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
P49575 UniProt NPD GO	PGLR_ASPPA	Polygalacturonase precursor (EC 3.2.1.15) (Pectinase) (PGL)	0.04	-	cyt	0					363
Q12554 UniProt NPD GO	PGLR3_ASPNG	Polygalacturonase-3 precursor (EC 3.2.1.15) (Polygalacturonase III) (PG-III) (PGC) (Pectinase-3)	0.04	-	mit	0					383
Q9SE93 UniProt NPD GO	PNAE_RAUSE	Polyneuridine-aldehyde esterase precursor (EC 3.1.1.78) (Polyneuridine aldehyde esterase)	0.04	-	cyt	1					264
P59943 UniProt NPD GO	KAX1C_LEIQH	Potassium channel toxin alpha-KTx 1.12 precursor (Charybdotoxin b) (ChTx-b)	0.04	-	exc	0	Secreted protein				59
P83407 UniProt NPD GO	KA191_MESMA	Potassium channel toxin alpha-KTx 19.1 (Neurotoxin BmBKTx1) (BmK37)	0.04	-	nuc	0	Secreted protein			1R1G	31
Q9TXD1 UniProt NPD GO	KAX24_CENNO	Potassium channel toxin alpha-KTx 2.4 (Noxiustoxin-2) (NTx2) (NTx-2)	0.04	-	nuc	0	Secreted protein				38
P59847 UniProt NPD GO	KAX25_CENLM	Potassium channel toxin alpha-KTx 2.5 (Hongotoxin-1) (HgTX1)	0.04	-	nuc	0	Secreted protein			1HLY	39
P59870 UniProt NPD GO	KAX55_MESTA	Potassium channel toxin alpha-KTx 5.5 (Tamapin-2)	0.04	-	nuc	0	Secreted protein				31
Q9FY75 UniProt NPD GO	POT7_ARATH	Potassium transporter 7 (AtPOT7) (AtHAK7)	0.04	-	end	12	Cell membrane; multi-pass membrane protein (Potential)				858
Q5R8Q2 UniProt NPD GO	KCNE1_PONPY	Potassium voltage-gated channel subfamily E member 1	0.04	-	mit	1 *	Membrane; single-pass type I membrane protein (By similarity)				129
Q9PT84 UniProt NPD GO	KCNH2_CHICK	Potassium voltage-gated channel subfamily H member 2 (Voltage-gated potassium channel subunit Kv11.1 ...	0.04	-	end	5	Membrane; multi-pass membrane protein				526
Q9FMP4 UniProt NPD GO	PM14_ARATH	Pre-mRNA branch site p14-like protein	0.04	-	mit	0	Nucleus (Potential)				124
Q12417 UniProt NPD GO	PRP46_YEAST	Pre-mRNA-splicing factor PRP46 (Pre-mRNA-processing protein 46) (Complexed with CEF1 protein 1) (PRP ...	0.04	-	cyt	0	Cytoplasm. Nucleus	spliceosome complex [IDA]			451
Q29432 UniProt NPD GO	PAG1_BOVIN	Pregnancy-associated glycoprotein 1 precursor (EC 3.4.23.-) (PAG 1) (Pregnancy-specific protein B) ( ...	0.04	-	exc	0	Secreted protein; extracellular space				380
P83499 UniProt NPD GO	PA59G_SHEEP	Pregnancy-associated glycoprotein 59g (EC 3.4.23.-) (ovPAG 59g) (Fragment)	0.04	-	cyt	0					25
Q28389 UniProt NPD GO	PAG_HORSE	Pregnancy-associated glycoprotein precursor (EC 3.4.23.-) (PAG)	0.04	-	mit	0	Secreted protein; extracellular space				388
O02100 UniProt NPD GO	HOP1_CAEEL	Presenilin hop-1	0.04	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				358
O62691 UniProt NPD GO	MCH_TARSY	Pro-MCH precursor (Fragment)	0.04	-	exc	1 *	Secreted protein (By similarity)				71
P31528 UniProt NPD GO	ACCO_DIACA	Probable 1-aminocyclopropane-1-carboxylate oxidase (EC 1.14.17.4) (ACC oxidase) (Ethylene-forming en ...	0.04	-	cyt	0					321
Q38854 UniProt NPD GO	DXS_ARATH	Probable 1-deoxy-D-xylulose-5-phosphate synthase, chloroplast precursor (EC 2.2.1.7) (1-deoxyxylulos ...	0.04	-	cyt	0	Plastid; chloroplast (Probable)				717
Q9VMN5 UniProt NPD GO	CH60C_DROME	Probable 60 kDa heat shock protein homolog 2, mitochondrial precursor (Hsp60) (60 kDa chaperonin) (C ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				576
P51678 UniProt NPD GO	CCR3_MOUSE	Probable C-C chemokine receptor type 3 (C-C CKR-3) (CC-CKR-3) (CCR-3) (CCR3) (CKR3) (Macrophage infl ...	0.04	-	end	7 *	Membrane; multi-pass membrane protein				359
Q19366 UniProt NPD GO	DPOD2_CAEEL	Probable DNA polymerase delta small subunit (EC 2.7.7.7)	0.04	-	cyt	0	Nucleus (By similarity)				451
Q8TDV5 UniProt NPD GO	GP119_HUMAN	Probable G-protein coupled receptor 119	0.04	-	end	7 *	Membrane; multi-pass membrane protein		300513		335
Q5UAW9 UniProt NPD GO	GP157_HUMAN	Probable G-protein coupled receptor 157	0.04	-	end	7 *	Membrane; multi-pass membrane protein				335
