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
Q99N69 UniProt NPD GO	LPXN_MOUSE	Leupaxin	0.30	-	nuc	0	Cytoplasm (By similarity)				386
Q58CR3 UniProt NPD GO	LIGA_BOVIN	Ligatin	0.30	-	mit	0	Membrane; peripheral membrane protein (By similarity)				579
P41646 UniProt NPD GO	CHLN_PINTH	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.30	-	cyt	0	Plastid; chloroplast				467
Q9Y8A5 UniProt NPD GO	LNKS_ASPTE	Lovastatin nonaketide synthase (EC 2.3.1.161) (EC 2.1.1.-) (LNKS)	0.30	-	end	0					3038
P01131 UniProt NPD GO	LDLR_BOVIN	Low-density lipoprotein receptor (LDL receptor) (Fragment)	0.30	-	nuc	1	Membrane; single-pass type I membrane protein				264
Q8TG06 UniProt NPD GO	PLB2_CANGA	Lysophospholipase 2 precursor (EC 3.1.1.5) (Phospholipase B 2)	0.30	-	exc	0	Secreted protein (Probable)				695
P24638 UniProt NPD GO	PPAL_MOUSE	Lysosomal acid phosphatase precursor (EC 3.1.3.2) (LAP)	0.30	-	end	2 *	Lysosome				423
P11279 UniProt NPD GO	LAMP1_HUMAN	Lysosome-associated membrane glycoprotein 1 precursor (LAMP-1) (CD107a antigen)	0.30	-	exc	1	Cell membrane; single-pass type I membrane protein. Endosome; endosomal membrane; single-pass type I ...	integral to plasma membrane [TAS] late endosome [IDA] lysosome [IDA] membrane fraction [TAS]	153330		416
Q5XI99 UniProt NPD GO	LAMP3_RAT	Lysosome-associated membrane glycoprotein 3 precursor (LAMP-3) (Lysosomal-associated membrane protei ...	0.30	-	nuc	1	Lysosome; lysosomal membrane; single-pass type I membrane protein (By similarity)				408
Q7TST5 UniProt NPD GO	LAMP3_MOUSE	Lysosome-associated membrane glycoprotein 3 precursor (LAMP-3) (Lysosomal-associated membrane protei ...	0.30	-	end	2 *	Lysosome; lysosomal membrane; single-pass type I membrane protein (By similarity)	lysosomal membrane [IDA]			411
P58215 UniProt NPD GO	LOXL3_HUMAN	Lysyl oxidase homolog 3 precursor (EC 1.4.3.-) (Lysyl oxidase-like protein 3)	0.30	-	exc	0	Secreted protein; extracellular space (Potential)	extracellular region [IDA]	607163		753
P04201 UniProt NPD GO	MAS_HUMAN	MAS proto-oncogene	0.30	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	165180		325
Q9FKY5 UniProt NPD GO	MLO10_ARATH	MLO-like protein 10 (AtMlo10)	0.30	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				569
P53624 UniProt NPD GO	MA121_DROME	Mannosyl-oligosaccharide alpha-1,2-mannosidase isoform 1 (EC 3.2.1.113) (Man(9)-alpha-mannosidase)	0.30	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				667
P10721 UniProt NPD GO	KIT_HUMAN	Mast/stem cell growth factor receptor precursor (EC 2.7.10.1) (SCFR) (Proto-oncogene tyrosine-protei ...	0.30	-	end	2	Membrane; single-pass type I membrane protein		164920	1T46	976
O42837 UniProt NPD GO	MTA1_SORMA	Mating type protein SmtA-1	0.30	-	cyt	0	Nucleus (Potential)				306
Q02990 UniProt NPD GO	MAT1_COCHE	Mating-type protein MAT-1	0.30	-	mit	0	Nucleus (Potential)				383
P52176 UniProt NPD GO	MMP9_BOVIN	Matrix metalloproteinase-9 precursor (EC 3.4.24.35) (MMP-9) (92 kDa type IV collagenase) (92 kDa gel ...	0.30	-	exc	0		extracellular space [ISS]			712
Q58T60 UniProt NPD GO	M5H42_BOMMX	Maximins 5/H4 type 2 precursor [Contains: Maximin-5; Maximin-H4]	0.30	-	end	0	Secreted protein				145
Q5GC92 UniProt NPD GO	MAXSB_BOMMX	Maximins-S type B/C precursor [Contains: Maximin-S1; Maximin-S3; Maximin-S3; Maximin-S5; Maximin-S2; ...	0.30	-	exc	0	Secreted protein				305
Q03104 UniProt NPD GO	MSC1_YEAST	Meiotic sister chromatid recombination protein 1	0.30	-	nuc	0		endoplasmic reticulum [IDA] mitochondrion [IDA]			513
Q68UT4 UniProt NPD GO	MRAP_PANTR	Melanocortin 2 receptor accessory protein (Fat cell-specific low molecular weight protein) (Fat tiss ...	0.30	-	nuc	1 *	Cell membrane. Endoplasmic reticulum. Cytoplasm; perinuclear region. Upon insulin stimulation, it is ...				172
Q6VE48 UniProt NPD GO	MCP_BOVIN	Membrane cofactor protein precursor (CD46 antigen)	0.30	-	mit	1	Acrosome; acrosomal inner membrane; single-pass type I membrane protein (By similarity). Inner acros ...				361
P13820 UniProt NPD GO	MSP1_PLAFN	Merozoite surface protein 1 precursor (Merozoite surface antigens) (PMMSA) (Fragment)	0.30	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				281
Q8W519 UniProt NPD GO	MMT1_MAIZE	Methionine S-methyltransferase (EC 2.1.1.12) (AdoMet:Met S-methyltransferase)	0.30	-	cyt	0	Cytoplasm (By similarity)				1091
