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
P32891 UniProt NPD GO	DLD1_YEAST	D-lactate dehydrogenase [cytochrome] 1, mitochondrial precursor (EC 1.1.2.4) (D-lactate ferricytochr ...	0.21	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA]			587
Q7FGZ2 UniProt NPD GO	RH1_ARATH	DEAD-box ATP-dependent RNA helicase 1 (EC 3.6.1.-)	0.21	-	cyt	0					512
Q5BN23 UniProt NPD GO	RGA1_BRACM	DELLA protein RGA1 (RGA-like protein 1) (BrRGA1)	0.21	-	cyt	0	Nucleus (By similarity)				573
Q8IUX4 UniProt NPD GO	ABC3F_HUMAN	DNA dC->dU-editing enzyme APOBEC-3F (EC 3.5.4.-) (Apolipoprotein B mRNA-editing enzyme catalytic pol ...	0.21	-	mit	0			608993		373
Q9VB62 UniProt NPD GO	DPOA2_DROME	DNA polymerase subunit alpha B (DNA polymerase alpha 73 kDa subunit)	0.21	-	cyt	0	Nucleus (By similarity)	alpha DNA polymerase:primase complex [ISS] nuclear envelope [ISS] nucleus [ISS]			653
Q9XED7 UniProt NPD GO	R51A2_MAIZE	DNA repair protein RAD51 homolog B (Rad51-like protein B) (RAD51B) (ZmRAD51b)	0.21	-	cyt	0	Nucleus				340
Q27297 UniProt NPD GO	RAD51_DROME	DNA repair protein Rad51 homolog (RecA protein homolog) (Protein spindle-A)	0.21	-	cyt	0	Nucleus (Probable)				336
P36601 UniProt NPD GO	RAD51_SCHPO	DNA repair protein rhp51 (RAD51 homolog)	0.21	-	cyt	0					365
P41138 UniProt NPD GO	ID3_RAT	DNA-binding protein inhibitor ID-3 (Inhibitor of DNA binding 3)	0.21	-	nuc	0	Nucleus				119
P41133 UniProt NPD GO	ID3_MOUSE	DNA-binding protein inhibitor ID-3 (Inhibitor of DNA binding 3) (ID-like protein inhibitor HLH 462)	0.21	-	nuc	0	Nucleus				119
Q9Y2S0 UniProt NPD GO	RPO1D_HUMAN	DNA-directed RNA polymerase I subunit D (EC 2.7.7.6) (DNA-directed RNA polymerase I 16 kDa polypepti ...	0.21	-	nuc	0	Nucleus				133
Q32P73 UniProt NPD GO	RPB9_BOVIN	DNA-directed RNA polymerase II subunit I (EC 2.7.7.6) (DNA-directed RNA polymerase II 14.5 kDa polyp ...	0.21	-	nuc	0	Nucleus (By similarity)				125
P36954 UniProt NPD GO	RPB9_HUMAN	DNA-directed RNA polymerase II subunit I (EC 2.7.7.6) (DNA-directed RNA polymerase II 14.5 kDa polyp ...	0.21	-	nuc	0	Nucleus		180662		125
P60898 UniProt NPD GO	RPB9_MOUSE	DNA-directed RNA polymerase II subunit I (EC 2.7.7.6) (DNA-directed RNA polymerase II 14.5 kDa polyp ...	0.21	-	nuc	0	Nucleus (By similarity)				125
P60899 UniProt NPD GO	RPB9_PIG	DNA-directed RNA polymerase II subunit I (EC 2.7.7.6) (DNA-directed RNA polymerase II 14.5 kDa polyp ...	0.21	-	nuc	0	Nucleus (By similarity)				125
Q8SL92 UniProt NPD GO	RPOA_EUGGA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.21	-	cyt	0	Plastid; chloroplast				216
Q1XDJ5 UniProt NPD GO	RPOA_PORYE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.21	-	cyt	0	Plastid; chloroplast				311
Q6B8R7 UniProt NPD GO	RPOC1_GRATL	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.21	-	cyt	0	Plastid; chloroplast				628
P20436 UniProt NPD GO	RPB8_YEAST	DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide (EC 2.7.7.6) (ABC14.4)	0.21	-	nuc	0	Nucleus	DNA-directed RNA polymerase I complex [TAS] DNA-directed RNA polymerase II, core complex [TAS] DNA-directed RNA polymerase III complex [TAS]		2B8K	146
O13896 UniProt NPD GO	RPC11_SCHPO	DNA-directed RNA polymerases III 12.5 kDa polypeptide (EC 2.7.7.6)	0.21	-	cyt	0	Nucleus (Potential)	DNA-directed RNA polymerase III complex [TAS]			109
Q04307 UniProt NPD GO	RPC11_YEAST	DNA-directed RNA polymerases III 12.5 kDa polypeptide (EC 2.7.7.6)	0.21	-	nuc	0	Nucleus (Potential)	DNA-directed RNA polymerase III complex [IDA]			110
P36108 UniProt NPD GO	DID4_YEAST	DOA4-independent degradation protein 4 (Vacuolar protein sorting-associated protein VPS2)	0.21	-	mit	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein	cytoplasm [IDA] ESCRT III complex [IDA]			151
Q01524 UniProt NPD GO	DEF6_HUMAN	Defensin 6 precursor (Defensin, alpha 6)	0.21	-	exc	0	Secreted protein		600471		100
Q5G860 UniProt NPD GO	DEF6_PANTR	Defensin 6 precursor (Defensin, alpha 6)	0.21	-	exc	0	Secreted protein				100
