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
P51086 UniProt NPD GO	CHS4_TRISU	Chalcone synthase 4 (EC 2.3.1.74) (Naringenin-chalcone synthase 4) (Fragment)	0.00	-	nuc	0					311
O22604 UniProt NPD GO	CFI_IPOPU	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase)	0.00	-	cyt	0					241
P51117 UniProt NPD GO	CFI_VITVI	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase)	0.00	-	cyt	0					234
Q9LKC3 UniProt NPD GO	CHI_ARALP	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase)	0.00	-	cyt	0					244
P83724 UniProt NPD GO	DNAK_NAEFO	Chaperone protein dnaK (NF024) (Fragment)	0.00	-		0					20
P80502 UniProt NPD GO	CH60_SOLTU	Chaperonin HSP60, mitochondrial (Fragment)	0.00	-	cyt	0	Mitochondrion				40
P60496 UniProt NPD GO	BABL_LILLO	Chemocyanin precursor (Basic blue protein) (Plantacyanin)	0.00	-	cyt	1 *					126
Q9UBR5 UniProt NPD GO	CKLF_HUMAN	Chemokine-like factor (C32)	0.00	-	end	4 *	Isoform CKLF1 is secreted, whereas isoforms CKLF2 and CKLF4 exist as integral membrane proteins	extracellular region [IDA] integral to membrane [IDA]			152
P17237 UniProt NPD GO	CRBL_ICASP	Chemotactic peptide (I-CP)	0.00	-		0	Secreted protein				13
P55003 UniProt NPD GO	CHS1_TUBUN	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Fragment)	0.00	-	mit	0	Cell membrane; multi-pass membrane protein				189
P84708 UniProt NPD GO	CAI_PHAVU	Chitinolytic alpha-amylase inhibitor PvCAI (EC 3.2.1.14) (Fragment)	0.00	-	cyt	0					25
Q6CVU2 UniProt NPD GO	ALG1_KLULA	Chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) (GDP-mannose-dolichol diphospho ...	0.00	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				447
P51803 UniProt NPD GO	CLCKA_RABIT	Chloride channel protein ClC-Ka (Chloride channel Ka) (ClC-K1)	0.00	-	end	10 *	Membrane; multi-pass membrane protein				687
P51804 UniProt NPD GO	CLCKB_RABIT	Chloride channel protein ClC-Kb (Chloride channel Kb) (ClC-K2)	0.00	-	end	10 *	Membrane; multi-pass membrane protein				678
P27489 UniProt NPD GO	CB23_LYCES	Chlorophyll a-b binding protein 13, chloroplast precursor (LHCII type III CAB-13)	0.00	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P14274 UniProt NPD GO	CB2A_LYCES	Chlorophyll a-b binding protein 1A, chloroplast precursor (LHCII type I CAB-1A) (LHCP) (Fragments)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P07370 UniProt NPD GO	CB2B_LYCES	Chlorophyll a-b binding protein 1B, chloroplast precursor (LHCII type I CAB-1B) (LHCP)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P14275 UniProt NPD GO	CB2C_LYCES	Chlorophyll a-b binding protein 1C, chloroplast precursor (LHCII type I CAB-1C) (LHCP) (Fragments)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P27521 UniProt NPD GO	CB24_ARATH	Chlorophyll a-b binding protein 4, chloroplast precursor (LHCI type III CAB-4) (LHCP)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				251
P27490 UniProt NPD GO	CB28_PEA	Chlorophyll a-b binding protein 8, chloroplast precursor (LHCII type I CAB-8)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				268
P07371 UniProt NPD GO	CB22_PEA	Chlorophyll a-b binding protein AB80, chloroplast precursor (LHCII type I CAB-AB80) (LHCP)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein			2BHW	269
P04159 UniProt NPD GO	CB21_PEA	Chlorophyll a-b binding protein AB96 (LHCII type I CAB-AB96) (LHCP) (Major 15) (Fragment)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				228
P27524 UniProt NPD GO	CB4A_LYCES	Chlorophyll a-b binding protein CP24 10A, chloroplast precursor (CAB-10A) (LHCP)	0.00	-	exc	2	Plastid; chloroplast				256
Q9XF88 UniProt NPD GO	CB4B_ARATH	Chlorophyll a-b binding protein CP29.2, chloroplast precursor (LHCII protein 4.2) (LHCB4.2)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				287
P12327 UniProt NPD GO	CB21_EUGGR	Chlorophyll a-b binding protein of LHCII type 1 (Chlorophyll a-b binding protein of LHCII type I) (C ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				127
P12328 UniProt NPD GO	CB21_LEMGI	Chlorophyll a-b binding protein of LHCII type I, chloroplast precursor (CAB) (LHCP)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				264
P27523 UniProt NPD GO	CB23_HORVU	Chlorophyll a-b binding protein of LHCII type III, chloroplast precursor (CAB)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				268
P15192 UniProt NPD GO	CB22_PINSY	Chlorophyll a-b binding protein type 2 member 2 (Chlorophyll a-b binding protein type II 2) (CAB) (L ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				150
P13869 UniProt NPD GO	CB12_PETHY	Chlorophyll a-b binding protein, chloroplast precursor (LHCI type II CAB)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				270
P59677 UniProt NPD GO	CLH1_CHEAL	Chlorophyllase type 1 (EC 3.1.1.14) (CaCLH1) (Chlorophyll-chlorophyllido hydrolase 1) (Chlase 1) (Fr ...	0.00	-	cyt	0					22
Q85FV9 UniProt NPD GO	RR19_CYAME	Chloroplast 30S ribosomal protein S19	0.00	-	mit	0	Plastid; chloroplast				94
P51337 UniProt NPD GO	RK11_PORPU	Chloroplast 50S ribosomal protein L11	0.00	-	cyt	0	Plastid; chloroplast				141
O78414 UniProt NPD GO	RK12_GUITH	Chloroplast 50S ribosomal protein L12	0.00	-	cyt	0	Plastid; chloroplast				129
P51339 UniProt NPD GO	RK12_PORPU	Chloroplast 50S ribosomal protein L12	0.00	-	cyt	0	Plastid; chloroplast				129
P51290 UniProt NPD GO	RK31_PORPU	Chloroplast 50S ribosomal protein L31	0.00	-	cyt	0	Plastid; chloroplast				70
P28529 UniProt NPD GO	ATPI_PAVLU	Chloroplast ATP synthase a chain (EC 3.6.3.14) (ATPase subunit IV) (Fragment)	0.00	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				17
Q02847 UniProt NPD GO	ATPI_ANTSP	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				248
P56758 UniProt NPD GO	ATPI_ARATH	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				249
P69371 UniProt NPD GO	ATPI_ATRBE	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
O63075 UniProt NPD GO	ATPI_CHLRE	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				238
Q9TM31 UniProt NPD GO	ATPI_CYACA	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				239
P30391 UniProt NPD GO	ATPI_EUGGR	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				251
P35008 UniProt NPD GO	ATPI_GALSU	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				233
O78480 UniProt NPD GO	ATPI_GUITH	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				248
Q9BBS5 UniProt NPD GO	ATPI_LOTJA	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
P17344 UniProt NPD GO	ATPI_MAIZE	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
P06289 UniProt NPD GO	ATPI_MARPO	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				248
Q9TL13 UniProt NPD GO	ATPI_NEPOL	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				239
Q40607 UniProt NPD GO	ATPI_OCHNE	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				233
Q9MTM0 UniProt NPD GO	ATPI_OENHO	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247

You are viewing entries 93101 to 93150 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.