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
Q8BVU5 UniProt NPD GO	NUDT9_MOUSE	ADP-ribose pyrophosphatase, mitochondrial precursor (EC 3.6.1.13) (ADP-ribose diphosphatase) (Adenos ...	0.25	-	mit	0	Mitochondrion (By similarity)	mitochondrion [TAS]			350
O08915 UniProt NPD GO	AIP_MOUSE	AH receptor-interacting protein (AIP) (Aryl-hydrocarbon receptor-interacting protein)	0.25	-	cyt	0	Cytoplasm	membrane fraction [IDA]			330
P0C156 UniProt NPD GO	ATPF_SACHY	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.25	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				183
Q6ENW7 UniProt NPD GO	ATPF_SACOF	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.25	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				183
Q70XV0 UniProt NPD GO	ATPA_AMBTC	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.25	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q6ENW6 UniProt NPD GO	ATPA_SACOF	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.25	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
P12112 UniProt NPD GO	ATPA_WHEAT	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.25	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				504
Q01915 UniProt NPD GO	ATPAM_SOYBN	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.25	-	cyt	0	Mitochondrion				508
Q03265 UniProt NPD GO	ATPA_MOUSE	ATP synthase subunit alpha, mitochondrial precursor (EC 3.6.3.14)	0.25	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			553
P15999 UniProt NPD GO	ATPA_RAT	ATP synthase subunit alpha, mitochondrial precursor (EC 3.6.3.14)	0.25	-	mit	0	Mitochondrion; mitochondrial inner membrane			2F43	553
P24487 UniProt NPD GO	ATPA_SCHPO	ATP synthase subunit alpha, mitochondrial precursor (EC 3.6.3.14)	0.25	-	mit	0	Mitochondrion	proton-transporting ATP synthase, catalytic... [TAS]			536
Q9H172 UniProt NPD GO	ABCG4_HUMAN	ATP-binding cassette sub-family G member 4	0.25	-	end	7	Membrane; multi-pass membrane protein (Probable)		607784		646
P70170 UniProt NPD GO	ABCC9_MOUSE	ATP-binding cassette transporter sub-family C member 9 (Sulfonylurea receptor 2)	0.25	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				1546
Q36863 UniProt NPD GO	CLPP1_CYAPA	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.25	-	nuc	0	Plastid; cyanelle				194
Q5A4E2 UniProt NPD GO	DED1_CANAL	ATP-dependent RNA helicase DED1 (EC 3.6.1.-)	0.25	-	nuc	0	Cytoplasm (By similarity)				672
Q5B0J9 UniProt NPD GO	DBP2_EMENI	ATP-dependent RNA helicase dbp2 (EC 3.6.1.-)	0.25	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				563
Q5KN60 UniProt NPD GO	IF4A_CRYNE	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.25	-	cyt	0	Cytoplasm (By similarity)				401
Q4P331 UniProt NPD GO	IF4A_USTMA	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.25	-	cyt	0	Cytoplasm (By similarity)				411
P09940 UniProt NPD GO	ATIF_PICJA	ATPase inhibitor, mitochondrial	0.25	-	nuc	0	Mitochondrion				63
P01096 UniProt NPD GO	ATIF1_BOVIN	ATPase inhibitor, mitochondrial precursor	0.25	-	nuc	0	Mitochondrion			1OHH	109
Q84VX3 UniProt NPD GO	ALF4_ARATH	Aberrant root formation protein 4	0.25	-	nuc	0	Nucleus				626
Q8VD66 UniProt NPD GO	ABHD4_MOUSE	Abhydrolase domain-containing protein 4 (EC 3.1.1.-) (Lyso-N-acylphosphatidylethanolamine lipase) (A ...	0.25	-	cyt	0					342
P02714 UniProt NPD GO	ACHG_TORCA	Acetylcholine receptor protein subunit gamma precursor	0.25	-	end	4	Membrane; multi-pass membrane protein			1LK1	506
P80052 UniProt NPD GO	CHIT_DIOJA	Acidic endochitinase (EC 3.2.1.14)	0.25	-	cyt	0					250
P19172 UniProt NPD GO	CHIA_ARATH	Acidic endochitinase precursor (EC 3.2.1.14)	0.25	-	exc	0	Intercellular space of infected plants				302
Q9Y573 UniProt NPD GO	IPP_HUMAN	Actin-binding protein IPP (MIPP protein)	0.25	-	cyt	0		actin cytoskeleton [TAS]	147485		584
