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
Q96WJ0 UniProt NPD GO	ERG7_PNECA	Lanosterol synthase (EC 5.4.99.7) (Oxidosqualene--lanosterol cyclase) (2,3-epoxysqualene--lanosterol ...	0.35	-	mit	0					719
P46532 UniProt NPD GO	LE19B_HORVU	Late embryogenesis abundant protein B19.1B	0.35	-	nuc	0					93
Q8JI38 UniProt NPD GO	CRVP_LATSE	Latisemin precursor	0.35	-	exc	0	Secreted protein				238
P50596 UniProt NPD GO	LEP_RAT	Leptin precursor (Obesity factor)	0.35	-	exc	0	Secreted protein (Probable)				167
O94257 UniProt NPD GO	LCMT1_SCHPO	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.35	-	cyt	0					310
Q5BKY1 UniProt NPD GO	LRC10_HUMAN	Leucine-rich repeat-containing protein 10	0.35	-	nuc	0	Nucleus (By similarity)				277
P41737 UniProt NPD GO	LRCH1_FELCA	Leucine-rich repeats and calponin homology domain-containing protein 1 (Neuronal protein) (Fragment) ...	0.35	-	nuc	0					251
Q5R482 UniProt NPD GO	LRRN3_PONPY	Leucine-rich repeats neuronal protein 3 precursor (Neuronal leucine-rich repeat protein 3) (NLRR-3)	0.35	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				708
O75325 UniProt NPD GO	LRRN5_HUMAN	Leucine-rich repeats neuronal protein 5 precursor (Glioma amplified on chromosome 1 protein)	0.35	-	end	1	Membrane; single-pass type I membrane protein (Potential)		605492		713
Q61211 UniProt NPD GO	LIGA_MOUSE	Ligatin	0.35	-	mit	0	Membrane; peripheral membrane				570
Q9JIT0 UniProt NPD GO	LMBR1_MOUSE	Limb region 1 protein	0.35	-	end	9 *	Membrane; multi-pass membrane protein (By similarity)				490
Q08108 UniProt NPD GO	PLB3_YEAST	Lysophospholipase 3 precursor (EC 3.1.1.5) (Phospholipase B 3)	0.35	-	exc	0	Secreted protein (Potential)	extracellular region [IDA]			686
P12526 UniProt NPD GO	MAS_RAT	MAS proto-oncogene	0.35	-	end	7 *	Membrane; multi-pass membrane protein				324
P49300 UniProt NPD GO	MMGL_MOUSE	Macrophage asialoglycoprotein-binding protein 1 (M-ASGP-BP) (Macrophage galactose/N-acetylgalactosam ...	0.35	-	cyt	1 *	Membrane; single-pass type II membrane protein				304
Q9WVL0 UniProt NPD GO	MAAI_MOUSE	Maleylacetoacetate isomerase (EC 5.2.1.2) (MAAI) (Glutathione S-transferase zeta 1) (EC 2.5.1.18) (G ...	0.35	-	mit	0	Cytoplasm (By similarity)	mitochondrion [IDA]		2CZ3	216
P12617 UniProt NPD GO	DCMC_ANSAN	Malonyl-CoA decarboxylase, mitochondrial precursor (EC 4.1.1.9) (MCD)	0.35	-	pox	0	Mitochondrion. In liver. Cytoplasm. In uropygial gland. Peroxisome				504
Q28889 UniProt NPD GO	KIT_FELCA	Mast/stem cell growth factor receptor precursor (EC 2.7.10.1) (SCFR) (Proto-oncogene tyrosine-protei ...	0.35	-	end	2	Membrane; single-pass type I membrane protein				978
P19788 UniProt NPD GO	MGP_MOUSE	Matrix Gla-protein precursor (MGP)	0.35	-	exc	0	Secreted protein				104
P07507 UniProt NPD GO	MGP_BOVIN	Matrix Gla-protein precursor (MGP) [Contains: Matrix Gla-protein long form; Matrix Gla-protein short ...	0.35	-	exc	0	Secreted protein				103
Q58T83 UniProt NPD GO	M3H33_BOMMX	Maximins 3/H3 type 3 precursor [Contains: Maximin-3; Maximin-H3]	0.35	-	end	0	Secreted protein				144
Q27433 UniProt NPD GO	MEC2_CAEEL	Mechanosensory protein 2	0.35	-	nuc	1					481
Q9D7W5 UniProt NPD GO	MED8_MOUSE	Mediator of RNA polymerase II transcription subunit 8 homolog (Activator-recruited cofactor 32 kDa c ...	0.35	-	nuc	0	Nucleus (By similarity)				268
Q9UHM6 UniProt NPD GO	OPN4_HUMAN	Melanopsin (Opsin-4)	0.35	-	end	6	Membrane; multi-pass membrane protein. Found in soma, dendrites and proximal part of axons of certai ...	integral to membrane [NAS]	606665		478
Q9SWR3 UniProt NPD GO	MMT1_WOLBI	Methionine S-methyltransferase (EC 2.1.1.12) (AdoMet:Met S-methyltransferase)	0.35	-	nuc	0	Cytoplasm				1088
Q62000 UniProt NPD GO	MIME_MOUSE	Mimecan precursor (Osteoglycin)	0.35	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				298
Q9BDJ7 UniProt NPD GO	MCR_SHEEP	Mineralocorticoid receptor (MR) (Fragment)	0.35	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic and nuclear in the absence of ligand ...				258
