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
O35760 UniProt NPD GO	IDI1_RAT	Isopentenyl-diphosphate delta-isomerase 1 (EC 5.3.3.2) (IPP isomerase 1) (Isopentenyl pyrophosphate ...	0.14	-	cyt	0	Peroxisome	peroxisome [IDA]			227
Q9R226 UniProt NPD GO	KHDR3_MOUSE	KH domain-containing, RNA-binding, signal transduction-associated protein 3 (Sam68-like mammalian pr ...	0.14	-	nuc	0	Nucleus. Localized in a compartment adjacent to the nucleolus, but distinct from the peri-nucleolar ...				346
Q9UKR3 UniProt NPD GO	KLK13_HUMAN	Kallikrein-13 precursor (EC 3.4.21.-) (Kallikrein-like protein 4) (KLK-L4)	0.14	-	mit	0	Secreted protein (Probable)	cytoplasm [IDA] extracellular region [TAS]	605505		277
Q5RCR2 UniProt NPD GO	KAIN_PONPY	Kallistatin precursor (Serpin A4)	0.14	-	cyt	0	Secreted protein (By similarity)				427
P06796 UniProt NPD GO	CASK_MOUSE	Kappa-casein precursor	0.14	-	mit	0	Secreted protein				181
Q02958 UniProt NPD GO	KRA61_SHEEP	Keratin, glycine/tyrosine-rich of hair	0.14	-	cyt	0					82
P59991 UniProt NPD GO	KR122_HUMAN	Keratin-associated protein 12-2 (Keratin-associated protein 12.2) (High sulfur keratin-associated pr ...	0.14	-	mit	0					146
Q9BYR8 UniProt NPD GO	KRA31_HUMAN	Keratin-associated protein 3-1 (Keratin-associated protein 3.1) (High sulfur keratin-associated prot ...	0.14	-	nuc	0					98
Q05758 UniProt NPD GO	ILV5_ARATH	Ketol-acid reductoisomerase, chloroplast precursor (EC 1.1.1.86) (Acetohydroxy-acid reductoisomerase ...	0.14	-	mit	0	Plastid; chloroplast				591
Q01292 UniProt NPD GO	ILV5_SPIOL	Ketol-acid reductoisomerase, chloroplast precursor (EC 1.1.1.86) (Acetohydroxy-acid reductoisomerase ...	0.14	-	mit	0	Plastid; chloroplast			1YVE	595
Q62781 UniProt NPD GO	ANRE_RAT	Kidney androgen-regulated protein precursor (KAP) (ARP)	0.14	-	nuc	0	Secreted protein (Potential)				120
P43632 UniProt NPD GO	KI2S4_HUMAN	Killer cell immunoglobulin-like receptor 2DS4 precursor (MHC class I NK cell receptor) (Natural kill ...	0.14	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	604955		304
Q9TWF9 UniProt NPD GO	KC2_ANESU	Kunitz-type kalicludin-2 (AsKC2) (Kalicludine-2)	0.14	-	nuc	0	Secreted protein. Found in nematocyst				58
O43278 UniProt NPD GO	SPIT1_HUMAN	Kunitz-type protease inhibitor 1 precursor (Hepatocyte growth factor activator inhibitor type 1) (HA ...	0.14	-	end	2 *	Secreted protein	extracellular region [TAS] membrane fraction [TAS]	605123	1YC0	529
P07702 UniProt NPD GO	LYS2_YEAST	L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (Alpha-aminoadipate reductase) (Alpha-AR)	0.14	-	cyt	0		cytoplasm [TAS]			1392
Q12572 UniProt NPD GO	LYS2_CANAL	L-aminoadipate-semialdehyde dehydrogenase large subunit (EC 1.2.1.31) (Alpha-aminoadipate reductase) ...	0.14	-	cyt	0					1391
P11163 UniProt NPD GO	ASPG2_YEAST	L-asparaginase 2 precursor (EC 3.5.1.1) (L-asparaginase II) (L-asparagine amidohydrolase II) (ASP II ...	0.14	-	end	0	Cell wall	endoplasmic reticulum [IDA] nuclear envelope [IDA] periplasmic space (sensu Fungi) [TAS]			362
P06811 UniProt NPD GO	LAC1_NEUCR	Laccase precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Laccase alle ...	0.14	-	end	0	Secreted protein (Potential)				619
P10574 UniProt NPD GO	LAC2_NEUCR	Laccase precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Laccase alle ...	0.14	-	end	0	Secreted protein (Potential)				619
Q811X6 UniProt NPD GO	CRYL1_RAT	Lambda-crystallin homolog	0.14	-	cyt	0					318
Q04782 UniProt NPD GO	ERG7_CANAL	Lanosterol synthase (EC 5.4.99.7) (Oxidosqualene--lanosterol cyclase) (2,3-epoxysqualene--lanosterol ...	0.14	-	cyt	0					728
P09444 UniProt NPD GO	LEA34_GOSHI	Late embryogenesis abundant protein D-34 (LEA D-34)	0.14	-	mit	0					264
Q39644 UniProt NPD GO	LEA5_CITSI	Late embryogenesis abundant protein Lea5	0.14	-	mit	0					97
P69139 UniProt NPD GO	H2A3_PSAMI	Late histone H2A.3, gonadal	0.14	-	nuc	0	Nucleus				125
Q64361 UniProt NPD GO	LXN_RAT	Latexin (Endogenous carboxypeptidase inhibitor) (ECI) (Tissue carboxypeptidase inhibitor) (TCI)	0.14	-	cyt	0	Cytoplasm (Probable)				223