P30175 UniProt NPD GO	ADF_LILLO	Actin-depolymerizing factor (ADF)	0.25	-	cyt	0					139
P45890 UniProt NPD GO	ARP6_DROME	Actin-like protein 13E (Actin-related protein 6) (dArp6)	0.25	-	cyt	0	Nucleus. Localized on centric heterochromatin				398
Q9GZN1 UniProt NPD GO	ARP6_HUMAN	Actin-related protein 6 (hArp6) (hARPX)	0.25	+	cyt	0					396
Q94519 UniProt NPD GO	ACPM_DROME	Acyl carrier protein, mitochondrial precursor (ACP) (NADH-ubiquinone oxidoreductase 9.6 kDa subunit) ...	0.25	-	mit	0	Mitochondrion				152
Q8JZN5 UniProt NPD GO	ACAD9_MOUSE	Acyl-CoA dehydrogenase family member 9, mitochondrial precursor (EC 1.3.99.-) (ACAD-9)	0.25	-	mit	0	Mitochondrion (Potential)	mitochondrion [IDA]			625
P11356 UniProt NPD GO	ACOX2_CANTR	Acyl-coenzyme A oxidase 2 (EC 1.3.3.6) (Acyl-CoA oxidase 2) (PXP-2)	0.25	-	cyt	0	Peroxisome				723
Q8BYI6 UniProt NPD GO	AYT1A_MOUSE	Acyltransferase-like 1-A (EC 2.3.1.-)	0.25	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)				544
P19754 UniProt NPD GO	ADCY1_BOVIN	Adenylate cyclase type 1 (EC 4.6.1.1) (Adenylate cyclase type I) (ATP pyrophosphate-lyase 1) (Ca(2+) ...	0.25	-	end	11	Membrane; multi-pass membrane protein			1AWK	1134
P26770 UniProt NPD GO	ADCY4_RAT	Adenylate cyclase type 4 (EC 4.6.1.1) (Adenylate cyclase type IV) (ATP pyrophosphate-lyase 4) (Adeny ...	0.25	-	end	12 *	Membrane; multi-pass membrane protein				1064
P51829 UniProt NPD GO	ADCY7_MOUSE	Adenylate cyclase type 7 (EC 4.6.1.1) (Adenylate cyclase type VII) (ATP pyrophosphate-lyase 7) (Aden ...	0.25	-	end	12 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]			1099
P49982 UniProt NPD GO	KAD_GIALA	Adenylate kinase (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK)	0.25	-	nuc	0					248
Q8GWW7 UniProt NPD GO	AGUA_ARATH	Agmatine deiminase (EC 3.5.3.12) (Agmatine iminohydrolase)	0.25	-	cyt	0				1VKP	383
Q5XI42 UniProt NPD GO	AL3B1_RAT	Aldehyde dehydrogenase 3B1 (EC 1.2.1.5)	0.25	-	mit	0					468
Q5R7C9 UniProt NPD GO	AK1C3_PONPY	Aldo-keto reductase family 1 member C3 homolog (EC 1.-.-.-) (Trans-1,2-dihydrobenzene-1,2-diol dehyd ...	0.25	-	cyt	0					323
Q08347 UniProt NPD GO	BDS1_YEAST	Alkyl/aryl-sulfatase BDS1 (EC 3.1.6.-) (Bacterially-derived sulfatase 1)	0.25	-	mit	0					646
O00116 UniProt NPD GO	ADAS_HUMAN	Alkyldihydroxyacetonephosphate synthase, peroxisomal precursor (EC 2.5.1.26) (Alkyl-DHAP synthase) ( ...	0.25	-	cyt	0	Peroxisome. Localized to the inner aspect of the peroxisomal membrane	peroxisome [IDA]	603051		658
O73919 UniProt NPD GO	CRYAA_ORYLA	Alpha crystallin A chain (Fragment)	0.25	-	nuc	0					145
Q60HG8 UniProt NPD GO	CRYAB_MACFA	Alpha crystallin B chain (Alpha(B)-crystallin)	0.25	-	mit	0					175
P26618 UniProt NPD GO	PGFRA_MOUSE	Alpha platelet-derived growth factor receptor precursor (EC 2.7.10.1) (PDGF-R-alpha)	0.25	-	end	2 *	Membrane; single-pass type I membrane protein				1089
Q6BVB2 UniProt NPD GO	ALG11_DEBHA	Alpha-1,2-mannosyltransferase ALG11 (EC 2.4.1.-) (Asparagine-linked glycosylation protein 11)	0.25	-	nuc	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				616
Q59LF2 UniProt NPD GO	ALG2_CANAL	Alpha-1,3-mannosyltransferase ALG2 (EC 2.4.1.-) (GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransfe ...	0.25	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				428
P21352 UniProt NPD GO	A1AG8_MUSCR	Alpha-1-acid glycoprotein 8 precursor (AGP 8) (Orosomucoid-8) (OMD 8)	0.25	-	exc	0	Secreted protein				207
P97714 UniProt NPD GO	ADA1D_MOUSE	Alpha-1D adrenergic receptor (Alpha 1D-adrenoceptor) (Alpha 1D-adrenoreceptor) (Alpha-1A adrenergic ...	0.25	+	end	7	Membrane; multi-pass membrane protein				562
P70126 UniProt NPD GO	SIA8E_MOUSE	Alpha-2,8-sialyltransferase 8E (EC 2.4.99.-) (ST8Sia V)	0.25	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				412

You are viewing entries 44901 to 44950 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.