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
P24742 UniProt NPD GO	CXHA_MATBI	Cytotoxin homolog maticotoxin A (Fragment)	0.00	-	cyt	0	Secreted protein				41
Q99489 UniProt NPD GO	OXDD_HUMAN	D-aspartate oxidase (EC 1.4.3.1) (DASOX) (DDO)	0.00	-	nuc	0	Peroxisome		124450		341
Q6CRI9 UniProt NPD GO	DTD_KLULA	D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-)	0.00	-	cyt	0	Cytoplasm (By similarity)				150
P22144 UniProt NPD GO	XYL2_PICST	D-xylulose reductase (EC 1.1.1.9) (Xylitol dehydrogenase) (XDH)	0.00	-	mit	0					363
P60486 UniProt NPD GO	DAZP2_RAT	DAZ-associated protein 2 (Deleted in azoospermia-associated protein 2)	0.00	-	cyt	0					108
P84798 UniProt NPD GO	DPOD3_BOVIN	DNA polymerase subunit delta 3 (DNA polymerase subunit delta p66) (p68) (Fragments)	0.00	-	cyt	0	Nucleus	nucleus [IC]			71
Q6FWE1 UniProt NPD GO	RAD59_CANGA	DNA repair protein RAD59	0.00	-	cyt	0	Nucleus (By similarity)				212
P87123 UniProt NPD GO	RPB11_SCHPO	DNA-directed RNA polymerase II 14.1 kDa polypeptide (EC 2.7.7.6)	0.00	-	cyt	0	Nucleus (By similarity)	DNA-directed RNA polymerase II, core complex [IDA]			123
O14459 UniProt NPD GO	RPB7_SCHPO	DNA-directed RNA polymerase II 19 kDa polypeptide (EC 2.7.7.6)	0.00	-	cyt	0	Nucleus	DNA-directed RNA polymerase II, holoenzyme [IC]			172
P38421 UniProt NPD GO	RPB7_ARATH	DNA-directed RNA polymerase II 19 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 5)	0.00	-	mit	0	Nucleus				176
P46279 UniProt NPD GO	RPB7_SOYBN	DNA-directed RNA polymerase II 19 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 5)	0.00	-	cyt	0	Nucleus				176
P35718 UniProt NPD GO	RPC25_YEAST	DNA-directed RNA polymerase III 25 kDa polypeptide (EC 2.7.7.6) (C25)	0.00	-	cyt	0	Nucleus (Potential)	DNA-directed RNA polymerase III complex [TAS]			212
Q923G2 UniProt NPD GO	RPB8_MOUSE	DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide (EC 2.7.7.6) (RPB17) (RPB8)	0.00	-	cyt	0	Nucleus; nucleolus (By similarity)				149
P52434 UniProt NPD GO	RPB8_HUMAN	DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide (EC 2.7.7.6) (RPB17) (RPB8) (RPABC3 ...	0.00	-	cyt	0	Nucleus; nucleolus	nucleus [TAS]	606023	2F3I	149
P84273 UniProt NPD GO	DAH11_LITDA	Dahlein-1.1	0.00	-		0	Secreted protein	extracellular region [IDA]			13
P84263 UniProt NPD GO	DAH12_LITDA	Dahlein-1.2	0.00	-		0	Secreted protein	extracellular region [IDA]			13
P84264 UniProt NPD GO	DAH41_LITDA	Dahlein-4.1	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			23
P84265 UniProt NPD GO	DAH42_LITDA	Dahlein-4.2	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			23
P84266 UniProt NPD GO	DAH43_LITDA	Dahlein-4.3	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			23
P84267 UniProt NPD GO	DAH51_LITDA	Dahlein-5.1	0.00	-		0	Secreted protein	extracellular region [IDA]			20
P84268 UniProt NPD GO	DAH52_LITDA	Dahlein-5.2	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			21
P84270 UniProt NPD GO	DAH54_LITDA	Dahlein-5.4	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			21
Q9SME9 UniProt NPD GO	DAD1_HORVU	Defender against cell death 1 (DAD-1)	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				114
O50070 UniProt NPD GO	DAD1_ORYSA	Defender against cell death 1 (DAD-1) (Defender against apoptotic death 1 protein)	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				114
O81214 UniProt NPD GO	DAD1_MAIZE	Defender against cell death 1 (DAD-1) (Fragment)	0.00	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				79
