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
P04653 UniProt NPD GO	CAS1_SHEEP	Alpha-S1-casein precursor	0.25	-	exc	0	Secreted protein				214
P53354 UniProt NPD GO	AMY1_AEDAE	Alpha-amylase I precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.25	-	nuc	0	Secreted protein				737
P81125 UniProt NPD GO	SNAA_BOVIN	Alpha-soluble NSF attachment protein (SNAP-alpha) (N-ethylmaleimide-sensitive factor attachment prot ...	0.25	-	cyt	0	Membrane; peripheral membrane protein				295
P54921 UniProt NPD GO	SNAA_RAT	Alpha-soluble NSF attachment protein (SNAP-alpha) (N-ethylmaleimide-sensitive factor attachment prot ...	0.25	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				295
Q96UR9 UniProt NPD GO	AOX_MONFR	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-) (MfAOX1)	0.25	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				358
O97646 UniProt NPD GO	AMEL_ORNAN	Amelogenin (Fragment)	0.25	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				121
O97647 UniProt NPD GO	AMEL_TACAC	Amelogenin (Fragment)	0.25	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				121
P19801 UniProt NPD GO	ABP1_HUMAN	Amiloride-sensitive amine oxidase [copper-containing] precursor (EC 1.4.3.6) (Diamine oxidase) (DAO) ...	0.25	-	vac	0	Secreted protein; extracellular space	peroxisome [NAS]	104610		751
P31347 UniProt NPD GO	ANGI_RABIT	Angiogenin (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.25	-	nuc	0	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			125
Q6P6B7 UniProt NPD GO	ANR16_HUMAN	Ankyrin repeat domain-containing protein 16	0.25	-	cyt	0					361
Q8BXP5 UniProt NPD GO	ANR33_MOUSE	Ankyrin repeat domain-containing protein 33	0.25	-	nuc	0					281
Q86W74 UniProt NPD GO	ANR46_HUMAN	Ankyrin repeat domain-containing protein 46 (Ankyrin repeat small protein) (ANK-S)	0.25	-	nuc	1	Membrane; single-pass membrane protein (Potential)				232
Q8WMX7 UniProt NPD GO	ASZ1_PAPAN	Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 (Germ cell-specific ankyrin ...	0.25	-	nuc	0	Cytoplasm (By similarity)				475
P40560 UniProt NPD GO	YIA1_YEAST	Ankyrin repeat-containing protein YIL001W	0.25	-	nuc	0		cytoplasm [IDA]			513
P46193 UniProt NPD GO	ANXA1_BOVIN	Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II) (Chromobindin-9) (p35) (Phospholipase A2 inhibi ...	0.25	-	cyt	0					346
Q95L54 UniProt NPD GO	ANXA8_BOVIN	Annexin A8 (Annexin VIII)	0.25	-	cyt	0					327
P32070 UniProt NPD GO	SM21_SCHMA	Antigen Sm21.7	0.25	-	cyt	0					184
P21958 UniProt NPD GO	TAP1_MOUSE	Antigen peptide transporter 1 (APT1) (Peptide transporter TAP1) (ATP-binding cassette sub-family B m ...	0.25	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. The transmembran ...				724
P12021 UniProt NPD GO	MUCAP_PIG	Apomucin (Mucin core protein) (Fragment)	0.25	-	nuc	0	Secreted protein				1150
O88879 UniProt NPD GO	APAF_MOUSE	Apoptotic protease-activating factor 1 (Apaf-1)	0.25	-	nuc	0	Cytoplasm (By similarity)	cytosol [IDA] nucleus [IDA] soluble fraction [IDA]			1249
Q9EQX0 UniProt NPD GO	GHRL_MOUSE	Appetite-regulating hormone precursor (Growth hormone secretagogue) (Growth hormone-releasing peptid ...	0.25	-	exc	0	Secreted protein	cytoplasm [IDA] extracellular region [IDA] extracellular space [ISS]			117
Q7T287 UniProt NPD GO	APTX_XENLA	Aprataxin homolog (Forkhead-associated domain histidine triad-like protein) (FHA-HIT)	0.25	-	nuc	0	Nucleus (By similarity)				347
O75342 UniProt NPD GO	LX12B_HUMAN	Arachidonate 12-lipoxygenase, 12R type (EC 1.13.11.-) (Epidermis-type lipoxygenase 12) (12R-lipoxyge ...	0.25	-	cyt	0			603741		701
Q02759 UniProt NPD GO	LX12L_RAT	Arachidonate 12-lipoxygenase, leukocyte-type (EC 1.13.11.31) (12-LOX)	0.25	-	cyt	0	Cytoplasm	cytosol [IDA] sarcolemma [ISS]			662
Q10170 UniProt NPD GO	RMT2_SCHPO	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.25	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				357
P53090 UniProt NPD GO	ARO8_YEAST	Aromatic amino acid aminotransferase 1 (EC 2.6.1.-) (Aromatic amino acid aminotransferase I)	0.25	-	cyt	0		cytoplasm [IDA]			500