P31168 UniProt NPD GO	COR47_ARATH	Dehydrin COR47 (Cold-induced COR47 protein)	0.21	-	nuc	0					265
Q27914 UniProt NPD GO	GRA3_TOXGO	Dense granule protein 3 precursor (Protein GRA 3) (P30)	0.21	-	exc	1 *	Located in dense granules of tachyzoites. Upon infection, associates with the parasitophorous vacuol ...				220
Q8K2D6 UniProt NPD GO	DCTD_MOUSE	Deoxycytidylate deaminase (EC 3.5.4.12) (dCMP deaminase)	0.21	-	nuc	0					178
Q5M9G0 UniProt NPD GO	DCTD_RAT	Deoxycytidylate deaminase (EC 3.5.4.12) (dCMP deaminase)	0.21	-	nuc	0					178
Q2QDF0 UniProt NPD GO	DNSL1_PIG	Deoxyribonuclease I-like 1 precursor (EC 3.1.21.-) (DNase I-like 1) (DNase X)	0.21	-	exc	2 *	Endoplasmic reticulum (By similarity)				315
O55111 UniProt NPD GO	DSG2_MOUSE	Desmoglein-2 precursor	0.21	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)	desmosome [IDA]			1122
P23743 UniProt NPD GO	DGKA_HUMAN	Diacylglycerol kinase alpha (EC 2.7.1.107) (Diglyceride kinase alpha) (DGK-alpha) (DAG kinase alpha) ...	0.21	-	cyt	0			125855		735
P12695 UniProt NPD GO	ODP2_YEAST	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochond ...	0.21	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA] pyruvate dehydrogenase complex (sensu Eukar... [TAS]			482
P18962 UniProt NPD GO	DAP2_YEAST	Dipeptidyl aminopeptidase B (EC 3.4.14.-) (DPAP B) (YSCV)	0.21	-	cyt	1 *	Vacuole; vacuolar membrane; single-pass type II membrane protein. Lysosome-like vacuoles	vacuolar membrane (sensu Fungi) [IDA]			818
Q8BVG4 UniProt NPD GO	DPP9_MOUSE	Dipeptidyl peptidase 9 (EC 3.4.14.5) (Dipeptidyl peptidase IX) (DP9) (Dipeptidyl peptidase-like prot ...	0.21	-	cyt	0	Cytoplasm; cytosol (By similarity)				862
P31981 UniProt NPD GO	DISI_CROBA	Disintegrin basilicin (Platelet aggregation activation inhibitor)	0.21	-	nuc	0	Secreted protein				72
P31988 UniProt NPD GO	DISI_BOTCO	Disintegrin cotiarin (Platelet aggregation activation inhibitor)	0.21	-	nuc	0	Secreted protein				72
P56618 UniProt NPD GO	DIUH1_TENMO	Diuretic hormone 1 (Diuretic hormone I) (DH I) (Diuretic peptide I) (DP I) (DH(37)) (DH37)	0.21	-	nuc	0	Secreted protein				37
P59910 UniProt NPD GO	DNJBD_HUMAN	DnaJ homolog subfamily B member 13 (Testis spermatocyte apoptosis-related gene 6 protein) (Testis an ...	0.21	-	cyt	0					316
Q78YY6 UniProt NPD GO	DCJ15_MOUSE	DnaJ homolog subfamily C member 15	0.21	-	nuc	0	Membrane; single-pass membrane protein (Potential)				149
Q922B6 UniProt NPD GO	TRAF7_MOUSE	E3 ubiquitin protein ligase TRAF7 (EC 6.3.2.-) (TNF receptor-associated factor 7)	0.21	-	nuc	0	Cytoplasmic vesicle (By similarity). Colocalizes with MAP3K3 to vesicle-like structures throughout t ...	ubiquitin ligase complex [ISS]			594
P41045 UniProt NPD GO	EFH5_LEITA	EF-hand protein 5 (EFH5)	0.21	-	nuc	0					186
Q5R9Z6 UniProt NPD GO	ELAV2_PONPY	ELAV-like protein 2	0.21	-	nuc	0					359
Q8CH84 UniProt NPD GO	ELAV2_RAT	ELAV-like protein 2 (Hu-antigen B) (HuB)	0.21	-	nuc	0					359
Q12926 UniProt NPD GO	ELAV2_HUMAN	ELAV-like protein 2 (Hu-antigen B) (HuB) (ELAV-like neuronal protein 1) (Nervous system-specific RNA ...	0.21	-	nuc	0			601673		359
P34715 UniProt NPD GO	EF1G_TRYCR	Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma)	0.21	-	cyt	0					411
Q6CPQ9 UniProt NPD GO	EF2_KLULA	Elongation factor 2 (EF-2)	0.21	-	cyt	0	Cytoplasm (By similarity)				842
P20863 UniProt NPD GO	GDF1_MOUSE	Embryonic growth/differentiation factor 1 precursor (GDF-1)	0.21	-	exc	0	Secreted protein				357
Q7M4F4 UniProt NPD GO	CUD1_SCHGR	Endocuticle structural glycoprotein SgAbd-1	0.21	-	nuc	0					184
Q6BTC2 UniProt NPD GO	ERV25_DEBHA	Endoplasmic reticulum vesicle protein 25 precursor	0.21	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				214
Q5ZMC0 UniProt NPD GO	EDF1_CHICK	Endothelial differentiation-related factor 1 homolog (EDF-1)	0.21	-	nuc	0	Nucleus (By similarity)				148

You are viewing entries 49401 to 49450 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.