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
P02608 UniProt NPD GO	MLRS_RABIT	Myosin regulatory light chain 2, skeletal muscle isoform type 2 (G2) (DTNB) (MLC-2)	0.15	+	cyt	0					169
P54357 UniProt NPD GO	MLC2_DROME	Myosin-2 essential light chain (Myosin II essential light chain) (Nonmuscle myosin essential light c ...	0.15	-	cyt	0					147
Q05623 UniProt NPD GO	MYBPH_CHICK	Myosin-binding protein H (MyBP-H) (H-protein) (86 kDa protein)	0.15	-	nuc	0					537
Q9SQI3 UniProt NPD GO	FATB_GOSHI	Myristoyl-acyl carrier protein thioesterase, chloroplast precursor (EC 3.1.2.-) (16:0-acyl-carrier p ...	0.15	-	mit	0	Plastid; chloroplast				413
Q00326 UniProt NPD GO	MYRO_BRANA	Myrosinase precursor (EC 3.2.1.147) (Sinigrinase) (Thioglucosidase)	0.15	-	exc	0	Vacuole				548
Q9CZR2 UniProt NPD GO	NALD2_MOUSE	N-acetylated-alpha-linked acidic dipeptidase 2 (EC 3.4.17.21) (N-acetylated-alpha-linked acidic dipe ...	0.15	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				740
P34059 UniProt NPD GO	GA6S_HUMAN	N-acetylgalactosamine-6-sulfatase precursor (EC 3.1.6.4) (N-acetylgalactosamine-6-sulfate sulfatase) ...	0.15	-	exc	0	Lysosome		253000		522
Q8VCS0 UniProt NPD GO	PGRP2_MOUSE	N-acetylmuramoyl-L-alanine amidase precursor (EC 3.5.1.28) (Peptidoglycan recognition protein long) ...	0.15	-	nuc	0	Secreted protein. Membrane	intracellular [ISS] membrane [ISS]			530
P82343 UniProt NPD GO	RENBP_MOUSE	N-acylglucosamine 2-epimerase (EC 5.1.3.8) (GlcNAc 2-epimerase) (N-acetyl-D-glucosamine 2-epimerase) ...	0.15	-	cyt	0					419
O35309 UniProt NPD GO	NMI_MOUSE	N-myc-interactor (Nmi) (N-myc and STAT interactor)	0.15	-	cyt	0	Cytoplasm				314
Q8CHK7 UniProt NPD GO	NQO1_CAVPO	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2) (Quinone reductase 1) (NAD(P)H:quinone oxidoreductase ...	0.15	-	mit	0	Cytoplasm (By similarity)				275
P26690 UniProt NPD GO	6DCS_SOYBN	NAD(P)H-dependent 6'-deoxychalcone synthase (EC 2.3.1.170)	0.15	-	cyt	0					315
P56752 UniProt NPD GO	NU5C_ARATH	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.15	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				746
Q8WHX3 UniProt NPD GO	NUCC_PSINU	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.15	-	cyt	0	Plastid; chloroplast				393
P12199 UniProt NPD GO	NUGC_MARPO	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.15	-	cyt	0	Plastid; chloroplast				169
Q8M9T7 UniProt NPD GO	NUIC_CHAGL	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.15	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				182
Q99KE1 UniProt NPD GO	MAOM_MOUSE	NAD-dependent malic enzyme, mitochondrial precursor (EC 1.1.1.38) (NAD-ME) (Malic enzyme 2)	0.15	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				589
P24919 UniProt NPD GO	NDUA5_NEUCR	NADH-ubiquinone oxidoreductase 29.9 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) ...	0.15	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				273
P17694 UniProt NPD GO	NUCM_BOVIN	NADH-ubiquinone oxidoreductase 49 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-49KD) (CI-49KD)	0.15	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side				430
O75306 UniProt NPD GO	NUCM_HUMAN	NADH-ubiquinone oxidoreductase 49 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.15	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side		602985		463
P15690 UniProt NPD GO	NUAM_BOVIN	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.15	-	mit	0	Mitochondrion; mitochondrial inner membrane				727
Q91VD9 UniProt NPD GO	NUAM_MOUSE	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.15	-	nuc	0	Mitochondrion; mitochondrial inner membrane (By similarity). Matrix and cytoplasmic side of the mito ...	mitochondrion [IDA]			727
P24968 UniProt NPD GO	NU1M_COTJA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.15	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
P48899 UniProt NPD GO	NU1M_CYACA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.15	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				344