Q865V1 UniProt NPD GO	LATH_EQUBA	Latherin (Fragment)	0.14	-	mit	0	Secreted protein (By similarity)				205
Q00689 UniProt NPD GO	GP63_LEIGU	Leishmanolysin precursor (EC 3.4.24.36) (Cell surface protease) (Major surface glycoprotein) (Protei ...	0.14	-	end	2 *	Cell membrane; lipid-anchor; GPI-anchor				621
Q6K669 UniProt NPD GO	AMPL2_ORYSA	Leucine aminopeptidase 2, chloroplast precursor (EC 3.4.11.1) (LAP 2) (Leucyl aminopeptidase 2) (Pro ...	0.14	-	cyt	0	Plastid; chloroplast (Potential)				598
Q75AW4 UniProt NPD GO	LCMT2_ASHGO	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-)	0.14	-	cyt	1					699
Q9DAM1 UniProt NPD GO	LRC34_MOUSE	Leucine-rich repeat-containing protein 34	0.14	-	cyt	0					415
P17777 UniProt NPD GO	LIF_RAT	Leukemia inhibitory factor precursor (LIF) (Cholinergic neuronal differentiation factor)	0.14	-	mit	0	Secreted protein				202
Q6S9C8 UniProt NPD GO	LKHA4_CHILA	Leukotriene A-4 hydrolase (EC 3.3.2.6) (LTA-4 hydrolase) (Leukotriene A(4) hydrolase)	0.14	-	cyt	0	Cytoplasm (By similarity)				610
Q9R0Q2 UniProt NPD GO	LT4R1_RAT	Leukotriene B4 receptor 1 (LTB4-R 1)	0.14	+	end	7 *	Membrane; multi-pass membrane protein				351
P17652 UniProt NPD GO	CHLB_CHLMO	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.14	-	cyt	0	Plastid; chloroplast				563
P37846 UniProt NPD GO	CHLB_EPHAL	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.14	-	cyt	0	Plastid; chloroplast				509
P11542 UniProt NPD GO	LIG4_PHACH	Ligninase H2 precursor (EC 1.11.1.14) (Diarylpropane peroxidase) (Lignin peroxidase) (LG4)	0.14	-	vac	0				1QPA	372
O46107 UniProt NPD GO	LIP1_DROME	Lipase 1 precursor (EC 3.1.1.-) (DmLip1)	0.14	-	end	0	Secreted protein (Probable)	extracellular region [NAS]			439
Q29524 UniProt NPD GO	LIPL_SHEEP	Lipoprotein lipase precursor (EC 3.1.1.34) (LPL)	0.14	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor				478
P10758 UniProt NPD GO	LITH_RAT	Lithostathine precursor (Pancreatic stone protein) (PSP) (Pancreatic thread protein) (PTP) (Islet of ...	0.14	-	exc	0					165
P51174 UniProt NPD GO	ACADL_MOUSE	Long-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.13) (LCAD)	0.14	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			430
P15650 UniProt NPD GO	ACADL_RAT	Long-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.13) (LCAD)	0.14	-	mit	0	Mitochondrion; mitochondrial matrix				430
Q9DE67 UniProt NPD GO	LUM_COTJA	Lumican precursor (Keratan sulfate proteoglycan lumican) (KSPG lumican)	0.14	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				343
P51886 UniProt NPD GO	LUM_RAT	Lumican precursor (Keratan sulfate proteoglycan lumican) (KSPG lumican)	0.14	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				338
Q43578 UniProt NPD GO	LCYB_TOBAC	Lycopene beta cyclase, chloroplast precursor (EC 1.14.-.-)	0.14	-	nuc	0	Plastid; chloroplast				500
Q9WU67 UniProt NPD GO	LY6I_MOUSE	Lymphocyte antigen Ly-6I precursor (Lymphocyte antigen Ly-6M)	0.14	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	plasma membrane [TAS]			134
P61125 UniProt NPD GO	TNFB_PANTR	Lymphotoxin-alpha precursor (LT-alpha) (TNF-beta) (Tumor necrosis factor ligand superfamily member 1 ...	0.14	-	nuc	0	Homotrimer: Secreted protein (By similarity). Heterotrimer: Membrane (By similarity)				205
Q95KH4 UniProt NPD GO	EDG4_MACFA	Lysophosphatidic acid receptor Edg-4 (LPA receptor 2) (LPA-2)	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				351
P16675 UniProt NPD GO	PPGB_MOUSE	Lysosomal protective protein precursor (EC 3.4.16.5) (Cathepsin A) (Carboxypeptidase C) (Protective ...	0.14	-	exc	0	Lysosome	mitochondrion [IDA]			474
P82174 UniProt NPD GO	LYS_GALME	Lysozyme (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.14	-	nuc	0					121
P11375 UniProt NPD GO	LYSC_EQUAS	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.14	-	nuc	0					129

You are viewing entries 58551 to 58600 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.