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
P63069 UniProt NPD GO	B2MG_SAGBM	Beta-2-microglobulin precursor	0.01	-	exc	0	Secreted protein				119
P63070 UniProt NPD GO	B2MG_SAGMM	Beta-2-microglobulin precursor	0.01	-	exc	0	Secreted protein				119
O77517 UniProt NPD GO	B2MG_SAGMN	Beta-2-microglobulin precursor	0.01	-	exc	0	Secreted protein				119
P63071 UniProt NPD GO	B2MG_SAGMY	Beta-2-microglobulin precursor	0.01	-	exc	0	Secreted protein				119
P55079 UniProt NPD GO	B2MG_SAGOE	Beta-2-microglobulin precursor	0.01	-	exc	0	Secreted protein				119
Q07717 UniProt NPD GO	B2MG_PIG	Beta-2-microglobulin precursor (Lactollin)	0.01	-	vac	0	Secreted protein				118
Q96KN2 UniProt NPD GO	CNDP1_HUMAN	Beta-Ala-His dipeptidase precursor (EC 3.4.13.20) (Serum carnosinase) (CNDP dipeptidase 1) (Glutamat ...	0.01	-	end	0	Secreted protein		609064		507
P55005 UniProt NPD GO	AMYB_MAIZE	Beta-amylase (EC 3.2.1.2) (1,4-alpha-D-glucan maltohydrolase)	0.01	-	cyt	0					488
O22585 UniProt NPD GO	AMYB_MEDSA	Beta-amylase (EC 3.2.1.2) (1,4-alpha-D-glucan maltohydrolase)	0.01	-	cyt	0					496
O65015 UniProt NPD GO	AMYB_TRIRP	Beta-amylase (EC 3.2.1.2) (1,4-alpha-D-glucan maltohydrolase)	0.01	-	cyt	0					496
P93594 UniProt NPD GO	AMYB_WHEAT	Beta-amylase (EC 3.2.1.2) (1,4-alpha-D-glucan maltohydrolase)	0.01	-	cyt	0					503
Q30KK6 UniProt NPD GO	DB121_PANTR	Beta-defensin 121 precursor (Defensin, beta 121)	0.01	-	nuc	0	Secreted protein (Potential)				76
Q30KQ1 UniProt NPD GO	DB133_HUMAN	Beta-defensin 133 precursor (Defensin, beta 133)	0.01	-	mit	1 *	Secreted protein (Potential)				61
Q30KJ6 UniProt NPD GO	DB133_PANTR	Beta-defensin 133 precursor (Defensin, beta 133)	0.01	-	vac	1 *	Secreted protein (Potential)				62
Q4QY38 UniProt NPD GO	DB134_HUMAN	Beta-defensin 134 precursor (Defensin, beta 134)	0.01	-	exc	1 *	Secreted protein (Potential)				66
Q30KJ5 UniProt NPD GO	DB134_PANTR	Beta-defensin 134 precursor (Defensin, beta 134)	0.01	-	end	0	Secreted protein (Potential)				59
Q30KJ4 UniProt NPD GO	DB135_PANTR	Beta-defensin 135 precursor (Defensin, beta 135)	0.01	-	end	2 *	Secreted protein (Potential)				78
O19039 UniProt NPD GO	BD02_SHEEP	Beta-defensin 2 precursor (BD-2) (sBD2)	0.01	-	exc	1 *	Secreted protein (By similarity)				64
Q6TU36 UniProt NPD GO	BD50_MOUSE	Beta-defensin 50 precursor (Defensin, beta 50) (BD-50) (mBD-50) (Defensin, beta 37) (Prostate beta-d ...	0.01	-	nuc	0	Secreted protein (By similarity)				73
Q9M0I2 UniProt NPD GO	EXPB3_ARATH	Beta-expansin 3 precursor (AtEXPB3) (At-EXPB3) (Ath-ExpBeta-1.6)	0.01	-	exc	0	Cell wall; peripheral membrane protein				264
O14412 UniProt NPD GO	GUB_ORPSP	Beta-glucanase precursor (EC 3.2.1.73) (Endo-beta-1,3-1,4 glucanase) (1,3-1,4-beta-D-glucan 4-glucan ...	0.01	-	vac	0	Secreted protein				245
P29091 UniProt NPD GO	BGLS_SCHCO	Beta-glucosidase (EC 3.2.1.21) (Gentiobiase) (Cellobiase) (Beta-D-glucoside glucohydrolase) (Fragmen ...	0.01	-	cyt	0					192
P29090 UniProt NPD GO	BGL3_ASPWE	Beta-glucosidase A-3 (EC 3.2.1.21) (Gentiobiase) (Cellobiase) (Beta-D-glucoside glucohydrolase) (Fra ...	0.01	-	cyt	0					63
P13723 UniProt NPD GO	HEXA_DICDI	Beta-hexosaminidase A precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-N-acetylhexosami ...	0.01	-	end	1 *	Lysosome				532
O97936 UniProt NPD GO	MSPA_SAGOE	Beta-microseminoprotein A1 precursor (msp-A1) (Fragment)	0.01	-	exc	0	Secreted protein. Sperm surface (By similarity)	extracellular region [TAS]			112