P38174 UniProt NPD GO	AMPM2_YEAST	Methionine aminopeptidase 2 (EC 3.4.11.18) (MetAP 2) (Peptidase M 2)	0.30	+	cyt	0		cytoplasm [TAS]			421
Q28103 UniProt NPD GO	MFAP3_BOVIN	Microfibril-associated glycoprotein 3 (Fragment)	0.30	-	nuc	0	Cell membrane; single-pass type I membrane protein (Potential)				175
P21787 UniProt NPD GO	P320_TRYBB	Microtubule-associated protein P320 (Fragment)	0.30	-	nuc	0					290
P29172 UniProt NPD GO	TAU_BOVIN	Microtubule-associated protein tau (Neurofibrillary tangle protein) (Paired helical filament-tau) (P ...	0.30	-	nuc	0	Cytoplasm; cytosol. Cell membrane. Mostly found in the axons of neurons, in the cytosol and in assoc ...				447
Q5RBL2 UniProt NPD GO	MIME_PONPY	Mimecan precursor (Osteoglycin)	0.30	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				298
Q9W4L1 UniProt NPD GO	RM33_DROME	Mitochondrial 39S ribosomal protein L33 (L33mt)	0.30	-	mit	0	Mitochondrion (Potential)	mitochondrion [ISS]			64
P10663 UniProt NPD GO	RT02_YEAST	Mitochondrial 40S ribosomal protein MRP2	0.30	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			115
P32787 UniProt NPD GO	MG101_YEAST	Mitochondrial genome maintenance protein MGM101, mitochondrial precursor	0.30	-	mit	0	Mitochondrion. Associated with the mitochondrial nucleoid structure	mitochondrial chromosome [IDA]			269
Q5KDU4 UniProt NPD GO	TIM13_CRYNE	Mitochondrial import inner membrane translocase subunit TIM13	0.30	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				99
Q4IB65 UniProt NPD GO	TIM9_GIBZE	Mitochondrial import inner membrane translocase subunit TIM9	0.30	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				87
Q90YI5 UniProt NPD GO	TIM8A_FUGRU	Mitochondrial import inner membrane translocase subunit Tim8 A	0.30	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				90
P87250 UniProt NPD GO	MTF1_KLULA	Mitochondrial replication protein MTF1 (Mitochondrial transcription factor MTTFB)	0.30	-	mit	0	Mitochondrion (By similarity)				335
P46746 UniProt NPD GO	RT11_PROWI	Mitochondrial ribosomal protein S11	0.30	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [ISS]			128
P23209 UniProt NPD GO	RT13_DAUCA	Mitochondrial ribosomal protein S13	0.30	-	nuc	0	Mitochondrion				116
P05488 UniProt NPD GO	RT13_TOBAC	Mitochondrial ribosomal protein S13	0.30	-	nuc	0	Mitochondrion				116
P53733 UniProt NPD GO	RT19_YEAST	Mitochondrial ribosomal protein S19	0.30	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			91
Q3SZ71 UniProt NPD GO	MPPB_BOVIN	Mitochondrial-processing peptidase subunit beta, mitochondrial precursor (EC 3.4.24.64) (Beta-MPP)	0.30	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				490
Q03346 UniProt NPD GO	MPPB_RAT	Mitochondrial-processing peptidase subunit beta, mitochondrial precursor (EC 3.4.24.64) (Beta-MPP) ( ...	0.30	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			489
P11913 UniProt NPD GO	MPPB_NEUCR	Mitochondrial-processing peptidase subunit beta, mitochondrial precursor (EC 3.4.24.64) (Beta-MPP) ( ...	0.30	-	mit	0	Mitochondrion; mitochondrial matrix				476
Q5J4W4 UniProt NPD GO	MPK2_ORYSA	Mitogen-activated protein kinase 2 (EC 2.7.11.24) (MAP kinase 2)	0.30	-	cyt	0					394
Q336X9 UniProt NPD GO	MPK6_ORYSA	Mitogen-activated protein kinase 6 (EC 2.7.11.24) (MAP kinase 6)	0.30	-	cyt	0					376
P14681 UniProt NPD GO	KSS1_YEAST	Mitogen-activated protein kinase KSS1 (EC 2.7.11.24) (MAP kinase KSS1) (Kinase suppressor of SST2)	0.30	-	cyt	0	Nucleus. Cytoplasm. Periplasm. KSS1 shuttles rapidly between the cytoplasm and the nucleus independe ...	nucleus [IDA]			368
O88406 UniProt NPD GO	SMAD7_RAT	Mothers against decapentaplegic homolog 7 (SMAD 7) (Mothers against DPP homolog 7) (Smad7)	0.30	-	nuc	0	Nucleus. Interaction with NEDD4L induces translocation from the nucleus to the cytoplasm (By similar ...				426
P01307 UniProt NPD GO	MOTI_PIG	Motilin precursor [Contains: Motilin; Motilin-associated peptide (MAP)]	0.30	-	mit	1 *	Secreted protein				119
P79295 UniProt NPD GO	MIS_PIG	Muellerian-inhibiting factor precursor (MIS) (Anti-Muellerian hormone) (AMH) (Muellerian-inhibiting ...	0.30	-	nuc	0	Secreted protein (By similarity)				575

You are viewing entries 40501 to 40550 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.