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
P97819 UniProt NPD GO	PA2G6_MOUSE	85 kDa calcium-independent phospholipase A2 (EC 3.1.1.4) (iPLA2) (CaI-PLA2) (Group VI phospholipase ...	0.23	-	mit	0	Cytoplasm				752
O43687 UniProt NPD GO	AKA7A_HUMAN	A-kinase anchor protein 7 isoforms alpha and beta (Protein kinase A-anchoring protein 7 isoforms alp ...	0.23	-	nuc	0	Isoform Alpha: Cell membrane; lateral cell membrane; lipid-anchor. Isoform Beta: Cell membrane; apic ...	apical plasma membrane [IDA] lateral plasma membrane [IDA] plasma membrane [TAS]	604693		103
P04709 UniProt NPD GO	ADT1_MAIZE	ADP,ATP carrier protein 1, mitochondrial precursor (ADP/ATP translocase 1) (Adenine nucleotide trans ...	0.23	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				387
Q2KI07 UniProt NPD GO	ARL8B_BOVIN	ADP-ribosylation factor-like protein 8B	0.23	-	cyt	0	Endosome; late endosome (By similarity). Lysosome (By similarity). Alternatively, may localize with ...				186
P52303 UniProt NPD GO	AP1B1_RAT	AP-1 complex subunit beta-1 (Adapter-related protein complex 1 beta-1 subunit) (Beta-adaptin 1) (Ada ...	0.23	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...			1W63	949
P56759 UniProt NPD GO	ATPF_ARATH	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.23	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				184
P51245 UniProt NPD GO	ATPX_PORPU	ATP synthase B' chain (EC 3.6.3.14) (Subunit II)	0.23	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				158
O79675 UniProt NPD GO	ATP6_PELSU	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.23	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
P12633 UniProt NPD GO	ATP5I_CRILO	ATP synthase e chain, mitochondrial (EC 3.6.3.14) (UV-inducible PU4 protein)	0.23	-	cyt	0					68
Q85FL4 UniProt NPD GO	ATPE_ADICA	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.23	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				132
P35435 UniProt NPD GO	ATPG_RAT	ATP synthase gamma chain, mitochondrial (EC 3.6.3.14)	0.23	-	mit	0	Mitochondrion	mitochondrial envelope [NAS]		2F43	273
P56383 UniProt NPD GO	AT5G2_MOUSE	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.23	-	cyt	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein				146
Q8S8Y3 UniProt NPD GO	ATPA_ATRBE	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.23	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q2L8Z1 UniProt NPD GO	ATPA_GOSHI	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.23	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q6EW63 UniProt NPD GO	ATPA_NYMAL	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.23	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q6ENH7 UniProt NPD GO	ATPA_ORYNI	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.23	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
P12084 UniProt NPD GO	ATPA_ORYSA	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.23	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
P19483 UniProt NPD GO	ATPA1_BOVIN	ATP synthase subunit alpha heart isoform, mitochondrial precursor (EC 3.6.3.14)	0.23	-	mit	0	Mitochondrion; mitochondrial inner membrane			2CK3	553
P26854 UniProt NPD GO	ATPAM_MARPO	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.23	-	cyt	0	Mitochondrion				513
Q5R546 UniProt NPD GO	ATPA_PONPY	ATP synthase subunit alpha, mitochondrial precursor (EC 3.6.3.14)	0.23	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				553
P31542 UniProt NPD GO	CLPAB_LYCES	ATP-dependent Clp protease ATP-binding subunit clpA homolog CD4B, chloroplast precursor	0.23	-	mit	0	Plastid; chloroplast				923
Q6BU54 UniProt NPD GO	DED1_DEBHA	ATP-dependent RNA helicase DED1 (EC 3.6.1.-)	0.23	-	cyt	0	Cytoplasm (By similarity)				630
O70596 UniProt NPD GO	IRK14_RAT	ATP-sensitive inward rectifier potassium channel 14 (Potassium channel, inwardly rectifying subfamil ...	0.23	-	end	3	Membrane; multi-pass membrane protein				434
P20649 UniProt NPD GO	PMA1_ARATH	ATPase 1, plasma membrane-type (EC 3.6.3.6) (Proton pump 1)	0.23	-	end	10	Cell membrane; multi-pass membrane protein (Probable)				948
