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
Q93714 UniProt NPD GO	IDH3A_CAEEL	Probable isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor (EC 1.1.1.41) (Isocit ...	0.00	-	cyt	0	Mitochondrion (By similarity)				358
P93257 UniProt NPD GO	MTDH_MESCR	Probable mannitol dehydrogenase (EC 1.1.1.255) (NAD-dependent mannitol dehydrogenase)	0.00	-	cyt	0					361
P34660 UniProt NPD GO	TOM7_CAEEL	Probable mitochondrial import receptor subunit TOM7 homolog (Translocase of outer membrane 7 kDa sub ...	0.00	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				58
Q9SR59 UniProt NPD GO	MDAR1_ARATH	Probable monodehydroascorbate reductase, cytoplasmic isoform 1 (EC 1.6.5.4) (MDAR 1)	0.00	-	cyt	0	Cytoplasm (Potential)	cytosol [IDA]			441
Q93WJ8 UniProt NPD GO	MDAR4_ARATH	Probable monodehydroascorbate reductase, cytoplasmic isoform 4 (EC 1.6.5.4) (MDAR 4)	0.00	-	cyt	0	Cytoplasm (Potential)				435
Q9BLM2 UniProt NPD GO	SCXE_ANDAU	Probable neurotoxin pcD-1008 precursor	0.00	-	exc	0	Secreted protein (Potential)				72
P26912 UniProt NPD GO	NLTP_PINPI	Probable nonspecific lipid-transfer protein (LTP) (Basic protein) (PBP) (Fragment)	0.00	-	cyt	0					36
Q9P7L5 UniProt NPD GO	OAT_SCHPO	Probable ornithine aminotransferase (EC 2.6.1.13) (Ornithine--oxo-acid aminotransferase)	0.00	-	cyt	0	Cytoplasm (By similarity)				438
Q6IR37 UniProt NPD GO	ZDH24_MOUSE	Probable palmitoyltransferase ZDHHC24 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 24) ( ...	0.00	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				284
Q2TGI5 UniProt NPD GO	ZDH24_RAT	Probable palmitoyltransferase ZDHHC24 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 24) ( ...	0.00	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				284
P52573 UniProt NPD GO	REHY_ORYSA	Probable peroxiredoxin (EC 1.11.1.15) (Thioredoxin peroxidase) (RAB24 protein)	0.00	-	cyt	0					220
Q09770 UniProt NPD GO	AGM2_SCHPO	Probable phosphoacetylglucosamine mutase 2 (EC 5.4.2.3) (PAGM) (Acetylglucosamine phosphomutase) (N- ...	0.00	-	cyt	0					542
Q06652 UniProt NPD GO	GPX4_CITSI	Probable phospholipid hydroperoxide glutathione peroxidase (EC 1.11.1.12) (PHGPx) (Salt-associated p ...	0.00	-	nuc	0	Cytoplasm (Potential)				167
Q9VAN0 UniProt NPD GO	SERC_DROME	Probable phosphoserine aminotransferase (EC 2.6.1.52) (PSAT)	0.00	-	cyt	0					364
P83647 UniProt NPD GO	PROFX_ORYSA	Probable profilin LP04 (Fragments)	0.00	-		0					13
Q9Y7T8 UniProt NPD GO	PSB3_SCHPO	Probable proteasome subunit beta type 3 (EC 3.4.25.1)	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS]			204
Q09841 UniProt NPD GO	PSB7_SCHPO	Probable proteasome subunit beta type 7 precursor (EC 3.4.25.1)	0.00	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				267
Q9C2D4 UniProt NPD GO	SC61G_NEUCR	Probable protein transport protein SEC61 subunit gamma	0.00	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				70
P42865 UniProt NPD GO	QOR_LEIAM	Probable quinone oxidoreductase (EC 1.6.5.5) (NADPH:quinone reductase) (P36)	0.00	-	cyt	0					340
Q5BJI9 UniProt NPD GO	SPCS2_BRARE	Probable signal peptidase complex subunit 2 (EC 3.4.-.-) (Microsomal signal peptidase 25 kDa subunit ...	0.00	-	end	2	Membrane; multi-pass membrane protein (Potential)				201
Q9VCA9 UniProt NPD GO	SPCS3_DROME	Probable signal peptidase complex subunit 3 (EC 3.4.-.-) (Microsomal signal peptidase 22 kDa subunit ...	0.00	-	mit	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (Potential)				179
