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
Q99538 UniProt NPD GO	LGMN_HUMAN	Legumain precursor (EC 3.4.22.34) (Asparaginyl endopeptidase) (Protease, cysteine 1)	0.22	-	exc	0	Lysosome (By similarity)		602620		433
Q10712 UniProt NPD GO	AMPL1_LYCES	Leucine aminopeptidase 1, chloroplast precursor (EC 3.4.11.1) (LAP 1) (Leucyl aminopeptidase 1) (Pro ...	0.22	-	mit	0	Plastid; chloroplast				571
Q8K4Z0 UniProt NPD GO	LGI2_MOUSE	Leucine-rich repeat LGI family member 2 precursor (Leucine-rich glioma-inactivated protein 2)	0.22	-	mit	0	Secreted protein (Potential)				550
Q8N0V4 UniProt NPD GO	LGI2_HUMAN	Leucine-rich repeat LGI family member 2 precursor (Leucine-rich glioma-inactivated protein 2) (LGI1- ...	0.22	-	mit	1 *	Secreted protein (Potential)		608301		545
Q8BZT5 UniProt NPD GO	LRC19_MOUSE	Leucine-rich repeat-containing protein 19 precursor	0.22	-	end	1	Membrane; single-pass type I membrane protein (Potential)				364
Q6NSJ5 UniProt NPD GO	LRC8E_HUMAN	Leucine-rich repeat-containing protein 8E	0.22	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				796
O00453 UniProt NPD GO	LST1_HUMAN	Leukocyte-specific transcript 1 protein (B144 protein)	0.22	-	nuc	1 *	Membrane; single-pass membrane protein. Also detected in a perinuclear region corresponding to the l ...	cytoplasm [IDA] Golgi apparatus [NAS] integral to membrane [IDA]	109170		97
Q9T467 UniProt NPD GO	CHLB_NEPOL	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.22	-	cyt	0	Plastid; chloroplast				531
P37823 UniProt NPD GO	CHLB_CHLHU	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.22	-	cyt	0	Plastid; chloroplast				431
P49923 UniProt NPD GO	LIPL_PIG	Lipoprotein lipase precursor (EC 3.1.1.34) (LPL)	0.22	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				478
P43137 UniProt NPD GO	LIT1_MOUSE	Lithostathine 1 precursor (Pancreatic stone protein 1) (PSP) (Pancreatic thread protein 1) (PTP) (Is ...	0.22	-	exc	0					165
P01391 UniProt NPD GO	NXL1_NAJKA	Long neurotoxin 1 (Neurotoxin 3) (Alpha-cobratoxin)	0.22	-	nuc	0	Secreted protein			1YI5	71
P15815 UniProt NPD GO	NXL2_BUNFL	Long neurotoxin 2 (Kappa-flavitoxin)	0.22	-	nuc	0	Secreted protein				66
P39002 UniProt NPD GO	LCF3_YEAST	Long-chain-fatty-acid--CoA ligase 3 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 3) (Fatty acid acti ...	0.22	-	cyt	0					694
O95573 UniProt NPD GO	ACSL3_HUMAN	Long-chain-fatty-acid--CoA ligase 3 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 3) (LACS 3)	0.22	-	mit	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...		602371		720
Q5R668 UniProt NPD GO	ACSL3_PONPY	Long-chain-fatty-acid--CoA ligase 3 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 3) (LACS 3)	0.22	-	mit	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...				720
P42523 UniProt NPD GO	LAGC_DICDI	Loose aggregate C protein precursor	0.22	-	exc	2 *	Membrane; single-pass type I membrane protein				888
P27645 UniProt NPD GO	FCGR3_RAT	Low affinity immunoglobulin gamma Fc region receptor III precursor (IgG Fc receptor III) (Fc-gamma R ...	0.22	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				267
P31636 UniProt NPD GO	SC5A4_PIG	Low affinity sodium-glucose cotransporter (Sodium/glucose cotransporter 3) (Na(+)/glucose cotranspor ...	0.22	-	end	14 *	Membrane; multi-pass membrane protein				660
P40988 UniProt NPD GO	FET4_YEAST	Low-affinity Fe(II) transport protein	0.22	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			552
P80071 UniProt NPD GO	LSHB_RANCA	Lutropin beta chain (Luteinizing hormone subunit beta) (LSH-beta) (LSH-B) (LH-B)	0.22	-	nuc	0	Secreted protein				112
P47992 UniProt NPD GO	XCL1_HUMAN	Lymphotactin precursor (XCL1) (Cytokine SCM-1) (ATAC) (Lymphotaxin) (SCM-1-alpha) (Small inducible c ...	0.22	-	exc	0	Secreted protein		600250	1J9O	114
O59863 UniProt NPD GO	PLB_KLULA	Lysophospholipase precursor (EC 3.1.1.5) (Phospholipase B) (KlPLB)	0.22	-	end	0	Secreted protein (Probable)				640
Q5REZ0 UniProt NPD GO	LAPM5_PONPY	Lysosomal-associated multitransmembrane protein	0.22	-	end	5 *	Lysosome; lysosomal membrane; multi-pass membrane protein (By similarity)				262
Q9GMT4 UniProt NPD GO	MAMC1_MACFA	MAM domain-containing protein 1 (Fragment)	0.22	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				451
