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
P21788 UniProt NPD GO	SP15_HEMPU	15 kDa calcium-binding protein (CABP)	0.09	-	cyt	0	Nucleus. Spindle. Nuclei of fertilized eggs and mitotic apparatus of dividing eggs				150
Q06397 UniProt NPD GO	CR18_ORYSA	18 kDa cold-induced protein	0.09	-	cyt	0					156
P19243 UniProt NPD GO	HSP11_PEA	18.1 kDa class I heat shock protein (HSP 18.1)	0.09	-	mit	0	Cytoplasm				158
Q8R5M5 UniProt NPD GO	ACMSD_RAT	2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (EC 4.1.1.45)	0.09	-	cyt	0					336
O75600 UniProt NPD GO	KBL_HUMAN	2-amino-3-ketobutyrate coenzyme A ligase, mitochondrial precursor (EC 2.3.1.29) (AKB ligase) (Glycin ...	0.09	-	mit	0	Mitochondrion	mitochondrion [NAS]	607422		419
P17407 UniProt NPD GO	21KD_DAUCA	21 kDa protein precursor (1.2 protein)	0.09	-	exc	1 *					193
Q60HC5 UniProt NPD GO	DHC24_MACFA	24-dehydrocholesterol reductase precursor (EC 1.3.1.-) (3-beta-hydroxysterol delta-24-reductase)	0.09	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity). ...	endoplasmic reticulum [ISS] endoplasmic reticulum membrane [ISS] nucleus [ISS]			516
Q15392 UniProt NPD GO	DHC24_HUMAN	24-dehydrocholesterol reductase precursor (EC 1.3.1.-) (3-beta-hydroxysterol delta-24-reductase) (Se ...	0.09	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Golgi apparatus ...	endoplasmic reticulum [IDA] endoplasmic reticulum membrane [NAS] nucleus [IDA]	606418		516
Q9Y3D5 UniProt NPD GO	RT18C_HUMAN	28S ribosomal protein S18c, mitochondrial precursor (MRP-S18-c) (Mrps18c) (MRP-S18-1)	0.09	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			142
Q5IFP1 UniProt NPD GO	3BHS_CANFA	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase (3Beta-HSD) [Includes: 3-beta-hydroxy-delt ...	0.09	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity). ...				372
Q5R6N3 UniProt NPD GO	HMDH_PONPY	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.09	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				888
P29266 UniProt NPD GO	3HIDH_RAT	3-hydroxyisobutyrate dehydrogenase, mitochondrial precursor (EC 1.1.1.31) (HIBADH)	0.09	-	mit	0	Mitochondrion				335
Q6BNP0 UniProt NPD GO	ERG27_DEBHA	3-keto-steroid reductase (EC 1.1.1.270)	0.09	-	cyt	0					346
Q56WD9 UniProt NPD GO	THIK2_ARATH	3-ketoacyl-CoA thiolase 2, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase 2) (Acetyl-CoA acy ...	0.09	-	cyt	0	Peroxisome. Peroxisomal targeting signal type 2 (PTS2-type) import is temperature and ATP-dependent, ...				462
P33290 UniProt NPD GO	THIKA_CANTR	3-ketoacyl-CoA thiolase A, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase A) (Acetyl-CoA acy ...	0.09	-	nuc	0	Peroxisome				408
P25325 UniProt NPD GO	THTM_HUMAN	3-mercaptopyruvate sulfurtransferase (EC 2.8.1.2) (MST)	0.09	-	cyt	0	Cytoplasm		602496		296
P81440 UniProt NPD GO	PHYB_ASPFI	3-phytase B (EC 3.1.3.8) (Myo-inositol-hexaphosphate 3-phosphohydrolase B) (3 phytase B) (Myo-inosit ...	0.09	-	nuc	0					28
P42756 UniProt NPD GO	RS11_DUNTE	40S ribosomal protein S11	0.09	-	nuc	0					157
