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
P43063 UniProt NPD GO	CDC28_CANAL	Cell division control protein 28 (EC 2.7.11.22)	0.15	-	cyt	0					317
Q05062 UniProt NPD GO	CDC42_CAEEL	Cell division control protein 42 homolog (CDC42CE)	0.15	-	cyt	0	Cell surface. Preferentially localized at the cell surface and especially condensed at cell boundari ...	integral to membrane [IDA]			191
Q39102 UniProt NPD GO	FTSH1_ARATH	Cell division protein ftsH homolog 1, chloroplast precursor (EC 3.4.24.-)	0.15	-	mit	0	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				716
Q06309 UniProt NPD GO	CRK1_LEIME	Cell division protein kinase 2 homolog CRK1 (EC 2.7.11.23)	0.15	-	cyt	0					301
Q9ES58 UniProt NPD GO	MOX2R_RAT	Cell surface glycoprotein OX2 receptor precursor (CD200 cell surface glycoprotein receptor) (OX102 a ...	0.15	-	mit	1	Membrane; single-pass type I membrane protein				327
P10123 UniProt NPD GO	CRAL_BOVIN	Cellular retinaldehyde-binding protein (CRALBP)	0.15	-	nuc	0	Cytoplasm				316
P48386 UniProt NPD GO	CHS1_CAMSI	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.15	-	cyt	0					389
P49440 UniProt NPD GO	CHSY_PHAVU	Chalcone synthase 17 (EC 2.3.1.74) (Naringenin-chalcone synthase 17)	0.15	-	nuc	0					389
Q9XJ57 UniProt NPD GO	CHS2_CITSI	Chalcone synthase 2 (EC 2.3.1.74) (Naringenin-chalcone synthase 2)	0.15	-	nuc	0					391
Q96562 UniProt NPD GO	CHS2_HORVU	Chalcone synthase 2 (EC 2.3.1.74) (Naringenin-chalcone synthase 2)	0.15	-	cyt	0					399
Q9FSB8 UniProt NPD GO	CHS2_RUTGR	Chalcone synthase 2 (EC 2.3.1.74) (Naringenin-chalcone synthase 2)	0.15	-	cyt	0					393
Q9FSB7 UniProt NPD GO	CHS3_RUTGR	Chalcone synthase 3 (EC 2.3.1.74) (Naringenin-chalcone synthase 3)	0.15	-	cyt	0					393
P48399 UniProt NPD GO	CHSC_IPOPU	Chalcone synthase C (EC 2.3.1.74) (Naringenin-chalcone synthase C) (CHS-C) (Fragment)	0.15	-	cyt	0					352
O08707 UniProt NPD GO	CCBP2_MOUSE	Chemokine-binding protein 2 (Chemokine-binding protein D6) (C-C chemokine receptor D6)	0.15	-	end	7 *	Membrane; multi-pass membrane protein				378
O09027 UniProt NPD GO	CCBP2_RAT	Chemokine-binding protein 2 (Chemokine-binding protein D6) (C-C chemokine receptor D6) (CCR10-relate ...	0.15	-	end	7 *	Membrane; multi-pass membrane protein				382
P32470 UniProt NPD GO	CHI1_APHAL	Chitinase 1 precursor (EC 3.2.1.14)	0.15	-	exc	0	Secreted protein				423
Q9SLP4 UniProt NPD GO	CHIT1_TULBA	Chitinase 1 precursor (EC 3.2.1.14) (Tulip bulb chitinase-1) (TBC-1)	0.15	-	vac	1 *					314
P29027 UniProt NPD GO	CHI2_RHIOL	Chitinase 2 precursor (EC 3.2.1.14)	0.15	-	exc	0	Secreted protein (Probable)				542
Q7YS85 UniProt NPD GO	CH3L1_BUBBU	Chitinase-3-like protein 1 (Mammary gland protein 40) (SPB-40)	0.15	-	cyt	0	Secreted protein; extracellular space			1TFV	361
Q8SPQ0 UniProt NPD GO	CH3L1_CAPHI	Chitinase-3-like protein 1 precursor (Mammary gland protein MGP-40) (BP40)	0.15	-	vac	0	Secreted protein; extracellular space			2B41	383
Q9V3D4 UniProt NPD GO	IDGF2_DROME	Chitinase-like protein Idgf2 precursor (Imaginal disk growth factor protein 2)	0.15	-	vac	0	Secreted protein. Secreted in hemolymph. It is probably transported to target tissues via hemolymph	extracellular region [NAS]		1JNE	440
Q9WVC8 UniProt NPD GO	S26A3_MOUSE	Chloride anion exchanger (Protein DRA) (Down-regulated in adenoma) (Solute carrier family 26 member ...	0.15	-	end	11	Membrane; multi-pass membrane protein (Probable)				757
P21564 UniProt NPD GO	CICH_TORMA	Chloride channel protein	0.15	-	end	11	Membrane; multi-pass membrane protein			2D4Z	805
