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
P92990 UniProt NPD GO	JP650_ARATH	Probable polygalacturonase non-catalytic subunit JP650 precursor (Aromatic-rich glycoprotein JP650)	0.26	+	mit	1 *	Secreted protein; extracellular space; apoplast (By similarity). Cell wall (By similarity). Associat ...				626
Q9UTC9 UniProt NPD GO	PFD2_SCHPO	Probable prefoldin subunit 2	0.26	-	nuc	0					114
O74524 UniProt NPD GO	PROD_SCHPO	Probable proline oxidase, mitochondrial precursor (EC 1.5.3.-) (Proline dehydrogenase)	0.26	-	mit	0					492
Q10236 UniProt NPD GO	RNHL_SCHPO	Probable ribonuclease HI large subunit (EC 3.1.26.4) (RNase HI large subunit) (RNase H(35))	0.26	-	nuc	0					326
Q10305 UniProt NPD GO	GDI1_SCHPO	Probable secretory pathway GDP dissociation inhibitor 1	0.26	-	nuc	0					440
P27450 UniProt NPD GO	CX32_ARATH	Probable serine/threonine-protein kinase Cx32, chloroplast precursor (EC 2.7.11.1)	0.26	-	nuc	0	Plastid; chloroplast (Potential)				419
O74377 UniProt NPD GO	SULH_SCHPO	Probable sulfate permease C3H7.02	0.26	-	end	11	Membrane; multi-pass membrane protein (Potential)				877
O74948 UniProt NPD GO	T2AG_SCHPO	Probable transcription initiation factor IIA small chain	0.26	-	mit	0	Nucleus (By similarity)				107
Q9P3K8 UniProt NPD GO	MCH1_NEUCR	Probable transporter MCH1	0.26	-	end	12	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				598
Q9P4X4 UniProt NPD GO	SEC17_SCHPO	Probable vesicular-fusion protein sec17 homolog	0.26	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				289
P24802 UniProt NPD GO	PLOD1_CHICK	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 precursor (EC 1.14.11.4) (Lysyl hydroxylase 1) (LH ...	0.26	-	cyt	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...				730
Q8UW82 UniProt NPD GO	GON3_VERMO	Progonadoliberin-3 precursor (Progonadoliberin III) (Salmon-type gonadotropin-releasing hormone) (sG ...	0.26	-	exc	1 *	Secreted protein	extracellular region [ISS]			90
Q8SPN1 UniProt NPD GO	PKR2_BOVIN	Prokineticin receptor 2 (PK-R2) (G-protein coupled receptor 73-like 1) (G-protein coupled receptor I ...	0.26	+	end	7	Membrane; multi-pass membrane protein				384
P06879 UniProt NPD GO	PRL_MOUSE	Prolactin precursor (PRL)	0.26	-	exc	0	Secreted protein				226
Q91513 UniProt NPD GO	PRLR_ORENI	Prolactin receptor precursor (PRL-R)	0.26	-	end	1	Membrane; single-pass type I membrane protein				630
Q4EW11 UniProt NPD GO	PRLHR_BOVIN	Prolactin-releasing peptide receptor (PrRP receptor) (PrRPR) (G-protein coupled receptor 10)	0.26	-	end	7	Membrane; multi-pass membrane protein				370
Q6VMN6 UniProt NPD GO	PRLHR_MOUSE	Prolactin-releasing peptide receptor (PrRP receptor) (PrRPR) (G-protein coupled receptor 10)	0.26	-	end	7	Membrane; multi-pass membrane protein				370
Q64121 UniProt NPD GO	PRLHR_RAT	Prolactin-releasing peptide receptor (PrRP receptor) (PrRPR) (G-protein coupled receptor 10) (UHR-1) ...	0.26	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [IPI]			370
P19085 UniProt NPD GO	PRO4_ORYSA	Prolamin PPROL precursor (Prolamin PPROL 4A) (Prolamin PPROL 7) (Prolamin PPROL 14)	0.26	-	vac	0	In rice prolamin accumulates as type I protein body, which originates directly from the endoplasmic ...				150
Q9UQ80 UniProt NPD GO	PA2G4_HUMAN	Proliferation-associated protein 2G4 (Cell cycle protein p38-2G4 homolog) (hG4-1) (ErbB3-binding pro ...	0.26	-	cyt	0	Cytoplasm. Nucleus; nucleolus. Tranlocates to the nucleus upon treatment with HRG	nucleus [IDA]	602145		393
Q5ZLK5 UniProt NPD GO	P4HA2_CHICK	Prolyl 4-hydroxylase alpha-2 subunit precursor (EC 1.14.11.2) (4-PH alpha-2) (Procollagen-proline,2- ...	0.26	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				534
O82261 UniProt NPD GO	DEGP2_ARATH	Protease Do-like 2, chloroplast precursor (EC 3.4.21.-)	0.26	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; stromal side	thylakoid membrane (sensu Viridiplantae) [IDA]			607
