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
P43450 UniProt NPD GO	CDK2_CARAU	Cell division protein kinase 2 (EC 2.7.11.22)	0.02	-	cyt	0					298
P43497 UniProt NPD GO	CWP2_YEAST	Cell wall protein CWP2 precursor (Low pH resistance protein 1)	0.02	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			92
P50568 UniProt NPD GO	RABP_XENLA	Cellular retinoic acid-binding protein (CRABP) (Retinoic acid-binding protein, cellular)	0.02	-	nuc	0	Cytoplasm				137
P62964 UniProt NPD GO	RABP1_BOVIN	Cellular retinoic acid-binding protein 1 (Cellular retinoic acid-binding protein I) (CRABP-I) (Retin ...	0.02	-	nuc	0	Cytoplasm			2CBR	136
P40220 UniProt NPD GO	RABP1_CHICK	Cellular retinoic acid-binding protein 1 (Cellular retinoic acid-binding protein I) (CRABP-I) (Retin ...	0.02	-	nuc	0	Cytoplasm				136
P29762 UniProt NPD GO	RABP1_HUMAN	Cellular retinoic acid-binding protein 1 (Cellular retinoic acid-binding protein I) (CRABP-I) (Retin ...	0.02	-	nuc	0	Cytoplasm		180230		136
P62965 UniProt NPD GO	RABP1_MOUSE	Cellular retinoic acid-binding protein 1 (Cellular retinoic acid-binding protein I) (CRABP-I) (Retin ...	0.02	-	nuc	0	Cytoplasm			1CBR	136
P30370 UniProt NPD GO	RABP2_CHICK	Cellular retinoic acid-binding protein 2 (Cellular retinoic acid-binding protein II) (CRABP-II) (Ret ...	0.02	-	cyt	0	Cytoplasm				36
P36190 UniProt NPD GO	CTXA1_CERCA	Ceratotoxin-A precursor 1	0.02	-	exc	1 *	Secreted protein				71
O17512 UniProt NPD GO	CTXA2_CERCA	Ceratotoxin-A precursor 2	0.02	-	end	1 *	Secreted protein				71
Q17313 UniProt NPD GO	CTXC1_CERCA	Ceratotoxin-C precursor	0.02	-	end	1 *	Secreted protein (By similarity)				67
O17513 UniProt NPD GO	CTXD_CERCA	Ceratotoxin-D precursor	0.02	-	exc	1 *	Secreted protein (By similarity)				71
P23435 UniProt NPD GO	CBLN1_HUMAN	Cerebellin precursor (Precerebellin)	0.02	-	mit	0	Secreted protein. Membrane. Might be bound to, or associated with, a membrane		600432		193
Q9R171 UniProt NPD GO	CBLN1_MOUSE	Cerebellin precursor (Precerebellin) (Brain protein D3)	0.02	-	mit	0	Secreted protein				193
Q9NTU7 UniProt NPD GO	CBLN4_HUMAN	Cerebellin-4 precursor (Cerebellin-like glycoprotein 1)	0.02	-	exc	0	Secreted protein (Potential)				201
Q8BME9 UniProt NPD GO	CBLN4_MOUSE	Cerebellin-4 precursor (Cerebellin-like glycoprotein 1)	0.02	-	exc	1 *	Secreted protein (Potential)				198
O22045 UniProt NPD GO	CHSD_IPONI	Chalcone synthase D (EC 2.3.1.74) (Naringenin-chalcone synthase D) (CHS-D)	0.02	-	mit	0					388
Q9MB38 UniProt NPD GO	CHS6_IPOBA	Chalcone synthase DII (EC 2.3.1.74) (Naringenin-chalcone synthase DII)	0.02	-	cyt	0					393
Q9MB36 UniProt NPD GO	CHS8_IPOBA	Chalcone synthase DIV (EC 2.3.1.74) (Naringenin-chalcone synthase DIV)	0.02	-	mit	0					388
Q9MB33 UniProt NPD GO	CHS1_IPOBA	Chalcone synthase LF1 (EC 2.3.1.74) (Naringenin-chalcone synthase LF1)	0.02	-	cyt	0					393
Q9MB40 UniProt NPD GO	CHS3_IPOBA	Chalcone synthase LF3 (EC 2.3.1.74) (Naringenin-chalcone synthase LF3)	0.02	-	mit	0					388
Q9MB39 UniProt NPD GO	CHS4_IPOBA	Chalcone synthase LF4 (EC 2.3.1.74) (Naringenin-chalcone synthase LF4)	0.02	-	cyt	0					393
Q43754 UniProt NPD GO	CFI_DIACA	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase)	0.02	-	cyt	0					221
O22651 UniProt NPD GO	CFI_RAPSA	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase)	0.02	-	cyt	0					247
O81980 UniProt NPD GO	CFI_SOYBN	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase) (Fragment)	0.02	-	cyt	0					172
P41088 UniProt NPD GO	CFI_ARATH	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase) (TRANSPARENT TESTA 5 protein)	0.02	-	cyt	0					246
P28012 UniProt NPD GO	CFI1_MEDSA	Chalcone--flavonone isomerase 1 (EC 5.5.1.6) (Chalcone isomerase 1)	0.02	-	cyt	0				1JX1	222
P28013 UniProt NPD GO	CFI2_MEDSA	Chalcone--flavonone isomerase 2 (EC 5.5.1.6) (Chalcone isomerase 2) (Fragment)	0.02	-	cyt	0					197
Q37683 UniProt NPD GO	CH60_TRYBB	Chaperonin HSP60, mitochondrial precursor (Protein Cpn60) (groEL protein) (Heat shock protein 60)	0.02	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				562
