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
P52806 UniProt NPD GO	YCF3_PINTH	Photosystem I assembly protein ycf3	0.19	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				169
Q39195 UniProt NPD GO	PST2_ARATH	Photosystem II 5 kDa protein, chloroplast precursor (PSII-T) (Nuclear encoded psbT) (PsbTn)	0.19	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				103
Q9ST21 UniProt NPD GO	PSK1_ORYSA	Phytosulfokines 1 precursor [Contains: Phytosulfokine-alpha (PSK-alpha) (Phytosulfokine-a); Phytosul ...	0.19	-	exc	0	Secreted protein				89
O48609 UniProt NPD GO	RRP3_HORVU	Plastid-specific 30S ribosomal protein 3, chloroplast precursor (PSRP-3)	0.19	-	mit	0	Plastid; chloroplast (By similarity)				181
P21556 UniProt NPD GO	PTAFR_CAVPO	Platelet-activating factor receptor (PAF-R)	0.19	-	end	7 *	Membrane; multi-pass membrane protein				342
P36989 UniProt NPD GO	TXP9_PLETR	Plectoxin-9 (Plectoxin IX) (PLT-IX) (PLTIX)	0.19	-	nuc	0	Secreted protein				46
Q9GYS1 UniProt NPD GO	MES6_CAEEL	Polycomb protein mes-6 (Maternal-effect sterile protein 6) (ESC homolog)	0.19	-	cyt	0	Nucleus				459
Q05091 UniProt NPD GO	PGIP_PYRCO	Polygalacturonase inhibitor precursor (Polygalacturonase-inhibiting protein)	0.19	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				330
P43311 UniProt NPD GO	PPO_VITVI	Polyphenol oxidase, chloroplast precursor (EC 1.10.3.1) (PPO) (Catechol oxidase)	0.19	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				607
Q9MAC5 UniProt NPD GO	PTBP1_ARATH	Polypyrimidine tract-binding protein homolog 1	0.19	-	nuc	0	Nucleus (Probable)				399
Q9FGL9 UniProt NPD GO	PTBP2_ARATH	Polypyrimidine tract-binding protein homolog 2	0.19	-	nuc	0	Nucleus (Probable)				429
O54912 UniProt NPD GO	KCNK3_RAT	Potassium channel subfamily K member 3 (Acid-sensitive potassium channel protein TASK-1) (TWIK-relat ...	0.19	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				411
P45628 UniProt NPD GO	KAX12_LEIQH	Potassium channel toxin alpha-KTx 1.2 precursor (Charybdotoxin-2) (ChTX-Lq2) (Toxin 18-2) (Lqh 18-2) ...	0.19	-	exc	0	Secreted protein			1LIR	59
Q6XLL8 UniProt NPD GO	KAX67_OPICA	Potassium channel toxin alpha-KTx 6.7 precursor (OcKTx2)	0.19	-	exc	0	Secreted protein (By similarity)				61
O64769 UniProt NPD GO	POT11_ARATH	Potassium transporter 11 (AtPOT11)	0.19	-	end	11	Cell membrane; multi-pass membrane protein (Potential)				792
P79197 UniProt NPD GO	KCNA5_MUSPF	Potassium voltage-gated channel subfamily A member 5 (Voltage-gated potassium channel subunit Kv1.5) ...	0.19	-	end	3	Membrane; multi-pass membrane protein				601
O88758 UniProt NPD GO	KCNS1_RAT	Potassium voltage-gated channel subfamily S member 1 (Voltage-gated potassium channel subunit Kv9.1) ...	0.19	-	end	3	Cell membrane; multi-pass membrane protein (By similarity). Membrane; multi-pass membrane protein (B ...	plasma membrane [ISS] voltage-gated potassium channel complex [ISS]			497
Q6BJ73 UniProt NPD GO	SPP2_DEBHA	Pre-mRNA-splicing factor SPP2	0.19	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				174
P31171 UniProt NPD GO	PREA_CYAPA	Prenyl transferase (EC 2.5.1.-)	0.19	+	cyt	0	Plastid; cyanelle				323
P05224 UniProt NPD GO	CAER3_XENLA	Preprocaerulein type-3 precursor (Preprocaerulein type III) [Contains: Caerulein]	0.19	-	exc	0	Secreted protein				169
Q37143 UniProt NPD GO	SECY_ANTSP	Preprotein translocase secY subunit	0.19	-	end	9 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				405
P11976 UniProt NPD GO	PSTA_DICDI	Prestalk protein precursor	0.19	-	nuc	0	Secreted protein				1046
Q8L4Y2 UniProt NPD GO	LPAT4_ARATH	Probable 1-acyl-sn-glycerol-3-phosphate acyltransferase 4 (EC 2.3.1.51) (Lysophosphatidyl acyltransf ...	0.19	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				378
O22567 UniProt NPD GO	DXS_ORYSA	Probable 1-deoxy-D-xylulose-5-phosphate synthase, chloroplast precursor (EC 2.2.1.7) (1-deoxyxylulos ...	0.19	-	cyt	0	Plastid; chloroplast (Probable)				720