Q9S7W1 UniProt NPD GO	CB4C_ARATH	Chlorophyll a-b binding protein CP29.3, chloroplast precursor (LHCII protein 4.3) (LHCB4.3)	0.15	-	end	3	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein	thylakoid membrane (sensu Viridiplantae) [IDA]			276
O46903 UniProt NPD GO	RR17_GUITH	Chloroplast 30S ribosomal protein S17	0.15	-	nuc	0	Plastid; chloroplast				90
P31162 UniProt NPD GO	RR19_PEA	Chloroplast 30S ribosomal protein S19	0.15	-	nuc	0	Plastid; chloroplast				91
Q32RN2 UniProt NPD GO	RR8_ZYGCR	Chloroplast 30S ribosomal protein S8	0.15	-	cyt	0	Plastid; chloroplast				132
Q85FI6 UniProt NPD GO	RK14_ADICA	Chloroplast 50S ribosomal protein L14	0.15	+	cyt	0	Plastid; chloroplast				122
P49555 UniProt NPD GO	RK19_ODOSI	Chloroplast 50S ribosomal protein L19	0.15	-	nuc	0	Plastid; chloroplast				120
P19167 UniProt NPD GO	RK23_EUGGR	Chloroplast 50S ribosomal protein L23	0.15	-	cyt	0	Plastid; chloroplast				100
Q9TLT2 UniProt NPD GO	RK3_CYACA	Chloroplast 50S ribosomal protein L3	0.15	-	cyt	0	Plastid; chloroplast				215
Q6EW32 UniProt NPD GO	RK33_NYMAL	Chloroplast 50S ribosomal protein L33	0.15	-	nuc	0	Plastid; chloroplast				68
P51313 UniProt NPD GO	RK4_PORPU	Chloroplast 50S ribosomal protein L4	0.15	-	cyt	0	Plastid; chloroplast				214
Q4G355 UniProt NPD GO	RK5_EMIHU	Chloroplast 50S ribosomal protein L5	0.15	-	cyt	0	Plastid; chloroplast				182
Q1XDI6 UniProt NPD GO	RK5_PORYE	Chloroplast 50S ribosomal protein L5	0.15	-	cyt	0	Plastid; chloroplast				181
P92935 UniProt NPD GO	TLC2_ARATH	Chloroplast ADP,ATP carrier protein 2, chloroplast precursor (ADP/ATP translocase 2) (Adenine nucleo ...	0.15	-	end	11	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				618
Q4QQV7 UniProt NPD GO	CH25H_RAT	Cholesterol 25-hydroxylase (EC 1.14.99.38) (Cholesterol 25-monooxygenase)	0.15	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				298
P19807 UniProt NPD GO	HNM1_YEAST	Choline transport protein	0.15	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [IMP]			563
P07186 UniProt NPD GO	CH19_DROME	Chorion protein S19	0.15	-	exc	1 *					173
P52195 UniProt NPD GO	MCPT1_PAPHA	Chymase precursor (EC 3.4.21.39) (Mast cell protease I)	0.15	-	vac	0	Mast cell granules				247
P35003 UniProt NPD GO	CTRL_HALRU	Chymotrypsin-like serine proteinase precursor (EC 3.4.21.-)	0.15	-	exc	0	Secreted protein; extracellular space				254
P15978 UniProt NPD GO	HA11_RAT	Class I histocompatibility antigen, Non-RT1.A alpha-1 chain precursor	0.15	-	exc	0	Membrane; single-pass type I membrane protein				319
Q9D273 UniProt NPD GO	MMAB_MOUSE	Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial precursor (EC 2.5.1.17) (Cob(I)alam ...	0.15	-	mit	0	Mitochondrion (By similarity)				237
Q91YQ3 UniProt NPD GO	CSDC2_MOUSE	Cold shock domain-containing protein C2 (RNA-binding protein PIPPin)	0.15	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). PIPPin-RNA complexes are located to the nucleus ...				154
P42889 UniProt NPD GO	COL_MYOCO	Colipase precursor	0.15	-	exc	0	Secreted protein				111
Q80X19 UniProt NPD GO	COEA1_MOUSE	Collagen alpha-1(XIV) chain precursor	0.15	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				1797
O35206 UniProt NPD GO	COFA1_MOUSE	Collagen alpha-1(XV) chain precursor [Contains: Endostatin (Endostatin-XV)]	0.15	-	mit	0				1DY2	1367
Q07643 UniProt NPD GO	CO9A2_MOUSE	Collagen alpha-2(IX) chain precursor	0.15	-	exc	0					688
Q92496 UniProt NPD GO	FHR4_HUMAN	Complement factor H-related protein 4 precursor (FHR-4)	0.15	-	exc	0	Secreted protein		605337		331
P23805 UniProt NPD GO	CONG_BOVIN	Conglutinin precursor	0.15	-	nuc	0					371

You are viewing entries 56751 to 56800 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.