Q9CQ40 UniProt NPD GO	RM49_MOUSE	Mitochondrial 39S ribosomal protein L49 (L49mt) (MRP-L49)	0.35	-	mit	0	Mitochondrion	mitochondrion [IDA]			166
P46764 UniProt NPD GO	RM05_ACACA	Mitochondrial 60S ribosomal protein L5	0.35	-	mit	1	Mitochondrion				177
P46749 UniProt NPD GO	RM05_PROWI	Mitochondrial 60S ribosomal protein L5	0.35	-	nuc	0	Mitochondrion				231
P41905 UniProt NPD GO	MRS1_SACDO	Mitochondrial RNA-splicing protein MRS1	0.35	-	mit	0					363
Q6NVC5 UniProt NPD GO	MIRO1_BRARE	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (MIRO-1) (Ras homolog gene family member T1)	0.35	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				619
Q9CZP5 UniProt NPD GO	BCS1_MOUSE	Mitochondrial chaperone BCS1 (BCS1-like protein)	0.35	-	cyt	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				418
P59942 UniProt NPD GO	MCCD1_HUMAN	Mitochondrial coiled-coil domain protein 1, mitochondrial precursor	0.35	-	nuc	0	Mitochondrion		609624		119
Q9VTN3 UniProt NPD GO	TIM13_DROME	Mitochondrial import inner membrane translocase subunit Tim13	0.35	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				92
Q9M1Z5 UniProt NPD GO	MPK10_ARATH	Mitogen-activated protein kinase 10 (EC 2.7.11.24) (MAP kinase 10) (AtMPK10)	0.35	-	cyt	0					393
O61443 UniProt NPD GO	MK14B_DROME	Mitogen-activated protein kinase 14B (EC 2.7.11.24) (MAP kinase p38b) (D-p38b)	0.35	-	mit	0	Nucleus	nucleus [NAS]			365
Q9DGE1 UniProt NPD GO	MK14B_BRARE	Mitogen-activated protein kinase 14b (EC 2.7.11.24) (Mitogen-activated protein kinase p38b) (MAP kin ...	0.35	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				348
Q40884 UniProt NPD GO	MAPK_PETHY	Mitogen-activated protein kinase homolog 1 (EC 2.7.11.24) (PMEK1)	0.35	-	cyt	0					384
P91753 UniProt NPD GO	MP62_LYTPI	Mitotic apparatus protein p62	0.35	-	exc	0	Nucleus				411
P53988 UniProt NPD GO	MOT2_MESAU	Monocarboxylate transporter 2 (MCT 2)	0.35	-	end	11 *	Cell membrane; multi-pass membrane protein (By similarity)				484
P84024 UniProt NPD GO	SMAD3_PIG	Mothers against decapentaplegic homolog 3 (SMAD 3) (Mothers against DPP homolog 3) (Mad3)	0.35	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...				425
P84025 UniProt NPD GO	SMAD3_RAT	Mothers against decapentaplegic homolog 3 (SMAD 3) (Mothers against DPP homolog 3) (Mad3)	0.35	-	nuc	0	Cytoplasm. In the cytoplasm in the absence of ligand. Nucleus. Migration to the nucleus when complex ...				425
P84022 UniProt NPD GO	SMAD3_HUMAN	Mothers against decapentaplegic homolog 3 (SMAD 3) (Mothers against DPP homolog 3) (Mad3) (hMAD-3) ( ...	0.35	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...	intracellular [IC]	603109	1U7F	425
Q8BUN5 UniProt NPD GO	SMAD3_MOUSE	Mothers against decapentaplegic homolog 3 (SMAD 3) (Mothers against DPP homolog 3) (Mad3) (mMad3)	0.35	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...	nucleus [IDA] plasma membrane [IDA]			425
Q9GKQ9 UniProt NPD GO	SMAD4_PIG	Mothers against decapentaplegic homolog 4 (SMAD 4) (Mothers against DPP homolog 4) (Smad4)	0.35	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...				552
Q99MP5 UniProt NPD GO	MOTI_CAVPO	Motilin precursor [Contains: Motilin; Motilin-associated peptide (MAP)]	0.35	-	mit	0	Secreted protein				127
Q9LJX0 UniProt NPD GO	MDR11_ARATH	Multidrug resistance protein 11 (P-glycoprotein 19)	0.35	-	end	10 *	Cell membrane; multi-pass membrane protein (Probable)				1252
Q9NR56 UniProt NPD GO	MBNL_HUMAN	Muscleblind-like protein (Triplet-expansion RNA-binding protein)	0.35	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]	606516		388
P56670 UniProt NPD GO	MAZ_MESAU	Myc-associated zinc finger protein (MAZI) (Purine-binding transcription factor) (Pur-1) (Fragment)	0.35	-	nuc	0	Nucleus				331
P29294 UniProt NPD GO	MYLK_RABIT	Myosin light chain kinase, smooth muscle (EC 2.7.11.18) (MLCK) (Telokin)	0.35	-	nuc	0					1147

You are viewing entries 36001 to 36050 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.