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
Q9M7X7 UniProt NPD GO	RL291_ARATH	60S ribosomal protein L29-1	0.31	-	nuc	0					61
Q9STR1 UniProt NPD GO	RL312_ARATH	60S ribosomal protein L31-2	0.31	-	cyt	0					119
P51421 UniProt NPD GO	RL32_MAIZE	60S ribosomal protein L32 (Fragment)	0.31	-	nuc	0					42
P14198 UniProt NPD GO	AAC4_DICDI	AAC-rich mRNA clone pLK330 protein (Fragment)	0.31	-	nuc	0					317
Q06567 UniProt NPD GO	YL253_YEAST	ABC1 family protein YLR253W	0.31	-	mit	0		mitochondrion [IDA]			569
Q9FLT5 UniProt NPD GO	ATH11_ARATH	ABC2 homolog 11	0.31	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				950
P97776 UniProt NPD GO	ADA18_RAT	ADAM 18 (A disintegrin and metalloproteinase domain 18) (Transmembrane metalloproteinase-like, disin ...	0.31	-	nuc	1	Membrane; single-pass type I membrane protein				445
Q9R157 UniProt NPD GO	ADA18_MOUSE	ADAM 18 precursor (A disintegrin and metalloproteinase domain 18) (Transmembrane metalloproteinase-l ...	0.31	-	end	1	Membrane; single-pass type I membrane protein				719
O77780 UniProt NPD GO	ADAM2_BOVIN	ADAM 2 precursor (A disintegrin and metalloproteinase domain 2) (Fertilin subunit beta) (PH-30) (PH3 ...	0.31	-	end	1	Membrane; single-pass type I membrane protein				745
O00189 UniProt NPD GO	AP4M1_HUMAN	AP-4 complex subunit mu-1 (Adapter-related protein complex 4 mu-1 subunit) (Mu subunit of AP-4) (AP- ...	0.31	-	nuc	0	Golgi apparatus; trans-Golgi network. Associated with the trans-Golgi network. Found in soma and den ...	Golgi trans cisterna [TAS] membrane coat adaptor complex [TAS]	602296		453
Q05933 UniProt NPD GO	ARPC3_YEAST	ARP2/3 complex 21 kDa subunit (p21-ARC)	0.31	-	cyt	0		Arp2/3 protein complex [IDA]			178
Q85FN3 UniProt NPD GO	ATPF_ADICA	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.31	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				184
P51244 UniProt NPD GO	ATPF_PORPU	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.31	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				183
P36542 UniProt NPD GO	ATPG_HUMAN	ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14)	0.31	-	mit	0	Mitochondrion	proton-transporting ATP synthase complex (s... [TAS]	108729		298
Q4R5B0 UniProt NPD GO	ATPG_MACFA	ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14)	0.31	-	mit	0	Mitochondrion				298
Q9ZXY0 UniProt NPD GO	ATP8_PAPHA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.31	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				68
Q96J66 UniProt NPD GO	ABCCB_HUMAN	ATP-binding cassette transporter sub-family C member 11 (Multidrug resistance-associated protein 8)	0.31	-	end	11	Membrane; multi-pass membrane protein		607040		1382
P24784 UniProt NPD GO	DBP1_YEAST	ATP-dependent RNA helicase DBP1 (EC 3.6.1.-) (DEAD box protein 1) (Helicase CA1)	0.31	+	nuc	0	Cytoplasm	cytoplasm [IDA]			617
Q9UHL0 UniProt NPD GO	DDX25_HUMAN	ATP-dependent RNA helicase DDX25 (EC 3.6.1.-) (DEAD box protein 25) (Gonadotropin-regulated testicul ...	0.31	-	cyt	0	Cytoplasm	cytoplasm [TAS]	607663	2G2J	483
P06634 UniProt NPD GO	DED1_YEAST	ATP-dependent RNA helicase DED1 (EC 3.6.1.-) (DEAD box protein 1)	0.31	-	nuc	0	Cytoplasm	cytoplasm [IC]			604
Q755W0 UniProt NPD GO	FAL1_ASHGO	ATP-dependent RNA helicase FAL1 (EC 3.6.1.-)	0.31	-	cyt	0	Nucleus; nucleolus (By similarity)				398
Q4WP13 UniProt NPD GO	DED1_ASPFU	ATP-dependent RNA helicase ded1 (EC 3.6.1.-)	0.31	-	cyt	0	Cytoplasm (By similarity)				674
Q4WX43 UniProt NPD GO	IF4A_ASPFU	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.31	-	cyt	0	Cytoplasm (By similarity)				406
P47943 UniProt NPD GO	IF4A_SCHPO	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.31	-	cyt	0	Cytoplasm (By similarity)				392
O13792 UniProt NPD GO	SUB2_SCHPO	ATP-dependent RNA helicase uap56 (EC 3.6.1.-)	0.31	-	cyt	0	Nucleus (By similarity)				434
