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
Q9SLL7 UniProt NPD GO	RL311_ARATH	60S ribosomal protein L31-1	0.26	-	cyt	0					119
Q6FS03 UniProt NPD GO	RL32_CANGA	60S ribosomal protein L32	0.26	-	nuc	0					131
P11874 UniProt NPD GO	RL7_DICDI	60S ribosomal protein L7	0.26	-	nuc	0					245
Q9R160 UniProt NPD GO	ADA24_MOUSE	ADAM 24 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 24) (Testase 1)	0.26	-	end	1	Membrane; single-pass type I membrane protein				761
Q9H2U9 UniProt NPD GO	ADAM7_HUMAN	ADAM 7 precursor (A disintegrin and metalloproteinase domain 7) (Sperm maturation-related glycoprote ...	0.26	-	end	1	Membrane; single-pass type I membrane protein		607310		754
P12857 UniProt NPD GO	ADT2_MAIZE	ADP,ATP carrier protein 2, mitochondrial precursor (ADP/ATP translocase 2) (Adenine nucleotide trans ...	0.26	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				387
Q9UJY4 UniProt NPD GO	GGA2_HUMAN	ADP-ribosylation factor-binding protein GGA2 (Golgi-localized, gamma ear-containing, ARF-binding pro ...	0.26	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein. End ...	Golgi trans face [IDA]	606005	1MHQ	613
Q8JZQ2 UniProt NPD GO	AF3G2_MOUSE	AFG3-like protein 2 (EC 3.4.24.-)	0.26	+	end	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA]			802
Q7YRC1 UniProt NPD GO	AIP_BOVIN	AH receptor-interacting protein (AIP) (Aryl-hydrocarbon receptor-interacting protein)	0.26	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			330
Q8TCF1 UniProt NPD GO	ZFAN1_HUMAN	AN1-type zinc finger protein 1	0.26	-	nuc	0					268
Q99186 UniProt NPD GO	AP2M_YEAST	AP-2 complex subunit mu (Clathrin coat assembly protein AP50) (Clathrin coat-associated protein AP50 ...	0.26	-	mit	0					491
P56296 UniProt NPD GO	ATPF_CHLVU	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.26	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				175
Q9BBS4 UniProt NPD GO	ATPF_LOTJA	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.26	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				184
P48186 UniProt NPD GO	ATPF_MAIZE	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.26	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				183
P08214 UniProt NPD GO	ATPF_PEA	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.26	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				172
P06528 UniProt NPD GO	ATPF_WHEAT	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.26	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				183
Q5RBW2 UniProt NPD GO	ATP5I_PONPY	ATP synthase e chain, mitochondrial (EC 3.6.3.14)	0.26	-	nuc	1 *					70
P00833 UniProt NPD GO	ATPE_SPIOL	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.26	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				134
P26360 UniProt NPD GO	ATPG3_IPOBA	ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14)	0.26	-	mit	0	Mitochondrion				326
P15998 UniProt NPD GO	ATPAM_ORYSA	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.26	-	cyt	0	Mitochondrion				509
P05493 UniProt NPD GO	ATPAM_PEA	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.26	-	cyt	0	Mitochondrion				507
P24459 UniProt NPD GO	ATPAM_PHAVU	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.26	-	cyt	0	Mitochondrion				508
P12862 UniProt NPD GO	ATPAM_WHEAT	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.26	-	cyt	0	Mitochondrion				509
Q9NP58 UniProt NPD GO	ABCB6_HUMAN	ATP-binding cassette sub-family B member 6, mitochondrial precursor (Mitochondrial ABC transporter 3 ...	0.26	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	ATP-binding cassette (ABC) transporter complex [NAS] mitochondrial envelope [IDA] mitochondrion [IDA]	605452		842
P33897 UniProt NPD GO	ABCD1_HUMAN	ATP-binding cassette sub-family D member 1 (Adrenoleukodystrophy protein) (ALDP)	0.26	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein	integral to peroxisomal membrane [NAS]	300475		745
Q4IF76 UniProt NPD GO	DBP2_GIBZE	ATP-dependent RNA helicase DBP2 (EC 3.6.1.-)	0.26	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				555
