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
Q9Y5J7 UniProt NPD GO	TIM9_HUMAN	Mitochondrial import inner membrane translocase subunit Tim9	0.22	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side	mitochondrial inner membrane presequence tr... [TAS]	607384	2BSK	89
Q8J1Z1 UniProt NPD GO	TIM9_NEUCR	Mitochondrial import inner membrane translocase subunit tim-9	0.22	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side				88
P48945 UniProt NPD GO	RT14_CHLS6	Mitochondrial ribosomal protein S14 (Fragment)	0.22	-	mit	0	Mitochondrion				53
Q9VAY3 UniProt NPD GO	MFRN_DROME	Mitoferrin	0.22	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [ISS]			379
P63085 UniProt NPD GO	MK01_MOUSE	Mitogen-activated protein kinase 1 (EC 2.7.11.24) (Extracellular signal-regulated kinase 2) (ERK-2) ...	0.22	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			357
P63086 UniProt NPD GO	MK01_RAT	Mitogen-activated protein kinase 1 (EC 2.7.11.24) (Extracellular signal-regulated kinase 2) (ERK-2) ...	0.22	-	cyt	0				4ERK	357
Q9WUI1 UniProt NPD GO	MK11_MOUSE	Mitogen-activated protein kinase 11 (EC 2.7.11.24) (Mitogen-activated protein kinase p38 beta) (MAP ...	0.22	-	cyt	0					364
P47811 UniProt NPD GO	MK14_MOUSE	Mitogen-activated protein kinase 14 (EC 2.7.11.24) (Mitogen-activated protein kinase p38 alpha) (MAP ...	0.22	-	cyt	0	Cytoplasm. Nucleus	cell [IDA] cytoplasm [IDA] nucleus [IDA] spindle pole [IDA]		1YWR	359
P21708 UniProt NPD GO	MK03_RAT	Mitogen-activated protein kinase 3 (EC 2.7.11.24) (Extracellular signal-regulated kinase 1) (ERK-1) ...	0.22	-	cyt	0	Isoform B: Nucleus	cytosol [IDA] insoluble fraction [IDA]			380
Q39024 UniProt NPD GO	MPK4_ARATH	Mitogen-activated protein kinase 4 (EC 2.7.11.24) (MAP kinase 4) (AtMPK4)	0.22	-	cyt	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation (Probable)				376
Q92207 UniProt NPD GO	HOG1_CANAL	Mitogen-activated protein kinase HOG1 (EC 2.7.11.24) (MAP kinase HOG1)	0.22	-	cyt	0					377
Q40531 UniProt NPD GO	NTF6_TOBAC	Mitogen-activated protein kinase homolog NTF6 (EC 2.7.11.24) (P43)	0.22	-	cyt	0					371
O35308 UniProt NPD GO	MOT3_MOUSE	Monocarboxylate transporter 3 (MCT 3) (Proton-coupled monocarboxylate transporter 3)	0.22	-	end	12 *	Cell membrane; multi-pass membrane protein				492
Q90632 UniProt NPD GO	MOT3_CHICK	Monocarboxylate transporter 3 (MCT 3) (Retinal epithelial membrane protein)	0.22	+	end	12 *	Cell membrane; multi-pass membrane protein				542
P57787 UniProt NPD GO	MOT4_MOUSE	Monocarboxylate transporter 4 (MCT 4)	0.22	-	end	12 *	Cell membrane; multi-pass membrane protein (By similarity)				470
Q63691 UniProt NPD GO	CD14_RAT	Monocyte differentiation antigen CD14 precursor (Myeloid cell-specific leucine-rich glycoprotein)	0.22	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	lipopolysaccharide receptor complex [IEP]			371
O75425 UniProt NPD GO	MSPD3_HUMAN	Motile sperm domain-containing protein 3	0.22	-	end	2	Membrane; multi-pass membrane protein (Potential)		609125		235
Q8C854 UniProt NPD GO	MYEF2_MOUSE	Myelin expression factor 2 (MyEF-2) (MEF-2)	0.22	-	cyt	0	Nucleus				591
Q9P2K5 UniProt NPD GO	MYEF2_HUMAN	Myelin expression factor 2 (MyEF-2) (MST156)	0.22	-	nuc	0	Nucleus				600
O00934 UniProt NPD GO	MYOA_TOXGO	Myosin A (MyoA) (TgM-A)	0.22	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Tightly associated with the plasma mem ...				831
Q63518 UniProt NPD GO	MYPC1_RAT	Myosin-binding protein C, slow-type (Slow MyBP-C) (C-protein, skeletal muscle slow-isoform) (Fragmen ...	0.22	-	nuc	0					621
P24334 UniProt NPD GO	MYX4_CRODU	Myotoxin-4 precursor (Crotamine-4) (Fragment)	0.22	-	nuc	0	Secreted protein				51
Q13613 UniProt NPD GO	MTMR1_HUMAN	Myotubularin-related protein 1 (EC 3.1.3.-)	0.22	-	cyt	0			300171		665
P81612 UniProt NPD GO	MYTA_MYTED	Mytilin-A	0.22	-	nuc	0	Secreted protein				34
Q90WG6 UniProt NPD GO	NEUA_ONCMY	N-acylneuraminate cytidylyltransferase (EC 2.7.7.43) (CMP-N-acetylneuraminic acid synthetase) (CMP-N ...	0.22	+	nuc	0	Nucleus (Probable)				432
