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
P51104 UniProt NPD GO	DFRA_DIACA	Dihydroflavonol-4-reductase (EC 1.1.1.219) (DFR) (Dihydrokaempferol 4-reductase)	0.01	-	nuc	0					360
P51105 UniProt NPD GO	DFRA_GERHY	Dihydroflavonol-4-reductase (EC 1.1.1.219) (DFR) (Dihydrokaempferol 4-reductase)	0.01	-	mit	1 *					366
P51106 UniProt NPD GO	DFRA_HORVU	Dihydroflavonol-4-reductase (EC 1.1.1.219) (DFR) (Dihydrokaempferol 4-reductase)	0.01	-	cyt	0					354
P51110 UniProt NPD GO	DFRA_VITVI	Dihydroflavonol-4-reductase (EC 1.1.1.219) (DFR) (Dihydrokaempferol 4-reductase)	0.01	-	nuc	0					337
P00378 UniProt NPD GO	DYR_CHICK	Dihydrofolate reductase (EC 1.5.1.3)	0.01	-	cyt	0				8DFR	189
P84545 UniProt NPD GO	DLDH_POPEU	Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase) (Fragment)	0.01	-		0					11
P80503 UniProt NPD GO	DLDH_SOLTU	Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase) (Fragment)	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix				40
O08749 UniProt NPD GO	DLDH_MOUSE	Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			509
P11179 UniProt NPD GO	ODO2_BOVIN	Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex (E ...	0.01	-		0	Mitochondrion				16
Q9SF23 UniProt NPD GO	FOLB1_ARATH	Dihydroneopterin aldolase (EC 4.1.2.25) (DHNA)	0.01	-	cyt	0				1SQL	146
P20051 UniProt NPD GO	PYRC_YEAST	Dihydroorotase (EC 3.5.2.3) (DHOase)	0.01	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			364
P09417 UniProt NPD GO	DHPR_HUMAN	Dihydropteridine reductase (EC 1.5.1.34) (HDHPR) (Quinoid dihydropteridine reductase)	0.01	-	cyt	0			261630	1HDR	244
Q9EQF6 UniProt NPD GO	DPYL5_MOUSE	Dihydropyrimidinase-related protein 5 (DRP-5) (Collapsin response mediator protein 5) (CRMP-5)	0.01	-	cyt	0	Cytoplasm (Potential)	cell soma [IDA] cytoplasm [IPI] dendrite [IDA]			564
Q9JHU0 UniProt NPD GO	DPYL5_RAT	Dihydropyrimidinase-related protein 5 (DRP-5) (ULIP6 protein)	0.01	-	cyt	0	Cytoplasm (Potential)	protein complex [IDA]			564
Q9BPU6 UniProt NPD GO	DPYL5_HUMAN	Dihydropyrimidinase-related protein 5 (DRP-5) (ULIP6 protein) (Collapsin response mediator protein 5 ...	0.01	-	cyt	0	Cytoplasm (Potential)		608383		564
Q4KLZ6 UniProt NPD GO	DAK_RAT	Dihydroxyacetone kinase (EC 2.7.1.29) (Glycerone kinase) (DHA kinase)	0.01	-	mit	0					578
P16549 UniProt NPD GO	FMO1_PIG	Dimethylaniline monooxygenase [N-oxide-forming] 1 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.01	-	nuc	0	Microsome				531
P17636 UniProt NPD GO	FMO1_RABIT	Dimethylaniline monooxygenase [N-oxide-forming] 1 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.01	-	end	0	Microsome				534
Q8HYJ9 UniProt NPD GO	FMO3_BOVIN	Dimethylaniline monooxygenase [N-oxide-forming] 3 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.01	-	nuc	0	Microsome (By similarity)				532
P32417 UniProt NPD GO	FMO3_RABIT	Dimethylaniline monooxygenase [N-oxide-forming] 3 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.01	-	nuc	1	Microsome				530
Q3ZCJ8 UniProt NPD GO	CATC_BOVIN	Dipeptidyl-peptidase 1 precursor (EC 3.4.14.1) (Dipeptidyl-peptidase I) (DPP-I) (DPPI) (Cathepsin C) ...	0.01	-	exc	0	Lysosome (By similarity)				463
P53634 UniProt NPD GO	CATC_HUMAN	Dipeptidyl-peptidase 1 precursor (EC 3.4.14.1) (Dipeptidyl-peptidase I) (DPP-I) (DPPI) (Cathepsin C) ...	0.01	-	exc	0	Lysosome	lysosome [TAS]	170650	1K3B	463
P97821 UniProt NPD GO	CATC_MOUSE	Dipeptidyl-peptidase 1 precursor (EC 3.4.14.1) (Dipeptidyl-peptidase I) (DPP-I) (DPPI) (Cathepsin C) ...	0.01	-	exc	0	Lysosome				462
P80067 UniProt NPD GO	CATC_RAT	Dipeptidyl-peptidase 1 precursor (EC 3.4.14.1) (Dipeptidyl-peptidase I) (DPP-I) (DPPI) (Cathepsin C) ...	0.01	-	exc	0	Lysosome	lysosome [TAS]		1JQP	462
