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
P49139 UniProt NPD GO	MAPK2_RABIT	MAP kinase-activated protein kinase 2 (EC 2.7.11.1) (MAPK-activated protein kinase 2) (MAPKAP kinase ...	0.34	-	cyt	0					330
P40484 UniProt NPD GO	MOB1_YEAST	Maintenance of ploidy protein MOB1 (MPS1 binder 1)	0.34	-	cyt	0		bud neck [IDA] spindle pole body [IDA]			236
Q9GSU4 UniProt NPD GO	HSP72_DROSI	Major heat shock 70 kDa protein Ba (Heat shock protein Hsp70Ba) (HSP70-87C1)	0.34	-	cyt	0					643
Q40240 UniProt NPD GO	MPA5A_LOLPR	Major pollen allergen Lol p 5a precursor (Lol p Va) (Lol p Ib)	0.34	-	nuc	0	Starch granule				308
Q5R9N2 UniProt NPD GO	MVP_PONPY	Major vault protein (MVP)	0.34	-	cyt	0	Cytoplasm (By similarity)				892
Q14764 UniProt NPD GO	MVP_HUMAN	Major vault protein (MVP) (Lung resistance-related protein)	0.34	-	cyt	0	Cytoplasm. 5%: Nucleus; nuclear envelope; nuclear pore complex. Translocates from the nucleus to the ...	cytoplasm [TAS] nucleus [TAS]	605088	1Y7X	892
Q9DD48 UniProt NPD GO	MKRN2_SERQU	Makorin-2 (Zinc finger protein YGHLC3HC4)	0.34	-	nuc	0					423
P24571 UniProt NPD GO	MASY_CUCMA	Malate synthase, glyoxysomal (EC 2.3.3.9)	0.34	-	cyt	0	Glyoxysome				566
O13065 UniProt NPD GO	MMP18_XENLA	Matrix metalloproteinase-18 precursor (EC 3.4.24.-) (MMP-18) (Collagenase-4) (xCol4)	0.34	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				467
Q58T43 UniProt NPD GO	M3H15_BOMMX	Maximins 3/H15 precursor [Contains: Maximin-3; Maximin-H15]	0.34	-	end	0	Secreted protein				144
Q96G25 UniProt NPD GO	MED8_HUMAN	Mediator of RNA polymerase II transcription subunit 8 homolog (Activator-recruited cofactor 32 kDa c ...	0.34	-	nuc	0	Nucleus	mediator complex [IDA]	607956		268
O88174 UniProt NPD GO	MCP_MOUSE	Membrane cofactor protein precursor (CD46 antigen)	0.34	-	end	2 *	Acrosome; acrosomal inner membrane; single-pass type I membrane protein. Inner acrosomal membrane of ...				365
Q9Z0M4 UniProt NPD GO	MCP_RAT	Membrane cofactor protein precursor (CD46 antigen)	0.34	-	nuc	2 *	Acrosome; acrosomal inner membrane; multi-pass membrane protein. Inner acrosomal membrane of spermat ...				355
Q9QXY7 UniProt NPD GO	XK_MOUSE	Membrane transport protein XK (XK-related protein 1) (XK homolog)	0.34	-	end	9 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			446
P50496 UniProt NPD GO	MSA2_PLAF1	Merozoite surface antigen 2 precursor (MSA-2)	0.34	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				286
P50497 UniProt NPD GO	MSA2_PLAF6	Merozoite surface antigen 2 precursor (MSA-2)	0.34	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				274
P42898 UniProt NPD GO	MTHR_HUMAN	Methylenetetrahydrofolate reductase (EC 1.5.1.20)	0.34	-	cyt	0			607093		656
Q5RFU5 UniProt NPD GO	MMAC_BRARE	Methylmalonic aciduria and homocystinuria type C homolog	0.34	-	cyt	0					250
P55001 UniProt NPD GO	MFAP2_HUMAN	Microfibrillar-associated protein 2 precursor (MFAP-2) (Microfibril-associated glycoprotein) (MAGP) ...	0.34	-	exc	0	Secreted protein; extracellular space; extracellular matrix		156790		183
P27424 UniProt NPD GO	MFAP2_BOVIN	Microfibrillar-associated protein 2 precursor (MFAP-2) (Microfibril-associated glycoprotein) (MAGP) ...	0.34	-	exc	0	Secreted protein; extracellular space; extracellular matrix				183
Q9QZJ6 UniProt NPD GO	MFAP5_MOUSE	Microfibrillar-associated protein 5 precursor (MFAP-5) (Microfibril-associated glycoprotein 2) (MAGP ...	0.34	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	microfibril [TAS]			164
Q9BXW4 UniProt NPD GO	MLP3C_HUMAN	Microtubule-associated proteins 1A/1B light chain 3C precursor (Microtubule-associated protein 1 lig ...	0.34	-	nuc	0	LC3-I: Cytoplasm. LC3-II: Intracytoplasmic membrane; lipid-anchor. LC3-II binds to the autophagic me ...	autophagic vacuole [ISS] organelle membrane [ISS]	609605		147
P81474 UniProt NPD GO	MISG_MISAN	Misgurin	0.34	-	nuc	0	Secreted protein				21
P49389 UniProt NPD GO	RM16_BRANA	Mitochondrial 60S ribosomal protein L16	0.34	-	mit	0	Mitochondrion				177
P26862 UniProt NPD GO	RM16_MARPO	Mitochondrial 60S ribosomal protein L16	0.34	-	nuc	0	Mitochondrion				135
