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
Q8CFJ9 UniProt NPD GO	WDR24_MOUSE	WD repeat protein 24	0.30	-	mit	0					790
Q6PE01 UniProt NPD GO	WDR57_MOUSE	WD repeat protein 57	0.30	-	cyt	0	Nucleus (By similarity)				358
P53962 UniProt NPD GO	YND5_YEAST	WD repeat protein YNL035C	0.30	-	nuc	0		nucleus [IDA]			389
Q08924 UniProt NPD GO	YP183_YEAST	WD repeat protein YPL183C	0.30	-	cyt	0	Cytoplasm	cytoplasm [IDA]			1013
Q9M3D6 UniProt NPD GO	WBC19_ARATH	White-brown complex homolog protein 19	0.30	-	end	7	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuolar lumen [IDA]			725
P06679 UniProt NPD GO	ZEAW_MAIZE	Zein-alpha 22C2 precursor (22 kDa zein 22C2) (Fragment)	0.30	-	exc	0					261
P24449 UniProt NPD GO	ZEAC_MAIZE	Zein-alpha PMS1 precursor (19 kDa zein PMS1)	0.30	-	exc	0					235
O93567 UniProt NPD GO	ZBTB7_CHICK	Zinc finger and BTB domain-containing protein 7 (Leukemia/lymphoma-related factor) (cLRF)	0.30	-	nuc	0	Nucleus (By similarity)				546
P17019 UniProt NPD GO	ZN708_HUMAN	Zinc finger protein 708 (Zinc finger protein 15-like 1) (Zinc finger protein KOX8)	0.30	-	nuc	0	Nucleus (Potential)				563
O62243 UniProt NPD GO	NAS1_CAEEL	Zinc metalloproteinase nas-1 precursor (EC 3.4.24.21) (Nematode astacin 1)	0.30	-	vac	0	Secreted protein (Potential)				270
Q21178 UniProt NPD GO	NAS17_CAEEL	Zinc metalloproteinase nas-17 precursor (EC 3.4.24.21) (Nematode astacin 17)	0.30	-	exc	0	Secreted protein (Potential)				429
Q5TJF6 UniProt NPD GO	KE4_CANFA	Zinc transporter SLC39A7 (Solute carrier family 39 member 7) (Histidine-rich membrane protein Ke4)	0.30	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				469
P23491 UniProt NPD GO	ZP3_MESAU	Zona pellucida sperm-binding protein 3 precursor (Zona pellucida glycoprotein ZP3) (Sperm receptor) ...	0.30	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				422
Q15119 UniProt NPD GO	PDK2_HUMAN	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (EC 2.7.11.2) (Pyruva ...	0.30	-	cyt	0	Mitochondrion; mitochondrial matrix		602525	2BU8	407
Q9C196 UniProt NPD GO	KAPR_ASPNG	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.30	-	cyt	0					411
P14619 UniProt NPD GO	KGP1B_HUMAN	cGMP-dependent protein kinase 1, beta isozyme (EC 2.7.11.12) (cGK 1 beta) (cGKI-beta)	0.30	-	cyt	0			176894		686
Q9P905 UniProt NPD GO	PALC_EMENI	pH-response regulator protein palC	0.30	-	mit	0					507
Q39760 UniProt NPD GO	DCS2_GOSAR	(+)-delta-cadinene synthase isozyme XC14 (EC 4.2.3.13) (D-cadinene synthase)	0.29	-	cyt	0					554
P42648 UniProt NPD GO	14331_ENTHI	14-3-3 protein 1 (14-3-3-1)	0.29	-	cyt	0					239
P93208 UniProt NPD GO	14332_LYCES	14-3-3 protein 2	0.29	-	nuc	0					254
Q6UFZ9 UniProt NPD GO	143B1_ONCMY	14-3-3 protein beta/alpha-1 (Protein 14-3-3B1)	0.29	-	nuc	0	Cytoplasm (By similarity)				244
Q5ZKC9 UniProt NPD GO	1433Z_CHICK	14-3-3 protein zeta	0.29	-	nuc	0	Cytoplasm (By similarity)				245
Q5R651 UniProt NPD GO	1433Z_PONPY	14-3-3 protein zeta/delta	0.29	-	nuc	0	Cytoplasm (By similarity)				245
P63104 UniProt NPD GO	1433Z_HUMAN	14-3-3 protein zeta/delta (Protein kinase C inhibitor protein 1) (KCIP-1)	0.29	-	nuc	0	Cytoplasm		601288	2C1N	245
P63103 UniProt NPD GO	1433Z_BOVIN	14-3-3 protein zeta/delta (Protein kinase C inhibitor protein 1) (KCIP-1) (Factor activating exoenzy ...	0.29	-	nuc	0	Cytoplasm			1A4O	245