Q74Z32 UniProt NPD GO	DPH3_ASHGO	Diphthamide biosynthesis protein 3	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				82
Q6BTW5 UniProt NPD GO	DPH3_DEBHA	Diphthamide biosynthesis protein 3	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				71
P0C0V4 UniProt NPD GO	DPH3_EMENI	Diphthamide biosynthesis protein 3	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				83
Q8STR6 UniProt NPD GO	DPH3_ENCCU	Diphthamide biosynthesis protein 3	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				93
Q6CMG4 UniProt NPD GO	DPH3_KLULA	Diphthamide biosynthesis protein 3	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				82
Q9UT33 UniProt NPD GO	DPH3_SCHPO	Diphthamide biosynthesis protein 3	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				79
Q6C0G3 UniProt NPD GO	DPH3_YARLI	Diphthamide biosynthesis protein 3	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				69
Q6C6T1 UniProt NPD GO	DPH4_YARLI	Diphthamide biosynthesis protein 4	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				163
Q6FXK9 UniProt NPD GO	DPH5_CANGA	Diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.01	-	cyt	0	Cytoplasm (By similarity)				298
Q5BFG0 UniProt NPD GO	DPH5_EMENI	Diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.01	-	cyt	0	Cytoplasm (By similarity)				285
P02886 UniProt NPD GO	DISA_DICDI	Discoidin I, A chain	0.01	-	mit	0	Cytoplasm				253
P42530 UniProt NPD GO	DIS2_DICDI	Discoidin-2 (Discoidin II)	0.01	-	cyt	0					257
Q29381 UniProt NPD GO	OST48_PIG	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit (EC 2.4.1.119) (Oligos ...	0.01	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				103
P48440 UniProt NPD GO	OST48_CHICK	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit (EC 2.4.1.119) (Oligos ...	0.01	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (Potentia ...				413
P80896 UniProt NPD GO	OST1_CHICK	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 65-I kDa subunit (EC 2.4.1.119) (Olig ...	0.01	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (Potentia ...				28
Q5E9C2 UniProt NPD GO	DAD1_BOVIN	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 (EC 2.4.1.119) (Oligosac ...	0.01	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				112
Q29036 UniProt NPD GO	DAD1_PIG	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 (EC 2.4.1.119) (Oligosac ...	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				112
Q5RBB4 UniProt NPD GO	DAD1_PONPY	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 (EC 2.4.1.119) (Oligosac ...	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				112
Q39080 UniProt NPD GO	DAD1_ARATH	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 (EC 2.4.1.119) (Oligosac ...	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				115
Q86YN1 UniProt NPD GO	DOPP1_HUMAN	Dolichyldiphosphatase 1 (EC 3.6.1.43) (Dolichyl pyrophosphate phosphatase 1)	0.01	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	integral to endoplasmic reticulum membrane [ISS]			238
P0C1M6 UniProt NPD GO	MASTA_POLDO	Dominulin-A	0.01	-		0	Secreted protein				17
P0C1M7 UniProt NPD GO	MASTB_POLDO	Dominulin-B	0.01	-		0	Secreted protein				17
Q9GLX0 UniProt NPD GO	DUFFY_BOVIN	Duffy antigen/chemokine receptor (CD234 antigen)	0.01	-	end	7	Membrane; multi-pass membrane protein				330
P82079 UniProt NPD GO	DYS1_LIMIN	Dynastin-1	0.01	-		0	Secreted protein				8
P82080 UniProt NPD GO	DYS2_LIMDU	Dynastin-2	0.01	-		0	Secreted protein				10
P82081 UniProt NPD GO	DYS3_LIMTE	Dynastin-3	0.01	-		0	Secreted protein				12

You are viewing entries 88101 to 88150 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.