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
Q9GMZ4 UniProt NPD GO	IL1RA_TURTR	Interleukin-1 receptor antagonist protein precursor (IL-1ra) (IRAP) (IL1 inhibitor) (IL-1RN)	0.08	-	exc	0	Secreted protein				177
Q9Z0M9 UniProt NPD GO	I18BP_MOUSE	Interleukin-18-binding protein precursor (IL-18BP) (Interferon gamma-inducing factor-binding protein ...	0.08	-	exc	0	Secreted protein (Potential)	extracellular region [ISS]			191
P49875 UniProt NPD GO	IL3_BOVIN	Interleukin-3 precursor (IL-3) (Multipotential colony-stimulating factor) (Hematopoietic growth fact ...	0.08	-	nuc	0	Secreted protein	extracellular space [ISS]			144
P10168 UniProt NPD GO	IL7_MOUSE	Interleukin-7 precursor (IL-7)	0.08	-	exc	0	Secreted protein	extracellular region [ISS]			154
Q4P8D2 UniProt NPD GO	MIA40_USTMA	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				247
Q94702 UniProt NPD GO	PPO1_PHYPO	Intron-encoded endonuclease I-PpoI (EC 3.1.-.-) (I-Ppo)	0.08	-	cyt	0				1IPP	163
P24133 UniProt NPD GO	INV_DEBOC	Invertase precursor (EC 3.2.1.26) (Beta-fructofuranosidase) (Saccharase)	0.08	-	cyt	1 *					533
P48200 UniProt NPD GO	IREB2_HUMAN	Iron-responsive element-binding protein 2 (IRE-BP 2) (Iron regulatory protein 2) (IRP2)	0.08	-	cyt	0	Cytoplasm	cytoplasm [NAS]	147582		963
O13285 UniProt NPD GO	IDH1_CANTR	Isocitrate dehydrogenase [NADP], mitochondrial precursor (EC 1.1.1.42) (Oxalosuccinate decarboxylase ...	0.08	-	mit	0	Mitochondrion				430
O13696 UniProt NPD GO	IDH1_SCHPO	Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehydroge ...	0.08	-	mit	0	Mitochondrion (By similarity)				356
Q68FX0 UniProt NPD GO	IDH3B_RAT	Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehydr ...	0.08	-	mit	0	Mitochondrion (By similarity)				385
O77784 UniProt NPD GO	IDH3B_BOVIN	Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehydr ...	0.08	-	mit	0	Mitochondrion				385
Q39472 UniProt NPD GO	IDI1_CLABR	Isopentenyl-diphosphate delta-isomerase I (EC 5.3.3.2) (IPP isomerase I) (Isopentenyl pyrophosphate ...	0.08	-	mit	0					287
Q07663 UniProt NPD GO	NEU1_ONCMA	Isoticin-neurophysin IT 1 precursor [Contains: Isotocin (IT); Neurophysin IT 1]	0.08	-	exc	1 *	Secreted protein				157
Q2LKX9 UniProt NPD GO	IXOSN_IXOSI	Ixosin	0.08	-	cyt	0					79
Q9PTT2 UniProt NPD GO	JELT_LEPLA	Jeltraxin precursor (Egg jelly pentraxin)	0.08	-	mit	0	Secreted protein	extracellular region [IDA]			225
Q68FQ2 UniProt NPD GO	JAM3_RAT	Junctional adhesion molecule C precursor (JAM-C) (Junctional adhesion molecule 3) (JAM-3)	0.08	-	end	1	Membrane; single-pass type I membrane protein (Potential)				310
P04261 UniProt NPD GO	K2C3_BOVIN	Keratin, type II cytoskeletal 60 kDa, component III (Fragment)	0.08	-	cyt	0					182
Q7Z4W3 UniProt NPD GO	KR193_HUMAN	Keratin-associated protein 19-3 (Glycine/tyrosine-rich protein) (GTHRP)	0.08	-	cyt	2 *					81
Q3SYF9 UniProt NPD GO	KR197_HUMAN	Keratin-associated protein 19-7	0.08	-	cyt	1 *					63
P02447 UniProt NPD GO	KRA31_CAPHI	Keratin-associated protein 3-1 (Keratin, high sulfur matrix protein, IIIB2) (M1.2 protein)	0.08	-	nuc	0					97
Q3LI64 UniProt NPD GO	KRA61_HUMAN	Keratin-associated protein 6-1	0.08	-	cyt	1 *					71
P79150 UniProt NPD GO	FGF7_CANFA	Keratinocyte growth factor precursor (KGF) (Fibroblast growth factor 7) (FGF-7) (HBGF-7)	0.08	-	mit	0	Secreted protein				194
P21781 UniProt NPD GO	FGF7_HUMAN	Keratinocyte growth factor precursor (KGF) (Fibroblast growth factor 7) (FGF-7) (HBGF-7)	0.08	-	cyt	0	Secreted protein		148180		194
Q5RAY8 UniProt NPD GO	FGF7_PONPY	Keratinocyte growth factor precursor (KGF) (Fibroblast growth factor 7) (FGF-7) (HBGF-7)	0.08	-	cyt	0	Secreted protein (By similarity)				194
Q497B3 UniProt NPD GO	KCP3_RAT	Keratinocytes-associated protein 3 (KCP-3)	0.08	-	end	4 *	Membrane; multi-pass membrane protein				240
