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
P46282 UniProt NPD GO	IL12B_BOVIN	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.12	-	exc	1 *	Secreted protein	extracellular space [NAS]			327
O02744 UniProt NPD GO	IL12B_FELCA	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.12	-	exc	1 *	Secreted protein				329
Q9XSV9 UniProt NPD GO	IL13_BOVIN	Interleukin-13 precursor (IL-13)	0.12	-	exc	0	Secreted protein				132
P79155 UniProt NPD GO	IL4_CAPHI	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.12	-	exc	0	Secreted protein	extracellular space [ISS]			135
P07750 UniProt NPD GO	IL4_MOUSE	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.12	-	exc	0	Secreted protein				140
O77515 UniProt NPD GO	IL5_FELCA	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (Eosinophil differentiation factor)	0.12	-	end	0	Secreted protein				134
P26894 UniProt NPD GO	IL8_PIG	Interleukin-8 precursor (IL-8) (CXCL8) (Alveolar macrophage chemotactic factor I) (AMCF-I)	0.12	-	exc	1 *	Secreted protein				103
Q757A5 UniProt NPD GO	MIA40_ASHGO	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.12	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				266
Q11133 UniProt NPD GO	MMP1_RANCA	Interstitial collagenase precursor (EC 3.4.24.7) (Matrix metalloproteinase-1) (MMP-1) (TC1)	0.12	-	exc	0					384
P03882 UniProt NPD GO	SCE1_YEAST	Intron-encoded endonuclease I-SceI (EC 3.1.-.-) (21S rRNA intron maturase) (Homing endonuclease omeg ...	0.12	-	cyt	0	Mitochondrion	mitochondrion [TAS]		1R7M	235
Q9Y746 UniProt NPD GO	INV_KLULA	Invertase precursor (EC 3.2.1.26) (Beta-fructofuranosidase) (Saccharase)	0.12	-	exc	0					609
Q9BQI0 UniProt NPD GO	IBA2_HUMAN	Ionized calcium-binding adapter molecule 2	0.12	-	nuc	0					150
Q5RDI4 UniProt NPD GO	IBA2_PONPY	Ionized calcium-binding adapter molecule 2	0.12	-	nuc	0					150
P54071 UniProt NPD GO	IDHP_MOUSE	Isocitrate dehydrogenase [NADP], mitochondrial precursor (EC 1.1.1.42) (Oxalosuccinate decarboxylase ...	0.12	-	cyt	0	Mitochondrion	mitochondrial inner membrane [IDA] mitochondrion [IDA]			523
Q58CP0 UniProt NPD GO	IDH3G_BOVIN	Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehyd ...	0.12	-	cyt	0	Mitochondrion (By similarity)				392
P49297 UniProt NPD GO	ACEA_LYCES	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.12	-	cyt	0	Glyoxysome				575
Q8IYV9 UniProt NPD GO	IZUM1_HUMAN	Izumo sperm-egg fusion protein 1 precursor (Sperm-specific protein izumo)	0.12	+	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [IDA]	609278		350
Q80UL9 UniProt NPD GO	JAML1_MOUSE	Junctional adhesion molecule-like precursor (mCrea7)	0.12	-	end	1	Cell membrane; cell-cell junction; single-pass type I membrane protein (By similarity). Localized at ...				379
Q9JLP1 UniProt NPD GO	KHDR3_RAT	KH domain-containing, RNA-binding, signal transduction-associated protein 3 (Sam68-like mammalian pr ...	0.12	-	nuc	0	Nucleus				346
Q9UKQ9 UniProt NPD GO	KLK9_HUMAN	Kallikrein-9 precursor (EC 3.4.21.-) (Kallikrein-like protein 3) (KLK-L3)	0.12	-	end	0	Secreted protein (Probable)	extracellular region [NAS]	605504		250
Q9UH77 UniProt NPD GO	KLHL3_HUMAN	Kelch-like protein 3	0.12	-	cyt	0			605775		587
Q3LI58 UniProt NPD GO	KR211_HUMAN	Keratin-associated protein 21-1	0.12	-	nuc	0					79
Q02195 UniProt NPD GO	FGF7_RAT	Keratinocyte growth factor precursor (KGF) (Fibroblast growth factor 7) (FGF-7) (HBGF-7)	0.12	-	mit	0				1QQL	194
Q91V45 UniProt NPD GO	KISSR_MOUSE	KiSS-1 receptor (KiSS-1R) (Kisspeptins receptor) (Metastin receptor) (G-protein coupled receptor 54) ...	0.12	-	end	6 *	Membrane; multi-pass membrane protein	cell surface [IDA]			396
Q7TSU7 UniProt NPD GO	KIRR2_MOUSE	Kin of IRRE-like protein 2 precursor (Kin of irregular chiasm-like protein 2)	0.12	-	end	1	Membrane; single-pass type I membrane protein (Potential)				700
