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
Q2HJF4 UniProt NPD GO	MAWBP_BOVIN	Probable isomerase MAWBP (EC 5.1.-.-)	0.02	-	cyt	0					288
O36017 UniProt NPD GO	LIPB_SCHPO	Probable lipoate-protein ligase (EC 6.-.-.-) (Lipoate biosynthesis protein) (Lipoyl ligase)	0.02	-	cyt	0					219
O82399 UniProt NPD GO	MDHG2_ARATH	Probable malate dehydrogenase, glyoxysomal precursor (EC 1.1.1.37)	0.02	-	nuc	0	Glyoxysome (Potential)				354
P07190 UniProt NPD GO	MAL2_DROME	Probable maltase H precursor (EC 3.2.1.20) (Larval visceral protein H)	0.02	-	exc	0					577
P42734 UniProt NPD GO	MTDH_ARATH	Probable mannitol dehydrogenase (EC 1.1.1.255) (NAD-dependent mannitol dehydrogenase)	0.02	-	cyt	0					360
Q43137 UniProt NPD GO	MTDH1_STYHU	Probable mannitol dehydrogenase 1 (EC 1.1.1.255) (NAD-dependent mannitol dehydrogenase 1)	0.02	-	mit	0					354
Q43138 UniProt NPD GO	MTDH3_STYHU	Probable mannitol dehydrogenase 3 (EC 1.1.1.255) (NAD-dependent mannitol dehydrogenase 3)	0.02	-	cyt	0					363
Q6CCY2 UniProt NPD GO	ARX1_YARLI	Probable metalloprotease ARX1 (EC 3.-.-.-) (Associated with ribosomal export complex protein 1)	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				484
Q7QC84 UniProt NPD GO	MMSA_ANOGA	Probable methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (EC 1.2.1.27 ...	0.02	-	cyt	0	Mitochondrion (By similarity)				521
O44477 UniProt NPD GO	TIM17_CAEEL	Probable mitochondrial import inner membrane translocase subunit Tim17	0.02	-	mit	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				181
Q9US30 UniProt NPD GO	RT19_SCHPO	Probable mitochondrial ribosomal protein S19	0.02	-	mit	0	Mitochondrion				108
Q12029 UniProt NPD GO	YO271_YEAST	Probable mitochondrial transport protein YOR271C	0.02	-	end	4	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)	mitochondrion [IDA]			327
Q9VJD2 UniProt NPD GO	MK1I1_DROME	Probable mitogen-activated protein kinase kinase-interacting protein	0.02	-	cyt	0					124
Q9BLM1 UniProt NPD GO	SCXD_ANDAU	Probable neurotoxin pcD-996 precursor	0.02	-	exc	0	Secreted protein (Potential)				72
Q9ZQV7 UniProt NPD GO	NAS2_HORVU	Probable nicotianamine synthase 2 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-a ...	0.02	-	cyt	0					335
Q9ZQV6 UniProt NPD GO	NAS4_HORVU	Probable nicotianamine synthase 4 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-a ...	0.02	-	nuc	0					329
Q9ZQV3 UniProt NPD GO	NAS6_HORVU	Probable nicotianamine synthase 6 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-a ...	0.02	-	nuc	0					328
Q9ZWH8 UniProt NPD GO	NAS7_HORVU	Probable nicotianamine synthase 7 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-a ...	0.02	-	nuc	0					329
O04403 UniProt NPD GO	NLT22_PARJU	Probable nonspecific lipid-transfer protein 2 precursor (LTP 2) (Major pollen allergen Par j 2.0102) ...	0.02	-	exc	0					133
Q18040 UniProt NPD GO	OAT_CAEEL	Probable ornithine aminotransferase, mitochondrial precursor (EC 2.6.1.13) (Ornithine--oxo-acid amin ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				422
Q10494 UniProt NPD GO	YDG7_SCHPO	Probable oxidoreductase C26F1.07 (EC 1.-.-.-)	0.02	-	cyt	0					321
P41510 UniProt NPD GO	PME_BRANA	Probable pectinesterase precursor (EC 3.1.1.11) (Pectin methylesterase) (PE)	0.02	-	vac	1 *					584
O13830 UniProt NPD GO	PTH2_SCHPO	Probable peptidyl-tRNA hydrolase 2 (EC 3.1.1.29) (PTH 2)	0.02	-	nuc	1 *					205
Q9LRS0 UniProt NPD GO	GOX1_ARATH	Probable peroxisomal (S)-2-hydroxy-acid oxidase 1 (EC 1.1.3.15) (Glycolate oxidase 1) (GOX 1) (Short ...	0.02	-	cyt	0	Peroxisome (By similarity)				367
Q09687 UniProt NPD GO	AGM1_SCHPO	Probable phosphoacetylglucosamine mutase 1 (EC 5.4.2.3) (PAGM) (Acetylglucosamine phosphomutase) (N- ...	0.02	-	cyt	0					518
