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
Q9LHS8 UniProt NPD GO	LBD33_ARATH	LOB domain-containing protein 33	0.31	-	mit	0					177
O04479 UniProt NPD GO	LBD6_ARATH	LOB domain-containing protein 6 (Protein ASYMMETRIC LEAVES2)	0.31	-	nuc	0	Nucleus				199
Q25092 UniProt NPD GO	LAMB_HIRME	Laminin B-chain (Fragment)	0.31	-	nuc	0					400
Q5TA78 UniProt NPD GO	LCE4A_HUMAN	Late cornified envelope protein 4A (Late envelope protein 8) (Small proline-rich-like epidermal diff ...	0.31	-	nuc	0					99
O75610 UniProt NPD GO	LEFTB_HUMAN	Left-right determination factor B precursor (Lefty-B protein)	0.31	-	vac	0	Secreted protein		603037		366
Q5J732 UniProt NPD GO	LEP_BUBBU	Leptin precursor (Obesity factor)	0.31	-	exc	0	Secreted protein (Probable)				167
Q9Z1P4 UniProt NPD GO	LGR5_MOUSE	Leucine-rich repeat-containing G-protein coupled receptor 5 precursor (G-protein coupled receptor 49 ...	0.31	-	end	7	Membrane; multi-pass membrane protein				907
Q9UNZ5 UniProt NPD GO	L10K_HUMAN	Leydig cell tumor 10 kDa protein homolog	0.31	-	nuc	0					99
P36437 UniProt NPD GO	CHLB_CHLRE	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.31	-	cyt	0	Plastid; chloroplast				687
P05455 UniProt NPD GO	LA_HUMAN	Lupus La protein (Sjoegren syndrome type B antigen) (SS-B) (La ribonucleoprotein) (La autoantigen)	0.31	-	nuc	0	Nucleus (Probable)	ribonucleoprotein complex [TAS]	109090	1ZH5	408
Q28005 UniProt NPD GO	LSHR_BOVIN	Lutropin-choriogonadotropic hormone receptor precursor (LH/CG-R) (LSH-R) (Luteinizing hormone recept ...	0.31	-	end	7	Membrane; multi-pass membrane protein				701
O02721 UniProt NPD GO	LSHR_CALJA	Lutropin-choriogonadotropic hormone receptor precursor (LH/CG-R) (LSH-R) (Luteinizing hormone recept ...	0.31	-	end	7	Membrane; multi-pass membrane protein				676
P19794 UniProt NPD GO	LSHB_EQUAS	Lutropin/choriogonadotropin beta chain precursor (LSH-B/CG-B) (Luteinizing hormone subunit beta)	0.31	-	nuc	0	Secreted protein				169
Q38932 UniProt NPD GO	LCYE_ARATH	Lycopene epsilon cyclase, chloroplast precursor (EC 1.14.-.-)	0.31	-	end	1	Plastid; chloroplast				524
Q02173 UniProt NPD GO	MPSF_CHICK	M-protein, striated muscle	0.31	-	nuc	0					1450
Q8JIY8 UniProt NPD GO	MK67I_BRARE	MKI67 FHA domain-interacting nucleolar phosphoprotein-like (Nucleolar phosphoprotein NOPP34-like pro ...	0.31	-	cyt	0	Nucleus; nucleolus (By similarity)				269
P34960 UniProt NPD GO	MMP12_MOUSE	Macrophage metalloelastase precursor (EC 3.4.24.65) (MME) (Matrix metalloproteinase-12) (MMP-12)	0.31	-	exc	0					462
Q9WUB9 UniProt NPD GO	MARCO_MESAU	Macrophage receptor MARCO (Macrophage receptor with collagenous structure)	0.31	-	gol	1 *	Membrane; single-pass type II membrane protein (Probable)				483
Q9UEW3 UniProt NPD GO	MARCO_HUMAN	Macrophage receptor MARCO (Macrophage receptor with collagenous structure) (Scavenger receptor class ...	0.31	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)	integral to plasma membrane [TAS]	604870		520
Q8INI8 UniProt NPD GO	HSP72_DROME	Major heat shock 70 kDa protein Ba (Heat shock protein 70Ba) (HSP70-87C1)	0.31	-	cyt	0					641
Q9BIS2 UniProt NPD GO	HSP73_DROME	Major heat shock 70 kDa protein Bb (Heat shock protein 70Bb) (HSP70-87C1)	0.31	-	cyt	0					641
Q9VG58 UniProt NPD GO	HSP74_DROME	Major heat shock 70 kDa protein Bbb (Heat shock protein 70Bbb) (HSP70-87C1)	0.31	-	cyt	0					641
Q9BIR7 UniProt NPD GO	HSP75_DROME	Major heat shock 70 kDa protein Bc (Heat shock protein 70Bc) (HSP70-87C1)	0.31	-	cyt	0					641
P53018 UniProt NPD GO	MSP32_CAEEL	Major sperm protein 32 (MSP)	0.31	-	cyt	0					190
Q8R3F5 UniProt NPD GO	FABD_MOUSE	Malonyl CoA-acyl carrier protein transacylase, mitochondrial precursor (EC 2.3.1.39) (MCT) (Mitochon ...	0.31	-	mit	0	Mitochondrion (By similarity)				381
O43451 UniProt NPD GO	MGA_HUMAN	Maltase-glucoamylase, intestinal [Includes: Maltase (EC 3.2.1.20) (Alpha-glucosidase); Glucoamylase ...	0.31	-	cyt	1 *	Cell membrane; single-pass type II membrane protein. Brush border		154360		1856
