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
Q96375 UniProt NPD GO	ABA2_CAPAN	Zeaxanthin epoxidase, chloroplast precursor (EC 1.14.13.90) (Xanthophyll epoxidase) (Beta-cyclohexen ...	0.14	-	mit	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Plastid; chloroplast; chlor ...				660
Q9QZ48 UniProt NPD GO	ZBT7A_RAT	Zinc finger and BTB domain-containing protein 7A (Leukemia/lymphoma-related factor) (Osteoclast-deri ...	0.14	-	cyt	0	Nucleus	nucleus [ISS]			569
P52743 UniProt NPD GO	ZN137_HUMAN	Zinc finger protein 137	0.14	-	nuc	0	Nucleus (Potential)		604079		207
Q9Y6M5 UniProt NPD GO	ZNT1_HUMAN	Zinc transporter 1 (ZnT-1) (Solute carrier family 30 member 1)	0.14	-	end	6 *	Cell membrane; multi-pass membrane protein (Probable)		609521		507
Q4R6K2 UniProt NPD GO	ZNT1_MACFA	Zinc transporter 1 (ZnT-1) (Solute carrier family 30 member 1)	0.14	-	end	6 *	Cell membrane; multi-pass membrane protein (Probable)				505
Q64726 UniProt NPD GO	ZA2G_MOUSE	Zinc-alpha-2-glycoprotein precursor (Zn-alpha-2-glycoprotein) (Zn-alpha-2-GP)	0.14	-	cyt	0	Secreted protein	extracellular region [ISS]			307
P08948 UniProt NPD GO	LITL_PHYSA	[Leu8]-phyllolitorin precursor	0.14	-	exc	0	Secreted protein				90
Q9D0I8 UniProt NPD GO	MRT4_MOUSE	mRNA turnover protein 4 homolog	0.14	-	cyt	0	Nucleus; nucleolus (By similarity)				239
Q8C570 UniProt NPD GO	RAE1L_MOUSE	mRNA-associated protein mrnp 41 (Rae1 protein homolog)	0.14	-	exc	0	Cytoplasm (By similarity). Nucleus (By similarity)				368
Q06063 UniProt NPD GO	DUS4_YEAST	tRNA-dihydrouridine synthase 4 (EC 1.-.-.-)	0.14	-	cyt	0					367
Q6BXN1 UniProt NPD GO	GLGB_DEBHA	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme)	0.13	-	cyt	0					711
O35083 UniProt NPD GO	PLCA_MOUSE	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (EC 2.3.1.51) (1-AGP acyltransferase 1) (1-AGPA ...	0.13	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				285
Q99943 UniProt NPD GO	PLCA_HUMAN	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (EC 2.3.1.51) (1-AGP acyltransferase 1) (1-AGPA ...	0.13	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [TAS]	603099		283
P37821 UniProt NPD GO	1A1C_MALDO	1-aminocyclopropane-1-carboxylate synthase (EC 4.4.1.14) (ACC synthase) (S-adenosyl-L-methionine met ...	0.13	-	mit	0				1M4N	473
Q9FEW9 UniProt NPD GO	OPR3_LYCES	12-oxophytodienoate reductase 3 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 3) (OPDA-reductas ...	0.13	-	cyt	0	Peroxisome				396
P42650 UniProt NPD GO	14333_ENTHI	14-3-3 protein 3 (14-3-3-3) (Fragment)	0.13	-	cyt	0					236
Q8MUA4 UniProt NPD GO	14332_ECHGR	14-3-3 protein homolog 2	0.13	-	cyt	0					248
Q8MM75 UniProt NPD GO	14332_ECHMU	14-3-3 protein homolog 2	0.13	-	cyt	0					248
P29306 UniProt NPD GO	1433X_MAIZE	14-3-3-like protein (Fragment)	0.13	-	nuc	0					61
P42644 UniProt NPD GO	14333_ARATH	14-3-3-like protein GF14 psi (General regulatory factor 3) (14-3-3-like protein RCI1)	0.13	-	cyt	0					255
P69834 UniProt NPD GO	ISPD_ARATH	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplast precursor (EC 2.7.7.60) (4-dip ...	0.13	-	cyt	0	Plastid; chloroplast (Probable)			1W77	302
O04973 UniProt NPD GO	LEU1A_LYCPN	2-isopropylmalate synthase A (EC 2.3.3.13) (Alpha-isopropylmalate synthase A) (Alpha-IPM synthetase ...	0.13	-	nuc	0					589
Q750E9 UniProt NPD GO	RPN11_ASHGO	26S proteasome regulatory subunit RPN11	0.13	-	mit	0					311
Q6FKS1 UniProt NPD GO	RPN11_CANGA	26S proteasome regulatory subunit RPN11	0.13	-	cyt	0					306
