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
Q63621 UniProt NPD GO	IL1AP_RAT	Interleukin-1 receptor accessory protein precursor (IL-1 receptor accessory protein) (IL-1RAcP)	0.05	-	end	1	Membrane; single-pass type I membrane protein				570
Q08334 UniProt NPD GO	I10R2_HUMAN	Interleukin-10 receptor beta chain precursor (IL-10R-B) (IL-10R2) (Cytokine receptor family 2 member ...	0.05	-	nuc	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS] interleukin-28 receptor complex [NAS] plasma membrane [TAS]	123889		325
Q4GZL1 UniProt NPD GO	IL15_BUBBU	Interleukin-15 precursor (IL-15)	0.05	-	exc	0	Secreted protein				162
P40221 UniProt NPD GO	IL15_CERAE	Interleukin-15 precursor (IL-15)	0.05	-	exc	0	Secreted protein				162
P40933 UniProt NPD GO	IL15_HUMAN	Interleukin-15 precursor (IL-15)	0.05	-	exc	0	IL15-S48AA: Secreted protein. IL15-S21AA: Cytoplasm. Nucleus. IL15-S21AA is not secreted, but rather ...	cytoplasm [TAS] endosome [TAS] extracellular region [NAS] extracellular space [TAS] Golgi apparatus [TAS] integral to plasma membrane [TAS] membrane fraction [TAS]	600554		162
P48092 UniProt NPD GO	IL15_MACMU	Interleukin-15 precursor (IL-15)	0.05	-	exc	0	Secreted protein				162
Q4U0U2 UniProt NPD GO	IL15_MACTH	Interleukin-15 precursor (IL-15)	0.05	-	exc	0	Secreted protein				162
Q9XSR0 UniProt NPD GO	IL18_CANFA	Interleukin-18 precursor (IL-18) (Interferon-gamma-inducing factor) (IFN-gamma-inducing factor) (Int ...	0.05	-	nuc	0	Secreted protein	extracellular region [TAS]			193
Q13478 UniProt NPD GO	IL18R_HUMAN	Interleukin-18 receptor 1 precursor (IL1 receptor-related protein) (IL-1Rrp) (CDw218a antigen)	0.05	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [TAS]	604494		541
P19114 UniProt NPD GO	IL2_SHEEP	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.05	-	exc	0	Secreted protein				155
Q7YS71 UniProt NPD GO	IL4_BUBBU	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.05	-	exc	0	Secreted protein				135
Q9P403 UniProt NPD GO	CIH1_COLLN	Intracellular hyphae protein 1 precursor	0.05	-	exc	0	Cell wall. Cell wall and surrounding interfacial matrix	extracellular region [IDA] hyphal cell wall [IDA]			230
P19890 UniProt NPD GO	IAPP_CRIGR	Islet amyloid polypeptide (Amylin)	0.05	-	nuc	0	Secreted protein				37
O94229 UniProt NPD GO	IDH1_KLULA	Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehydroge ...	0.05	-	pox	0	Mitochondrion (By similarity)				361
P41564 UniProt NPD GO	IDH3G_MACFA	Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehyd ...	0.05	-	cyt	0	Mitochondrion				355
O24529 UniProt NPD GO	7OMT8_MEDSA	Isoflavone-7-O-methyltransferase 8 (EC 2.1.1.150) (Isoflavone-O-methyltransferase 8) (7-IOMT-8)	0.05	-	cyt	0				1FPX	352
P08703 UniProt NPD GO	IPNS_PENCH	Isopenicillin N synthetase (EC 1.21.3.1) (IPNS) (Isopenicillin N synthase)	0.05	-	cyt	0					331
Q38929 UniProt NPD GO	IDI1_ARATH	Isopentenyl-diphosphate delta-isomerase I (EC 5.3.3.2) (IPP isomerase I) (Isopentenyl pyrophosphate ...	0.05	-	cyt	0					233
Q9Y624 UniProt NPD GO	JAM1_HUMAN	Junctional adhesion molecule A precursor (JAM-A) (Junctional adhesion molecule 1) (JAM-1) (Platelet ...	0.05	-	end	2 *	Cell membrane; cell-cell junction; tight junction; single-pass type I membrane protein. Localized at ...	intercellular junction [TAS]	605721	1NBQ	299
Q9UKR0 UniProt NPD GO	KLK12_HUMAN	Kallikrein-12 precursor (EC 3.4.21.-) (Kallikrein-like protein 5) (KLK-L5)	0.05	-	exc	0	Secreted protein (Probable)	extracellular region [NAS] soluble fraction [IDA]	605539		248
Q91VE3 UniProt NPD GO	KLK7_MOUSE	Kallikrein-7 precursor (EC 3.4.21.-) (Stratum corneum chymotryptic enzyme) (Thymopsin)	0.05	-	exc	0	Secreted protein (By similarity)				249
P34975 UniProt NPD GO	OPRK_RAT	Kappa-type opioid receptor (KOR-1)	0.05	-	end	7	Membrane; multi-pass membrane protein				380
