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
Q9BV57 UniProt NPD GO	MTND_HUMAN	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase (EC 1.13.-.-) (Aci-reductone dioxygenase) (ARD) ...	0.12	-	cyt	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Nucleus	cytoplasm [IDA] nucleus [IDA] plasma membrane [IDA]			179
Q8H185 UniProt NPD GO	ARD4_ARATH	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 4 (EC 1.13.-.-) (Aci-reductone dioxygenase 4)	0.12	-	cyt	0					187
Q9P8U3 UniProt NPD GO	GEL3_ASPFU	1,3-beta-glucanosyltransferase gel3 precursor (EC 2.4.1.-) (Glucan elongating glucanosyltransferase ...	0.12	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)				552
Q9Y8H3 UniProt NPD GO	GLGB_EMENI	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme)	0.12	-	cyt	0					686
O15120 UniProt NPD GO	PLCB_HUMAN	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (EC 2.3.1.51) (1-AGP acyltransferase 2) (1-AGPAT ...	0.12	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [ISS]	608594		278
P31238 UniProt NPD GO	ACCO1_DORSP	1-aminocyclopropane-1-carboxylate oxidase 1 (EC 1.14.17.4) (ACC oxidase 1) (Ethylene-forming enzyme) ...	0.12	-	cyt	0					327
Q39705 UniProt NPD GO	ACCO2_DORSP	1-aminocyclopropane-1-carboxylate oxidase 2 (EC 1.14.17.4) (ACC oxidase 2) (Ethylene-forming enzyme) ...	0.12	-	cyt	0					325
P10967 UniProt NPD GO	ACCO3_LYCES	1-aminocyclopropane-1-carboxylate oxidase homolog (Protein E8)	0.12	-	cyt	0					363
P83004 UniProt NPD GO	13SB_FAGES	13S globulin basic chain	0.12	-	cyt	0					194
Q6UFZ8 UniProt NPD GO	143B2_ONCMY	14-3-3 protein beta/alpha-2 (Protein 14-3-3B2)	0.12	-	nuc	0	Cytoplasm (By similarity)				244
P06208 UniProt NPD GO	LEU1_YEAST	2-isopropylmalate synthase (EC 2.3.3.13) (Alpha-isopropylmalate synthase) (Alpha-IPM synthetase)	0.12	-	cyt	0	Mitochondrion. Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]			619
Q01939 UniProt NPD GO	PRS8_YEAST	26S protease regulatory subunit 8 homolog (SUG1 protein) (Protein CIM3) (TAT-binding protein TBY1)	0.12	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	nucleus [IDA] proteasome regulatory particle, base subcom... [IDA]			404
Q9LT08 UniProt NPD GO	PSDE_ARATH	26S proteasome non-ATPase regulatory subunit 14 (26S proteasome regulatory subunit rpn11)	0.12	-	cyt	0		nucleus [TAS]			308
Q08937 UniProt NPD GO	ROC2_NICSY	29 kDa ribonucleoprotein B, chloroplast precursor (CP29B)	0.12	-	mit	0	Plastid; chloroplast				291
Q9Y7D2 UniProt NPD GO	HMDH_ASPTE	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.12	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				1068
Q12577 UniProt NPD GO	HMDH_GIBFU	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.12	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				976
Q6P7I0 UniProt NPD GO	3HAO_XENLA	3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) (3-HAO) (3-hydroxyanthranilic acid dioxygenase) ...	0.12	-	cyt	0	Cytoplasm (By similarity)				282
O59930 UniProt NPD GO	LEU3_PHACH	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.12	-	mit	0	Cytoplasm				380
P51196 UniProt NPD GO	FABH_PORPU	3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.41) (3-oxoacyl-[acyl-carrier-protein] synthase ...	0.12	-	end	0	Plastid; chloroplast				326
P19684 UniProt NPD GO	ROC5_NICSY	33 kDa ribonucleoprotein, chloroplast precursor	0.12	-	mit	0	Plastid; chloroplast				324
Q68EV6 UniProt NPD GO	RM28_XENLA	39S ribosomal protein L28, mitochondrial precursor (L28mt) (MRP-L28)	0.12	-	cyt	0	Mitochondrion (By similarity)				253
P23248 UniProt NPD GO	RS3B_YEAST	40S ribosomal protein S1-B (RP10B)	0.12	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			254
