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
Q96S97 UniProt NPD GO	MYADM_HUMAN	Myeloid-associated differentiation marker (SB135)	0.10	-	end	8 *	Membrane; multi-pass membrane protein (Probable)		609959		322
Q5R887 UniProt NPD GO	MYL3_PONPY	Myosin light polypeptide 3	0.10	-	cyt	0					194
P09542 UniProt NPD GO	MYL3_MOUSE	Myosin light polypeptide 3 (Myosin light chain 1, slow-twitch muscle B/ventricular isoform) (MLC1SB) ...	0.10	-	cyt	0					203
P16409 UniProt NPD GO	MYL3_RAT	Myosin light polypeptide 3 (Myosin light chain 1, slow-twitch muscle B/ventricular isoform) (MLC1SB) ...	0.10	-	cyt	0					199
P08590 UniProt NPD GO	MYL3_HUMAN	Myosin light polypeptide 3 (Myosin light chain 1, slow-twitch muscle B/ventricular isoform) (MLC1SB) ...	0.10	-	cyt	0		muscle myosin [TAS]	608751		194
Q01449 UniProt NPD GO	MLRA_HUMAN	Myosin regulatory light chain 2, atrial isoform (Myosin light chain 2a) (MLC-2a) (MLC2a) (Myosin reg ...	0.10	-	mit	0		myosin [NAS]			175
P51667 UniProt NPD GO	MLRV_MOUSE	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform (MLC-2) (MLC-2v)	0.10	-	cyt	0					165
P07461 UniProt NPD GO	MLR_HALRO	Myosin regulatory light chain, smooth muscle	0.10	-	cyt	0					153
P12029 UniProt NPD GO	MYX2_CROVC	Myotoxin-2 (Myotoxin II)	0.10	-	nuc	0	Secreted protein				43
O80998 UniProt NPD GO	MB21_ARATH	Myrosinase-binding protein-like At2g25980	0.10	-	cyt	0					449
O02467 UniProt NPD GO	ASPG_SPOFR	N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase (EC 3.5.1.26) (Glycosylasparaginase) (Aspartylglucos ...	0.10	-	cyt	0	Lysosome				320
Q9Y3Q0 UniProt NPD GO	NALD2_HUMAN	N-acetylated-alpha-linked acidic dipeptidase 2 (EC 3.4.17.21) (N-acetylated-alpha-linked acidic dipe ...	0.10	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)	integral to membrane [NAS]			740
Q6FQ55 UniProt NPD GO	ECO1_CANGA	N-acetyltransferase ECO1 (EC 2.3.1.-) (Establishment of cohesion protein 1)	0.10	-	nuc	0	Nucleus (By similarity)				261
Q07923 UniProt NPD GO	LOT6_YEAST	NAD(P)H-dependent FMN reductase LOT6 (EC 1.5.1.29) (FMN reductase LOT6) (Azoreductase LOT6) (Low tem ...	0.10	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]		1T0I	191
Q3V4X4 UniProt NPD GO	NU2C_ACOCL	NAD(P)H-quinone oxidoreductase chain 2 (EC 1.6.5.-) (NAD(P)H dehydrogenase I, chain 2) (NDH-1, chain ...	0.10	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q85FP1 UniProt NPD GO	NU2C_ADICA	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.10	-	end	12 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				498
Q70XV5 UniProt NPD GO	NU2C_AMBTC	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.10	-	end	12 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q33532 UniProt NPD GO	NU2C_HORVU	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.10	-	end	14 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
P46619 UniProt NPD GO	NU2C_MAIZE	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.10	-	end	14 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
P06257 UniProt NPD GO	NU2C_MARPO	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.10	-	end	14 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				501
P12125 UniProt NPD GO	NU2C_ORYSA	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.10	-	end	14 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q6YXR9 UniProt NPD GO	NU2C_PHYPA	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.10	-	end	13 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				501
P0C159 UniProt NPD GO	NU2C_SACHY	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.10	-	end	14 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				510
Q67ID9 UniProt NPD GO	NU2C_SISMO	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.10	-	end	12 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
P58282 UniProt NPD GO	NU2C_WHEAT	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.10	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q6EW00 UniProt NPD GO	NU4C_NYMAL	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.10	-	end	14 *	Plastid; chloroplast				500
P58419 UniProt NPD GO	NU4C_OENHO	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.10	-	end	13 *	Plastid; chloroplast				500
Q85FH3 UniProt NPD GO	NU4LC_ADICA	NAD(P)H-quinone oxidoreductase chain 4L, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4L) ...	0.10	-	end	3 *	Plastid; chloroplast				99
Q85FG9 UniProt NPD GO	NUCC_ADICA	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.10	-	cyt	0	Plastid; chloroplast				394
Q95H42 UniProt NPD GO	NUCC_WHEAT	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.10	-	cyt	0	Plastid; chloroplast				393
Q9TKV4 UniProt NPD GO	NUIC_NEPOL	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.10	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				173
Q5R5S0 UniProt NPD GO	NDUA9_PONPY	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial precursor (EC 1.6.5.3) ( ...	0.10	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				377
P52504 UniProt NPD GO	NUMM_RAT	NADH-ubiquinone oxidoreductase 13 kDa-A subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) ...	0.10	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				116
Q23883 UniProt NPD GO	NUCM_DICDI	NADH-ubiquinone oxidoreductase 49 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (NADH dehydrogenase subunit ...	0.10	-	cyt	0	Mitochondrion				406
Q94511 UniProt NPD GO	NUAM_DROME	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.10	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity). Matrix and cytoplasmic side of the mito ...				731
P24918 UniProt NPD GO	NUAM_NEUCR	NADH-ubiquinone oxidoreductase 78 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.10	-	mit	0	Mitochondrion; mitochondrial inner membrane				744
P08834 UniProt NPD GO	NU1M_CITLA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.10	-	end	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				316
Q8M893 UniProt NPD GO	NU1M_EMBAL	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.10	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q9T9Z0 UniProt NPD GO	NU1M_GORGO	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.10	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
P26845 UniProt NPD GO	NU1M_MARPO	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.10	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				328
O79670 UniProt NPD GO	NU1M_PELSU	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.10	-	vac	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				322
P16672 UniProt NPD GO	NU1M_RANCA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.10	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
Q53AV2 UniProt NPD GO	NU1M_SAGLE	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.10	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
O78694 UniProt NPD GO	NU1M_SAGOE	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.10	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
P03892 UniProt NPD GO	NU2M_BOVIN	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.10	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q9MIY9 UniProt NPD GO	NU2M_BRARE	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.10	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348
P48903 UniProt NPD GO	NU2M_CHOCR	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.10	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				497
Q34951 UniProt NPD GO	NU2M_LUMTE	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.10	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				335
O21078 UniProt NPD GO	NU2M_MYXGL	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.10	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348
Q35140 UniProt NPD GO	NU2M_NEUCR	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.10	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				583

You are viewing entries 64751 to 64800 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.