Q60436 UniProt NPD GO	ARS2_CRIGR	Arsenite-resistance protein 2 (Fragment)	0.25	+	cyt	0					290
P50430 UniProt NPD GO	ARSB_RAT	Arylsulfatase B (EC 3.1.6.12) (ASB) (N-acetylgalactosamine-4-sulfatase) (G4S) (Fragment)	0.25	-	cyt	0	Lysosome				473
Q9BN10 UniProt NPD GO	API_PARTN	Aspartyl protease inhibitor precursor (Pt-API-1)	0.25	-	exc	0	Secreted protein (Potential)				226
Q9BXN1 UniProt NPD GO	ASPN_HUMAN	Asporin precursor (Periodontal ligament-associated protein 1) (PLAP-1)	0.25	+	nuc	0	Secreted protein; extracellular space; extracellular matrix		608135		379
Q8WXF7 UniProt NPD GO	SPG3A_HUMAN	Atlastin (GTP-binding protein 3) (Guanine nucleotide-binding protein 3) (Brain-specific GTP-binding ...	0.25	-	end	2			606439		558
Q59VY1 UniProt NPD GO	ATG5_CANAL	Autophagy protein 5	0.25	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				278
Q525E4 UniProt NPD GO	ATG5_MAGGR	Autophagy protein 5	0.25	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				314
Q3MQ04 UniProt NPD GO	ATG5_PIG	Autophagy protein 5	0.25	-	cyt	0	Cytoplasm (By similarity)				275
Q9H1Y0 UniProt NPD GO	ATG5_HUMAN	Autophagy protein 5 (APG5-like) (Apoptosis-specific protein)	0.25	-	cyt	0	Cytoplasm. Colocalizes with nonmuscle actin	autophagic vacuole [IDA]	604261		275
Q9LU77 UniProt NPD GO	PIN2_ARATH	Auxin efflux carrier component 2 (AtPIN2) (Auxin efflux carrier AGR) (Polar-auxin-transport efflux c ...	0.25	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				647
Q6AT10 UniProt NPD GO	IAA15_ORYSA	Auxin-responsive protein IAA15 (Indoleacetic acid-induced protein 15)	0.25	-	nuc	0	Nucleus (By similarity)				212
Q9JLT6 UniProt NPD GO	BID_RAT	BH3-interacting domain death agonist (BID) (p22 BID) [Contains: BH3-interacting domain death agonist ...	0.25	-	cyt	0	Cytoplasm. When uncleaved, it is predominantly cytoplasmic. Mitochodrion; mitochondrial membrane. p1 ...				196
Q14201 UniProt NPD GO	BTG3_HUMAN	BTG3 protein (Tob5 protein) (Abundant in neuroepithelium area protein)	0.25	-	nuc	0		cytoplasm [IDA]	605674		252
P11362 UniProt NPD GO	FGFR1_HUMAN	Basic fibroblast growth factor receptor 1 precursor (EC 2.7.10.1) (FGFR-1) (bFGF-R) (Fms-like tyrosi ...	0.25	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] membrane fraction [NAS]	101600	2FGI	822
P16092 UniProt NPD GO	FGFR1_MOUSE	Basic fibroblast growth factor receptor 1 precursor (EC 2.7.10.1) (FGFR-1) (bFGF-R) (MFR)	0.25	-	end	1	Membrane; single-pass type I membrane protein			2CKN	822
Q28740 UniProt NPD GO	BASI_RABIT	Basigin precursor (CD147 antigen)	0.25	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Colocalizes with SLC16A1 and SLC ...				270
Q9MBD8 UniProt NPD GO	BI1_ORYSA	Bax inhibitor 1 (BI-1) (OsBI-1)	0.25	+	end	7 *	Membrane; multi-pass membrane protein (Potential)				249
Q9M2J9 UniProt NPD GO	BET11_ARATH	Bet1-like SNARE 1-1 (AtBET11) (Bet1/Sft1-like SNARE 14a) (AtBS14a)	0.25	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				122
P55164 UniProt NPD GO	CRBA2_CHICK	Beta crystallin A2 (Beta-A2-crystallin)	0.25	-	cyt	0					196
P02524 UniProt NPD GO	CRBB3_RAT	Beta crystallin B3 (Beta-B3-crystallin)	0.25	-	cyt	0					210
Q9Z0F0 UniProt NPD GO	B3GT4_MOUSE	Beta-1,3-galactosyltransferase 4 (EC 2.4.1.62) (Beta-1,3-GalTase 4) (Beta3Gal-T4) (b3Gal-T4) (Gangli ...	0.25	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				371
P02665 UniProt NPD GO	CASB_RAT	Beta-casein precursor	0.25	-	exc	0	Secreted protein				231
Q56UC9 UniProt NPD GO	INV7_ORYSA	Beta-fructofuranosidase, insoluble isoenzyme 7 precursor (EC 3.2.1.26) (Sucrose hydrolase 7) (Invert ...	0.25	-	vac	0	Secreted protein; extracellular space; apoplast (Probable). Cell wall (Probable). Associated to the ...				596
P29853 UniProt NPD GO	BGAL_ASPNG	Beta-galactosidase precursor (EC 3.2.1.23) (Lactase) (Tilactase) (Lactase-N)	0.25	-	cyt	0					1006

You are viewing entries 44951 to 45000 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.