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
Q06838 UniProt NPD GO	ATP9_PICPJ	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein) (Fragment)	0.00	-	mit	1 *					29
P61829 UniProt NPD GO	ATP9_YEAST	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein) (Oligomycin resistance p ...	0.00	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)	proton-transporting ATP synthase complex, c... [TAS]			76
P26965 UniProt NPD GO	ATPA_BRYMA	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				29
P31476 UniProt NPD GO	ATPB_EUGGR	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				480
P49647 UniProt NPD GO	ATPB_ODOSI	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				475
Q6ENG7 UniProt NPD GO	ATPB_ORYNI	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
Q6L392 UniProt NPD GO	ATPB_SACHY	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
Q6ENV6 UniProt NPD GO	ATPB_SACOF	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
O03064 UniProt NPD GO	ATPB_ADIRA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				396
P83505 UniProt NPD GO	ATPB_BRARA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				32
P81663 UniProt NPD GO	ATPBM_PINPS	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) (Fragment)	0.00	-		0	Mitochondrion				15
Q07233 UniProt NPD GO	ATPB_SCHGA	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) (Fragment)	0.00	-	cyt	0	Mitochondrion				158
Q24751 UniProt NPD GO	ATPB_DROVI	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14) (Fragment)	0.00	-	mit	0	Mitochondrion				228
Q7Z4Y8 UniProt NPD GO	AT5L2_HUMAN	ATP synthase subunit g 2, mitochondrial (EC 3.6.3.14) (ATPase subunit g 2)	0.00	-	cyt	0					100
Q28852 UniProt NPD GO	ATP5L_BOVIN	ATP synthase subunit g, mitochondrial (EC 3.6.3.14) (ATPase subunit g)	0.00	-	cyt	0					102
O75964 UniProt NPD GO	ATP5L_HUMAN	ATP synthase subunit g, mitochondrial (EC 3.6.3.14) (ATPase subunit g)	0.00	-	cyt	0					103
Q9CPQ8 UniProt NPD GO	ATP5L_MOUSE	ATP synthase subunit g, mitochondrial (EC 3.6.3.14) (ATPase subunit g)	0.00	-	cyt	0		mitochondrial inner membrane [IDA] mitochondrion [IDA]			103
Q5RFH0 UniProt NPD GO	ATP5L_PONPY	ATP synthase subunit g, mitochondrial (EC 3.6.3.14) (ATPase subunit g)	0.00	-	cyt	0					103
P81671 UniProt NPD GO	CLPA_PINPS	ATP-dependent Clp protease ATP-binding subunit clpA homolog (Fragments)	0.00	-	cyt	0	Plastid; chloroplast (By similarity)				30
P84565 UniProt NPD GO	CLPA_POPEU	ATP-dependent Clp protease ATP-binding subunit clpA homolog (Fragments)	0.00	-	cyt	0	Plastid; chloroplast				72
Q70XY2 UniProt NPD GO	CLPP_AMBTC	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	nuc	0	Plastid; chloroplast				202
Q85BZ1 UniProt NPD GO	CLPP_ANTFO	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	cyt	0	Plastid; chloroplast				204
Q7YJV2 UniProt NPD GO	CLPP_CALFE	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	cyt	0	Plastid; chloroplast				202
P30063 UniProt NPD GO	CLPP_EPIVI	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	cyt	0	Plastid				196
Q5SD28 UniProt NPD GO	CLPP_HUPLU	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	cyt	0	Plastid; chloroplast				209
