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
P46650 UniProt NPD GO	IL6_CERTO	Interleukin-6 precursor (IL-6)	0.28	-	exc	0	Secreted protein	extracellular region [ISS] extracellular space [ISS]			212
P41683 UniProt NPD GO	IL6_FELCA	Interleukin-6 precursor (IL-6)	0.28	-	mit	0	Secreted protein				208
Q9MZR1 UniProt NPD GO	IL6_RABIT	Interleukin-6 precursor (IL-6)	0.28	-	exc	0	Secreted protein				241
Q25BC2 UniProt NPD GO	IL6_VULVU	Interleukin-6 precursor (IL-6)	0.28	-	exc	0	Secreted protein (By similarity)				207
Q6FW26 UniProt NPD GO	MIA40_CANGA	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.28	-	nuc	1	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				404
Q12425 UniProt NPD GO	ISA2_YEAST	Iron sulfur assembly protein 2	0.28	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial intermembrane space [IDA]			185
P23442 UniProt NPD GO	IAPP_MESAU	Islet amyloid polypeptide precursor (Amylin)	0.28	-	nuc	0	Secreted protein				92
P12968 UniProt NPD GO	IAPP_MOUSE	Islet amyloid polypeptide precursor (Diabetes-associated peptide) (DAP) (Amylin)	0.28	-	exc	0	Secreted protein				93
P53982 UniProt NPD GO	IDHH_YEAST	Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) (Oxalosuccinate decarboxylase) (IDH) (NADP(+)-specific ...	0.28	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA] peroxisome [IDA]			420
O94198 UniProt NPD GO	ACEA_ASHGO	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.28	-	pox	0	Peroxisome				560
Q9D9J7 UniProt NPD GO	IZUM1_MOUSE	Izumo sperm-egg fusion protein 1 precursor (Sperm-specific protein izumo)	0.28	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [IDA]			397
P40309 UniProt NPD GO	KHA1_YEAST	K(+)/H(+) antiporter 1	0.28	-	end	12 *	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			873
O43240 UniProt NPD GO	KLK10_HUMAN	Kallikrein-10 precursor (EC 3.4.21.-) (Protease serine-like 1) (Normal epithelial cell-specific 1)	0.28	-	mit	0	Secreted protein (Probable)	extracellular region [TAS]	602673		276
Q9QYN3 UniProt NPD GO	KLK11_MOUSE	Kallikrein-11 precursor (EC 3.4.21.-) (Hippostasin)	0.28	-	mit	0	Secreted protein	extracellular region [IDA]			276
P11840 UniProt NPD GO	CASK_BUBBU	Kappa-casein precursor	0.28	-	exc	0	Secreted protein				190
P50422 UniProt NPD GO	CASK_NEMGO	Kappa-casein precursor	0.28	-	exc	0	Secreted protein				192
Q96M94 UniProt NPD GO	KHL15_HUMAN	Kelch-like protein 15	0.28	-	cyt	0					604
Q6R648 UniProt NPD GO	KR111_CAPHI	Keratin-associated protein 11-1 (High sulfur keratin-associated protein 11.1)	0.28	-	nuc	0					159
P43626 UniProt NPD GO	KI2L1_HUMAN	Killer cell immunoglobulin-like receptor 2DL1 precursor (MHC class I NK cell receptor) (Natural kill ...	0.28	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	604936	1NKR	348
P43627 UniProt NPD GO	KI2L2_HUMAN	Killer cell immunoglobulin-like receptor 2DL2 precursor (MHC class I NK cell receptor) (Natural kill ...	0.28	-	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [ISS]	604937	2DLI	348
Q25297 UniProt NPD GO	KM11B_LEIIN	Kinetoplastid membrane protein 11B	0.28	-	nuc	0	Cytoplasm. Associated with microtubules. Flagellum. Associated with the flagellum and flagellar pock ...	microtubule cytoskeleton [ISS]			92
O08677 UniProt NPD GO	KNG1_MOUSE	Kininogen-1 precursor [Contains: Kininogen-1 heavy chain; Bradykinin; Kininogen-1 light chain]	0.28	-	exc	0	Secreted protein; extracellular space				661
Q95N18 UniProt NPD GO	SCF_MUSVI	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF)	0.28	-	nuc	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				274
Q8N5Z0 UniProt NPD GO	AADAT_HUMAN	Kynurenine/alpha-aminoadipate aminotransferase mitochondrial precursor (KAT/AadAT) (Kynurenine--oxog ...	0.28	-	mit	0	Mitochondrion (Potential)				425
P29038 UniProt NPD GO	LDH_MAIZE	L-lactate dehydrogenase (EC 1.1.1.27) (LDH)	0.28	+	cyt	0					354
P61968 UniProt NPD GO	LMO4_HUMAN	LIM domain transcription factor LMO4 (LIM domain only protein 4) (LMO-4) (Breast tumor autoantigen)	0.28	-	nuc	0		transcription factor complex [ISS]	603129		165