O97949 UniProt NPD GO	MSPJ_SAGOE	Beta-microseminoprotein J1 precursor (msp-J1)	0.01	-	exc	1 *	Secreted protein. Sperm surface (By similarity)	extracellular region [NAS]			114
Q16143 UniProt NPD GO	SYUB_HUMAN	Beta-synuclein	0.01	-	cyt	0	Cytoplasm		602569		134
Q63754 UniProt NPD GO	SYUB_RAT	Beta-synuclein (Phosphoneuroprotein 14) (PNP 14)	0.01	-	cyt	0	Cytoplasm (By similarity)				137
P33567 UniProt NPD GO	SYUB_BOVIN	Beta-synuclein (Phosphoneuroprotein 14) (PNP 14) (14 kDa brain-specific protein)	0.01	-	cyt	0	Cytoplasm				134
Q5RFG2 UniProt NPD GO	BHMT_PONPY	Betaine--homocysteine S-methyltransferase (EC 2.1.1.5)	0.01	-	cyt	0	Cytoplasm (By similarity)				406
Q7SIA2 UniProt NPD GO	SYEP_CRIGR	Bifunctional aminoacyl-tRNA synthetase [Includes: Glutamyl-tRNA synthetase (EC 6.1.1.17) (Glutamate- ...	0.01	-	cyt	0				1R1B	49
Q99148 UniProt NPD GO	PUR2_YARLI	Bifunctional purine biosynthetic protein ADE1 [Includes: Phosphoribosylamine--glycine ligase (EC 6.3 ...	0.01	-	cyt	0					788
P07244 UniProt NPD GO	PUR2_YEAST	Bifunctional purine biosynthetic protein ADE5,7 [Includes: Phosphoribosylamine--glycine ligase (EC 6 ...	0.01	-	cyt	0		cytoplasm [IDA]			802
P52843 UniProt NPD GO	ST2A1_MOUSE	Bile salt sulfotransferase 1 (EC 2.8.2.14) (Hydroxysteroid sulfotransferase) (ST)	0.01	-	cyt	0	Cytoplasm				285
P84546 UniProt NPD GO	ACCC_POPEU	Biotin carboxylase (EC 6.3.4.14) (Acetyl-CoA carboxylase subunit A) (EC 6.4.1.2) (ACC) (Fragments)	0.01	-	cyt	0					40
P78986 UniProt NPD GO	BSD_ASPTE	Blasticidin-S deaminase (EC 3.5.4.23)	0.01	-	cyt	0				1WN6	130
P07095 UniProt NPD GO	APL1_PETMA	Blood plasma apolipoprotein LAL1 precursor	0.01	-	exc	0	Secreted protein				105
Q07488 UniProt NPD GO	BCB1_ARATH	Blue copper protein precursor (Blue copper-binding protein) (AtBCB) (Stellacyanin) (Phytocyanin 1)	0.01	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				196
P51490 UniProt NPD GO	OPSB_BOVIN	Blue-sensitive opsin (BOP) (Blue cone photoreceptor pigment)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				349
P42991 UniProt NPD GO	BOML_PSEGU	Bombesin-like peptide L (PG-L)	0.01	-		0	Secreted protein				13
P01505 UniProt NPD GO	BMN_BOMVA	Bombinin	0.01	-	cyt	0	Secreted protein				24
P10521 UniProt NPD GO	BOL1_MEGPE	Bombolitin-1 (Bombolitin I)	0.01	-		0	Secreted protein				17
P26733 UniProt NPD GO	BXB1_BOMMO	Bombyxin B-1 precursor (BBX-B1) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin B-1 B ...	0.01	-	end	0	Secreted protein				89
Q17196 UniProt NPD GO	BXB11_BOMMO	Bombyxin B-11 precursor (BBX-B11) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin B-11 ...	0.01	-	mit	0	Secreted protein				93
P26739 UniProt NPD GO	BXB5_BOMMO	Bombyxin B-5 precursor (BBX-B5) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin B-5 B ...	0.01	-	mit	0	Secreted protein				90
P26741 UniProt NPD GO	BXB7_BOMMO	Bombyxin B-7 precursor (BBX-B7) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin B-7 B ...	0.01	-	vac	0	Secreted protein				90
P26743 UniProt NPD GO	BXB9_BOMMO	Bombyxin B-9 precursor (BBX-B9) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin B-9 B ...	0.01	-	mit	0	Secreted protein				90
P00771 UniProt NPD GO	COGS_UCAPU	Brachyurin (EC 3.4.21.32) (Collagenolytic protease)	0.01	-	mit	0				1AZZ	226
P84832 UniProt NPD GO	BRK10_ASCTR	Bradykinin-like peptide AR-10	0.01	-		0	Secreted protein	extracellular region [IDA]			10
P84823 UniProt NPD GO	BRK12_ASCTR	Bradykinin-like peptide AV-12	0.01	-		0	Secreted protein	extracellular region [IDA]			12

You are viewing entries 86851 to 86900 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.