Q32539 UniProt NPD GO	NU5C_LACSA	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.22	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				742
Q6ENB0 UniProt NPD GO	NU5C_ORYNI	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.22	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				734
P12129 UniProt NPD GO	NU5C_ORYSA	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.22	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				734
Q33066 UniProt NPD GO	NU5C_SORBI	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.22	-	end	14 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				702
Q6L3D4 UniProt NPD GO	NUCC_SACHY	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.22	-	cyt	0	Plastid; chloroplast				393
Q6ENP1 UniProt NPD GO	NUCC_SACOF	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.22	-	cyt	0	Plastid; chloroplast				393
Q25337 UniProt NPD GO	SIR2_LEIMA	NAD-dependent deacetylase SIR2 homolog (EC 3.5.1.-) (LMSIR2RP)	0.22	-	mit	0	Nucleus (Potential)				381
Q9CXZ1 UniProt NPD GO	NUYM_MOUSE	NADH-ubiquinone oxidoreductase 18 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.22	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)	mitochondrion [IDA] respiratory chain complex I (sensu Eukaryota) [IDA]			175
Q94VI4 UniProt NPD GO	NU1M_VARFL	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.22	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				319
O05000 UniProt NPD GO	NU2M_ARATH	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.22	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				499
P24970 UniProt NPD GO	NU2M_BALPH	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.22	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q96061 UniProt NPD GO	NU2M_RHIUN	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.22	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P24975 UniProt NPD GO	NU4M_BALPH	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.22	-	end	13 *					459
Q38PR3 UniProt NPD GO	NU4M_MAMPR	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.22	-	end	12 *					455
Q591Y7 UniProt NPD GO	NU4M_MICSM	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.22	-	end	12 *					459
Q9G2W9 UniProt NPD GO	NU4M_MYXGL	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.22	-	end	13 *					458
P03912 UniProt NPD GO	NU4M_XENLA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.22	-	end	10 *					461
Q35648 UniProt NPD GO	NU5M_PANTR	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.22	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				603
Q35543 UniProt NPD GO	NU5M_PETMA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.22	-	end	13 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				598
Q96069 UniProt NPD GO	NU5M_RHIUN	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.22	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
P16435 UniProt NPD GO	NCPR_HUMAN	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.22	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Anchored to the ...	endoplasmic reticulum [TAS]	124015	1B1C	676
P22570 UniProt NPD GO	ADRO_HUMAN	NADPH:adrenodoxin oxidoreductase, mitochondrial precursor (EC 1.18.1.2) (Adrenodoxin reductase) (AR) ...	0.22	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	103270		491
P82861 UniProt NPD GO	ADRO_SALFO	NADPH:adrenodoxin oxidoreductase, mitochondrial precursor (EC 1.18.1.2) (Adrenodoxin reductase) (AR) ...	0.22	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				498
Q01345 UniProt NPD GO	NHEB_ONCMY	Na(+)/H(+) exchanger beta (Na(+)/H(+) antiporter) (Beta-NHE)	0.22	-	end	13 *	Cell membrane; basolateral cell membrane; multi-pass membrane protein				759
Q8WY41 UniProt NPD GO	NANO1_HUMAN	Nanos homolog 1 (NOS-1) (EC_Rep1a)	0.22	-	nuc	0	Cytoplasm; perinuclear region	cytoplasm [IDA]	608226		292

You are viewing entries 48651 to 48700 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.