P09581 UniProt NPD GO	CSF1R_MOUSE	Macrophage colony-stimulating factor 1 receptor precursor (CSF-1-R) (EC 2.7.10.1) (Fms proto-oncogen ...	0.22	-	nuc	1	Membrane; single-pass type I membrane protein				977
Q00495 UniProt NPD GO	CSF1R_RAT	Macrophage colony-stimulating factor 1 receptor precursor (CSF-1-R) (EC 2.7.10.1) (Fms proto-oncogen ...	0.22	-	nuc	1	Membrane; single-pass type I membrane protein				978
Q5UJH8 UniProt NPD GO	PRIO_BUBBU	Major prion protein precursor (PrP) (CD230 antigen)	0.22	-	exc	3 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				264
P04925 UniProt NPD GO	PRIO_MOUSE	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.22	-	nuc	2 *	Cell membrane; lipid-anchor; GPI-anchor	endoplasmic reticulum [IDA] Golgi apparatus [IDA] lipid raft [IDA] plasma membrane [IDA]		1Y16	254
P40245 UniProt NPD GO	PRIO_AOTTR	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen) (Fragment)	0.22	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				239
Q3SYU9 UniProt NPD GO	MVP_BOVIN	Major vault protein (MVP)	0.22	-	cyt	0	Cytoplasm (By similarity)				890
P38156 UniProt NPD GO	MAL31_YEAST	Maltose permease MAL31 (Maltose transport protein MAL31)	0.22	-	end	8	Membrane; multi-pass membrane protein				614
Q02292 UniProt NPD GO	MATA_NEUAF	Mating type protein A-1 (Mt A-1)	0.22	-	cyt	0	Nucleus (Potential)				286
P41243 UniProt NPD GO	MATK_RAT	Megakaryocyte-associated tyrosine-protein kinase (EC 2.7.10.2) (Tyrosine-protein kinase CTK) (Protei ...	0.22	-	cyt	0	Cytoplasm (Probable)				467
Q60696 UniProt NPD GO	PME17_MOUSE	Melanocyte protein Pmel 17 precursor (Silver locus protein)	0.22	-	end	1	Membrane; single-pass type I membrane protein (Potential)				626
Q9CPR8 UniProt NPD GO	MAGG1_MOUSE	Melanoma-associated antigen G1 (MAGE-G1 antigen) (Necdin-like protein 2)	0.22	-	nuc	0	Cytoplasm. Nucleus				279
Q11001 UniProt NPD GO	AMPM_MANSE	Membrane alanyl aminopeptidase precursor (EC 3.4.11.-) (Aminopeptidase N-like protein) (CryIA(C) rec ...	0.22	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				990
Q15049 UniProt NPD GO	MLC1_HUMAN	Membrane protein MLC1	0.22	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane of membrane fraction [TAS]	605908		376
Q60HE7 UniProt NPD GO	MLC1_MACFA	Membrane protein MLC1	0.22	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				376
Q03645 UniProt NPD GO	MSA2_PLAFZ	Merozoite surface antigen 2 precursor (MSA-2)	0.22	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				300
P55949 UniProt NPD GO	MT1_CALSI	Metallothionein-1B (MT-1B) (Metallothionein-IB) (MT-IB) [Contains: Metallothionein-1A (MT-1A) (Metal ...	0.22	-	nuc	0				1DMF	59
O75431 UniProt NPD GO	MTX2_HUMAN	Metaxin-2	0.22	-	cyt	0	Mitochondrion; mitochondrial outer membrane	mitochondrial outer membrane [TAS]	608555		263
Q2QMG2 UniProt NPD GO	MCCA_ORYSA	Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial precursor (EC 6.4.1.4) (3-methylcrotony ...	0.22	-	mit	0	Mitochondrion; mitochondrial matrix (Probable)				737
P16332 UniProt NPD GO	MUTA_MOUSE	Methylmalonyl-CoA mutase, mitochondrial precursor (EC 5.4.99.2) (MCM) (Methylmalonyl-CoA isomerase)	0.22	-	mit	0	Mitochondrion; mitochondrial matrix				748
Q80ZK0 UniProt NPD GO	RT10_MOUSE	Mitochondrial 28S ribosomal protein S10 (S10mt) (MRP-S10)	0.22	-	cyt	0	Mitochondrion (By similarity)				160
Q9HF53 UniProt NPD GO	RT02_ASHGO	Mitochondrial 40S ribosomal protein MRP2	0.22	-	mit	0	Mitochondrion (By similarity)				114
P38860 UniProt NPD GO	MTG2_YEAST	Mitochondrial GTPase 2	0.22	-	cyt	0	Mitochondrion	extrinsic to membrane [IDA] mitochondrial inner membrane [IDA]			499
P38702 UniProt NPD GO	LEU5_YEAST	Mitochondrial carrier protein LEU5	0.22	-	cyt	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			357
Q5KFM0 UniProt NPD GO	TIM8_CRYNE	Mitochondrial import inner membrane translocase subunit TIM8	0.22	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				88
Q2KIV2 UniProt NPD GO	TIM9_BOVIN	Mitochondrial import inner membrane translocase subunit Tim9	0.22	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				89

You are viewing entries 48601 to 48650 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.