Q95046 UniProt NPD GO	CH60_TRYCR	Chaperonin HSP60, mitochondrial precursor (Protein Cpn60) (groEL protein) (Heat shock protein 60)	0.02	-	cyt	0	Mitochondrion; mitochondrial matrix				562
Q93WU3 UniProt NPD GO	CVMT1_OCIBA	Chavicol O-methyltransferase (EC 2.1.1.146) ((Iso)eugenol O-methyltransferase CVOMT1) (S-adenosysl-L ...	0.02	-	mit	0					356
Q99788 UniProt NPD GO	CML1_HUMAN	Chemokine receptor-like 1 (G-protein coupled receptor DEZ) (G-protein coupled receptor ChemR23)	0.02	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602351		373
Q9JK79 UniProt NPD GO	CKLF_RAT	Chemokine-like factor	0.02	-	end	4 *	Isoform CKLF1: Secreted protein. Isoform CKLF2: Membrane; multi-pass membrane protein (Potential)				151
P30580 UniProt NPD GO	CHS2_AJEDE	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2) (Class-II chitin synt ...	0.02	-	mit	0	Cell membrane; multi-pass membrane protein				189
P30578 UniProt NPD GO	CHS3_AJECA	Chitin synthase 3 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 3) (Class-II chitin synt ...	0.02	-	cyt	0	Cell membrane; multi-pass membrane protein				189
Q5R7A2 UniProt NPD GO	ALG1_PONPY	Chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) (GDP-mannose-dolichol diphospho ...	0.02	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				464
Q9BT22 UniProt NPD GO	ALG1_HUMAN	Chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) (GDP-mannose-dolichol diphospho ...	0.02	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (Probabl ...		608540		464
P51800 UniProt NPD GO	CLCKA_HUMAN	Chloride channel protein ClC-Ka (Chloride channel Ka) (ClC-K1)	0.02	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602024		687
P51801 UniProt NPD GO	CLCKB_HUMAN	Chloride channel protein ClC-Kb (Chloride channel Kb) (ClC-K2)	0.02	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	607364		687
P12329 UniProt NPD GO	CB21_MAIZE	Chlorophyll a-b binding protein 1, chloroplast precursor (LHCII type I CAB-1) (LHCP)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				262
P12330 UniProt NPD GO	CB21_ORYSA	Chlorophyll a-b binding protein 1, chloroplast precursor (LHCII type I CAB-1) (LHCP)	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P13851 UniProt NPD GO	CB21_SINAL	Chlorophyll a-b binding protein 1, chloroplast precursor (LHCII type I CAB-1) (LHCP)	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				266
P04779 UniProt NPD GO	CB21_PETSP	Chlorophyll a-b binding protein 13, chloroplast precursor (LHCII type I CAB-13) (LHCP)	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				266
P09756 UniProt NPD GO	CB23_SOYBN	Chlorophyll a-b binding protein 3, chloroplast precursor (LHCII type I CAB-3) (LHCP)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				263
Q00827 UniProt NPD GO	CB48_MAIZE	Chlorophyll a-b binding protein 48, chloroplast precursor (LHCII type I CAB-48) (LHCP)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				264
Q03965 UniProt NPD GO	L181_CHLEU	Chlorophyll a-b binding protein L1818, chloroplast precursor	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				270
P27497 UniProt NPD GO	CB29_MAIZE	Chlorophyll a-b binding protein M9, chloroplast precursor (LHCII type I CAB-M9) (LHCP)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P08221 UniProt NPD GO	CB21_CUCSA	Chlorophyll a-b binding protein of LHCII type I, chloroplast precursor (CAB) (LHCP) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				255
P15195 UniProt NPD GO	CB23_POLMU	Chlorophyll a-b binding protein type 1 member F3, chloroplast precursor (Chlorophyll a-b binding pro ...	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P10049 UniProt NPD GO	CB21_PINTH	Chlorophyll a-b binding protein type I, chloroplast precursor (CAB) (LHCP)	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				266

You are viewing entries 82751 to 82800 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.