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
P04784 UniProt NPD GO	CB21_WHEAT	Chlorophyll a-b binding protein, chloroplast precursor (LHCII type I CAB) (LHCP)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				266
P06671 UniProt NPD GO	CB22_MAIZE	Chlorophyll a-b binding protein, chloroplast precursor (LHCII type I CAB) (LHCP)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
P20866 UniProt NPD GO	CB2_PHYPA	Chlorophyll a-b binding protein, chloroplast precursor (LHCII type I CAB) (LHCP)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				269
P12332 UniProt NPD GO	CB21_SILPR	Chlorophyll a-b binding protein, chloroplast precursor (LHCII type I CAB) (LHCP) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				205
P12471 UniProt NPD GO	CB21_SOYBN	Chlorophyll a-b binding protein, chloroplast precursor (LHCII type I CAB) (LHCP) (Fragment)	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				245
Q70XX0 UniProt NPD GO	RR19_AMBTC	Chloroplast 30S ribosomal protein S19	0.02	-	mit	0	Plastid; chloroplast				92
Q8M9U8 UniProt NPD GO	RR19_CHAGL	Chloroplast 30S ribosomal protein S19	0.02	-	mit	0	Plastid; chloroplast				92
Q5SD12 UniProt NPD GO	RR19_HUPLU	Chloroplast 30S ribosomal protein S19	0.02	-	mit	0	Plastid; chloroplast				92
Q9TL19 UniProt NPD GO	RR19_NEPOL	Chloroplast 30S ribosomal protein S19	0.02	-	mit	0	Plastid; chloroplast				92
P21508 UniProt NPD GO	RR8_EUGGR	Chloroplast 30S ribosomal protein S8	0.02	-	cyt	0	Plastid; chloroplast				140
O78413 UniProt NPD GO	RK1_GUITH	Chloroplast 50S ribosomal protein L1	0.02	-	nuc	0	Plastid; chloroplast				234
O46915 UniProt NPD GO	RK13_GUITH	Chloroplast 50S ribosomal protein L13	0.02	-	cyt	0	Plastid; chloroplast				143
Q9TLU2 UniProt NPD GO	RK14_CYACA	Chloroplast 50S ribosomal protein L14	0.02	-	nuc	0	Plastid; chloroplast				121
Q6END7 UniProt NPD GO	RK14_ORYNI	Chloroplast 50S ribosomal protein L14	0.02	-	cyt	0	Plastid; chloroplast				123
P12137 UniProt NPD GO	RK14_ORYSA	Chloroplast 50S ribosomal protein L14	0.02	-	cyt	0	Plastid; chloroplast				123
P49560 UniProt NPD GO	RK24_ODOSI	Chloroplast 50S ribosomal protein L24	0.02	-	cyt	0	Plastid; chloroplast				77
Q9TLV5 UniProt NPD GO	RK31_CYACA	Chloroplast 50S ribosomal protein L31	0.02	-	nuc	0	Plastid; chloroplast				75
Q85AE6 UniProt NPD GO	ATPI_ANTFO	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				248
P56295 UniProt NPD GO	ATPI_CHLVU	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.02	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
Q9MUS9 UniProt NPD GO	ATPI_MESVI	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
Q8H0M1 UniProt NPD GO	QORH_SPIOL	Chloroplastic quinone-oxidoreductase homolog (EC 1.-.-.-) (ceQORH)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast inner membrane				329
Q91VA1 UniProt NPD GO	CTL4_MOUSE	Choline transporter-like protein 4 (Solute carrier family 44 member 4)	0.02	-	end	10 *	Membrane; multi-pass membrane protein (By similarity)				707
Q95000 UniProt NPD GO	CHLE1_BRALA	Cholinesterase 1 (EC 3.1.1.8) (Fragment)	0.02	-	cyt	0					357
P24512 UniProt NPD GO	CH16_DROVI	Chorion protein S16	0.02	-	exc	0					139
P24513 UniProt NPD GO	CH18_DROGR	Chorion protein S18	0.02	-	vac	0					166
P07184 UniProt NPD GO	CH18_DROME	Chorion protein S18	0.02	-	mit	0					172
Q2T9X3 UniProt NPD GO	CLLD6_BOVIN	Chronic lymphocytic leukemia deletion region gene 6 protein homolog (CLL deletion region gene 6 prot ...	0.02	-	cyt	0					196
Q9DFZ3 UniProt NPD GO	CHUR_CHICK	Churchill protein	0.02	-	mit	0					112
P01052 UniProt NPD GO	ICIA_SOLTU	Chymotrypsin inhibitor I, A, B and C subunits	0.02	-	cyt	0					71
P40313 UniProt NPD GO	CTRL_HUMAN	Chymotrypsin-like protease CTRL-1 precursor (EC 3.4.21.-)	0.02	-	exc	0		extracellular space [TAS]	118888		264
P83986 UniProt NPD GO	CARI_CICAR	Cicerarin (Fragment)	0.02	-		0					20
P48523 UniProt NPD GO	CADH1_ARATH	Cinnamyl-alcohol dehydrogenase (EC 1.1.1.195) (CAD)	0.02	-	nuc	0					365
P56871 UniProt NPD GO	CIRA_CHAPA	Circulin-A (CIRA)	0.02	-	nuc	0				1BH4	30
P84641 UniProt NPD GO	CIRC_CHAPA	Circulin-C (CIRC)	0.02	-	nuc	0					30
P84644 UniProt NPD GO	CIRF_CHAPA	Circulin-F (CIRF)	0.02	-	nuc	0					29
P84543 UniProt NPD GO	CISY_POPEU	Citrate synthase (EC 2.3.3.1) (Fragments)	0.02	-		0					20
O75390 UniProt NPD GO	CISY_HUMAN	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	118950		466
Q9CZU6 UniProt NPD GO	CISY_MOUSE	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			464
P34085 UniProt NPD GO	CISY_NEUCR	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.02	-	nuc	0	Mitochondrion; mitochondrial matrix				469
P00889 UniProt NPD GO	CISY_PIG	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix			4CTS	464
Q39962 UniProt NPD GO	CBPR_HEVBR	Citrate-binding protein precursor	0.02	-	mit	0	Lutoid (vacuole); tonoplast				238
P35737 UniProt NPD GO	2DMB_MOUSE	Class II histocompatibility antigen, M beta 1 chain precursor (H2-M beta 1 chain)	0.02	-	end	1 *	Endosome; late endosome; late endosomal membrane; single-pass type I membrane protein. Lysosome; lys ...				261
Q9CQX5 UniProt NPD GO	CLDND_MOUSE	Claudin domain-containing protein 1	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				253
Q3MHK4 UniProt NPD GO	CLD11_BOVIN	Claudin-11	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein				207
Q4R3L1 UniProt NPD GO	CLD11_MACFA	Claudin-11	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)				207
Q5REK8 UniProt NPD GO	CLD11_PONPY	Claudin-11	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)				200
O75508 UniProt NPD GO	CLD11_HUMAN	Claudin-11 (Oligodendrocyte-specific protein)	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]	601326		207
P56749 UniProt NPD GO	CLD12_HUMAN	Claudin-12	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			244
Q9ET43 UniProt NPD GO	CLD12_MOUSE	Claudin-12	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			244
Q5R9K1 UniProt NPD GO	CLD12_PONPY	Claudin-12	0.02	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)				244

You are viewing entries 82801 to 82850 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.