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
Q8CBC6 UniProt NPD GO	LRRN3_MOUSE	Leucine-rich repeats neuronal protein 3 precursor (Neuronal leucine-rich repeat protein 3) (NLRR-3)	0.25	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				707
Q9P2J5 UniProt NPD GO	SYLC_HUMAN	Leucyl-tRNA synthetase, cytoplasmic (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS)	0.25	-	cyt	0	Cytoplasm (By similarity)		151350		1176
Q3UP87 UniProt NPD GO	ELNE_MOUSE	Leukocyte elastase precursor (EC 3.4.21.37) (Elastase-2) (Neutrophil elastase)	0.25	-	exc	0					265
P36208 UniProt NPD GO	CHLB_GINBI	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.25	-	cyt	0	Plastid; chloroplast				513
Q28880 UniProt NPD GO	LAP_BOVIN	Lingual antimicrobial peptide precursor	0.25	-	mit	1 *	Secreted protein				64
O60135 UniProt NPD GO	LCF1_SCHPO	Long-chain-fatty-acid--CoA ligase 1 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 1) (Fatty acid acti ...	0.25	-	nuc	0					676
P50895 UniProt NPD GO	LU_HUMAN	Lutheran blood group glycoprotein precursor (B-CAM cell surface glycoprotein) (Auberger B antigen) ( ...	0.25	-	nuc	1	Membrane; single-pass type I membrane protein	cell surface [IEP] integral to plasma membrane [TAS] plasma membrane [TAS]	111200		628
Q8N2G4 UniProt NPD GO	LYPD1_HUMAN	Ly6/PLAUR domain-containing protein 1 precursor	0.25	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)				141
O88188 UniProt NPD GO	LY86_MOUSE	Lymphocyte antigen 86 precursor (MD-1 protein)	0.25	-	exc	0	Secreted protein; extracellular space. Associated with CD180 at the cell surface				162
P37879 UniProt NPD GO	SYK_CRIGR	Lysyl-tRNA synthetase (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS)	0.25	-	cyt	0	Cytoplasm				597
O49621 UniProt NPD GO	MLO1_ARATH	MLO-like protein 1 (AtMlo1) (MLO protein homolog 1) (AtMLO-H1)	0.25	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				526
Q94KB9 UniProt NPD GO	MLO3_ARATH	MLO-like protein 3 (AtMlo3)	0.25	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				508
Q10746 UniProt NPD GO	MIP2A_RAT	Macrophage inflammatory protein 2-alpha (MIP2-alpha) (CINC-2-alpha)	0.25	-	nuc	0	Secreted protein				68
P21757 UniProt NPD GO	MSRE_HUMAN	Macrophage scavenger receptor types I and II (Macrophage acetylated LDL receptor I and II) (Scavenge ...	0.25	-	mit	1	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]	153622		451
Q01239 UniProt NPD GO	HCC1_CRYCO	Major basic nuclear protein 1 (Protein p14 alpha/beta chain)	0.25	-	cyt	0	Nucleus				113
Q5BLZ2 UniProt NPD GO	M6PBP_PIG	Mannose-6-phosphate receptor-binding protein 1 (Cargo selection protein TIP47)	0.25	-	cyt	0	Cytoplasm (By similarity). Endosome (By similarity). Membrane associated on endosomes. Detected in t ...				439
P15088 UniProt NPD GO	CBPA3_HUMAN	Mast cell carboxypeptidase A precursor (EC 3.4.17.1) (MC-CPA) (Carboxypeptidase A3)	0.25	-	exc	0	Secretory granules	secretory granule [NAS]	114851		417
P55032 UniProt NPD GO	MMP7_FELCA	Matrilysin precursor (EC 3.4.24.23) (Pump-1 protease) (Uterine metalloproteinase) (Matrix metallopro ...	0.25	-	mit	0					262
P53690 UniProt NPD GO	MMP14_MOUSE	Matrix metalloproteinase-14 precursor (EC 3.4.24.80) (MMP-14) (Membrane-type matrix metalloproteinas ...	0.25	-	end	1	Membrane; single-pass type I membrane protein (Potential)				582
Q5R4T7 UniProt NPD GO	MKKS_PONPY	McKusick-Kaufman/Bardet-Biedl syndromes putative chaperonin	0.25	-	cyt	0					570
Q5REZ6 UniProt NPD GO	M4A10_PONPY	Membrane-spanning 4-domains subfamily A member 10	0.25	-	end	3	Membrane; multi-pass membrane protein (By similarity)				264
O00255 UniProt NPD GO	MEN1_HUMAN	Menin	0.25	-	mit	0	Nucleus. Concentrated in nuclear body-like structures. Relocates to the nuclear matrix upon gamma ir ...	histone methyltransferase complex [IDA] nucleus [IDA]	145000		615
P12032 UniProt NPD GO	TIMP1_MOUSE	Metalloproteinase inhibitor 1 precursor (TIMP-1) (Erythroid potentiating activity) (EPA) (Tissue inh ...	0.25	-	nuc	0	Secreted protein	basement membrane [IDA]			205
P27087 UniProt NPD GO	MTB_COLVI	Metallothionein B (MTB) (Fragment)	0.25	-	nuc	0					43
Q9FV50 UniProt NPD GO	AMP1D_ARATH	Methionine aminopeptidase 1D, chloroplast/mitochondrial precursor (EC 3.4.11.18) (MetAP 1D) (MAP 1D) ...	0.25	-	mit	0	Plastid; chloroplast. Mitochondrion				350