P27069 UniProt NPD GO	RS14_KLULA	40S ribosomal protein S14 (RP59)	0.12	-	cyt	0					137
P39516 UniProt NPD GO	RS14B_YEAST	40S ribosomal protein S14-B (RP59B)	0.12	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS] small nucleolar ribonucleoprotein complex [IPI]			137
P51429 UniProt NPD GO	RS15_NAEGR	40S ribosomal protein S15 (Fragment)	0.12	-	nuc	0					120
P48149 UniProt NPD GO	RS15A_DROME	40S ribosomal protein S15Aa	0.12	-	cyt	0					129
Q7KR04 UniProt NPD GO	RS15B_DROME	40S ribosomal protein S15Ab	0.12	-	cyt	0					129
Q6XIM8 UniProt NPD GO	RS15A_DROYA	40S ribosomal protein S15a	0.12	-	cyt	0					129
P79016 UniProt NPD GO	RS19B_SCHPO	40S ribosomal protein S19-B (S16-B)	0.12	-	cyt	0					143
Q6CXT6 UniProt NPD GO	RS21_KLULA	40S ribosomal protein S21	0.12	-	nuc	0					87
O93798 UniProt NPD GO	RS21_NEUCR	40S ribosomal protein S21 (CRP7)	0.12	-	nuc	0					87
P46792 UniProt NPD GO	RS22_AGABI	40S ribosomal protein S22 (Ribosomal protein S15a)	0.12	-	mit	0					130
P0C0W1 UniProt NPD GO	RS22A_YEAST	40S ribosomal protein S22-A (S24) (YS22) (RP50) (YP58)	0.12	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]		1S1H	129
P79009 UniProt NPD GO	RS25A_SCHPO	40S ribosomal protein S25-A (S31-A)	0.12	-	nuc	0					89
O74172 UniProt NPD GO	RS25B_SCHPO	40S ribosomal protein S25-B (S31-B)	0.12	-	nuc	0					88
P35997 UniProt NPD GO	RS27A_YEAST	40S ribosomal protein S27-A (YS20) (RP61)	0.12	-	nuc	0		cytoplasm [IDA] cytosolic small ribosomal subunit (sensu Eu... [TAS]			82
P38711 UniProt NPD GO	RS27B_YEAST	40S ribosomal protein S27-B (YS20) (RP61)	0.12	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			82
Q6FLC3 UniProt NPD GO	RS28_CANGA	40S ribosomal protein S28	0.12	-	cyt	0					67
O61590 UniProt NPD GO	RS28_OSTOS	40S ribosomal protein S28	0.12	-	nuc	0					66
Q6PAM0 UniProt NPD GO	AAKB2_MOUSE	5'-AMP-activated protein kinase subunit beta-2 (AMPK beta-2 chain)	0.12	-	nuc	0					271
Q9YHT4 UniProt NPD GO	HEM0_BRARE	5-aminolevulinate synthase, erythroid-specific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevuli ...	0.12	-	cyt	0	Mitochondrion; mitochondrial matrix				583
Q09189 UniProt NPD GO	AZR1_SCHPO	5-azacytidine resistance protein azr1	0.12	+	mit	0					288
Q75Z89 UniProt NPD GO	5HT2A_BOVIN	5-hydroxytryptamine 2A receptor (5-HT-2A) (Serotonin receptor 2A) (5-HT-2)	0.12	-	end	7	Cell membrane; multi-pass membrane protein. Localizes to the post-synaptic thickening of axo-dendrit ...				470
Q8K010 UniProt NPD GO	OPLA_MOUSE	5-oxoprolinase (EC 3.5.2.9) (5-oxo-L-prolinase) (Pyroglutamase) (5-OPase)	0.12	-	cyt	0					1288
Q9MAP3 UniProt NPD GO	RK11_ARATH	50S ribosomal protein L11, chloroplast precursor (CL11)	0.12	-	mit	0	Plastid; chloroplast (Probable)	cytosolic ribosome (sensu Eukaryota) [IDA]			222
P59680 UniProt NPD GO	K6PF1_YARLI	6-phosphofructokinase subunit alpha (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (6PF-1 ...	0.12	-	cyt	0	Cytoplasm (By similarity)				953
P28256 UniProt NPD GO	CH60_GALSU	60 kDa chaperonin (Protein Cpn60) (groEL protein)	0.12	-	nuc	0	Plastid; chloroplast				534
Q6B911 UniProt NPD GO	CH60_GRATL	60 kDa chaperonin (Protein Cpn60) (groEL protein)	0.12	-	nuc	0	Plastid; chloroplast				528
O88202 UniProt NPD GO	LPP60_RAT	60 kDa lysophospholipase (EC 3.1.1.5) [Includes: L-asparaginase (EC 3.5.1.1) (L-asparagine amidohydr ...	0.12	-	cyt	0					564
P35979 UniProt NPD GO	RL12_MOUSE	60S ribosomal protein L12	0.12	-	nuc	0		cytoplasm [IDA] nucleolus [IDA] nucleus [IDA]		1WIB	165

You are viewing entries 60701 to 60750 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.