P34659 UniProt NPD GO	RUXF_CAEEL	Probable small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF)	0.00	-	cyt	0	Nucleus (By similarity)				85
O74966 UniProt NPD GO	RUXG_SCHPO	Probable small nuclear ribonucleoprotein G (snRNP-G) (Sm protein G) (Sm-G) (SmG)	0.00	-	cyt	0	Nucleus (Potential)				77
Q85AI0 UniProt NPD GO	CYST_ANTFO	Probable sulfate transport system permease protein cysT	0.00	-	end	7 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Probable)				288
P56343 UniProt NPD GO	CYST_CHLVU	Probable sulfate transport system permease protein cysT	0.00	-	end	6 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Probable)				266
Q5Z6B1 UniProt NPD GO	SEN2_ORYSA	Probable tRNA-splicing endonuclease subunit Sen2 (EC 3.1.27.9) (tRNA-intron endonuclease Sen2)	0.00	-	cyt	1	Nucleus (By similarity)				293
Q6C6X6 UniProt NPD GO	TPMT_YARLI	Probable thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.00	-	cyt	0	Cytoplasm (By similarity)				213
Q17424 UniProt NPD GO	THIO2_CAEEL	Probable thioredoxin-2	0.00	-	cyt	0					119
Q61IU9 UniProt NPD GO	TPPC3_CAEBR	Probable trafficking protein particle complex subunit 3	0.00	-	nuc	0	Golgi apparatus; cis-Golgi network (By similarity)				181
Q9CA23 UniProt NPD GO	UFM1_ARATH	Probable ubiquitin-fold modifier 1 precursor	0.00	-	cyt	0					93
O14046 UniProt NPD GO	VATO_SCHPO	Probable vacuolar ATP synthase 20 kDa proteolipid subunit (EC 3.6.3.14)	0.00	-	end	5 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				199
Q9FKL9 UniProt NPD GO	XTH12_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 12 precursor (EC 2.4.1.207) (At-XTH12) (X ...	0.00	-	vac	1 *	Secreted protein; extracellular space; apoplast (Probable)	cell wall [IDA] cytoplasm [IDA]			285
Q8S3W4 UniProt NPD GO	ZIP8_ARATH	Probable zinc transporter 8 precursor (ZRT/IRT-like protein 8)	0.00	-	end	8 *	Cell membrane; multi-pass membrane protein (Potential)				347
Q68HB4 UniProt NPD GO	PROF_BOMMO	Profilin	0.00	-	cyt	0					126
Q9FUB8 UniProt NPD GO	PROF_BRANA	Profilin	0.00	-	cyt	0					134
Q6QNF8 UniProt NPD GO	PROF_NAEGR	Profilin	0.00	-	cyt	0					132
Q9XF38 UniProt NPD GO	PROF_PYRCO	Profilin (Allergen Pyr c 4) (Pyr c 3)	0.00	-	cyt	0					131
Q9XF37 UniProt NPD GO	PROF_APIGR	Profilin (Minor pollen allergen Api g 4)	0.00	-	cyt	0					134
Q8SAE6 UniProt NPD GO	PROF_DAUCA	Profilin (Minor pollen allergen Dau c 4)	0.00	-	cyt	0					134
Q5FX67 UniProt NPD GO	PROF_CUCME	Profilin (Pollen allergen Cuc m 2)	0.00	-	cyt	0					131
Q9SNW7 UniProt NPD GO	PROF1_LILLO	Profilin-1	0.00	-	cyt	0					131
Q9XF40 UniProt NPD GO	PROF1_MALDO	Profilin-1 (GD4-1) (Pollen allergen Mal d 4.0301)	0.00	-	cyt	0					131
O65809 UniProt NPD GO	PROF1_SOYBN	Profilin-1 (GmPRO1) (Allergen Gly m 3.0101)	0.00	-	cyt	0					131
O24169 UniProt NPD GO	PROF1_OLEEU	Profilin-1 (Pollen allergen Ole e 2)	0.00	-	cyt	0					134
Q9XG85 UniProt NPD GO	PROF1_PARJU	Profilin-1 (Pollen allergen Par j 3.0101)	0.00	-	cyt	0					132
P26199 UniProt NPD GO	PROF1_DICDI	Profilin-1 (Profilin I)	0.00	-	cyt	0					126
P68696 UniProt NPD GO	PRO1A_ACACA	Profilin-1A (Profilin IA) (Acidic profilin IA)	0.00	-	cyt	0				1PRQ	125
Q95VF7 UniProt NPD GO	PRO1B_ACACA	Profilin-1B (Profilin IB) (Acidic profilin IB)	0.00	-	cyt	0				1ACF	125
O24170 UniProt NPD GO	PROF2_OLEEU	Profilin-2 (Pollen allergen Ole e 2)	0.00	-	cyt	0					134
Q9T0M8 UniProt NPD GO	PROF2_PARJU	Profilin-2 (Pollen allergen Par j 3.0102)	0.00	-	cyt	0					131

You are viewing entries 97201 to 97250 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.