P84527 UniProt NPD GO	KIWEL_ACTCH	Kiwellin (Allergen Act c ?)	0.08	-	nuc	0	Secreted protein (Potential)				189
P49223 UniProt NPD GO	SPIT3_HUMAN	Kunitz-type protease inhibitor 3 precursor (HKIB9)	0.08	-	exc	0	Secreted protein (Probable)				69
P31713 UniProt NPD GO	ISH1_STOHE	Kunitz-type proteinase inhibitor SHPI-1	0.08	-	nuc	0	Secreted protein. Found in nematocyst			1SHP	55
Q9FE01 UniProt NPD GO	APX2_ORYSA	L-ascorbate peroxidase 2, cytosolic (EC 1.11.1.11) (APXb)	0.08	-	cyt	0	Cytoplasm (Probable)				251
P27545 UniProt NPD GO	LASS1_MOUSE	LAG1 longevity assurance homolog 1 (UOG-1 protein)	0.08	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				350
Q43533 UniProt NPD GO	LIM1_LILLO	LIM1 protein precursor	0.08	-	exc	0					90
P56193 UniProt NPD GO	LAC1_THACU	Laccase 1 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.08	-	exc	0	Secreted protein				576
Q9N290 UniProt NPD GO	A4GAT_GORGO	Lactosylceramide 4-alpha-galactosyltransferase (EC 2.4.1.228) (Alpha-1,4-galactosyltransferase) (UDP ...	0.08	-	cyt	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	integral to Golgi membrane [ISS]			327
O88829 UniProt NPD GO	SIAT9_MOUSE	Lactosylceramide alpha-2,3-sialyltransferase (EC 2.4.99.9) (CMP-NeuAc:lactosylceramide alpha-2,3-sia ...	0.08	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	Golgi membrane [ISS]			359
Q9Z127 UniProt NPD GO	LAT1_MOUSE	Large neutral amino acids transporter small subunit 1 (L-type amino acid transporter 1) (4F2 light c ...	0.08	-	end	9	Membrane; multi-pass membrane protein (Probable)				512
Q63016 UniProt NPD GO	LAT1_RAT	Large neutral amino acids transporter small subunit 1 (L-type amino acid transporter 1) (4F2 light c ...	0.08	-	end	9	Membrane; multi-pass membrane protein (Probable)				512
P04736 UniProt NPD GO	H2A2_PSAMI	Late histone H2A.2.1	0.08	-	nuc	0	Nucleus				123
P82615 UniProt NPD GO	LATH_HORSE	Latherin precursor (Dander allergen Equ c 4/Equ c 5)	0.08	-	exc	0	Secreted protein (Potential)				228
Q9JI61 UniProt NPD GO	LRAT_RAT	Lecithin retinol acyltransferase (EC 2.3.1.135) (Phosphatidylcholine--retinol O-acyltransferase)	0.08	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				231
Q9JI60 UniProt NPD GO	LRAT_MOUSE	Lecithin retinol acyltransferase (EC 2.3.1.135) (Phosphatidylcholine--retinol O-acyltransferase) (Ph ...	0.08	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				231
P16352 UniProt NPD GO	LEC_CROJU	Lectin (Fragment)	0.08	-	nuc	0					24
P05046 UniProt NPD GO	LEC_SOYBN	Lectin precursor (Agglutinin) (SBA)	0.08	-	exc	0				2SBA	285
O89017 UniProt NPD GO	LGMN_MOUSE	Legumain precursor (EC 3.4.22.34) (Asparaginyl endopeptidase) (Protease, cysteine 1)	0.08	-	exc	0	Lysosome	apical part of cell [IDA] late endosome [IDA]			435
Q9R0J8 UniProt NPD GO	LGMN_RAT	Legumain precursor (EC 3.4.22.34) (Asparaginyl endopeptidase) (Protease, cysteine 1)	0.08	-	exc	0	Lysosome (By similarity)				435
P43150 UniProt NPD GO	GP63_LEIME	Leishmanolysin C1 precursor (EC 3.4.24.36) (Cell surface protease) (Major surface glycoprotein) (Pro ...	0.08	-	cyt	2 *					646
Q06031 UniProt NPD GO	GP63_CRIFA	Leishmanolysin homolog precursor (EC 3.4.24.36) (Cell surface protease) (Major surface glycoprotein) ...	0.08	-	mit	1 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				652
Q8IZ02 UniProt NPD GO	LRC34_HUMAN	Leucine-rich repeat-containing protein 34	0.08	-	mit	0					419
Q9SEV0 UniProt NPD GO	BAN_ARATH	Leucoanthocyanidin reductase (EC 1.3.1.77) (LAR) (Protein BANYULS) (Anthocyanin spotted testa) (ast) ...	0.08	-	cyt	0					340
Q61470 UniProt NPD GO	CD37_MOUSE	Leukocyte antigen CD37	0.08	-	end	4 *	Membrane; multi-pass membrane protein				281

You are viewing entries 68301 to 68350 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.