Q85PQ7 UniProt NPD GO	NU2M_CYNPE	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.15	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P92476 UniProt NPD GO	NU2M_EQUAS	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.15	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
P48905 UniProt NPD GO	NU2M_FELCA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.15	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q38PS1 UniProt NPD GO	NU2M_MAMPR	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.15	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q85PQ3 UniProt NPD GO	NU2M_NANBI	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.15	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q2TGY4 UniProt NPD GO	NU2M_NASNA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.15	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
O79875 UniProt NPD GO	NU2M_PIG	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.15	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q9ZZ53 UniProt NPD GO	NU2M_SQUAC	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.15	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348
Q4JQI6 UniProt NPD GO	NU2M_TETNG	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.15	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348
Q534D9 UniProt NPD GO	NU2M_VULVU	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.15	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q34878 UniProt NPD GO	NU4M_LEMCA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.15	-	end	12 *					459
P24998 UniProt NPD GO	NU4M_PISOC	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.15	-	end	13 *					460
Q35541 UniProt NPD GO	NU4LM_PETMA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.15	-	end	3 *					96
P24978 UniProt NPD GO	NU5M_BALPH	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.15	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
Q8W9M6 UniProt NPD GO	NU5M_DUGDU	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.15	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				603
O03174 UniProt NPD GO	NU5M_LATCH	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.15	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				611
P92669 UniProt NPD GO	NU5M_MACRO	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.15	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				602
Q37314 UniProt NPD GO	NU6M_DICDI	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.15	-	end	5 *					226
Q9Y5S8 UniProt NPD GO	NOX1_HUMAN	NADPH oxidase homolog 1 (NOX-1) (NOH-1) (NADH/NADPH mitogenic oxidase subunit P65-MOX) (Mitogenic ox ...	0.15	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]	300225		564
Q9WV87 UniProt NPD GO	NOX1_RAT	NADPH oxidase homolog 1 (NOX-1) (NOH-1) (NADH/NADPH mitogenic oxidase subunit P65-MOX) (Mitogenic ox ...	0.15	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				563
Q7SXP2 UniProt NPD GO	ULA1_BRARE	NEDD8-activating enzyme E1 regulatory subunit (Amyloid protein-binding protein 1) (APP-BP1)	0.15	-	nuc	0					533
P61081 UniProt NPD GO	UBC12_HUMAN	NEDD8-conjugating enzyme Ubc12 (EC 6.3.2.-) (Ubiquitin-conjugating enzyme E2 M) (NEDD8 protein ligas ...	0.15	-	nuc	0			603173	1Y8X	183
P61082 UniProt NPD GO	UBC12_MOUSE	NEDD8-conjugating enzyme Ubc12 (EC 6.3.2.-) (Ubiquitin-conjugating enzyme E2 M) (NEDD8 protein ligas ...	0.15	-	nuc	0					183
Q6DCZ9 UniProt NPD GO	UBC12_XENLA	NEDD8-conjugating enzyme Ubc12 (EC 6.3.2.-) (Ubiquitin-conjugating enzyme E2 M) (NEDD8 protein ligas ...	0.15	-	nuc	0					183
O94760 UniProt NPD GO	DDAH1_HUMAN	NG,NG-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18) (Dimethylargininase-1) (Dimethylargini ...	0.15	-	cyt	0			604743		284
Q05965 UniProt NPD GO	FL3H_MATIN	Naringenin,2-oxoglutarate 3-dioxygenase (EC 1.14.11.9) (Flavonone-3-hydroxylase) (F3H) (FHT) (Fragme ...	0.15	-	cyt	0					357

You are viewing entries 57251 to 57300 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.