Q06323 UniProt NPD GO	PSME1_HUMAN	Proteasome activator complex subunit 1 (Proteasome activator 28-alpha subunit) (PA28alpha) (PA28a) ( ...	0.26	-	cyt	0		cytoplasm [TAS] proteasome complex (sensu Eukaryota) [TAS]	600654	1AVO	249
Q95K48 UniProt NPD GO	POTE1_MACFA	Protection of telomeres 1 (POT1-like telomere end-binding protein)	0.26	-	cyt	0	Nucleus (By similarity). Colocalizes with telomeric DNA (By similarity)				634
Q9NUX5 UniProt NPD GO	POTE1_HUMAN	Protection of telomeres 1 (hPot1) (POT1-like telomere end-binding protein)	0.26	-	nuc	0	Nucleus. Colocalizes with telomeric DNA		606478	1XJV	634
Q3U128 UniProt NPD GO	APCD1_MOUSE	Protein APCDD1 precursor (Adenomatosis polyposis coli down-regulated 1 protein homolog)	0.26	-	mit	1 *	Membrane; single-pass type I membrane protein (Potential)				514
Q9CRC6 UniProt NPD GO	CJ032_MOUSE	Protein C10orf32 homolog	0.26	-	nuc	0					105
Q9BRX8 UniProt NPD GO	CJ058_HUMAN	Protein C10orf58 precursor	0.26	-	cyt	1 *	Secreted protein (Potential)				229
Q9CQE8 UniProt NPD GO	CN166_MOUSE	Protein C14orf166 homolog	0.26	-	mit	0	Or: Nucleus (By similarity). Or: Cytoplasm; perinuclear region (By similarity). May localize at the ...				244
Q9BGL9 UniProt NPD GO	CF015_MACMU	Protein C6orf15 homolog precursor (rmSTG)	0.26	-	exc	0	Secreted protein (Potential)				314
Q9BRR3 UniProt NPD GO	CI125_HUMAN	Protein C9orf125	0.26	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				403
Q5R868 UniProt NPD GO	CI125_PONPY	Protein C9orf125 homolog	0.26	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				403
P53829 UniProt NPD GO	CAF40_YEAST	Protein CAF40 (40 kDa CCR4-associated factor)	0.26	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)	CCR4-NOT complex [IPI]			373
Q9H1Q7 UniProt NPD GO	F113A_HUMAN	Protein FAM113A (Sarcoma antigen NY-SAR-23)	0.26	-	cyt	0					454
Q7Z5A7 UniProt NPD GO	F19A5_HUMAN	Protein FAM19A5 precursor (Chemokine-like protein TAFA-5)	0.26	-	mit	1 *	Secreted protein				125
Q91WE9 UniProt NPD GO	F19A5_MOUSE	Protein FAM19A5 precursor (Chemokine-like protein TAFA-5)	0.26	-	mit	1 *	Secreted protein (By similarity)				125
Q68FB1 UniProt NPD GO	FA44B_XENTR	Protein FAM44B	0.26	-	nuc	0					169
Q8TCH9 UniProt NPD GO	YV04_HUMAN	Protein FLJ23865	0.26	-	nuc	0					128
Q07928 UniProt NPD GO	GAT3_YEAST	Protein GAT3	0.26	-	nuc	0					141
Q3SZ31 UniProt NPD GO	HS020_BOVIN	Protein HSPC020 homolog	0.26	-	nuc	0					121
Q6FX62 UniProt NPD GO	PBN1_CANGA	Protein PBN1	0.26	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				416
O42825 UniProt NPD GO	RHO1_CANAL	Protein RHO1	0.26	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				198
P38163 UniProt NPD GO	SNI2_YEAST	Protein SNI2 (Suppressor of RHO3 protein 77)	0.26	-	mit	0		plasma membrane [IPI]			1010
P38869 UniProt NPD GO	SVP26_YEAST	Protein SVP26 (Sed5 compartment vesicle protein of 26 kDa)	0.26	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein. Early Golgi	endoplasmic reticulum [IDA] integral to Golgi membrane [IDA]			228
P32626 UniProt NPD GO	UTR4_YEAST	Protein UTR4 (Unknown transcript 4 protein)	0.26	-	nuc	0		cytoplasm [IDA] nucleus [IDA]		2G80	241
O96014 UniProt NPD GO	WNT11_HUMAN	Protein Wnt-11 precursor	0.26	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix		603699		354
Q2QLC7 UniProt NPD GO	WNT2_CARPS	Protein Wnt-2 precursor	0.26	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
Q2QLH2 UniProt NPD GO	WNT2_OTOGA	Protein Wnt-2 precursor	0.26	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
P28110 UniProt NPD GO	WNT7A_CHECA	Protein Wnt-7a (Fragment)	0.26	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P28129 UniProt NPD GO	WNT7A_MELGA	Protein Wnt-7a (Fragment)	0.26	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123

You are viewing entries 44551 to 44600 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.