Q9D5V2 UniProt NPD GO	KLH10_MOUSE	Kelch-like protein 10	0.05	-	cyt	0	Cytoplasm				608
Q6JEL3 UniProt NPD GO	KLH10_RAT	Kelch-like protein 10	0.05	-	cyt	0	Cytoplasm (By similarity)				608
Q80TF4 UniProt NPD GO	KLH13_MOUSE	Kelch-like protein 13 (BTB and kelch domain-containing protein 2)	0.05	-	cyt	0					604
Q9BYP8 UniProt NPD GO	KR171_HUMAN	Keratin-associated protein 17-1 (Keratin-associated protein 16.1)	0.05	-	nuc	0					105
Q6L8G5 UniProt NPD GO	KR510_HUMAN	Keratin-associated protein 5-10 (Keratin-associated protein 5.10) (Ultrahigh sulfur keratin-associat ...	0.05	-	nuc	0					202
Q9D3I6 UniProt NPD GO	KRA71_MOUSE	Keratin-associated protein 7-1 (High glycine-tyrosine keratin-associated protein 7.1)	0.05	-	mit	0					87
Q28580 UniProt NPD GO	KRA71_SHEEP	Keratin-associated protein 7-1 (High glycine-tyrosine keratin-associated protein 7.1) (HGT-C2) (HGT ...	0.05	-	cyt	0					85
Q8N6L1 UniProt NPD GO	KCP2_HUMAN	Keratinocytes-associated protein 2 (KCP-2)	0.05	-	mit	4 *	Membrane; multi-pass membrane protein				162
P83037 UniProt NPD GO	ILLB_LEUGL	Kunitz-type trypsin inhibitor LlTI, beta chain	0.05	-	cyt	0	Secreted protein			1LT2	42
P32734 UniProt NPD GO	ID5B_PROJU	Kunitz-type trypsin inhibitor beta chain	0.05	-	nuc	0					38
Q9H9P8 UniProt NPD GO	L2HDH_HUMAN	L-2-hydroxyglutarate dehydrogenase, mitochondrial precursor (EC 1.1.99.2) (Duranin)	0.05	-	nuc	0	Mitochondrion	integral to membrane [IDA] integral to mitochondrial inner membrane [NAS] mitochondrion [IDA]	609584		463
Q9ZSD6 UniProt NPD GO	ASPG_LUPLU	L-asparaginase precursor (EC 3.5.1.1) (L-asparagine amidohydrolase) [Contains: L-asparaginase subuni ...	0.05	-	cyt	0					325
P10867 UniProt NPD GO	GGLO_RAT	L-gulonolactone oxidase (EC 1.1.3.8) (LGO) (L-gulono-gamma-lactone oxidase) (GLO)	0.05	-	mit	1	Microsome; microsomal membrane; single-pass membrane protein	microsome [TAS]			439
P13774 UniProt NPD GO	LDH_PLAFA	L-lactate dehydrogenase (EC 1.1.1.27) (LDH-P) (Fragment)	0.05	-	nuc	0					42
Q12729 UniProt NPD GO	LAC1_PLEOS	Laccase 1 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.05	-	end	0	Secreted protein				529
Q99049 UniProt NPD GO	LAC3_TRAVI	Laccase 3 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.05	-	exc	0	Secreted protein				473
Q5BHG4 UniProt NPD GO	LBUA_EMENI	Lactobacillus up-regulated protein precursor	0.05	-	exc	0					175
P46417 UniProt NPD GO	LGUL_SOYBN	Lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I)	0.05	-	cyt	0					219
Q42891 UniProt NPD GO	LGUL_LYCES	Lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (Glx I) (Ke ...	0.05	-	cyt	0					185
P11995 UniProt NPD GO	LSP1A_DROME	Larval serum protein 1 alpha chain precursor (Hexamerin 1 alpha)	0.05	-	mit	0	Secreted protein; extracellular space	larval serum protein complex [IDA]			816
P61505 UniProt NPD GO	TXL1_LASPA	Lasiotoxin-1 (LpTX1)	0.05	-	nuc	0	Secreted protein				49
P61506 UniProt NPD GO	TXL2_LASPA	Lasiotoxin-2 (LpTX2)	0.05	-	nuc	0	Secreted protein				49
P80691 UniProt NPD GO	LSPI_CARPA	Latex serine proteinase inhibitor	0.05	-	cyt	1 *	Secreted protein; extracellular space				184
P08902 UniProt NPD GO	LECA_DIOGR	Lectin alpha chain [Contains: Lectin beta chain; Lectin gamma chain]	0.05	-	cyt	0				1VLN	237
P58907 UniProt NPD GO	LECA_DIOVI	Lectin alpha chain [Contains: Lectin beta chain; Lectin gamma-1 chain; Lectin gamma-2 chain] (Fragme ...	0.05	-	nuc	0					50
P16404 UniProt NPD GO	LEC_ERYCO	Lectin precursor (ECorL)	0.05	-	exc	0				1SFY	281
P16300 UniProt NPD GO	LEC_PHALU	Lectin precursor (LBL)	0.05	-	exc	1 *					262
P08148 UniProt NPD GO	GP63_LEIMA	Leishmanolysin precursor (EC 3.4.24.36) (Cell surface protease) (Major surface glycoprotein) (Protei ...	0.05	-	cyt	1 *	Cell membrane; lipid-anchor; GPI-anchor			1LML	602

You are viewing entries 74751 to 74800 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.