Q6UWL6 UniProt NPD GO	KIRR2_HUMAN	Kin of IRRE-like protein 2 precursor (Kin of irregular chiasm-like protein 2) (Nephrin-like protein ...	0.12	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]	607762		708
P10753 UniProt NPD GO	KRX6C_MOUSE	Krox-6.1B- protein (Fragment)	0.12	-	nuc	0	Nucleus (Potential)				55
Q6BI19 UniProt NPD GO	KYNU_DEBHA	Kynureninase (EC 3.7.1.3) (L-kynurenine hydrolase)	0.12	-	cyt	0	Cytoplasm (By similarity)				460
O88867 UniProt NPD GO	KMO_RAT	Kynurenine 3-monooxygenase (EC 1.14.13.9) (Kynurenine 3-hydroxylase)	0.12	-	end	2	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				478
Q14657 UniProt NPD GO	LAGE3_HUMAN	L antigen family member 3 (ITBA2 protein) (ESO-3 protein)	0.12	-	cyt	0			300060		143
Q9LJK3 UniProt NPD GO	LAG12_ARATH	LAG1 longevity assurance homolog 2 (LAG1 homolog 2)	0.12	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				296
Q95114 UniProt NPD GO	MFGM_BOVIN	Lactadherin precursor (Milk fat globule-EGF factor 8) (MFG-E8) (MGP57/53) (PAS-6/PAS-7 glycoprotein) ...	0.12	-	exc	0					427
Q4R5F2 UniProt NPD GO	LGUL_MACFA	Lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (Glx I) (Ke ...	0.12	-	cyt	0		cytoplasm [ISS]			183
P16351 UniProt NPD GO	LEC_CROST	Lectin (Fragment)	0.12	-	nuc	0					24
P82151 UniProt NPD GO	LEC6_TACTR	Lectin L6	0.12	-	cyt	0	L-granules				221
Q8RX72 UniProt NPD GO	AMPL2_ARATH	Leucine aminopeptidase 2, chloroplast precursor (EC 3.4.11.1) (LAP 2) (Leucyl aminopeptidase 2) (Pro ...	0.12	-	mit	0	Plastid; chloroplast (Potential)				581
Q8TCA0 UniProt NPD GO	LRC20_HUMAN	Leucine-rich repeat-containing protein 20	0.12	-	nuc	0					184
Q5M8M9 UniProt NPD GO	LRC52_MOUSE	Leucine-rich repeat-containing protein 52 precursor	0.12	-	end	1	Membrane; single-pass membrane protein (Potential)				314
P09056 UniProt NPD GO	LIF_MOUSE	Leukemia inhibitory factor precursor (LIF) (Differentiation-stimulating factor) (D factor)	0.12	-	mit	0	Secreted protein			1LKI	203
Q5TM23 UniProt NPD GO	LST1_MACMU	Leukocyte-specific transcript 1 protein	0.12	-	nuc	0	Membrane; single-pass membrane protein (By similarity). Also detected in a perinuclear region corres ...				93
P30349 UniProt NPD GO	LKHA4_RAT	Leukotriene A-4 hydrolase (EC 3.3.2.6) (LTA-4 hydrolase) (Leukotriene A(4) hydrolase)	0.12	-	cyt	0	Cytoplasm				609
Q15722 UniProt NPD GO	LT4R1_HUMAN	Leukotriene B4 receptor 1 (LTB4-R 1) (P2Y purinoceptor 7) (P2Y7) (Chemoattractant receptor-like 1) ( ...	0.12	+	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601531		352
P59358 UniProt NPD GO	THNB_PHOLI	Ligatoxin B	0.12	-	mit	0	Secreted protein				46
Q695L6 UniProt NPD GO	CHLL_LARDC	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.12	-	nuc	0	Plastid; chloroplast				291
O47041 UniProt NPD GO	CHLL_PICAB	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.12	-	nuc	0	Plastid; chloroplast				291
P37844 UniProt NPD GO	CHLB_BAZTR	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.12	-	cyt	0	Plastid; chloroplast				103
P37852 UniProt NPD GO	CHLB_POLCU	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.12	-	cyt	0	Plastid; chloroplast				100
P11965 UniProt NPD GO	PERX_TOBAC	Lignin-forming anionic peroxidase precursor (EC 1.11.1.7) (TOPA)	0.12	-	end	1 *	Secreted protein (By similarity)				324
Q9MB73 UniProt NPD GO	LGT_CITUN	Limonoid UDP-glucosyltransferase (EC 2.4.1.210) (Limonoid glucosyltransferase) (Limonoid GTase) (LGT ...	0.12	-	mit	0					511
P61871 UniProt NPD GO	LIP_RHINI	Lipase precursor (EC 3.1.1.3) (Triacylglycerol lipase) (Lipase II) (RNL)	0.12	-	exc	0	Secreted protein; extracellular space			1LGY	392

You are viewing entries 61351 to 61400 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.