Q9BBQ9 UniProt NPD GO	CLPP_LOTJA	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	nuc	0	Plastid; chloroplast				196
P12208 UniProt NPD GO	CLPP_MARPO	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	cyt	0	Plastid; chloroplast				203
Q6EW27 UniProt NPD GO	CLPP_NYMAL	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	mit	0	Plastid; chloroplast				202
Q68RY2 UniProt NPD GO	CLPP_PANGI	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	nuc	0	Plastid; chloroplast				196
Q6YXM7 UniProt NPD GO	CLPP_PHYPA	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	cyt	0	Plastid; chloroplast				199
Q8WHZ7 UniProt NPD GO	CLPP_PSINU	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	cyt	0	Plastid; chloroplast				198
Q9M3K5 UniProt NPD GO	CLPP_SPIOL	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	nuc	0	Plastid; chloroplast				196
P12210 UniProt NPD GO	CLPP_TOBAC	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.00	-	nuc	0	Plastid; chloroplast				196
P48883 UniProt NPD GO	CLPP_HORVU	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				24
P16548 UniProt NPD GO	A95EF_DROME	Accessory gland-specific peptide 95EF precursor (Male accessory gland secretory protein 316)	0.00	-	vac	1 *	Secreted protein				52
P14610 UniProt NPD GO	THIL_PIG	Acetyl-CoA acetyltransferase (EC 2.3.1.9) (Acetoacetyl-CoA thiolase) (Fragment)	0.00	-	nuc	0	Mitochondrion				26
Q12598 UniProt NPD GO	THIA_CANTR	Acetyl-CoA acetyltransferase IA (EC 2.3.1.9) (Peroxisomal acetoacetyl-CoA thiolase) (Thiolase IA)	0.00	-	pox	0	Peroxisome				402
Q04677 UniProt NPD GO	THIB_CANTR	Acetyl-CoA acetyltransferase IB (EC 2.3.1.9) (Peroxisomal acetoacetyl-CoA thiolase) (Thiolase IB)	0.00	-	pox	0	Peroxisome				402
Q6FPF3 UniProt NPD GO	ACH1_CANGA	Acetyl-CoA hydrolase (EC 3.1.2.1) (Acetyl-CoA deacylase) (Acetyl-CoA acylase)	0.00	-	cyt	0	Cytoplasm (By similarity)				526
P14144 UniProt NPD GO	ACHA_NATTE	Acetylcholine receptor protein subunit alpha (Fragment)	0.00	-	cyt	0	Membrane; multi-pass membrane protein				127
Q867X3 UniProt NPD GO	ACES_CULPP	Acetylcholinesterase (EC 3.1.1.7) (AChE) (Fragment)	0.00	-	cyt	0					132
Q867X2 UniProt NPD GO	ACES_CULQU	Acetylcholinesterase (EC 3.1.1.7) (AChE) (Fragment)	0.00	-	cyt	0					132
Q86GC9 UniProt NPD GO	ACES_CULTO	Acetylcholinesterase (EC 3.1.1.7) (AChE) (Fragment)	0.00	-	cyt	0					132
P35904 UniProt NPD GO	ACH1_ACHFU	Achatin-1 (Achatin-I)	0.00	-		0					4
P27061 UniProt NPD GO	PPA1_LYCES	Acid phosphatase 1 precursor (EC 3.1.3.2) (Apase-1(1))	0.00	-	exc	0					255
P58242 UniProt NPD GO	ASM3B_MOUSE	Acid sphingomyelinase-like phosphodiesterase 3b precursor (EC 3.1.4.-) (ASM-like phosphodiesterase 3 ...	0.00	-	exc	0	Secreted protein (By similarity)				456
P29060 UniProt NPD GO	CHIA_TOBAC	Acidic endochitinase precursor (EC 3.2.1.14)	0.00	-	end	0	Cell wall				291
P22582 UniProt NPD GO	LECA1_PSOSC	Acidic lectin A1 (Fragment)	0.00	-		0					15
P10165 UniProt NPD GO	PRP1_RAT	Acidic proline-rich protein PRP18 precursor (Fragment)	0.00	-	nuc	0					23
P01001 UniProt NPD GO	IAC2_BOVIN	Acrosin inhibitors IIA and IIB (BUSI-II)	0.00	-	nuc	0	Secreted protein			2BUS	57

You are viewing entries 92401 to 92450 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.