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
Q63270 UniProt NPD GO	IREB1_RAT	Iron-responsive element-binding protein 1 (IRE-BP 1) (Iron regulatory protein 1) (IRP1) (Ferritin re ...	0.03	-	cyt	0	Cytoplasm				889
Q07333 UniProt NPD GO	IAPP_LEPEU	Islet amyloid polypeptide (Amylin) (Fragment)	0.03	-	nuc	0	Secreted protein				23
Q29119 UniProt NPD GO	IAPP_PIG	Islet amyloid polypeptide (Amylin) (Fragment)	0.03	-	nuc	0	Secreted protein				32
Q9Z2K8 UniProt NPD GO	IDHC_MICOH	Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) (Cytosolic NADP-isocitrate dehydrogenase) ...	0.03	-	pox	0	Cytoplasm				414
P41562 UniProt NPD GO	IDHC_RAT	Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) (Cytosolic NADP-isocitrate dehydrogenase) ...	0.03	-	pox	0	Cytoplasm				414
P20699 UniProt NPD GO	ACEA_HELAN	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL) (Fragment)	0.03	-	nuc	0	Glyoxysome				58
Q9JHI5 UniProt NPD GO	IVD_MOUSE	Isovaleryl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.10) (IVD)	0.03	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			424
P30810 UniProt NPD GO	JHEB_TRINI	Juvenile hormone esterase, isoform B (EC 3.1.1.59) (JH esterase) (JHE-B) (Fragments)	0.03	-	cyt	0					63
P15948 UniProt NPD GO	K1B22_MOUSE	Kallikrein 1-related peptidase b22 precursor (EC 3.4.21.35) (Glandular kallikrein K22) (Tissue kalli ...	0.03	-	end	0					259
Q61754 UniProt NPD GO	K1B24_MOUSE	Kallikrein 1-related peptidase b24 precursor (EC 3.4.21.35) (Glandular kallikrein K24) (Tissue kalli ...	0.03	-	end	0					263
P84704 UniProt NPD GO	CX14A_CONVL	Kappa-conotoxin vil14a	0.03	-	nuc	0	Secreted protein				27
Q3KRE6 UniProt NPD GO	KLDC2_RAT	Kelch domain-containing protein 2	0.03	-	cyt	0					406
Q4G5Y1 UniProt NPD GO	KLDC2_MOUSE	Kelch domain-containing protein 2 (Endothelial differentiation inhibitory protein TNG)	0.03	-	cyt	0					406
Q3LI63 UniProt NPD GO	KR201_HUMAN	Keratin-associated protein 20-1	0.03	-	cyt	1 *					56
Q3LI67 UniProt NPD GO	KRA63_HUMAN	Keratin-associated protein 6-3	0.03	-	cyt	0					103
Q8IUC3 UniProt NPD GO	KRA71_HUMAN	Keratin-associated protein 7-1 (High tyrosine-glycine keratin-associated protein 7.1)	0.03	-	cyt	0					87
P10410 UniProt NPD GO	TOXK_WILMR	Killer toxin HM-1 precursor	0.03	-	end	0	Secreted protein			1WKT	125
Q9UUH3 UniProt NPD GO	YKI9_SCHPO	Kinase C630.09c (EC 2.7.-.-)	0.03	-	cyt	0	Cytoplasm. Nucleus				277
P50113 UniProt NPD GO	LYS5_YEAST	L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase (EC 2.7.8.-) (AASD-PPT)	0.03	-	cyt	0		cytoplasm [TAS]			272
P37064 UniProt NPD GO	ASO_CUCPM	L-ascorbate oxidase (EC 1.10.3.3) (Ascorbase) (ASO)	0.03	-	cyt	0				1ASQ	552
P24792 UniProt NPD GO	ASO_CUCMA	L-ascorbate oxidase precursor (EC 1.10.3.3) (Ascorbase) (ASO)	0.03	-	end	1 *					579
P14133 UniProt NPD GO	ASO_CUCSA	L-ascorbate oxidase precursor (EC 1.10.3.3) (Ascorbase) (ASO)	0.03	-	mit	1 *					587
P50287 UniProt NPD GO	ASPG1_ARATH	L-asparaginase 1 precursor (EC 3.5.1.1) (L-asparagine amidohydrolase 1) [Contains: L-asparaginase 1 ...	0.03	-	cyt	0					315
Q09927 UniProt NPD GO	PPR1_SCHPO	L-azetidine-2-carboxylic acid acetyltransferase (EC 2.3.1.-)	0.03	-	cyt	0					209
Q3ZC33 UniProt NPD GO	GGLO_BOVIN	L-gulonolactone oxidase (EC 1.1.3.8) (LGO) (L-gulono-gamma-lactone oxidase) (GLO)	0.03	-	mit	1	Microsome; microsomal membrane; single-pass membrane protein (By similarity)				439