Q13724 UniProt NPD GO	GCS1_HUMAN	Mannosyl-oligosaccharide glucosidase (EC 3.2.1.106) (Processing A-glucosidase I)	0.31	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein	endoplasmic reticulum [TAS] membrane fraction [TAS]	606056		837
P36027 UniProt NPD GO	MID2_YEAST	Mating process protein MID2 (Serine-rich protein SMS1) (Protein kinase A interference protein)	0.31	-	exc	1	Membrane; peripheral membrane protein (Potential)	integral to plasma membrane [IDA]			376
Q10116 UniProt NPD GO	MATD_NEUCR	Mating-type protein A-3 (Mt A-3)	0.31	-	cyt	0	Nucleus (Potential)				324
Q5RDP6 UniProt NPD GO	MGP_PONPY	Matrix Gla-protein precursor (MGP)	0.31	-	exc	0	Secreted protein (By similarity)				103
P08494 UniProt NPD GO	MGP_RAT	Matrix Gla-protein precursor (MGP)	0.31	-	exc	0	Secreted protein				103
P14761 UniProt NPD GO	MAT1_ASTLO	Maturase-like protein 1	0.31	-	cyt	0	Plastid				456
Q5GC94 UniProt NPD GO	MAXSA_BOMMX	Maximins-S type A precursor [Contains: Maximin-S1; Maximin-S2; Maximin-S3; Maximin-S3; Maximin-S4; M ...	0.31	-	exc	0	Secreted protein				235
Q5GC91 UniProt NPD GO	MAXSD_BOMMX	Maximins-S type D precursor [Contains: Maximin-S1; Maximin-S3; Maximin-S5; Maximin-S2; Maximin-S3; M ...	0.31	-	exc	0	Secreted protein				270
Q9MZ01 UniProt NPD GO	MCHR1_PIG	Melanin-concentrating hormone receptor 1 (MCH receptor 1) (MCHR-1) (MCH-R1) (MCH1R) (MCH-1R) (MCHR) ...	0.31	-	mit	2 *	Membrane; multi-pass membrane protein				121
O02839 UniProt NPD GO	MCP_PIG	Membrane cofactor protein precursor (CD46 antigen)	0.31	-	mit	1	Acrosome; acrosomal inner membrane; single-pass type I membrane protein (By similarity). Inner acros ...				363
Q8K480 UniProt NPD GO	MFRP_MOUSE	Membrane frizzled-related protein (Membrane-type frizzled-related protein)	0.31	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)				584
Q56Y85 UniProt NPD GO	AMP2B_ARATH	Methionine aminopeptidase 2B (EC 3.4.11.18) (MetAP 2B) (MAP 2B) (Peptidase M 2B)	0.31	+	cyt	0	Cytoplasm				439
Q60HE5 UniProt NPD GO	MTHR_MACFA	Methylenetetrahydrofolate reductase (EC 1.5.1.20)	0.31	-	cyt	0					656
Q8QHI2 UniProt NPD GO	MCR_CHICK	Mineralocorticoid receptor (MR) (Fragment)	0.31	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic and nuclear in the absence of ligand ...				147
P53944 UniProt NPD GO	MTQ1_YEAST	Mitochondrial N5-glutamine methyltransferase MTQ1 (EC 2.1.1.-)	0.31	-	mit	0	Mitochondrion	mitochondrion [IDA]			314
Q2HJF8 UniProt NPD GO	MIRO1_BOVIN	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (MIRO-1) (Ras homolog gene family member T1)	0.31	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				631
Q6C6V8 UniProt NPD GO	MG101_YARLI	Mitochondrial genome maintenance protein MGM101, mitochondrial precursor	0.31	-	mit	0	Mitochondrion. Associated with the mitochondrial nucleoid structure (By similarity)				289
Q6C6Z2 UniProt NPD GO	TIM9_YARLI	Mitochondrial import inner membrane translocase subunit TIM9	0.31	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				85
P57745 UniProt NPD GO	TIM9_ZYGBA	Mitochondrial import inner membrane translocase subunit Tim9	0.31	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				87
Q5RDJ0 UniProt NPD GO	TIM9B_PONPY	Mitochondrial import inner membrane translocase subunit Tim9 B (TIMM10B) (Tim10b)	0.31	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				102
Q8GYQ5 UniProt NPD GO	MPK12_ARATH	Mitogen-activated protein kinase 12 (EC 2.7.11.24) (MAP kinase 12) (AtMPK12)	0.31	-	cyt	0					372
Q09892 UniProt NPD GO	STY1_SCHPO	Mitogen-activated protein kinase sty1 (EC 2.7.11.24) (MAP kinase sty1) (MAP kinase spc1)	0.31	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			349
Q8N6T7 UniProt NPD GO	SIRT6_HUMAN	Mono-ADP-ribosyltransferase sirtuin-6 (EC 2.4.2.31) (SIR2-like protein 6)	0.31	-	nuc	0	Nucleus (By similarity). Predominantly	nucleus [ISS]	606211		355
P03972 UniProt NPD GO	MIS_BOVIN	Muellerian-inhibiting factor precursor (MIS) (Anti-Muellerian hormone) (AMH) (Muellerian-inhibiting ...	0.31	-	mit	0	Secreted protein				575

You are viewing entries 39601 to 39650 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.