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
Q95108 UniProt NPD GO	THIOM_BOVIN	Thioredoxin, mitochondrial precursor (Mt-Trx) (MTRX) (Thioredoxin-2)	0.05	-	mit	0	Mitochondrion				166
P47938 UniProt NPD GO	THIO1_DROME	Thioredoxin-1 (DmTrx-1) (Protein deadhead)	0.05	-	mit	0	Nucleus				107
P60226 UniProt NPD GO	THIO1_DROYA	Thioredoxin-1 (Trx-1) (Protein deadhead)	0.05	-	mit	0	Nucleus (By similarity)				107
P35705 UniProt NPD GO	PRDX3_BOVIN	Thioredoxin-dependent peroxide reductase, mitochondrial precursor (EC 1.11.1.15) (Peroxiredoxin-3) ( ...	0.05	-	mit	0	Mitochondrion			1ZYE	257
P34978 UniProt NPD GO	TA2R_RAT	Thromboxane A2 receptor (TXA2-R) (Prostanoid TP receptor) (TXR2)	0.05	-	end	6 *	Membrane; multi-pass membrane protein				341
P82538 UniProt NPD GO	TL26_ARATH	Thylakoid lumenal 25.6 kDa protein, chloroplast precursor	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				230
P01250 UniProt NPD GO	THP2_BOVIN	Thymopoietin-2 (Thymopoietin II)	0.05	-	cyt	0					49
Q9DFJ9 UniProt NPD GO	TYB_GILMI	Thymosin beta	0.05	-	nuc	0	Cytoplasm (By similarity)				43
P21752 UniProt NPD GO	TYB9_BOVIN	Thymosin beta-9 (Thymosin beta-10) [Contains: Thymosin beta-8]	0.05	-	nuc	0	Cytoplasm			1HJ0	41
Q91641 UniProt NPD GO	THIB_XENLA	Thyroid hormone-induced protein B precursor	0.05	-	exc	0	Or: Membrane; peripheral membrane protein. Or: Secreted protein; extracellular space				688
P17164 UniProt NPD GO	FUCO_RAT	Tissue alpha-L-fucosidase precursor (EC 3.2.1.51) (Alpha-L-fucosidase I) (Alpha-L-fucoside fucohydro ...	0.05	-	mit	1 *	Lysosome				462
Q94FY7 UniProt NPD GO	TOCC_ARATH	Tocopherol cyclase, chloroplast precursor (Vitamin E pathway gene 1 protein) (Sucrose export defecti ...	0.05	-	cyt	0	Plastid; chloroplast; chloroplast inner membrane (By similarity)				488
P00759 UniProt NPD GO	KLK2_RAT	Tonin precursor (EC 3.4.21.35) (Esterase 1) (S2 kallikrein) (RGK-2) (RSKG-5)	0.05	-	exc	0				1TON	259
P61542 UniProt NPD GO	APT2_ANTEL	Toxin APETx2	0.05	-	nuc	0	Secreted protein (Probable). Found in nematocyst (Probable)			1WXN	42
P84713 UniProt NPD GO	TXMO1_CONMO	Toxin Mo1659	0.05	-		0	Secreted protein	extracellular region [IDA]			13
P60271 UniProt NPD GO	SCX1_PARSC	Toxin PBITx1 (sITx10)	0.05	-	nuc	0	Secreted protein				25
Q923Y7 UniProt NPD GO	TAAR4_RAT	Trace amine-associated receptor 4 (Trace amine receptor 2) (TaR-2)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				347
Q5QD12 UniProt NPD GO	TAA7A_MOUSE	Trace amine-associated receptor 7a	0.05	-	end	7 *	Membrane; multi-pass membrane protein				358
Q32L78 UniProt NPD GO	TPC6B_BOVIN	Trafficking protein particle complex subunit 6B	0.05	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)				158
Q86SZ2 UniProt NPD GO	TPC6B_HUMAN	Trafficking protein particle complex subunit 6B	0.05	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)			2BJN	158
Q6GQN8 UniProt NPD GO	MECR_BRARE	Trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.38)	0.05	-	mit	0	Mitochondrion (By similarity)				377
Q9DCS3 UniProt NPD GO	MECR_MOUSE	Trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.38)	0.05	-	mit	0	Mitochondrion (By similarity)				373
P01134 UniProt NPD GO	TGFA_RAT	Transforming growth factor alpha precursor (TGF-alpha) (EGF-like TGF) (ETGF) (TGF type 1)	0.05	-	end	1	Precursor form: Cell membrane; single-pass type I membrane protein. Mature form: Secreted protein; e ...	extracellular space [IDA] integral to plasma membrane [TAS] nucleus [IDA]			159
Q6YXL2 UniProt NPD GO	IF1C_PHYPA	Translation initiation factor IF-1, chloroplast	0.05	-	nuc	0	Plastid; chloroplast				78
P14741 UniProt NPD GO	EI2BA_YEAST	Translation initiation factor eIF-2B subunit alpha (eIF-2B GDP-GTP exchange factor subunit alpha) (G ...	0.05	-	cyt	0		eukaryotic translation initiation factor 2B... [IDA] multi-eIF complex [IDA]			305
