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
Q99133 UniProt NPD GO	RAD51_USTMA	DNA repair protein RAD51	0.11	-	cyt	0					339
P25454 UniProt NPD GO	RAD51_YEAST	DNA repair protein RAD51	0.11	-	cyt	0		condensed nuclear chromosome [IDA]		1SZP	400
P41134 UniProt NPD GO	ID1_HUMAN	DNA-binding protein inhibitor ID-1 (Inhibitor of DNA binding 1)	0.11	-	nuc	0	Nucleus	nucleus [IC]	600349		155
Q8SQU1 UniProt NPD GO	RPB9_ENCCU	DNA-directed RNA polymerase II subunit 9 (EC 2.7.7.6)	0.11	-	nuc	0	Nucleus (By similarity)				108
Q9MUV0 UniProt NPD GO	RPOA_MESVI	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.11	-	cyt	0	Plastid; chloroplast				316
O65740 UniProt NPD GO	DEF2_CAPAN	Defensin J1-2 precursor	0.11	-	vac	1 *	Secreted protein				74
Q99LB2 UniProt NPD GO	DHRS4_MOUSE	Dehydrogenase/reductase SDR family member 4 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase/NADP- ...	0.11	-	mit	0	Peroxisome (By similarity)	mitochondrion [IDA]			260
Q92629 UniProt NPD GO	SGCD_HUMAN	Delta-sarcoglycan (SG-delta) (35 kDa dystrophin-associated glycoprotein) (35DAG)	0.11	-	mit	1 *	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein	plasma membrane [TAS] sarcoglycan complex [TAS]	606685		290
Q5RFG0 UniProt NPD GO	ECH1_PONPY	Delta3,5-delta2,4-dienoyl-CoA isomerase, mitochondrial precursor (EC 5.3.3.-)	0.11	-	pox	0	Mitochondrion (By similarity). Peroxisome (By similarity)				328
O00115 UniProt NPD GO	DNS2A_HUMAN	Deoxyribonuclease-2-alpha precursor (EC 3.1.22.1) (Deoxyribonuclease II alpha) (DNase II alpha) (Aci ...	0.11	-	exc	0	Lysosome	lysosome [TAS]	126350		360
P53630 UniProt NPD GO	BIOD_YEAST	Dethiobiotin synthetase (EC 6.3.3.3) (Dethiobiotin synthase) (DTB synthetase) (DTBS)	0.11	-	cyt	0				1M3T	237
Q9LZX6 UniProt NPD GO	DAPA1_ARATH	Dihydrodipicolinate synthase 1, chloroplast precursor (EC 4.2.1.52) (DHDPS 1)	0.11	-	mit	0	Plastid; chloroplast				365
P28019 UniProt NPD GO	DYR_AEDAL	Dihydrofolate reductase (EC 1.5.1.3)	0.11	-	cyt	0					186
P09624 UniProt NPD GO	DLDH_YEAST	Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase) ( ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix	glycine cleavage complex [TAS] mitochondrial nucleoid [IDA] oxoglutarate dehydrogenase complex (sensu E... [IDA]		1V59	499
Q62950 UniProt NPD GO	DPYL1_RAT	Dihydropyrimidinase-related protein 1 (DRP-1) (Collapsin response mediator protein 1) (CRMP-1)	0.11	-	cyt	0	Cytoplasm (Potential)				572
P97427 UniProt NPD GO	DPYL1_MOUSE	Dihydropyrimidinase-related protein 1 (DRP-1) (Collapsin response mediator protein 1) (CRMP-1) (ULIP ...	0.11	-	cyt	0	Cytoplasm (Potential)	cell soma [IDA] dendrite [IDA]		1KCX	572
P50285 UniProt NPD GO	FMO1_MOUSE	Dimethylaniline monooxygenase [N-oxide-forming] 1 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.11	-	nuc	1	Microsome				532
P36365 UniProt NPD GO	FMO1_RAT	Dimethylaniline monooxygenase [N-oxide-forming] 1 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.11	-	nuc	1	Microsome				532
Q8K2I3 UniProt NPD GO	FMO2_MOUSE	Dimethylaniline monooxygenase [N-oxide-forming] 2 (EC 1.14.13.8) (Pulmonary flavin-containing monoox ...	0.11	-	end	1	Microsome (By similarity)				534
Q5REK0 UniProt NPD GO	FMO2_PONPY	Dimethylaniline monooxygenase [N-oxide-forming] 2 (EC 1.14.13.8) (Pulmonary flavin-containing monoox ...	0.11	-	end	1	Microsome (By similarity)				534