P38858 UniProt NPD GO	SOL3_YEAST	Probable 6-phosphogluconolactonase 3 (EC 3.1.1.31) (6PGL)	0.19	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			280
P70585 UniProt NPD GO	GPR19_RAT	Probable G-protein coupled receptor 19	0.19	-	end	7	Membrane; multi-pass membrane protein				415
Q9ES90 UniProt NPD GO	GPR35_MOUSE	Probable G-protein coupled receptor 35	0.19	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				307
Q9BXC0 UniProt NPD GO	GPR81_HUMAN	Probable G-protein coupled receptor 81 (G-protein coupled receptor 104)	0.19	-	end	6 *	Membrane; multi-pass membrane protein		606923		346
Q93126 UniProt NPD GO	GPR9_BALAM	Probable G-protein coupled receptor No9	0.19	-	end	7 *	Membrane; multi-pass membrane protein				476
Q8SRG3 UniProt NPD GO	AMP12_ENCCU	Probable M1-family aminopeptidase 2 (EC 3.4.11.-)	0.19	-	cyt	0					864
Q09527 UniProt NPD GO	KAD6_CAEEL	Probable adenylate kinase isoenzyme 6 (EC 2.7.4.3) (ATP-AMP transphosphorylase 6)	0.19	-	cyt	0	Nucleus (By similarity)				182
Q09629 UniProt NPD GO	KADY_CAEEL	Probable adenylate kinase isoenzyme ZK673.2 (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.19	-	cyt	0					222
Q69R21 UniProt NPD GO	ALDO4_ORYSA	Probable aldehyde oxidase 4 (EC 1.2.3.1) (AO-4)	0.19	-	cyt	0					837
Q21929 UniProt NPD GO	CBR2_CAEEL	Probable carbonyl reductase [NADPH] (EC 1.1.1.184) (NADPH-dependent carbonyl reductase)	0.19	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				251
Q20168 UniProt NPD GO	COPB2_CAEEL	Probable coatomer subunit beta' (Beta'-coat protein) (Beta'-COP)	0.19	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				1000
P82711 UniProt NPD GO	C6A19_DROME	Probable cytochrome P450 6a19 (EC 1.14.-.-) (CYPVIA19)	0.19	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				503
P54889 UniProt NPD GO	P5CS_CAEEL	Probable delta 1-pyrroline-5-carboxylate synthetase (P5CS) [Includes: Glutamate 5-kinase (EC 2.7.2.1 ...	0.19	-	mit	0					800
P34497 UniProt NPD GO	GLNA_CAEEL	Probable glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase)	0.19	-	cyt	0	Cytoplasm (By similarity)				367
P53301 UniProt NPD GO	CRH1_YEAST	Probable glycosidase CRH1 precursor (EC 3.2.-.-) (Congo red hypersensitive protein 1)	0.19	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential). Localized at the cell surface, particularly in ...	cell wall (sensu Fungi) [IDA] incipient bud site [IDA]			507
Q09627 UniProt NPD GO	ILB2_CAEEL	Probable insulin-like peptide beta-type 2 precursor	0.19	-	exc	0	Secreted protein (Potential)				106
Q5TUE9 UniProt NPD GO	RM23_ANOGA	Probable mitochondrial 39S ribosomal protein L23 (L23mt) (MRP-L23)	0.19	-	mit	0	Mitochondrion (By similarity)				151
Q9UTK3 UniProt NPD GO	NPT1_SCHPO	Probable nicotinate phosphoribosyltransferase (EC 2.4.2.11) (NAPRTase)	0.19	-	cyt	0					410
O94626 UniProt NPD GO	ORN_SCHPO	Probable oligoribonuclease (EC 3.1.-.-)	0.19	-	cyt	0					180
Q3U4I7 UniProt NPD GO	CJ033_MOUSE	Probable oxidoreductase C10orf33 homolog (EC 1.-.-.-)	0.19	-	mit	0					580
P24396 UniProt NPD GO	PEL18_LYCES	Probable pectate lyase P18 precursor (EC 4.2.2.2) (Style development-specific protein 9612)	0.19	-	nuc	0	Secreted protein				404
Q6K439 UniProt NPD GO	PAP2_ORYSA	Probable plastid-lipid-associated protein 2, chloroplast precursor (Fibrillin-like protein 2)	0.19	-	mit	0	Plastid; chloroplast (Potential)				319
O14450 UniProt NPD GO	PFD6_SCHPO	Probable prefoldin subunit 6	0.19	-	nuc	0					114
Q5M7W7 UniProt NPD GO	SYPM_RAT	Probable prolyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.15) (Proline--tRNA ligase) (ProRS ...	0.19	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				475
P50605 UniProt NPD GO	SDC_CAEEL	Probable syndecan precursor	0.19	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				288
O60156 UniProt NPD GO	SEN34_SCHPO	Probable tRNA-splicing endonuclease subunit sen34 (EC 3.1.27.9) (tRNA-intron endonuclease sen34)	0.19	-	cyt	0					284

You are viewing entries 52251 to 52300 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.