Q9SME8 UniProt NPD GO	DAD2_HORVU	Defender against cell death 2 (DAD-2)	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				114
O22622 UniProt NPD GO	DAD2_ARATH	Defender against cell death 2 (DAD-2) (AtDAD2)	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				115
Q9LDR4 UniProt NPD GO	ERG24_ARATH	Delta(14)-sterol reductase (EC 1.3.1.70) (C-14 sterol reductase) (Sterol C14-reductase) (Protein FAC ...	0.00	-	end	9 *	Membrane; multi-pass membrane protein (Probable)				369
O74212 UniProt NPD GO	FAD5_MORAP	Delta-5 fatty acid desaturase (EC 1.14.19.-)	0.00	-	nuc	4	Membrane; multi-pass membrane protein (Potential)				446
Q9ZT29 UniProt NPD GO	SC5D_TOBAC	Delta-7-sterol-C5(6)-desaturase (EC 1.3.3.-) (Delta-7-C-5 sterol desaturase) (Delta7-sterol-C5-desat ...	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				271
Q39208 UniProt NPD GO	SC5D1_ARATH	Delta-7-sterol-C5(6)-desaturase 1 (EC 1.3.3.-) (Delta-7-C-5 sterol desaturase 1) (Delta7-sterol-C5-d ...	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				281
P69748 UniProt NPD GO	CXD6A_CONAI	Delta-conotoxin AVIA (Delta-AVIA)	0.00	-	cyt	0	Secreted protein (By similarity)				27
P60179 UniProt NPD GO	CXD66_CONAA	Delta-conotoxin Am 2766	0.00	-	nuc	0	Secreted protein			1YZ2	26
P69751 UniProt NPD GO	CXD6E_CONCT	Delta-conotoxin CVIE (Delta-CVIE)	0.00	-	cyt	0	Secreted protein (By similarity)				27
P69750 UniProt NPD GO	CXD6A_CONCN	Delta-conotoxin CnVIA (Delta-CnVIA)	0.00	-	mit	1 *	Secreted protein (By similarity)				31
P69752 UniProt NPD GO	CXD6B_CONER	Delta-conotoxin EVIB (Delta-EVIB) (Delta-EVIA)	0.00	-	cyt	0	Secreted protein (By similarity)				29
P69753 UniProt NPD GO	CXD6A_CONMA	Delta-conotoxin MVIA (Delta-MVIA)	0.00	-	cyt	0	Secreted protein (By similarity)				32
P69754 UniProt NPD GO	CXD6B_CONMA	Delta-conotoxin MVIB (Delta-MVIB)	0.00	-	cyt	1 *	Secreted protein (By similarity)				32
P69755 UniProt NPD GO	CXD6C_CONMA	Delta-conotoxin MVIC (Delta-MVIC)	0.00	-	cyt	0	Secreted protein (By similarity)				32
P69756 UniProt NPD GO	CXD6D_CONMA	Delta-conotoxin MVID (Delta-MVID)	0.00	-	cyt	1 *	Secreted protein (By similarity)				32
P56710 UniProt NPD GO	CXD6_CONNI	Delta-conotoxin NgVIA	0.00	-	cyt	0	Secreted protein				31
Q9XZK5 UniProt NPD GO	CXSO6_CONST	Delta-conotoxin SVIE precursor (Delta-SVIE) (Conotoxin SO6) (Conotoxin 4)	0.00	-	exc	1 *	Secreted protein				82
P69757 UniProt NPD GO	CXD6A_CONSE	Delta-conotoxin SmVIA (Delta-SmVIA)	0.00	-	cyt	0	Secreted protein (By similarity)				31
Q6FRN2 UniProt NPD GO	DHYS_CANGA	Deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.00	-	cyt	0					385
P49366 UniProt NPD GO	DHYS_HUMAN	Deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.00	-	cyt	0			600944	1RQD	369
P49365 UniProt NPD GO	DHYS_NEUCR	Deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.00	-	cyt	0					353
Q6CG56 UniProt NPD GO	DHYS_YARLI	Deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.00	-	cyt	0					346
P38791 UniProt NPD GO	DHYS_YEAST	Deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.00	-	cyt	0		cytoplasm [IDA]			387
Q74ZF0 UniProt NPD GO	DUT_ASHGO	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphatase)	0.00	-	cyt	0					153
P32518 UniProt NPD GO	DUT_LYCES	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphatase) (P18 ...	0.00	-	cyt	0					169

You are viewing entries 94251 to 94300 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.