Q5AF54 UniProt NPD GO	TIM13_CANAL	Mitochondrial import inner membrane translocase subunit TIM13	0.34	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				109
Q59SI2 UniProt NPD GO	TIM14_CANAL	Mitochondrial import inner membrane translocase subunit TIM14 (Presequence translocated-associated m ...	0.34	-	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				157
P48990 UniProt NPD GO	TIM54_CANAL	Mitochondrial import inner membrane translocase subunit TIM54	0.34	-	cyt	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				400
Q9Y0V3 UniProt NPD GO	TIM9B_DROME	Mitochondrial import inner membrane translocase subunit Tim9B (Tim10b)	0.34	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				117
Q9VFB2 UniProt NPD GO	RT10_DROME	Mitochondrial ribosomal protein S10 (MRP-S10)	0.34	-	mit	0	Mitochondrion (By similarity)	mitochondrial ribosome [ISS]			173
P26872 UniProt NPD GO	RT13_MARPO	Mitochondrial ribosomal protein S13	0.34	-	nuc	0	Mitochondrion				120
P27361 UniProt NPD GO	MK03_HUMAN	Mitogen-activated protein kinase 3 (EC 2.7.11.24) (Extracellular signal-regulated kinase 1) (ERK-1) ...	0.34	-	cyt	0			601795		379
Q9ERH6 UniProt NPD GO	MOAP1_MOUSE	Modulator of apoptosis 1 (MAP-1)	0.34	+	nuc	0					352
Q03835 UniProt NPD GO	GLRX3_YEAST	Monothiol glutaredoxin-3	0.34	-	mit	0		intracellular [TAS] nucleus [IDA]			285
O18845 UniProt NPD GO	MOTI_SHEEP	Motilin precursor [Contains: Motilin; Motilin-associated peptide (MAP)]	0.34	-	exc	0	Secreted protein				115
Q96BX8 UniProt NPD GO	MOL2A_HUMAN	Mps one binder kinase activator-like 2A (Mob1 homolog 2A) (MOB-LAK) (Protein Mob3A)	0.34	-	nuc	0					217
Q8TDD5 UniProt NPD GO	MCLN3_HUMAN	Mucolipin-3	0.34	-	end	5	Membrane; multi-pass membrane protein (Potential)		607400		553
P21439 UniProt NPD GO	MDR3_HUMAN	Multidrug resistance protein 3 (EC 3.6.3.44) (P-glycoprotein 3)	0.34	-	end	10	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	602347		1279
Q9C8H0 UniProt NPD GO	MRP13_ARATH	Multidrug resistance-associated protein 13 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPas ...	0.34	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				1495
O95255 UniProt NPD GO	MRP6_HUMAN	Multidrug resistance-associated protein 6 (ATP-binding cassette sub-family C member 6) (Anthracyclin ...	0.34	-	end	12 *	Membrane; multi-pass membrane protein (By similarity)	plasma membrane [TAS]	603234		1503
P56270 UniProt NPD GO	MAZ_HUMAN	Myc-associated zinc finger protein (MAZI) (Purine-binding transcription factor) (Pur-1) (ZF87) (ZIF8 ...	0.34	-	nuc	0	Nucleus (Probable)		600999		477
Q99750 UniProt NPD GO	MDFI_HUMAN	MyoD family inhibitor (Myogenic repressor I-mf)	0.34	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [TAS]	604971		246
P19626 UniProt NPD GO	MLR2_CAEEL	Myosin regulatory light chain 2	0.34	-	mit	0					170
Q84WP6 UniProt NPD GO	NAC43_ARATH	NAC domain-containing protein 43 (ANAC043) (NAC SECONDARY WALL THICKENING PROMOTING FACTOR 1) (Prote ...	0.34	-	nuc	0	Nucleus (Probable)				365
Q8HVU9 UniProt NPD GO	NUIC_CHAST	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.34	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				166
Q2L959 UniProt NPD GO	NUIC_GOSHI	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.34	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
Q8IXJ6 UniProt NPD GO	SIRT2_HUMAN	NAD-dependent deacetylase sirtuin-2 (EC 3.5.1.-) (SIR2-like) (SIR2-like protein 2)	0.34	-	nuc	0	Cytoplasm. Colocalizes with microtubules	chromatin silencing complex [NAS] cytoplasm [IDA] microtubule [IDA]	604480	1J8F	389
Q12644 UniProt NPD GO	NUIM_NEUCR	NADH-ubiquinone oxidoreductase 23 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.34	-	mit	0					219
P03907 UniProt NPD GO	NU4M_GORGO	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.34	-	end	12 *					459
Q85DA7 UniProt NPD GO	NU4M_LEPST	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.34	-	end	11 *					459

You are viewing entries 36851 to 36900 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.