Q9JM63 UniProt NPD GO	IRK10_MOUSE	ATP-sensitive inward rectifier potassium channel 10 (Potassium channel, inwardly rectifying subfamil ...	0.31	-	mit	2	Membrane; multi-pass membrane protein				379
Q14500 UniProt NPD GO	IRK12_HUMAN	ATP-sensitive inward rectifier potassium channel 12 (Potassium channel, inwardly rectifying subfamil ...	0.31	-	end	3	Membrane; multi-pass membrane protein		602323		433
Q91ZF1 UniProt NPD GO	IRK15_RAT	ATP-sensitive inward rectifier potassium channel 15 (Potassium channel, inwardly rectifying subfamil ...	0.31	-	mit	2	Membrane; multi-pass membrane protein				405
P11497 UniProt NPD GO	COA1_RAT	Acetyl-CoA carboxylase 1 (EC 6.4.1.2) (ACC-alpha) [Includes: Biotin carboxylase (EC 6.3.4.14)]	0.31	-	nuc	0	Cytoplasm				2345
P23578 UniProt NPD GO	ACRO_MOUSE	Acrosin precursor (EC 3.4.21.10) [Contains: Acrosin light chain; Acrosin heavy chain]	0.31	-	nuc	0		acrosomal matrix [TAS]			436
O18823 UniProt NPD GO	AOAH_RABIT	Acyloxyacyl hydrolase precursor (EC 3.1.1.77) [Contains: Acyloxyacyl hydrolase small subunit; Acylox ...	0.31	-	end	0					575
P34179 UniProt NPD GO	ADAM_CROAD	Adamalysin-2 (EC 3.4.24.46) (Adamalysin II) (Proteinase II)	0.31	-	nuc	0				4AIG	203
Q920P5 UniProt NPD GO	KAD5_MOUSE	Adenylate kinase isoenzyme 5 (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.31	-	cyt	0	Cytoplasm				193
P07897 UniProt NPD GO	PGCA_RAT	Aggrecan core protein precursor (Cartilage-specific proteoglycan core protein) (CSPCP)	0.31	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [IDA]		1TDQ	2124
Q9VC44 UniProt NPD GO	ALLS_DROME	Allatostatins Ast precursor [Contains: Drostatin-1; Drostatin-2; Drostatin-3; Drostatin-4; Drostatin ...	0.31	-	exc	0	Secreted protein				151
P81076 UniProt NPD GO	AIF1_PIG	Allograft inflammatory factor 1 (AIF-1) (Daintain)	0.31	-	nuc	0					146
P06904 UniProt NPD GO	CRYAA_ALLMI	Alpha crystallin A chain	0.31	-	mit	0					173
O12984 UniProt NPD GO	CRYAA_ANAPL	Alpha crystallin A chain (Fragment)	0.31	-	nuc	0					149
P68281 UniProt NPD GO	CRYAA_CAVPO	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.31	-	cyt	0					173
P02494 UniProt NPD GO	CRYAA_EULFU	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.31	-	cyt	0					173
P68283 UniProt NPD GO	CRYAA_PEDCA	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.31	-	cyt	0					173
P02485 UniProt NPD GO	CRYAA_TAMME	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.31	-	cyt	0					170
P05811 UniProt NPD GO	CRYAB_MESAU	Alpha crystallin B chain (Alpha(B)-crystallin)	0.31	-	mit	0					175
P41316 UniProt NPD GO	CRYAB_RABIT	Alpha crystallin B chain (Alpha(B)-crystallin)	0.31	-	mit	0					175
Q11130 UniProt NPD GO	FUT7_HUMAN	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.31	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...	Golgi apparatus [TAS] integral to membrane [TAS]	602030		342
P56433 UniProt NPD GO	FUT5_PANTR	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.65) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferas ...	0.31	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				374
Q09326 UniProt NPD GO	MGAT2_RAT	Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.143) (Mannoside ace ...	0.31	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				442
O19054 UniProt NPD GO	ADA2B_PROHA	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.31	-	end	6 *	Membrane; multi-pass membrane protein				389
Q02989 UniProt NPD GO	LITA_LATMA	Alpha-latroinsectotoxin precursor (Alpha-LIT) (Fragment)	0.31	-	cyt	0	Secreted protein				1411
Q8CFA2 UniProt NPD GO	GCST_MOUSE	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.31	+	mit	0	Mitochondrion (By similarity)				403

You are viewing entries 39151 to 39200 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.