P63102 UniProt NPD GO	1433Z_RAT	14-3-3 protein zeta/delta (Protein kinase C inhibitor protein 1) (KCIP-1) (Mitochondrial import stim ...	0.29	-	nuc	0	Cytoplasm				245
P63101 UniProt NPD GO	1433Z_MOUSE	14-3-3 protein zeta/delta (Protein kinase C inhibitor protein 1) (KCIP-1) (SEZ-2)	0.29	-	nuc	0	Cytoplasm	mitochondrion [IDA] nucleus [IDA]			245
P48348 UniProt NPD GO	14338_ARATH	14-3-3-like protein GF14 kappa (General regulatory factor 8)	0.29	-	cyt	0					248
O00233 UniProt NPD GO	PSD9_HUMAN	26S proteasome non-ATPase regulatory subunit 9 (26S proteasome regulatory subunit p27)	0.29	-	nuc	0		proteasome regulatory particle (sensu Eukar... [NAS]	603146		223
Q5U3F8 UniProt NPD GO	3HAO_BRARE	3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) (3-HAO) (3-hydroxyanthranilic acid dioxygenase) ...	0.29	-	cyt	0	Cytoplasm (By similarity)				287
Q03201 UniProt NPD GO	RT10_YEAST	30S ribosomal protein S10, mitochondrial precursor (Mitochondrial ribosomal small subunit protein 10 ...	0.29	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			203
Q99N89 UniProt NPD GO	RM43_MOUSE	39S ribosomal protein L43, mitochondrial precursor (L43mt) (MRP-L43) (Mitochondrial ribosomal protei ...	0.29	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IDA]			183
Q756Q5 UniProt NPD GO	MRP10_ASHGO	40S ribosomal protein MRP10, mitochondrial precursor (Mitochondrial ribosomal protein 10)	0.29	-	nuc	0	Mitochondrion (By similarity)				95
Q9WVH0 UniProt NPD GO	RS13_CRIGR	40S ribosomal protein S13	0.29	-	nuc	0					150
Q9DFR6 UniProt NPD GO	RS13_GILMI	40S ribosomal protein S13	0.29	-	nuc	0					150
P42036 UniProt NPD GO	RS143_ARATH	40S ribosomal protein S14-3	0.29	-	cyt	0	Cytoplasm				150
P16149 UniProt NPD GO	RS16_LUPPO	40S ribosomal protein S16	0.29	-	nuc	0	Cytoplasm				145
P46294 UniProt NPD GO	RS16_ORYSA	40S ribosomal protein S16	0.29	-	mit	0	Cytoplasm				149
Q8ITC3 UniProt NPD GO	RS19_AEQIR	40S ribosomal protein S19	0.29	-	nuc	0					144
Q9W6X9 UniProt NPD GO	RS24_ORYLA	40S ribosomal protein S24	0.29	-	mit	0					132
P69061 UniProt NPD GO	RS27A_KLULA	40S ribosomal protein S27a	0.29	+	nuc	0					74
O43999 UniProt NPD GO	RS3A_EIMTE	40S ribosomal protein S3a (EtS3a)	0.29	+	nuc	0					263
Q98998 UniProt NPD GO	5HT1A_XENLA	5-hydroxytryptamine 1A receptor (5-HT-1A) (Serotonin receptor 1A) (5-HT1A) (X5-HT1A)	0.29	-	end	7 *	Membrane; multi-pass membrane protein				408
P79748 UniProt NPD GO	5HT1D_FUGRU	5-hydroxytryptamine 1D receptor (5-HT-1D) (Serotonin receptor 1D) (5HT1D) (F1D)	0.29	-	end	7 *	Membrane; multi-pass membrane protein				379
P31387 UniProt NPD GO	5HT5B_MOUSE	5-hydroxytryptamine 5B receptor (5-HT-5B) (Serotonin receptor 5B)	0.29	-	end	7	Membrane; multi-pass membrane protein				370
P50406 UniProt NPD GO	5HT6R_HUMAN	5-hydroxytryptamine 6 receptor (5-HT-6) (Serotonin receptor 6)	0.29	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601109		440
O22795 UniProt NPD GO	RK28_ARATH	50S ribosomal protein L28, chloroplast precursor	0.29	-	mit	0	Plastid; chloroplast	plastid ribosome [NAS]			143
P22685 UniProt NPD GO	RLA0_DICDI	60S acidic ribosomal protein P0	0.29	-	nuc	0					305
Q967Y7 UniProt NPD GO	RLA0_EIMTE	60S acidic ribosomal protein P0	0.29	-	mit	0					314
O96647 UniProt NPD GO	RL10_BOMMA	60S ribosomal protein L10 (QM protein homolog)	0.29	-	mit	0					219

You are viewing entries 40901 to 40950 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.