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
Q28234 UniProt NPD GO	IL12B_CEREL	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.13	-	exc	1 *	Secreted protein	extracellular space [ISS]			327
Q865W9 UniProt NPD GO	IL12B_LAMGL	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.13	-	exc	1 *	Secreted protein				330
Q9N0W9 UniProt NPD GO	IL13_CANFA	Interleukin-13 precursor (IL-13)	0.13	-	exc	0	Secreted protein				131
Q95253 UniProt NPD GO	IL15_PIG	Interleukin-15 precursor (IL-15)	0.13	-	mit	0	Secreted protein				162
P55030 UniProt NPD GO	IL4_FELCA	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.13	-	exc	1 *	Secreted protein				133
P20096 UniProt NPD GO	IL4_RAT	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.13	-	exc	0	Secreted protein				147
Q9XT91 UniProt NPD GO	IL5_MACEU	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (Eosinophil differentiation factor)	0.13	-	vac	0	Secreted protein				139
P03878 UniProt NPD GO	SCE2_YEAST	Intron-encoded DNA endonuclease aI4 precursor (DNA endonuclease I-SceII) [Contains: Truncated, nonfu ...	0.13	-	end	6 *	Mitochondrion	mitochondrion [TAS]			556
P10596 UniProt NPD GO	INV4_YEAST	Invertase 4 precursor (EC 3.2.1.26) (Beta-fructofuranosidase 4) (Saccharase)	0.13	-	vac	0					532
Q96WT3 UniProt NPD GO	FET3_CANGA	Iron transport multicopper oxidase FET3 precursor (EC 1.-.-.-)	0.13	-	end	1	Cell membrane; single-pass type I membrane protein; extracellular side (Potential)				635
P70404 UniProt NPD GO	IDH3G_MOUSE	Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehyd ...	0.13	-	mit	0	Mitochondrion	mitochondrion [IDA]			393
Q9BX67 UniProt NPD GO	JAM3_HUMAN	Junctional adhesion molecule C precursor (JAM-C) (Junctional adhesion molecule 3) (JAM-3) (JAM-2)	0.13	-	end	1	Membrane; single-pass type I membrane protein (Potential)		606871		310
P12992 UniProt NPD GO	ESTJ_HELVI	Juvenile hormone esterase precursor (EC 3.1.1.59) (JH esterase)	0.13	-	exc	0					564
P01398 UniProt NPD GO	NXL1_BUNMU	Kappa-1-bungarotoxin precursor (Long neurotoxin 2) (Neuronal-bungarotoxin) (Toxin F)	0.13	-	nuc	0	Secreted protein			2NBT	87
Q29150 UniProt NPD GO	CASK_UNCUN	Kappa-casein (Fragment)	0.13	-	nuc	0	Secreted protein				146
Q8N7A1 UniProt NPD GO	KLDC1_HUMAN	Kelch domain-containing protein 1	0.13	-	cyt	0					406
Q02957 UniProt NPD GO	KRA61_RABIT	Keratin, glycine/tyrosine-rich of hair	0.13	-	cyt	1 *					79
Q6L8H2 UniProt NPD GO	KRA53_HUMAN	Keratin-associated protein 5-3 (Keratin-associated protein 5.3) (Ultrahigh sulfur keratin-associated ...	0.13	-	nuc	0					238
P06168 UniProt NPD GO	ILV5_YEAST	Ketol-acid reductoisomerase, mitochondrial precursor (EC 1.1.1.86) (Acetohydroxy-acid reductoisomera ...	0.13	-	mit	0	Mitochondrion	mitochondrial nucleoid [IDA] mitochondrion [IDA]			395
P22313 UniProt NPD GO	KHR1_YEAST	Killer toxin KHR precursor (Killer of heat resistant)	0.13	-	mit	0					296
P83609 UniProt NPD GO	BMTIA_BOOMI	Kunitz-type serine protease inhibitor BmTI-A (Fragments)	0.13	-	nuc	0	Secreted protein				121
Q750P5 UniProt NPD GO	KYNU_ASHGO	Kynureninase (EC 3.7.1.3) (L-kynurenine hydrolase)	0.13	-	cyt	0	Cytoplasm (By similarity)				447
Q6DIZ8 UniProt NPD GO	KMO_XENTR	Kynurenine 3-monooxygenase (EC 1.14.13.9) (Kynurenine 3-hydroxylase)	0.13	-	cyt	2	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				473
Q99MB5 UniProt NPD GO	LMO3_RAT	LIM-only protein 3 (Neuronal-specific transcription factor DAT1)	0.13	-	nuc	0					145
P37138 UniProt NPD GO	LIM2B_XENLA	LIM/homeobox protein xLIM-2B (Fragment)	0.13	-	nuc	0	Nucleus (Probable)				39
Q04760 UniProt NPD GO	LGUL_HUMAN	Lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (Glx I) (Ke ...	0.13	-	cyt	0		cytoplasm [TAS]	138750	1QIP	183
P38604 UniProt NPD GO	ERG7_YEAST	Lanosterol synthase (EC 5.4.99.7) (Oxidosqualene--lanosterol cyclase) (2,3-epoxysqualene--lanosterol ...	0.13	-	mit	0	Lipid particle; lipid particle membrane; peripheral membrane protein. Endoplasmic reticulum; endopla ...	lipid particle [IDA] plasma membrane [TAS]			730
