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
Q71SS4 UniProt NPD GO	DERL1_BOVIN	Derlin-1 (Degradation in endoplasmic reticulum protein 1) (Der1-like protein 1)	0.00	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				251
Q5R9W3 UniProt NPD GO	DERL1_PONPY	Derlin-1 (Degradation in endoplasmic reticulum protein 1) (Der1-like protein 1)	0.00	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				251
Q9BUN8 UniProt NPD GO	DERL1_HUMAN	Derlin-1 (Degradation in endoplasmic reticulum protein 1) (Der1-like protein 1) (DERtrin-1)	0.00	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA] integral to endoplasmic reticulum membrane [IDA]	608813		251
Q5RC74 UniProt NPD GO	DERL2_PONPY	Derlin-2 (Degradation in endoplasmic reticulum protein 2) (Der1-like protein 2)	0.00	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	integral to endoplasmic reticulum membrane [ISS]			239
Q9GZP9 UniProt NPD GO	DERL2_HUMAN	Derlin-2 (Degradation in endoplasmic reticulum protein 2) (Der1-like protein 2) (DERtrin-2) (F-LANa) ...	0.00	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA] integral to endoplasmic reticulum membrane [IDA]			239
P83638 UniProt NPD GO	DDSK_PHYDS	Dermadistinctin-K (DD K)	0.00	-	cyt	0	Secreted protein				33
P83642 UniProt NPD GO	DDQ2_PHYDS	Dermadistinctin-Q2 (DD Q2)	0.00	-	cyt	0	Secreted protein				25
P80281 UniProt NPD GO	DMS5_PHYSA	Dermaseptin-5 (DS V)	0.00	-	cyt	0	Secreted protein				29
P81487 UniProt NPD GO	DMS5_PHYBI	Dermaseptin-B5 (Dermaseptin-BV)	0.00	-	cyt	0	Secreted protein				26
P83914 UniProt NPD GO	DLP_SCHMA	Dermaseptin-like peptide (SmDLP)	0.00	-	cyt	0					27
Q7LZ48 UniProt NPD GO	TKN1_TORMA	Des[Ser(1)Pro(2)] scyliorhinin-2 (Des[Ser(1)Pro(2)] scyliorhinin II)	0.00	-		0	Secreted protein				16
P22241 UniProt NPD GO	DRPD_CRAPL	Desiccation-related protein PCC27-45	0.00	-	cyt	0					151
P23170 UniProt NPD GO	25KD_SARPE	Development-specific 25 kDa protein	0.00	-	cyt	0					258
Q9Y295 UniProt NPD GO	DRG1_HUMAN	Developmentally-regulated GTP-binding protein 1 (DRG 1)	0.00	-	mit	0	Cytoplasm		603952		367
P32233 UniProt NPD GO	DRG1_MOUSE	Developmentally-regulated GTP-binding protein 1 (DRG 1) (Protein NEDD3) (Neural precursor cell expre ...	0.00	-	cyt	0	Cytoplasm				367
P43690 UniProt NPD GO	DRG1_XENLA	Developmentally-regulated GTP-binding protein 1 (DRG 1) (xDRG)	0.00	-	mit	0	Cytoplasm				367
Q7PCJ9 UniProt NPD GO	SAT2_PIG	Diamine acetyltransferase 2 (EC 2.3.1.57) (Spermidine/spermine N(1)-acetyltransferase 2) (Polyamine ...	0.00	-	cyt	0	Intracellular organelles (By similarity)				170
P0C007 UniProt NPD GO	CYNT_HALAU	Dicynthaurin	0.00	-	nuc	0	Secreted protein				30
P24847 UniProt NPD GO	DAPA2_WHEAT	Dihydrodipicolinate synthase 2, chloroplast precursor (EC 4.2.1.52) (DHDPS 2)	0.00	-	mit	0	Plastid; chloroplast				377
Q42800 UniProt NPD GO	DAPA_SOYBN	Dihydrodipicolinate synthase, chloroplast precursor (EC 4.2.1.52) (DHDPS)	0.00	-	cyt	0	Plastid; chloroplast				332
O18480 UniProt NPD GO	DLDH_MANSE	Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase) (E3)	0.00	-	mit	0	Cytoplasm (Potential)				497
P49819 UniProt NPD GO	DLDH_CANFA	Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase)	0.00	-	mit	0	Mitochondrion; mitochondrial matrix				509
Q60HG3 UniProt NPD GO	DLDH_MACFA	Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase)	0.00	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				509
P09623 UniProt NPD GO	DLDH_PIG	Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase)	0.00	-	mit	0	Mitochondrion; mitochondrial matrix				509
P09622 UniProt NPD GO	DLDH_HUMAN	Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase) ( ...	0.00	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	238331	2F5Z	509
P11180 UniProt NPD GO	ODP2_BOVIN	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1. ...	0.00	-		0	Mitochondrion; mitochondrial matrix				10
Q6V3X0 UniProt NPD GO	PYRD_SACCA	Dihydroorotate dehydrogenase (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (DHODase) (DHOD)	0.00	-	cyt	0	Cytoplasm (By similarity)				314