O42275 UniProt NPD GO	ACES_ELEEL	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.23	-	end	1 *					633
P16579 UniProt NPD GO	CHI6_POPTR	Acidic endochitinase WIN6 precursor (EC 3.2.1.14)	0.23	-	exc	0					340
Q25379 UniProt NPD GO	ACT3_LYTPI	Actin, cytoskeletal 3 (LPC3) (Fragment)	0.23	-	cyt	0	Cytoplasm. Cytoskeleton				172
Q9ZSK4 UniProt NPD GO	ADF3_ARATH	Actin-depolymerizing factor 3 (ADF 3) (AtADF3)	0.23	-	cyt	0					139
P47117 UniProt NPD GO	ARP3_YEAST	Actin-like protein 3 (Actin-related protein 3) (Actin-like protein ARP3)	0.23	-	nuc	0		Arp2/3 protein complex [IDA]			449
Q28043 UniProt NPD GO	AVR2A_BOVIN	Activin receptor type 2A precursor (EC 2.7.11.30) (Activin receptor type IIA) (ACTR-IIA)	0.23	-	end	1	Membrane; single-pass type I membrane protein				513
Q85FZ0 UniProt NPD GO	ACP_CYAME	Acyl carrier protein (ACP)	0.23	-	nuc	0	Plastid; chloroplast				91
Q9H845 UniProt NPD GO	ACAD9_HUMAN	Acyl-CoA dehydrogenase family member 9, mitochondrial precursor (EC 1.3.99.-) (ACAD-9)	0.23	-	mit	0	Mitochondrion (Potential)				621
Q92604 UniProt NPD GO	LGAT1_HUMAN	Acyl-CoA:lysophosphatidylglycerol acyltransferase 1 (EC 2.3.1.-)	0.23	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	cytoplasm [IDA]			370
Q63448 UniProt NPD GO	ACOX3_RAT	Acyl-coenzyme A oxidase 3, peroxisomal (EC 1.3.3.6) (Pristanoyl-CoA oxidase) (Branched-chain acyl-Co ...	0.23	-	nuc	0	Peroxisome				700
O14734 UniProt NPD GO	ACOT8_HUMAN	Acyl-coenzyme A thioesterase 8 (EC 3.1.2.2) (Acyl-CoA thioesterase 8) (Peroxisomal acyl-coenzyme A t ...	0.23	-	pox	0	Peroxisome	peroxisome [TAS]	608123		319
Q9Y0Y2 UniProt NPD GO	PURA_DROME	Adenylosuccinate synthetase (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPSase)	0.23	-	cyt	0	Cytoplasm (By similarity)				447
Q60604 UniProt NPD GO	ADSV_MOUSE	Adseverin (Scinderin) (Gelsolin-like protein)	0.23	-	cyt	0					715
Q28046 UniProt NPD GO	ADSV_BOVIN	Adseverin (Scinderin) (SC)	0.23	-	cyt	0		cell cortex [IDA] cytoplasm [IDA]			715
P10968 UniProt NPD GO	AGI1_WHEAT	Agglutinin isolectin 1 precursor (WGA1) (Isolectin A)	0.23	-	exc	0				7WGA	212
Q7G192 UniProt NPD GO	ALDO2_ARATH	Aldehyde oxidase 2 (EC 1.2.3.1) (AO-2) (AtAO-2) (AtAO3)	0.23	-	cyt	0					1321
Q64FW2 UniProt NPD GO	RETST_MOUSE	All-trans-retinol 13,14-reductase precursor (EC 1.3.99.23) (All-trans-13,14-dihydroretinol saturase) ...	0.23	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum membrane [IDA] nuclear outer membrane [IDA]			609
P02478 UniProt NPD GO	CRYAA_HORSE	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.23	-	cyt	0					173
Q91312 UniProt NPD GO	CRYAB_RANCA	Alpha crystallin B chain (Alpha(B)-crystallin)	0.23	-	cyt	0					173
P02512 UniProt NPD GO	CRYAB_SQUAC	Alpha crystallin B chain (Alpha(B)-crystallin)	0.23	-	mit	0					177
Q8HZR3 UniProt NPD GO	FUT4_BOVIN	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.23	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				398
Q6C9T3 UniProt NPD GO	ALG11_YARLI	Alpha-1,2-mannosyltransferase ALG11 (EC 2.4.1.-) (Asparagine-linked glycosylation protein 11)	0.23	+	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				635
P81105 UniProt NPD GO	A1AT6_MOUSE	Alpha-1-antitrypsin 1-6 precursor (Serine protease inhibitor 1-6) (Alpha-1 protease inhibitor 6)	0.23	-	end	0	Secreted protein				412
Q07977 UniProt NPD GO	SIA8B_RAT	Alpha-2,8-sialyltransferase 8B (EC 2.4.99.-) (ST8Sia II) (Sialyltransferase X) (STX)	0.23	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				375
P06238 UniProt NPD GO	A2MG_RAT	Alpha-2-macroglobulin precursor (Alpha-2-M)	0.23	-	mit	0	Secreted protein				1472
P06280 UniProt NPD GO	AGAL_HUMAN	Alpha-galactosidase A precursor (EC 3.2.1.22) (Melibiase) (Alpha-D-galactoside galactohydrolase) (Al ...	0.23	-	mit	0	Lysosome	cytoplasm [IMP] extracellular region [IDA] Golgi apparatus [IMP] lysosome [IMP]	301500	1R47	429

You are viewing entries 47051 to 47100 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.