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
P70677 UniProt NPD GO	CASP3_MOUSE	Caspase-3 precursor (EC 3.4.22.-) (CASP-3) (Apopain) (Cysteine protease CPP32) (Yama protein) (CPP-3 ...	0.21	-	nuc	0	Cytoplasm	cytoplasm [IDA]			277
Q8MKI5 UniProt NPD GO	CASP3_CANFA	Caspase-3 precursor (EC 3.4.22.-) (CASP-3) [Contains: Caspase-3 p17 subunit; Caspase-3 p12 subunit]	0.21	-	nuc	0	Cytoplasm				277
Q95ND5 UniProt NPD GO	CASP3_PIG	Caspase-3 precursor (EC 3.4.22.-) (CASP-3) [Contains: Caspase-3 p17 subunit; Caspase-3 p12 subunit]	0.21	-	nuc	0	Cytoplasm				277
P55214 UniProt NPD GO	CASP7_MESAU	Caspase-7 precursor (EC 3.4.22.-) (CASP-7) (ICE-like apoptotic protease 3) (ICE-LAP3) (Apoptotic pro ...	0.21	-	nuc	0	Cytoplasm				303
Q91WM2 UniProt NPD GO	CECR5_MOUSE	Cat eye syndrome critical region protein 5 homolog precursor	0.21	-	nuc	0					419
Q9AXH0 UniProt NPD GO	CATA_AVIMR	Catalase (EC 1.11.1.6)	0.21	-	cyt	0	Peroxisome (By similarity)				492
P45739 UniProt NPD GO	CATA_HELAN	Catalase (EC 1.11.1.6)	0.21	-	cyt	0	Peroxisome (By similarity)				492
P78574 UniProt NPD GO	CATA_ASPFU	Catalase A (EC 1.11.1.6) (Fast catalase)	0.21	-	cyt	0					750
P30264 UniProt NPD GO	CATA1_LYCES	Catalase isozyme 1 (EC 1.11.1.6)	0.21	-	cyt	0	Peroxisome (By similarity)				492
P49284 UniProt NPD GO	CATA1_SOLTU	Catalase isozyme 1 (EC 1.11.1.6)	0.21	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492
P25802 UniProt NPD GO	CYSP1_OSTOS	Cathepsin B-like cysteine proteinase 1 precursor (EC 3.4.22.-)	0.21	-	cyt	0					341
Q9UBX1 UniProt NPD GO	CATF_HUMAN	Cathepsin F precursor (EC 3.4.22.41) (CATSF)	0.21	-	exc	0	Lysosome	lysosome [TAS]	603539	1M6D	484
Q3T0I2 UniProt NPD GO	CATH_BOVIN	Cathepsin H precursor (EC 3.4.22.16) [Contains: Cathepsin H mini chain; Cathepsin H heavy chain; Cat ...	0.21	-	mit	0	Lysosome (By similarity)				335
Q9WUU7 UniProt NPD GO	CATZ_MOUSE	Cathepsin Z precursor (EC 3.4.22.-)	0.21	-	vac	0	Lysosome				306
Q99MA0 UniProt NPD GO	CITE4_RAT	Cbp/p300-interacting transactivator 4 (MSG1-related protein 2) (MRG-2)	0.21	-	nuc	0	Nucleus. Cytoplasm (By similarity)				179
Q5R7X9 UniProt NPD GO	RAD1_PONPY	Cell cycle checkpoint protein RAD1 (EC 3.1.11.2) (DNA repair exonuclease rad1 homolog)	0.21	-	cyt	0	Nucleus (By similarity)				282
O60671 UniProt NPD GO	RAD1_HUMAN	Cell cycle checkpoint protein RAD1 (EC 3.1.11.2) (DNA repair exonuclease rad1 homolog) (Rad1-like DN ...	0.21	-	cyt	0	Nucleus	nucleus [IC]	603153		282
Q10905 UniProt NPD GO	CRN4_CAEEL	Cell death-related nuclease 4 precursor (EC 3.1.-.-)	0.21	-	cyt	0					298
Q64261 UniProt NPD GO	CDK6_MOUSE	Cell division protein kinase 6 (EC 2.7.11.22) (Serine/threonine-protein kinase PLSTIRE) (CRK2)	0.21	-	cyt	0					326
Q8R2Y2 UniProt NPD GO	MUC18_MOUSE	Cell surface glycoprotein MUC18 precursor (Melanoma-associated antigen MUC18) (Melanoma cell adhesio ...	0.21	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				648
P53996 UniProt NPD GO	CNBP_MOUSE	Cellular nucleic acid-binding protein (CNBP) (Zinc finger protein 9)	0.21	-	nuc	0	Cytoplasm. Endoplasmic reticulum	cytosol [IDA] endoplasmic reticulum [IDA] nucleus [IDA]			178
Q61147 UniProt NPD GO	CERU_MOUSE	Ceruloplasmin precursor (EC 1.16.3.1) (Ferroxidase)	0.21	-	exc	0	Secreted protein				1062
P13114 UniProt NPD GO	CHSY_ARATH	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase) (TRANSPARENT TESTA 4 protein)	0.21	-	cyt	0					395