Q7Z891 UniProt NPD GO	PYRD_SACPA	Dihydroorotate dehydrogenase (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (DHODase) (DHOD)	0.00	-	cyt	0	Cytoplasm (By similarity)				314
P28272 UniProt NPD GO	PYRD_YEAST	Dihydroorotate dehydrogenase (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (DHODase) (DHOD)	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA] extrinsic to membrane [IDA]			314
Q95LA2 UniProt NPD GO	FMO1_CANFA	Dimethylaniline monooxygenase [N-oxide-forming] 1 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.00	-	nuc	1	Microsome				531
P49328 UniProt NPD GO	FMO1_CAVPO	Dimethylaniline monooxygenase [N-oxide-forming] 1 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.00	-		0	Microsome				19
Q60HG6 UniProt NPD GO	CATC_MACFA	Dipeptidyl-peptidase 1 precursor (EC 3.4.14.1) (Dipeptidyl-peptidase I) (DPP-I) (DPPI) (Cathepsin C) ...	0.00	-	end	0	Lysosome (By similarity)				463
O97578 UniProt NPD GO	CATC_CANFA	Dipeptidyl-peptidase 1 precursor (EC 3.4.14.1) (Dipeptidyl-peptidase I) (DPP-I) (DPPI) (Cathepsin C) ...	0.00	-	cyt	0	Lysosome (By similarity)				435
P83681 UniProt NPD GO	DPP3_BLACR	Dipeptidyl-peptidase 3 (EC 3.4.14.4) (Dipeptidyl-peptidase III) (DPP III) (Dipeptidyl aminopeptidase ...	0.00	-	cyt	0	Membrane; multi-pass membrane protein				73
Q6MY91 UniProt NPD GO	DPH5_ASPFU	Diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.00	-	cyt	0	Cytoplasm (By similarity)				285
P18684 UniProt NPD GO	DIPD_PROTE	Diptericin-D precursor	0.00	-	exc	0					101
P27047 UniProt NPD GO	DRR4_PEA	Disease resistance response protein DRRG49-C	0.00	-	cyt	0					158
P13239 UniProt NPD GO	DRR1_PEA	Disease resistance response protein Pi176	0.00	-	cyt	0					159
P14710 UniProt NPD GO	DRR3_PEA	Disease resistance response protein Pi49 (PR10)	0.00	-	cyt	0					158
P81999 UniProt NPD GO	DNJBB_CANFA	DnaJ homolog subfamily B member 11 (Fragments)	0.00	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen				48
P82539 UniProt NPD GO	DNJC1_CANFA	DnaJ homolog subfamily C member 1 (DnaJ protein homolog MTJ1) (Fragment)	0.00	-		0	Nucleus; nuclear membrane; multi-pass membrane protein. Microsome; microsomal membrane; multi-pass m ...				20
Q9Z1P1 UniProt NPD GO	DPM2_CRIGR	Dolichol phosphate-mannose biosynthesis regulatory protein	0.00	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				83
Q9Z324 UniProt NPD GO	DPM2_MOUSE	Dolichol phosphate-mannose biosynthesis regulatory protein	0.00	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				83
Q9Z325 UniProt NPD GO	DPM2_RAT	Dolichol phosphate-mannose biosynthesis regulatory protein	0.00	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IPI] microsome [IMP]			83
O94633 UniProt NPD GO	DPM3_SCHPO	Dolichol-phosphate mannosyltransferase subunit 3 (Dolichol-phosphate mannose synthase subunit 3) (Do ...	0.00	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [IGI]			90
Q9P2X0 UniProt NPD GO	DPM3_HUMAN	Dolichol-phosphate mannosyltransferase subunit 3 (Dolichol-phosphate mannose synthase subunit 3) (Do ...	0.00	-	vac	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [TAS] mannosyltransferase complex [TAS]	605951		92
P53730 UniProt NPD GO	ALG12_YEAST	Dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl-alpha-1,6-mannosyltransferase (EC 2.4.1.-) (Mannosyltrans ...	0.00	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			551
Q24319 UniProt NPD GO	OST48_DROME	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit precursor (EC 2.4.1.11 ...	0.00	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (Potentia ...				449
P80897 UniProt NPD GO	OST2_CHICK	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 65-II kDa subunit (EC 2.4.1.119) (Oli ...	0.00	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (Potentia ...				36
O13113 UniProt NPD GO	DAD1_CHICK	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 (EC 2.4.1.119) (Oligosac ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				123

You are viewing entries 94301 to 94350 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.