Q99678 UniProt NPD GO	GPR20_HUMAN	Probable G-protein coupled receptor 20	0.04	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601908		358
P50132 UniProt NPD GO	GPR4_PIG	Probable G-protein coupled receptor 4 (G-protein coupled receptor 19)	0.04	-	end	6 *	Membrane; multi-pass membrane protein				362
Q9EQQ3 UniProt NPD GO	GPR63_MOUSE	Probable G-protein coupled receptor 63 (PSP24-beta) (PSP24-2)	0.04	-	end	7	Membrane; multi-pass membrane protein				425
Q8CIM5 UniProt NPD GO	GPR84_MOUSE	Probable G-protein coupled receptor 84	0.04	-	end	7 *	Membrane; multi-pass membrane protein				396
Q86Y34 UniProt NPD GO	GPR97_HUMAN	Probable G-protein coupled receptor 97 precursor (G-protein coupled receptor PGR26)	0.04	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]			549
Q9VSE7 UniProt NPD GO	MTH7_DROME	Probable G-protein coupled receptor Mth-like 7 precursor (Protein methuselah-like 7)	0.04	-	end	5	Membrane; multi-pass membrane protein (Potential)				491
P87015 UniProt NPD GO	ASPG1_SCHPO	Probable L-asparaginase 1 precursor (EC 3.5.1.1) (L-asparagine amidohydrolase 1)	0.04	-	exc	0	Cell wall (By similarity)				360
Q9P7P7 UniProt NPD GO	LDH_SCHPO	Probable L-lactate dehydrogenase (EC 1.1.1.27) (L-LDH)	0.04	-	mit	0	Cytoplasm (By similarity)				330
Q7G765 UniProt NPD GO	NADO2_ORYSA	Probable NAD(P)H-dependent oxidoreductase 2 (EC 1.-.-.-)	0.04	-	cyt	0					322
Q93873 UniProt NPD GO	NUCM_CAEEL	Probable NADH-ubiquinone oxidoreductase 49 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6 ...	0.04	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				482
P80616 UniProt NPD GO	METK_MAIZE	Probable S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synth ...	0.04	-		0					15
P50306 UniProt NPD GO	METL_CAEEL	Probable S-adenosylmethionine synthetase C06E7.3 (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoM ...	0.04	-	nuc	0					404
O82422 UniProt NPD GO	SPY_HORVU	Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY (EC 2.4.1.-) (HvSP ...	0.04	-	cyt	0	Nucleus (By similarity)				944
Q40255 UniProt NPD GO	ALDH_LINUS	Probable aldehyde dehydrogenase (EC 1.2.1.3) (Flax-inducible sequence 1)	0.04	-	mit	0					551
Q09913 UniProt NPD GO	ALLC_SCHPO	Probable allantoicase (EC 3.5.3.4) (Allantoate amidinohydrolase)	0.04	-	nuc	0					342
Q10174 UniProt NPD GO	YAV5_SCHPO	Probable aminotransferase C27F1.05c (EC 2.6.1.-)	0.04	-	cyt	0					484
Q9LWR2 UniProt NPD GO	TIP43_ORYSA	Probable aquaporin TIP4.3 (Tonoplast intrinsic protein 4.3) (OsTIP4.3)	0.04	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				251
Q9LF54 UniProt NPD GO	POLC2_ARATH	Probable calcium-binding protein At5g17480	0.04	-	cyt	0					83
Q95JN5 UniProt NPD GO	AT133_MACFA	Probable cation-transporting ATPase 13A3 (EC 3.6.3.-) (ATPase family homolog up-regulated in senesce ...	0.04	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				492
O42937 UniProt NPD GO	COPB2_SCHPO	Probable coatomer subunit beta' (Beta'-coat protein) (Beta'-COP)	0.04	-	mit	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				796
Q9LT77 UniProt NPD GO	CPR1_ARATH	Probable cysteine proteinase At3g19400 precursor (EC 3.4.22.-)	0.04	-	exc	1 *					362
Q9P5L0 UniProt NPD GO	CYB5_NEUCR	Probable cytochrome b5	0.04	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				139
Q20779 UniProt NPD GO	COX6A_CAEEL	Probable cytochrome c oxidase polypeptide VIa, mitochondrial precursor (EC 1.9.3.1)	0.04	-	nuc	1	Mitochondrion; mitochondrial inner membrane (By similarity)				128
O80505 UniProt NPD GO	ALG8_ARATH	Probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl ...	0.04	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				383
O17214 UniProt NPD GO	FUMH_CAEEL	Probable fumarate hydratase, mitochondrial precursor (EC 4.2.1.2) (Fumarase)	0.04	-	mit	0	Mitochondrion (By similarity)				501

You are viewing entries 78001 to 78050 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.