UniProt NPD GO	NU1C_CUCSA	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q49KU3 UniProt NPD GO	NU1C_EUCGG	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q3C1P9 UniProt NPD GO	NU1C_NICSY	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				363
Q6EVZ5 UniProt NPD GO	NU1C_NYMAL	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				361
Q6ENA2 UniProt NPD GO	NU1C_ORYNI	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.02	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				362
P12124 UniProt NPD GO	NU1C_ORYSA	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.02	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				362
Q6L3D5 UniProt NPD GO	NU1C_SACHY	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				362
Q6ENP2 UniProt NPD GO	NU1C_SACOF	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				362
Q95H43 UniProt NPD GO	NU1C_WHEAT	NAD(P)H-quinone oxidoreductase subunit 1, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 1) ...	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				362
Q8H9D2 UniProt NPD GO	NQR_SOLTU	NAD(P)H:quinone oxidoreductase (EC 1.6.5.2) (NAD(P)H:QR)	0.02	-	cyt	0					194
Q02377 UniProt NPD GO	NDUA1_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.02	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; matrix side				70
Q9WU08 UniProt NPD GO	NDUA1_CRIGR	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.02	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; matrix side				70
Q8SPF0 UniProt NPD GO	NDUA1_GORGO	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.02	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; matrix side				70
O15239 UniProt NPD GO	NDUA1_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.02	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; matrix side		300078		70
Q7JGX4 UniProt NPD GO	NDUA1_PANPA	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.02	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; matrix side				70
Q02371 UniProt NPD GO	NDUA3_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.02	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				83
Q62425 UniProt NPD GO	NDUA4_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.02	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; matrix side	mitochondrial inner membrane [IDA] mitochondrion [IDA]		1LEG	82
Q02365 UniProt NPD GO	NDUB3_BOVIN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.02	-	cyt	1	Mitochondrion; mitochondrial inner membrane; matrix side				97
O43676 UniProt NPD GO	NDUB3_HUMAN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.02	-	cyt	1	Mitochondrion; mitochondrial inner membrane; matrix side		603839		97
P83291 UniProt NPD GO	NCB5R_ARATH	NADH-cytochrome b5 reductase-like protein (EC 1.6.2.2) (B5R)	0.02	-	mit	0	Mitochondrion; mitochondrial intermembrane space	mitochondrial intermembrane space [TAS]			328
P19404 UniProt NPD GO	NUHM_HUMAN	NADH-ubiquinone oxidoreductase 24 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3)	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane		600532		249
P80265 UniProt NPD GO	NDUA9_SOLTU	NADH-ubiquinone oxidoreductase 38.5 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-38.5KD) (CI-38 ...	0.02	-	nuc	0	Mitochondrion; mitochondrial matrix				22
P48897 UniProt NPD GO	NU1M_ALBCO	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.02	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				299

You are viewing entries 84401 to 84450 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.