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
P06907 UniProt NPD GO	MYP0_RAT	Myelin P0 protein precursor (Myelin protein zero) (Myelin peripheral protein) (MPP)	0.09	-	end	2 *	Membrane; single-pass type I membrane protein			1NEU	248
P54695 UniProt NPD GO	MYOF_DICDI	Myosin IF heavy chain (Fragment)	0.09	-	mit	0					86
P07462 UniProt NPD GO	MLE_HALRO	Myosin catalytic light chain, smooth muscle	0.09	-	cyt	0					151
P02606 UniProt NPD GO	MLEC_CHICK	Myosin light chain 1, cardiac muscle (A1 catalytic) (Alkali)	0.09	-	nuc	0					193
P53014 UniProt NPD GO	MLE_CAEEL	Myosin, essential light chain (Myosin light chain alkali)	0.09	-	cyt	0					153
Q90233 UniProt NPD GO	MYPC3_AMBME	Myosin-binding protein C, cardiac-type (Cardiac MyBP-C) (C-protein, cardiac muscle isoform) (CPRO ax ...	0.09	-	cyt	0					510
P37702 UniProt NPD GO	MYRO_ARATH	Myrosinase precursor (EC 3.2.1.147) (Sinigrinase) (Thioglucosidase)	0.09	-	exc	0	Vacuole (By similarity)				541
Q757J9 UniProt NPD GO	TRPF_ASHGO	N-(5'-phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) (PRAI)	0.09	-	nuc	0					210
P87800 UniProt NPD GO	MLB3_VISAL	N-acetyl-D-galactosamine-specific lectin III B chain (ML-3B) (ML-III B)	0.09	-	cyt	0					262
P23336 UniProt NPD GO	GGTA1_MOUSE	N-acetyllactosaminide alpha-1,3-galactosyltransferase (EC 2.4.1.87) (Galactosyltransferase) (UDP-gal ...	0.09	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				394
Q52QH4 UniProt NPD GO	NAC68_ORYSA	NAC domain-containing protein 68 (ONAC068)	0.09	-	cyt	0	Nucleus (Probable)				318
P15559 UniProt NPD GO	NQO1_HUMAN	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2) (Quinone reductase 1) (NAD(P)H:quinone oxidoreductase ...	0.09	-	mit	0	Cytoplasm	cytoplasm [TAS]	125860	2F1O	274
Q876L8 UniProt NPD GO	XYL1_TRIRE	NAD(P)H-dependent D-xylose reductase (EC 1.1.1.-) (XR)	0.09	-	cyt	0					324
Q67ID0 UniProt NPD GO	NU2C_ALLTE	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.09	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q67IC4 UniProt NPD GO	NU2C_ASPOF	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.09	-	end	9 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q67IB5 UniProt NPD GO	NU2C_MAIRA	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.09	-	end	9 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q67IB2 UniProt NPD GO	NU2C_MUIMA	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.09	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q67IA9 UniProt NPD GO	NU2C_MUSCM	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.09	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q67IA6 UniProt NPD GO	NU2C_NAREL	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.09	-	end	12 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q67IE2 UniProt NPD GO	NU2C_PHOTN	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.09	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q67IA3 UniProt NPD GO	NU2C_YUCGL	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.09	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
P11647 UniProt NPD GO	NU4C_MAIZE	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.09	-	end	14 *	Plastid; chloroplast				500
Q6YXQ3 UniProt NPD GO	NU4C_PHYPA	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.09	-	end	14 *	Plastid; chloroplast				501
Q6ENP7 UniProt NPD GO	NU4C_SACOF	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.09	-	end	14 *	Plastid; chloroplast				500
Q6ENA5 UniProt NPD GO	NU4LC_ORYNI	NAD(P)H-quinone oxidoreductase chain 4L, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4L) ...	0.09	-	end	3 *	Plastid; chloroplast				101
P12128 UniProt NPD GO	NU4LC_ORYSA	NAD(P)H-quinone oxidoreductase chain 4L, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4L) ...	0.09	-	end	3 *	Plastid; chloroplast				101
Q6L3D8 UniProt NPD GO	NU4LC_SACHY	NAD(P)H-quinone oxidoreductase chain 4L, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4L) ...	0.09	-	end	3 *	Plastid; chloroplast				101
Q6ENP5 UniProt NPD GO	NU4LC_SACOF	NAD(P)H-quinone oxidoreductase chain 4L, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4L) ...	0.09	-	end	3 *	Plastid; chloroplast				101
Q85FH9 UniProt NPD GO	NU5C_ADICA	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.09	-	end	18 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (By similarity)				729
Q859V1 UniProt NPD GO	NU5C_ANTFO	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.09	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				732
Q9TL56 UniProt NPD GO	NU5C_CARCG	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.09	-	end	14 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				743
Q9MUL0 UniProt NPD GO	NUCC_MESVI	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.09	-	cyt	0	Plastid; chloroplast				391
Q9BBT6 UniProt NPD GO	NUGC_LOTJA	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.09	-	cyt	0	Plastid; chloroplast				158
P31174 UniProt NPD GO	NUGC_SOYBN	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.09	-	cyt	0	Plastid; chloroplast				158
O95178 UniProt NPD GO	NDUB2_HUMAN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial precursor (EC 1.6.5.3) (E ...	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side		603838		105
Q9CPU2 UniProt NPD GO	NDUB2_MOUSE	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial precursor (EC 1.6.5.3) (E ...	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)	mitochondrion [IDA]			105
Q9CQH3 UniProt NPD GO	NDUB5_MOUSE	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial precursor (EC 1.6.5.3) (E ...	0.09	-	mit	1	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			189
P52503 UniProt NPD GO	NUMM_MOUSE	NADH-ubiquinone oxidoreductase 13 kDa-A subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) ...	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				116
Q26783 UniProt NPD GO	NUKM_TRYBB	NADH-ubiquinone oxidoreductase 20 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.09	-	mit	0					202
O22769 UniProt NPD GO	NUHM_ARATH	NADH-ubiquinone oxidoreductase 24 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3)	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity). Matrix and cytoplasmic side of the mito ...				255
P25708 UniProt NPD GO	NUBM_BOVIN	NADH-ubiquinone oxidoreductase 51 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				464
Q9FGI6 UniProt NPD GO	NUAM_ARATH	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity). Matrix and cytoplasmic side of the mito ...				748
O47868 UniProt NPD GO	NU1M_ALLMI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.09	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				321
Q85UK4 UniProt NPD GO	NU1M_COTCH	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.09	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
Q9T9W3 UniProt NPD GO	NU1M_PANTR	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.09	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q94VF8 UniProt NPD GO	NU1M_VARJO	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.09	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				320
Q37376 UniProt NPD GO	NU2M_ACACA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.09	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				527
P34848 UniProt NPD GO	NU2M_ANOGA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.09	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				341
Q37704 UniProt NPD GO	NU2M_ARTSF	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.09	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				296
P03895 UniProt NPD GO	NU2M_DROYA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.09	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				341

You are viewing entries 66551 to 66600 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.