P61969 UniProt NPD GO	LMO4_MOUSE	LIM domain transcription factor LMO4 (LIM domain only protein 4) (LMO-4) (Breast tumor autoantigen)	0.28	-	nuc	0		transcription factor complex [IDA]		1RUT	165
P15522 UniProt NPD GO	LCTN_CAMDR	Lactophorin precursor (Whey protein)	0.28	-	exc	0		extracellular region [IEP]			155
O49816 UniProt NPD GO	LEA1_CICAR	Late embryogenesis abundant protein 1 (CapLEA-1)	0.28	-	nuc	0					177
O49817 UniProt NPD GO	LEA2_CICAR	Late embryogenesis abundant protein 2 (CapLEA-2)	0.28	-	nuc	0					155
P11218 UniProt NPD GO	AGI_URTDI	Lectin/endochitinase precursor (EC 3.2.1.14) (Agglutinin) (UDA)	0.28	-	exc	0				1IQB	372
Q9TU09 UniProt NPD GO	LEP_HORSE	Leptin precursor (Obesity factor) (Fragment)	0.28	-	nuc	0	Secreted protein (Probable)				145
Q7SZE3 UniProt NPD GO	L2GL2_BRARE	Lethal(2) giant larvae protein homolog 2 (Protein penner)	0.28	-	nuc	0					1020
Q9NZU1 UniProt NPD GO	FLRT1_HUMAN	Leucine-rich repeat transmembrane protein FLRT1 precursor (Fibronectin-like domain-containing leucin ...	0.28	-	nuc	1	Membrane; single-pass type I membrane protein (Probable)	extracellular matrix (sensu Metazoa) [NAS] integral to plasma membrane [NAS]	604806		646
Q8VCH9 UniProt NPD GO	LRC3B_MOUSE	Leucine-rich repeat-containing protein 3B precursor (Leucine-rich repeat protein LRP15)	0.28	-	end	1 *					259
Q8R2R5 UniProt NPD GO	LRC61_MOUSE	Leucine-rich repeat-containing protein 61	0.28	-	nuc	0					259
Q9ESY6 UniProt NPD GO	LRRN3_RAT	Leucine-rich repeats neuronal protein 3 precursor (Neuronal leucine-rich repeat protein 3) (NLRR-3)	0.28	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				707
P41213 UniProt NPD GO	LDOX_MAIZE	Leucoanthocyanidin dioxygenase (EC 1.14.11.19) (LDOX) (Leucocyanidin oxygenase) (Leucoanthocyanidin ...	0.28	-	mit	0					395
P80229 UniProt NPD GO	ILEU_PIG	Leukocyte elastase inhibitor (LEI) (Serpin B1) (Leukocyte neutral proteinase inhibitor) (LNPI)	0.28	-	nuc	0	Cytoplasm				378
Q5PPG7 UniProt NPD GO	LIGA_RAT	Ligatin	0.28	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				570
O70601 UniProt NPD GO	LAT_RAT	Linker for activation of T-cells family member 1 (36 kDa phospho-tyrosine adapter protein) (pp36) (p ...	0.28	-	nuc	1 *	Cell membrane; single-pass type III membrane protein. Present in lipid rafts (By similarity)				241
P97544 UniProt NPD GO	LPP3_RAT	Lipid phosphate phosphohydrolase 3 (EC 3.1.3.4) (Phosphatidic acid phosphatase 2b) (Phosphatidate ph ...	0.28	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA]			312
O04979 UniProt NPD GO	LONH1_SPIOL	Lon protease homolog 1, mitochondrial precursor (EC 3.4.21.-)	0.28	-	cyt	0	Mitochondrion; mitochondrial matrix (Potential)				875
P33121 UniProt NPD GO	ACSL1_HUMAN	Long-chain-fatty-acid--CoA ligase 1 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 1) (LACS 1) (Palmit ...	0.28	-	cyt	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...		152425		698
O60488 UniProt NPD GO	ACSL4_HUMAN	Long-chain-fatty-acid--CoA ligase 4 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 4) (LACS 4)	0.28	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...		300387		711
Q91WC3 UniProt NPD GO	ACSL6_MOUSE	Long-chain-fatty-acid--CoA ligase 6 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 6) (LACS 6)	0.28	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...	mitochondrion [IDA]			697
Q8CB67 UniProt NPD GO	LRP11_MOUSE	Low-density lipoprotein receptor-related protein 11 precursor	0.28	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				483
Q14849 UniProt NPD GO	MLN64_HUMAN	MLN 64 protein (StAR-related lipid transfer protein 3) (StARD3) (START domain-containing protein 3) ...	0.28	-	end	3	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein	cytoplasm [TAS]	607048	1EM2	445
Q85FX6 UniProt NPD GO	ACSF_CYAME	Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (EC 1.14.13.81) (Mg-protoporphyrin ...	0.28	-	cyt	0	Plastid; chloroplast				335
P82910 UniProt NPD GO	HSP70_DROME	Major heat shock 70 kDa protein Aa (Heat shock protein 70Aa) (HSP70-87A7)	0.28	-	cyt	0					642

You are viewing entries 42401 to 42450 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.