O74374 UniProt NPD GO	PGM_SCHPO	Probable phosphoglucomutase (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.02	-	cyt	0	Cytoplasm (By similarity)				554
P91427 UniProt NPD GO	PGK_CAEEL	Probable phosphoglycerate kinase (EC 2.7.2.3)	0.02	-	cyt	0	Cytoplasm				417
O24031 UniProt NPD GO	GPX4_LYCES	Probable phospholipid hydroperoxide glutathione peroxidase (EC 1.11.1.12) (PHGPx)	0.02	-	cyt	0	Cytoplasm (Potential)				169
Q9LEF0 UniProt NPD GO	GPX4_MESCR	Probable phospholipid hydroperoxide glutathione peroxidase (EC 1.11.1.12) (PHGPx)	0.02	-	cyt	0	Cytoplasm (Potential)				170
O23968 UniProt NPD GO	GPX4_HELAN	Probable phospholipid hydroperoxide glutathione peroxidase (EC 1.11.1.12) (PHGPx) (Glutathione perox ...	0.02	-	cyt	0	Cytoplasm (Potential)				180
Q2N2K1 UniProt NPD GO	PHYK1_SOYBN	Probable phytol kinase 1, chloroplast precursor (EC 2.7.-.-)	0.02	-	end	5	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				302
Q9BAC3 UniProt NPD GO	RRP3_EUGMU	Probable plastid-specific 30S ribosomal protein 3 (PSRP-3)	0.02	-	mit	0	Plastid; chloroplast				101
O78422 UniProt NPD GO	RRP3_GUITH	Probable plastid-specific 30S ribosomal protein 3 (PSRP-3)	0.02	-	cyt	0	Plastid; chloroplast				99
Q8X077 UniProt NPD GO	PSA2_NEUCR	Probable proteasome subunit alpha type 2 (EC 3.4.25.1)	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				249
P38661 UniProt NPD GO	PDIA6_MEDSA	Probable protein disulfide-isomerase A6 precursor (EC 5.3.4.1) (P5)	0.02	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				364
Q8L940 UniProt NPD GO	PDXL3_ARATH	Probable pyridoxin biosynthesis PDX1-like protein 3	0.02	-	cyt	0					309
Q39963 UniProt NPD GO	PDX1_HEVBR	Probable pyridoxin biosynthesis protein ER1 (PDX1 homolog) (Ethylene-inducible protein HEVER)	0.02	-	cyt	0					309
Q9FT25 UniProt NPD GO	PDX1_PHAVU	Probable pyridoxin biosynthesis protein PDX1 (pvPDX1)	0.02	-	cyt	0					312
Q9UU90 UniProt NPD GO	RNP2_SCHPO	Probable ribonuclease P protein subunit 2 (EC 3.1.26.5)	0.02	-	cyt	0	Nucleus (Potential)				139
Q9SJA7 UniProt NPD GO	SOX_ARATH	Probable sarcosine oxidase (EC 1.5.3.1)	0.02	-	cyt	0					416
O14434 UniProt NPD GO	SCYD_ASPFU	Probable scytalone dehydratase (EC 4.2.1.94)	0.02	-	cyt	0					168
O62461 UniProt NPD GO	SELD_CAEEL	Probable selenide, water dikinase (EC 2.7.9.3) (Selenophosphate synthetase) (Selenium donor protein) ...	0.02	-	mit	0					378
Q9N4G9 UniProt NPD GO	RUXG_CAEEL	Probable small nuclear ribonucleoprotein G (snRNP-G) (Sm protein G) (Sm-G) (SmG)	0.02	-	nuc	0	Nucleus (By similarity)				77
P53589 UniProt NPD GO	SUCB2_CAEEL	Probable succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.4) (Succiny ...	0.02	-	nuc	0	Mitochondrion (By similarity)				415
Q6BLV6 UniProt NPD GO	ETR1_DEBHA	Probable trans-2-enoyl-CoA reductase 1, mitochondrial precursor (EC 1.3.1.38)	0.02	-	cyt	0	Mitochondrion (By similarity)				378
Q9W1G0 UniProt NPD GO	TALDO_DROME	Probable transaldolase (EC 2.2.1.2)	0.02	-	cyt	0	Cytoplasm (Probable)				331
Q9M0G4 UniProt NPD GO	TYDC2_ARATH	Probable tyrosine decarboxylase 2 (EC 4.1.1.25)	0.02	-	nuc	0					545
Q94DM8 UniProt NPD GO	UFM1_ORYSA	Probable ubiquitin-fold modifier 1 precursor	0.02	-	cyt	0					102
Q9HE15 UniProt NPD GO	UPP2_SCHPO	Probable uracil phosphoribosyltransferase 2 (EC 2.4.2.9) (UMP pyrophosphorylase 2) (UPRTase 2)	0.02	-	cyt	0					220
Q40144 UniProt NPD GO	XTH1_LYCES	Probable xyloglucan endotransglucosylase/hydrolase 1 precursor (EC 2.4.1.207) (LeXTH1)	0.02	-	end	1 *	Secreted protein; extracellular space; apoplast (Probable)				296

You are viewing entries 85201 to 85250 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.