O00148 UniProt NPD GO	DDX39_HUMAN	ATP-dependent RNA helicase DDX39 (EC 3.6.1.-) (DEAD box protein 39) (Nuclear RNA helicase URH49)	0.26	-	cyt	0	Nucleus (By similarity)	nucleus [ISS]			427
Q43128 UniProt NPD GO	PMA10_ARATH	ATPase 10, plasma membrane-type (EC 3.6.3.6) (Proton pump 10)	0.26	-	end	9	Membrane; multi-pass membrane protein				947
Q9SH76 UniProt NPD GO	PMA6_ARATH	ATPase 6, plasma membrane-type (EC 3.6.3.6) (Proton pump 6)	0.26	-	end	9	Membrane; multi-pass membrane protein				949
Q8TB40 UniProt NPD GO	ABHD4_HUMAN	Abhydrolase domain-containing protein 4 (EC 3.1.1.-) (Lyso-N-acylphosphatidylethanolamine lipase) (A ...	0.26	-	cyt	0					342
O46201 UniProt NPD GO	A98AB_DROME	Accessory gland protein 98AB precursor	0.26	-	nuc	0	Secreted protein (Potential)	extracellular region [TAS]			31
Q05955 UniProt NPD GO	ADY4_YEAST	Accumulates dyads protein 4	0.26	-	nuc	0	Localizes to the meiotic outer plaque of the SPB, at the end of the meiotic spindles	spindle pole body [IDA]			493
P39058 UniProt NPD GO	CEFG_CEPAC	Acetyl-CoA--deacetylcephalosporin C acetyltransferase precursor (EC 2.3.1.175) (DCPC-ATF) (DAC acety ...	0.26	-	mit	0					444
P18916 UniProt NPD GO	ACHG_RAT	Acetylcholine receptor protein subunit gamma precursor	0.26	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [IMP]			519
P25229 UniProt NPD GO	CAPZA_XENLA	Actin-binding protein chain A (ABP-A) (Fragment)	0.26	-	nuc	0	Nucleus				256
P32390 UniProt NPD GO	ARP3_SCHPO	Actin-like protein 3 (Actin-related protein 3)	0.26	-	nuc	0		actin cortical patch [IDA]			427
Q6C982 UniProt NPD GO	ARP6_YARLI	Actin-like protein ARP6	0.26	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				387
Q9D864 UniProt NPD GO	ARP6_MOUSE	Actin-related protein 6 (mArp6)	0.26	+	cyt	0					396
Q8NER5 UniProt NPD GO	ACV1C_HUMAN	Activin receptor type 1C precursor (EC 2.7.11.30) (ACTR-IC) (Activin receptor-like kinase 7) (ALK-7) ...	0.26	-	end	1	Membrane; single-pass type I membrane protein	activin receptor complex [IDA]	608981		493
Q6P756 UniProt NPD GO	NECP2_RAT	Adaptin ear-binding coat-associated protein 2 (NECAP-2)	0.26	-	cyt	0	Membrane-associated; membranes of clathrin-coated vesicles. Colocalizes with AP-2 at the plasma memb ...	clathrin vesicle coat [ISS] coated pit [ISS]			263
Q25464 UniProt NPD GO	FP2_MYTGA	Adhesive plaque matrix protein 2 precursor (Foot protein 2) (MGFP2) (MGFP-2)	0.26	-	exc	0	Secreted protein				473
Q9EQH2 UniProt NPD GO	ARTS1_MOUSE	Adipocyte-derived leucine aminopeptidase precursor (EC 3.4.11.-) (A-LAP) (ARTS-1) (Aminopeptidase PI ...	0.26	-	cyt	0	Secreted protein (By similarity)	cytoplasm [IDA] cytosol [ISS] endoplasmic reticulum [ISS] endoplasmic reticulum lumen [ISS] extracellular region [ISS] integral to membrane [ISS]			930
P48034 UniProt NPD GO	ADO_BOVIN	Aldehyde oxidase (EC 1.2.3.1)	0.26	-	cyt	0	Cytoplasm				1339
Q9W6S5 UniProt NPD GO	ALLC_XENLA	Allantoicase (EC 3.5.3.4) (Allantoate amidinohydrolase)	0.26	-	cyt	0					389
P15990 UniProt NPD GO	CRYAA_SPAEH	Alpha crystallin A chain	0.26	-	cyt	0					196
P68287 UniProt NPD GO	CRYAA_GALCR	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.26	-	cyt	0					173
P68286 UniProt NPD GO	CRYAA_PERPO	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.26	-	cyt	0					173
P26619 UniProt NPD GO	PGFRA_XENLA	Alpha platelet-derived growth factor receptor precursor (EC 2.7.10.1) (PDGF-R-alpha)	0.26	-	end	3 *	Membrane; single-pass type I membrane protein				1087
Q7SA35 UniProt NPD GO	ALG10_NEUCR	Alpha-1,2 glucosyltransferase alg-10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10) (Dolichyl-phos ...	0.26	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				770
Q09325 UniProt NPD GO	MGAT1_RAT	Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.101) (N-glycosyl-ol ...	0.26	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				447

You are viewing entries 43901 to 43950 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.