P07046 UniProt NPD GO	3SHD_NEUCR	3-dehydroshikimate dehydratase (EC 4.2.1.-) (DHS dehydratase) (DHSase)	0.13	-	exc	0					359
P48020 UniProt NPD GO	HMDH1_SOLTU	3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (EC 1.1.1.34) (HMG-CoA reductase 1) (HMGR1) (HMGR) ...	0.13	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				596
P21775 UniProt NPD GO	THIKA_RAT	3-ketoacyl-CoA thiolase A, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase A) (Acetyl-CoA acy ...	0.13	-	nuc	0	Peroxisome				424
Q59RQ2 UniProt NPD GO	TSC10_CANAL	3-ketodihydrosphingosine reductase TSC10 (EC 1.1.1.102) (3-dehydrosphinganine reductase) (KDS reduct ...	0.13	-	cyt	0	Endoplasmic reticulum (By similarity)				271
P27582 UniProt NPD GO	FABG6_BRANA	3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) (3-ketoacyl-acyl carrier protein reductase ...	0.13	-	nuc	2	Plastid; chloroplast. And non-photosynthetic plastids				201
Q93X67 UniProt NPD GO	FABG2_BRANA	3-oxoacyl-[acyl-carrier-protein] reductase 2, chloroplast precursor (EC 1.1.1.100) (3-ketoacyl-acyl ...	0.13	-	cyt	0	Plastid; chloroplast. Plastid. And non-photosynthetic plastids (By similarity)				328
Q949M2 UniProt NPD GO	FABG4_BRANA	3-oxoacyl-[acyl-carrier-protein] reductase 4 (EC 1.1.1.100) (3-ketoacyl-acyl carrier protein reducta ...	0.13	-	cyt	0	Plastid; chloroplast (By similarity). Plastid (By similarity). And non-photosynthetic plastids (By s ...				254
O00092 UniProt NPD GO	PHYA_ASPFU	3-phytase A precursor (EC 3.1.3.8) (Myo-inositol-hexaphosphate 3-phosphohydrolase A) (3 phytase A) ( ...	0.13	-	exc	0	Secreted protein			1SKB	465
Q99N93 UniProt NPD GO	RM16_MOUSE	39S ribosomal protein L16, mitochondrial precursor (L16mt) (MRP-L16)	0.13	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IDA]			251
P49604 UniProt NPD GO	GATA_USTMA	4-aminobutyrate aminotransferase (EC 2.6.1.19) (Gamma-amino-N-butyrate transaminase) (GABA transamin ...	0.13	-	mit	0					510
P33192 UniProt NPD GO	RS13_CANMA	40S ribosomal protein S13 (S15)	0.13	-	nuc	0					150
P46295 UniProt NPD GO	RS14_CHLRE	40S ribosomal protein S14	0.13	-	cyt	0					153
P62244 UniProt NPD GO	RS15A_HUMAN	40S ribosomal protein S15a	0.13	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	603674		129
P62245 UniProt NPD GO	RS15A_MOUSE	40S ribosomal protein S15a	0.13	-	cyt	0					129
P62246 UniProt NPD GO	RS15A_RAT	40S ribosomal protein S15a	0.13	-	cyt	0					129
P39697 UniProt NPD GO	RT19_ARATH	40S ribosomal protein S19, mitochondrial precursor	0.13	-	cyt	0	Mitochondrion				212
P58234 UniProt NPD GO	RS19A_SCHPO	40S ribosomal protein S19-A (S16-A)	0.13	-	cyt	0					144
Q612Q9 UniProt NPD GO	RS21_CAEBR	40S ribosomal protein S21	0.13	-	nuc	0					88
P49197 UniProt NPD GO	RS21_CAEEL	40S ribosomal protein S21	0.13	-	nuc	0		ribosome [NAS]			88
Q6FMF8 UniProt NPD GO	RS21_CANGA	40S ribosomal protein S21	0.13	-	nuc	0					87
P05765 UniProt NPD GO	RS21_RAT	40S ribosomal protein S21	0.13	-	nuc	0		ribosome [ISS]			83
Q96W54 UniProt NPD GO	RS22_CANAL	40S ribosomal protein S22	0.13	-	cyt	0					129
Q6FMW9 UniProt NPD GO	RS22_CANGA	40S ribosomal protein S22	0.13	-	cyt	0					129
Q7RV75 UniProt NPD GO	RS22_NEUCR	40S ribosomal protein S22	0.13	-	cyt	0					130
O74330 UniProt NPD GO	RS27_SCHPO	40S ribosomal protein S27	0.13	-	cyt	0					83
Q6PS50 UniProt NPD GO	RS28_BOMMO	40S ribosomal protein S28	0.13	-	cyt	0					65

You are viewing entries 59251 to 59300 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.