Q7T0Z0 UniProt NPD GO	SYMM_XENLA	Methionyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.10) (Methionine--tRNA ligase 2) (Mitoch ...	0.25	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				562
Q5E9C8 UniProt NPD GO	MMAC_BOVIN	Methylmalonic aciduria and homocystinuria type C homolog	0.25	-	cyt	0					280
Q9Y4U1 UniProt NPD GO	MMAC_HUMAN	Methylmalonic aciduria and homocystinuria type C protein	0.25	-	mit	0			609831		282
Q3T100 UniProt NPD GO	MGST3_BOVIN	Microsomal glutathione S-transferase 3 (EC 2.5.1.18) (Microsomal GST-3)	0.25	-	end	4 *	Microsome; microsomal membrane; multi-pass membrane protein (Potential)				152
Q9MYX8 UniProt NPD GO	TAU_PAPHA	Microtubule-associated protein tau (Neurofibrillary tangle protein) (Paired helical filament-tau) (P ...	0.25	-	nuc	0	Cytoplasm; cytosol (By similarity). Cell membrane (By similarity). Mostly found in the axons of neur ...				382
Q5XGJ0 UniProt NPD GO	TIM16_XENTR	Mitochondrial import inner membrane translocase subunit TIM16	0.25	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				125
Q75DU7 UniProt NPD GO	TIM8_ASHGO	Mitochondrial import inner membrane translocase subunit TIM8	0.25	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				87
Q4IJW4 UniProt NPD GO	TIM8_GIBZE	Mitochondrial import inner membrane translocase subunit TIM8	0.25	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				93
Q59R24 UniProt NPD GO	TIM9_CANAL	Mitochondrial import inner membrane translocase subunit TIM9	0.25	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				110
Q5ZIR8 UniProt NPD GO	TIM9_CHICK	Mitochondrial import inner membrane translocase subunit Tim9	0.25	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				89
Q9Y0V2 UniProt NPD GO	TIM9B_CAEEL	Mitochondrial import inner membrane translocase subunit Tim9B (Tim10b) (Tim-10b)	0.25	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein				111
O45319 UniProt NPD GO	TIM13_CAEEL	Mitochondrial import inner membrane translocase subunit tim-13	0.25	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				108
P23644 UniProt NPD GO	TOM40_YEAST	Mitochondrial import receptor subunit TOM40 (Mitochondrial import-site-protein ISP42) (Translocase o ...	0.25	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrial outer membrane translocase co... [IPI] mitochondrion [IDA]			387
P48858 UniProt NPD GO	RT12_CHOCR	Mitochondrial ribosomal protein S12	0.25	-	mit	0	Mitochondrion				127
P46753 UniProt NPD GO	RT02_ACACA	Mitochondrial ribosomal protein S2	0.25	-	nuc	0	Mitochondrion				312
P21547 UniProt NPD GO	RT03_SCHPO	Mitochondrial ribosomal protein S3	0.25	-	nuc	0	Mitochondrion				227
P53779 UniProt NPD GO	MK10_HUMAN	Mitogen-activated protein kinase 10 (EC 2.7.11.24) (Stress-activated protein kinase JNK3) (c-Jun N-t ...	0.25	-	cyt	0	Cytoplasm		602897	1PMV	464
Q61831 UniProt NPD GO	MK10_MOUSE	Mitogen-activated protein kinase 10 (EC 2.7.11.24) (Stress-activated protein kinase JNK3) (c-Jun N-t ...	0.25	-	cyt	0	Cytoplasm; perinuclear region				464
Q39022 UniProt NPD GO	MPK2_ARATH	Mitogen-activated protein kinase 2 (EC 2.7.11.24) (MAP kinase 2) (AtMPK2)	0.25	-	cyt	0					376
P45983 UniProt NPD GO	MK08_HUMAN	Mitogen-activated protein kinase 8 (EC 2.7.11.24) (Stress-activated protein kinase JNK1) (c-Jun N-te ...	0.25	-	cyt	0			601158	1UKI	427
O42099 UniProt NPD GO	MK08B_CYPCA	Mitogen-activated protein kinase 8B (EC 2.7.11.24) (Stress-activated protein kinase JNKb) (c-Jun N-t ...	0.25	-	cyt	0					427
P79996 UniProt NPD GO	MK09_CHICK	Mitogen-activated protein kinase 9 (EC 2.7.11.24) (Stress-activated protein kinase JNK2) (c-Jun N-te ...	0.25	-	nuc	0					382
P49186 UniProt NPD GO	MK09_RAT	Mitogen-activated protein kinase 9 (EC 2.7.11.24) (Stress-activated protein kinase JNK2) (c-Jun N-te ...	0.25	-	nuc	0		nucleus [ISS]			423
Q99J21 UniProt NPD GO	MCLN1_MOUSE	Mucolipin-1 (Mucolipidin)	0.25	-	end	6	Cell membrane; multi-pass membrane protein (By similarity). Endosome; late endosome; late endosomal ...				580
P21448 UniProt NPD GO	MDR1_CRIGR	Multidrug resistance protein 1 (EC 3.6.3.44) (P-glycoprotein 1) (CD243 antigen)	0.25	+	end	11 *	Membrane; multi-pass membrane protein				1276

You are viewing entries 45401 to 45450 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.