P26018 UniProt NPD GO	CHS1_HORVU	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.21	-	cyt	0					398
O23730 UniProt NPD GO	CHS4_BROFI	Chalcone synthase 4 (EC 2.3.1.74) (Naringenin-chalcone synthase 4)	0.21	-	cyt	0					394
Q9SBL5 UniProt NPD GO	CHS4_SORBI	Chalcone synthase 4 (EC 2.3.1.74) (Naringenin-chalcone synthase 4)	0.21	-	cyt	0					401
P48396 UniProt NPD GO	CHSB_IPONI	Chalcone synthase B (EC 2.3.1.74) (Naringenin-chalcone synthase B) (CHS-B) (Fragment)	0.21	-	cyt	0					363
P48404 UniProt NPD GO	CHSB_IPOTR	Chalcone synthase B (EC 2.3.1.74) (Naringenin-chalcone synthase B) (CHS-B) (Fragment)	0.21	-	mit	0					366
Q7ZVB1 UniProt NPD GO	CHM1B_BRARE	Charged multivesicular body protein 1b (Chromatin-modifying protein 1b) (CHMP1b)	0.21	-	nuc	0	Cytoplasm (By similarity)				199
O13933 UniProt NPD GO	ALG1_SCHPO	Chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) (GDP-mannose-dolichol diphospho ...	0.21	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				424
O35454 UniProt NPD GO	CLCN6_MOUSE	Chloride channel protein 6 (ClC-6)	0.21	-	end	7	Membrane; multi-pass membrane protein				870
Q95MF9 UniProt NPD GO	CLIC1_RABIT	Chloride intracellular channel protein 1	0.21	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	brush border [ISS] cytoplasm [ISS] membrane fraction [ISS] soluble fraction [ISS]			240
Q4G348 UniProt NPD GO	RR11_EMIHU	Chloroplast 30S ribosomal protein S11	0.21	-	nuc	0	Plastid; chloroplast				130
Q8MA02 UniProt NPD GO	RR16_CHAGL	Chloroplast 30S ribosomal protein S16	0.21	-	nuc	0	Plastid; chloroplast				83
Q68S24 UniProt NPD GO	RR16_PANGI	Chloroplast 30S ribosomal protein S16	0.21	-	mit	0	Plastid; chloroplast				78
P32087 UniProt NPD GO	RR16_SOLTU	Chloroplast 30S ribosomal protein S16	0.21	-	mit	0	Plastid; chloroplast				88
Q85FI4 UniProt NPD GO	RR3_ADICA	Chloroplast 30S ribosomal protein S3	0.21	-	mit	0	Plastid; chloroplast				217
Q8S8V5 UniProt NPD GO	RR3_ATRBE	Chloroplast 30S ribosomal protein S3	0.21	-	cyt	0	Plastid; chloroplast				218
Q85FV7 UniProt NPD GO	RR3_CYAME	Chloroplast 30S ribosomal protein S3	0.21	-	cyt	0	Plastid; chloroplast				205
Q4G359 UniProt NPD GO	RR3_EMIHU	Chloroplast 30S ribosomal protein S3	0.21	-	cyt	0	Plastid; chloroplast				216
O46900 UniProt NPD GO	RR3_GUITH	Chloroplast 30S ribosomal protein S3	0.21	-	mit	0	Plastid; chloroplast				216
P09595 UniProt NPD GO	RR3_SPIOL	Chloroplast 30S ribosomal protein S3	0.21	-	mit	0	Plastid; chloroplast				217
Q3ZJ39 UniProt NPD GO	RR4_PSEAK	Chloroplast 30S ribosomal protein S4	0.21	-	mit	0	Plastid; chloroplast				205
P42343 UniProt NPD GO	RR8_OENAM	Chloroplast 30S ribosomal protein S8 (Fragment)	0.21	-	nuc	0	Plastid; chloroplast				74
Q85FU8 UniProt NPD GO	RK18_CYAME	Chloroplast 50S ribosomal protein L18	0.21	-	mit	0	Plastid; chloroplast				109
P51309 UniProt NPD GO	RK22_PORPU	Chloroplast 50S ribosomal protein L22	0.21	-	mit	0	Plastid; chloroplast				116
Q1XDH9 UniProt NPD GO	RK22_PORYE	Chloroplast 50S ribosomal protein L22	0.21	-	mit	0	Plastid; chloroplast				117
Q9B1K8 UniProt NPD GO	RK23_LOTJA	Chloroplast 50S ribosomal protein L23	0.21	-	nuc	0	Plastid; chloroplast				93
Q32RN3 UniProt NPD GO	RK5_ZYGCR	Chloroplast 50S ribosomal protein L5	0.21	-	mit	0	Plastid; chloroplast				184
P46558 UniProt NPD GO	KICB1_CAEEL	Choline kinase B1 (EC 2.7.1.32)	0.21	-	mit	0					371

You are viewing entries 49301 to 49350 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.