P25460 UniProt NPD GO	RS11_MAIZE	40S ribosomal protein S11	0.09	-	nuc	0	Cytoplasm				159
Q9AT34 UniProt NPD GO	RS15A_DAUCA	40S ribosomal protein S15a	0.09	-	cyt	0	Cytoplasm (By similarity)				129
Q90YQ4 UniProt NPD GO	RS19_ICTPU	40S ribosomal protein S19	0.09	-	cyt	0					147
P27073 UniProt NPD GO	RS19_EMENI	40S ribosomal protein S19 (S16)	0.09	-	cyt	0					148
Q9FNP8 UniProt NPD GO	RS193_ARATH	40S ribosomal protein S19-3	0.09	-	cyt	0					143
P51403 UniProt NPD GO	RS2_CAEEL	40S ribosomal protein S2	0.09	-	nuc	0					272
Q3ZBH8 UniProt NPD GO	RS20_BOVIN	40S ribosomal protein S20	0.09	-	nuc	0					119
P60866 UniProt NPD GO	RS20_HUMAN	40S ribosomal protein S20	0.09	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	603682		119
P60867 UniProt NPD GO	RS20_MOUSE	40S ribosomal protein S20	0.09	-	nuc	0					119
P60868 UniProt NPD GO	RS20_RAT	40S ribosomal protein S20	0.09	-	nuc	0					119
P23403 UniProt NPD GO	RS20_XENLA	40S ribosomal protein S20 (S22)	0.09	-	nuc	0					119
Q4GXP2 UniProt NPD GO	RS21_BIPLU	40S ribosomal protein S21	0.09	-	nuc	0					83
Q9P844 UniProt NPD GO	RS21_CANAL	40S ribosomal protein S21	0.09	-	nuc	0					87
Q90YQ2 UniProt NPD GO	RS21_ICTPU	40S ribosomal protein S21	0.09	-	nuc	0					83
Q6AZJ9 UniProt NPD GO	RS21_XENLA	40S ribosomal protein S21	0.09	-	nuc	0					83
Q6DDC6 UniProt NPD GO	RS21_XENTR	40S ribosomal protein S21	0.09	-	nuc	0					83
Q8I7D5 UniProt NPD GO	RS23_CIOIN	40S ribosomal protein S23	0.09	-	nuc	0					143
Q8SR65 UniProt NPD GO	RS23_ENCCU	40S ribosomal protein S23	0.09	-	mit	0					140
Q74ZD8 UniProt NPD GO	RS28_ASHGO	40S ribosomal protein S28	0.09	-	cyt	0					67
P33285 UniProt NPD GO	RS28_KLULA	40S ribosomal protein S28 (S33)	0.09	-	cyt	0					67
P33286 UniProt NPD GO	RS28_KLUMA	40S ribosomal protein S28 (S33)	0.09	-	cyt	0					67
Q10421 UniProt NPD GO	RS28_SCHPO	40S ribosomal protein S28 (S33)	0.09	-	cyt	0					68
Q3E7X9 UniProt NPD GO	RS28A_YEAST	40S ribosomal protein S28-A (S33) (YS27)	0.09	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			67
Q9N3X2 UniProt NPD GO	RS4_CAEEL	40S ribosomal protein S4	0.09	-	mit	0					259
P87158 UniProt NPD GO	RS4A_SCHPO	40S ribosomal protein S4-A	0.09	-	mit	0					262
Q9USW5 UniProt NPD GO	RS4B_SCHPO	40S ribosomal protein S4-B	0.09	-	mit	0					262
Q9P4W9 UniProt NPD GO	RS4C_SCHPO	40S ribosomal protein S4-C	0.09	-	mit	0					262
P80848 UniProt NPD GO	CWP28_ARATH	48 kDa cell wall protein (Fragment)	0.09	-		0	Cell wall				10
O54950 UniProt NPD GO	AAKG1_MOUSE	5'-AMP-activated protein kinase subunit gamma-1 (AMPK gamma-1 chain) (AMPKg)	0.09	-	cyt	0		nucleus [IDA]			330
Q6FU96 UniProt NPD GO	RIB7_CANGA	5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193) (HTP reductase)	0.09	-	nuc	0					244
P33312 UniProt NPD GO	RIB7_YEAST	5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193) (HTP reductase)	0.09	-	cyt	0					244
Q16951 UniProt NPD GO	5HTB2_APLCA	5-hydroxytryptamine 2 receptor (5-HTB2) (Serotonin receptor 2)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				421

You are viewing entries 65501 to 65550 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.