P89886 UniProt NPD GO	TMA20_YEAST	Translation machinery-associated protein 20	0.05	-	nuc	0	Cytoplasm	cytoplasm [IDA]			181
P51571 UniProt NPD GO	SSRD_HUMAN	Translocon-associated protein subunit delta precursor (TRAP-delta) (Signal sequence receptor subunit ...	0.05	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	translocon complex [NAS]	300090		173
Q5REH6 UniProt NPD GO	SSRD_PONPY	Translocon-associated protein subunit delta precursor (TRAP-delta) (Signal sequence receptor subunit ...	0.05	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				173
Q64302 UniProt NPD GO	T4S1_MOUSE	Transmembrane 4 L6 family member 1 (Tumor-associated antigen L6) (Membrane component surface marker ...	0.05	-	end	4 *	Membrane; multi-pass membrane protein				202
Q9BZW5 UniProt NPD GO	TM6S1_HUMAN	Transmembrane 6 superfamily member 1	0.05	-	end	9 *	Membrane; multi-pass membrane protein (Potential)	membrane [NAS]	606562		370
P58749 UniProt NPD GO	TM6S1_MOUSE	Transmembrane 6 superfamily member 1	0.05	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				370
Q04562 UniProt NPD GO	YD107_YEAST	Transmembrane 9 superfamily protein YDR107C precursor	0.05	-	end	9	Membrane; multi-pass membrane protein (Probable)				672
Q5R8Y6 UniProt NPD GO	TM9S2_PONPY	Transmembrane 9 superfamily protein member 2 precursor	0.05	-	end	9	Endosome; endosomal membrane; multi-pass membrane protein (Probable)				663
Q99805 UniProt NPD GO	TM9S2_HUMAN	Transmembrane 9 superfamily protein member 2 precursor (p76)	0.05	-	end	9	Endosome; endosomal membrane; multi-pass membrane protein (Probable)	endosome [TAS] integral to plasma membrane [TAS]	604678		663
Q71RG4 UniProt NPD GO	TMUB2_HUMAN	Transmembrane and ubiquitin-like domain-containing protein 2	0.05	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				321
Q8K1T0 UniProt NPD GO	TMPS3_MOUSE	Transmembrane protease, serine 3 (EC 3.4.21.-)	0.05	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein				453
P56983 UniProt NPD GO	TM14A_MOUSE	Transmembrane protein 14A	0.05	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				99
Q8BY79 UniProt NPD GO	TMM20_MOUSE	Transmembrane protein 20	0.05	-	end	10	Membrane; multi-pass membrane protein (Potential)				368
Q60774 UniProt NPD GO	TM45A_MOUSE	Transmembrane protein 45a (Dermal papilla-derived protein 7 homolog) (19.5)	0.05	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				273
Q9QYZ9 UniProt NPD GO	TMSP8_MOUSE	Transmembrane serine protease 8 precursor (EC 3.4.21.-) (Distal intestinal serine protease)	0.05	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Probable)	anchored to plasma membrane [ISS]			310
P36186 UniProt NPD GO	TPI1_GIALA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.05	-	mit	0					257
P36187 UniProt NPD GO	TPI2_GIALA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.05	-	mit	0					257
Q9HGY8 UniProt NPD GO	TPIS_ASPOR	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.05	-	cyt	0					251
P02587 UniProt NPD GO	TNNC2_PIG	Troponin C, skeletal muscle	0.05	-	cyt	0					159
P54624 UniProt NPD GO	TRYA_DROER	Trypsin alpha precursor (EC 3.4.21.4)	0.05	-	exc	0	Secreted protein; extracellular space				256
P35004 UniProt NPD GO	TRYB_DROME	Trypsin beta precursor (EC 3.4.21.4)	0.05	-	exc	0	Secreted protein; extracellular space				253
P42276 UniProt NPD GO	TRYDG_DROME	Trypsin delta/gamma precursor (EC 3.4.21.4)	0.05	-	exc	0	Secreted protein; extracellular space				253
P80301 UniProt NPD GO	ITI1_BRANA	Trypsin inhibitor (RTI)	0.05	-	cyt	0	Secreted protein				60
P32877 UniProt NPD GO	IT1B_PSOTE	Trypsin inhibitor 1B (WTI-1B)	0.05	-	cyt	0					172
P83395 UniProt NPD GO	ITR4_CYCPE	Trypsin inhibitor 4 (Trypsin inhibitor IV) (CyPTI-IV)	0.05	-	nuc	0	Secreted protein				29

You are viewing entries 75801 to 75850 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.