Q8HXW0 UniProt NPD GO	GGLO_PIG	L-gulonolactone oxidase (EC 1.1.3.8) (LGO) (L-gulono-gamma-lactone oxidase) (GLO)	0.03	-	end	1	Microsome; microsomal membrane; single-pass membrane protein (By similarity)				439
Q7SI97 UniProt NPD GO	LDH_PLABA	L-lactate dehydrogenase (EC 1.1.1.27)	0.03	-	end	1 *				1OC4	316
P84793 UniProt NPD GO	LDH_PLABE	L-lactate dehydrogenase (EC 1.1.1.27)	0.03	-	end	1 *					316
Q95028 UniProt NPD GO	LDH_DROME	L-lactate dehydrogenase (EC 1.1.1.27) (LDH)	0.03	-	cyt	0	Cytoplasm (By similarity)				332
P22988 UniProt NPD GO	LDHA_HORVU	L-lactate dehydrogenase A (EC 1.1.1.27) (LDH-A)	0.03	-	cyt	0					356
Q9W7L4 UniProt NPD GO	LDHB_SCEUN	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.03	-	mit	0	Cytoplasm (By similarity)				334
P13490 UniProt NPD GO	LDHB_RABIT	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B) (LDH heart subunit) (LDH-H) (Fragment)	0.03	-	cyt	0	Cytoplasm (By similarity)				217
Q40227 UniProt NPD GO	LIM3_LILLO	LIM3 protein precursor	0.03	-	exc	0					90
Q99044 UniProt NPD GO	LAC1_TRAVI	Laccase 1 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.03	-	exc	0	Secreted protein				520
Q12739 UniProt NPD GO	LAC2_PLEOS	Laccase 2 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.03	-	exc	0	Secreted protein				533
Q12718 UniProt NPD GO	LAC2_TRAVE	Laccase 2 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.03	-	vac	0	Secreted protein			1GYC	519
Q02081 UniProt NPD GO	LAC4_THACU	Laccase 4 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.03	-	exc	0	Secreted protein				531
Q12542 UniProt NPD GO	LAC2_AGABI	Laccase-2 precursor (EC 1.10.3.2) (Laccase II) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase ...	0.03	-	exc	0	Secreted protein				520
P83315 UniProt NPD GO	LCTN_LAMGL	Lactophorin (Whey protein) (Fragment)	0.03	-		0		extracellular region [ISS]			18
Q9UHI5 UniProt NPD GO	LAT2_HUMAN	Large neutral amino acids transporter small subunit 2 (L-type amino acid transporter 2) (hLAT2)	0.03	-	end	12 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS] plasma membrane [TAS]	604235		535
P80683 UniProt NPD GO	CUA3A_TENMO	Larval cuticle protein A3A (TM-A3A) (TM-LCP A3A)	0.03	-	cyt	0					134
Q9TXD9 UniProt NPD GO	CUF1_TENMO	Larval cuticle protein F1 (Tml-F1)	0.03	-	cyt	0		extracellular region [IC]			162
P11996 UniProt NPD GO	LSP1B_DROME	Larval serum protein 1 beta chain precursor (Hexamerin 1 beta)	0.03	-	end	0	Secreted protein; extracellular space	larval serum protein complex [IDA]			789
Q24388 UniProt NPD GO	LSP2_DROME	Larval serum protein 2 precursor (LSP-2) (Hexamerin 2)	0.03	-	vac	0	Secreted protein; extracellular space	larval serum protein complex [IDA]			701
P80686 UniProt NPD GO	CUH1C_TENMO	Larval/pupal cuticle protein H1C precursor (TM-H1C) (TM-PCP H1C) (TMLPCP-22)	0.03	-	mit	1 *					211
Q9BGL2 UniProt NPD GO	LRAT_BOVIN	Lecithin retinol acyltransferase (EC 2.3.1.135) (Phosphatidylcholine--retinol O-acyltransferase)	0.03	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				230
P83955 UniProt NPD GO	LG29_VIGUS	Lectin 29 kDa subunit (Hemagglutinin 29 kDa subunit) (Fragment)	0.03	-		0					15
P17346 UniProt NPD GO	LEC2_MEGRO	Lectin BRA-2	0.03	-	cyt	0					173
P23558 UniProt NPD GO	LEC1_LABAL	Lectin I (Seed lectin anti-H(O)) (LAA-I)	0.03	-	cyt	0					250
P58908 UniProt NPD GO	LECA_DIORO	Lectin alpha chain [Contains: Lectin beta chain; Lectin gamma-1 chain; Lectin gamma-2 chain] (Fragme ...	0.03	-	nuc	0					49

You are viewing entries 80401 to 80450 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.