P07793 UniProt NPD GO	H2A4_PSAMI	Late histone H2A.2.2	0.13	-	nuc	0	Nucleus				119
Q6PJG9 UniProt NPD GO	LRFN4_HUMAN	Leucine-rich repeat and fibronectin type-III domain-containing protein 4 precursor	0.13	-	end	1	Membrane; single-pass type I membrane protein (Potential)				635
Q80XU8 UniProt NPD GO	LRFN4_MOUSE	Leucine-rich repeat and fibronectin type-III domain-containing protein 4 precursor	0.13	-	end	1	Membrane; single-pass type I membrane protein (Potential)				636
P0C192 UniProt NPD GO	LRC4B_MOUSE	Leucine-rich repeat-containing protein 4B precursor	0.13	-	end	1	Membrane; single-pass membrane protein (Potential)				709
O43261 UniProt NPD GO	LEU1_HUMAN	Leukemia-associated protein 1 (Deleted in lymphocytic leukemia 1)	0.13	-	exc	0			605765		78
P07979 UniProt NPD GO	GUB_NICPL	Lichenase precursor (EC 3.2.1.73) (Endo-beta-1,3-1,4 glucanase)	0.13	-	exc	1 *					370
Q9UUS2 UniProt NPD GO	LIDS_GAEGR	Linoleate diol synthase (EC 1.13.11.44) (Linoleate (8R)-dioxygenase) (Linoleate 8-dioxygenase)	0.13	-	cyt	0					978
P18428 UniProt NPD GO	LBP_HUMAN	Lipopolysaccharide-binding protein precursor (LBP)	0.13	-	exc	0	Secreted protein	extracellular region [NAS] extracellular space [TAS]	151990		481
P11151 UniProt NPD GO	LIPL_BOVIN	Lipoprotein lipase precursor (EC 3.1.1.34) (LPL) (Fragment)	0.13	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor				465
P37831 UniProt NPD GO	LOX1_SOLTU	Lipoxygenase 1 (EC 1.13.11.12)	0.13	-	cyt	0	Cytoplasm (By similarity)				861
P29250 UniProt NPD GO	LOX2_ORYSA	Lipoxygenase 2 (EC 1.13.11.12) (Lipoxygenase L-2)	0.13	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA]			870
P38416 UniProt NPD GO	LOXB_LYCES	Lipoxygenase B (EC 1.13.11.12)	0.13	-	nuc	0	Cytoplasm				859
Q29191 UniProt NPD GO	LITH_PIG	Lithostathine precursor [Contains: Lithostathine A chain] (Fragment)	0.13	-	exc	0					122
P83428 UniProt NPD GO	LOCU_LOCMI	Locustin	0.13	-	nuc	0	Secreted protein	extracellular region [NAS]			55
P01382 UniProt NPD GO	NXL1_NAJOX	Long neurotoxin 1 (Neurotoxin I)	0.13	-	nuc	0	Secreted protein			1W6B	73
P97849 UniProt NPD GO	S27A1_RAT	Long-chain fatty acid transport protein 1 (EC 6.2.1.-) (Fatty acid transport protein 1) (FATP-1) (So ...	0.13	-	end	1 *	Cell membrane; peripheral membrane protein. Intracellular membrane; peripheral membrane protein. Pla ...				646
Q4R3Y4 UniProt NPD GO	S27A4_MACFA	Long-chain fatty acid transport protein 4 (EC 6.2.1.-) (Fatty acid transport protein 4) (FATP-4) (So ...	0.13	-	nuc	2 *	Membrane; multi-pass membrane protein (Probable)				643
Q5RDY4 UniProt NPD GO	S27A4_PONPY	Long-chain fatty acid transport protein 4 (EC 6.2.1.-) (Fatty acid transport protein 4) (FATP-4) (So ...	0.13	-	nuc	2 *	Membrane; multi-pass membrane protein (Probable)				643
Q9CZW4 UniProt NPD GO	ACSL3_MOUSE	Long-chain-fatty-acid--CoA ligase 3 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 3) (LACS 3)	0.13	-	mit	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...				720
Q63151 UniProt NPD GO	ACSL3_RAT	Long-chain-fatty-acid--CoA ligase 3 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 3) (LACS 3) (Brain ...	0.13	-	mit	1 *	Mitochondrion; mitochondrial outer membrane; single-pass type III membrane protein (By similarity). ...				720
P47912 UniProt NPD GO	LCF4_YEAST	Long-chain-fatty-acid--CoA ligase 4 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 4) (Fatty acid acti ...	0.13	-	cyt	0		cytoplasm [IDA] lipid particle [IDA]			694
P08637 UniProt NPD GO	FCG3A_HUMAN	Low affinity immunoglobulin gamma Fc region receptor III-A precursor (IgG Fc receptor III-2) (Fc-gam ...	0.13	-	end	1	Cell membrane; single-pass type I membrane protein (Potential). Secreted protein. Exists also as a s ...	plasma membrane [TAS]	146740		254
P82891 UniProt NPD GO	PPA2_DROME	Low molecular weight phosphotyrosine protein phosphatase 2 (EC 3.1.3.48) (Low molecular weight cytos ...	0.13	-	mit	0	Cytoplasm				164

You are viewing entries 59901 to 59950 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.