P49326 UniProt NPD GO	FMO5_HUMAN	Dimethylaniline monooxygenase [N-oxide-forming] 5 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.11	-	end	1	Microsome	microsome [NAS]	603957		532
O17397 UniProt NPD GO	DIML_CAEEL	Diminuto-like protein	0.11	-	mit	1 *					525
Q4I5M4 UniProt NPD GO	DPH2_GIBZE	Diphthamide biosynthesis protein 2	0.11	-	mit	1	Cytoplasm (By similarity)				535
P31986 UniProt NPD GO	DISI_CROVL	Disintegrin lutosin (Platelet aggregation activation inhibitor)	0.11	-	nuc	0	Secreted protein				73
P83658 UniProt NPD GO	DISS_ECHCA	Disintegrin schistatin	0.11	-	nuc	0	Secreted protein			1TEJ	64
Q9UF47 UniProt NPD GO	DNJ5B_HUMAN	DnaJ homolog subfamily C member 5B (Beta cysteine string protein) (Beta-CSP)	0.11	-	nuc	0	Membrane; lipid-anchor (By similarity)				199
P04844 UniProt NPD GO	RIB2_HUMAN	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunit precursor (EC 2.4.1.11 ...	0.11	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	oligosaccharyl transferase complex [TAS]	180490		631
Q91YQ5 UniProt NPD GO	RIB1_MOUSE	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kDa subunit precursor (EC 2.4.1.11 ...	0.11	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				608
P07153 UniProt NPD GO	RIB1_RAT	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kDa subunit precursor (EC 2.4.1.11 ...	0.11	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	oligosaccharyl transferase complex [ISS] rough endoplasmic reticulum membrane [IPI]			605
P53223 UniProt NPD GO	CAX4_YEAST	Dolichyldiphosphatase (EC 3.6.1.43) (Dolichyl pyrophosphate phosphatase)	0.11	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IDA]			239
Q13163 UniProt NPD GO	MP2K5_HUMAN	Dual specificity mitogen-activated protein kinase kinase 5 (EC 2.7.12.2) (MAP kinase kinase 5) (MAPK ...	0.11	-	cyt	0			602520		438
Q9D0T2 UniProt NPD GO	DUS12_MOUSE	Dual specificity protein phosphatase 12 (EC 3.1.3.48) (EC 3.1.3.16) (Dual specificity phosphatase T- ...	0.11	-	cyt	0	Nucleus (By similarity)				339
Q8NEJ0 UniProt NPD GO	DUS18_HUMAN	Dual specificity protein phosphatase 18 (EC 3.1.3.48) (EC 3.1.3.16) (Low molecular weight dual speci ...	0.11	-	mit	0	Cytoplasm. Nucleus			2ESB	188
Q6NT99 UniProt NPD GO	DUS23_MOUSE	Dual specificity protein phosphatase 23 (EC 3.1.3.48) (EC 3.1.3.16) (Low molecular mass dual specifi ...	0.11	-	cyt	0	Cytoplasm; cytosol. Mainly. Nucleus (By similarity). Weakly nuclear (By similarity)				150
Q04651 UniProt NPD GO	ERV41_YEAST	ER-derived vesicles protein ERV41	0.11	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	ER to Golgi transport vesicle [IDA] integral to endoplasmic reticulum membrane [IDA] integral to Golgi membrane [IDA]			352
Q90257 UniProt NPD GO	ES1_BRARE	ES1 protein, mitochondrial precursor	0.11	-	cyt	0	Mitochondrion (Potential)				270
Q02917 UniProt NPD GO	NO552_SOYBN	Early nodulin 55-2 precursor (N-55-2) (Nodulin-315)	0.11	-	exc	0	Peribacteroid membrane (Potential)				187
P81996 UniProt NPD GO	ECHB_ECHCA	Echicetin subunit beta	0.11	-	cyt	0	Secreted protein				123
P97687 UniProt NPD GO	ENP1_RAT	Ectonucleoside triphosphate diphosphohydrolase 1 (EC 3.6.1.5) (NTPDase1) (Ecto-ATP diphosphohydrolas ...	0.11	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				511
P13549 UniProt NPD GO	EF1A0_XENLA	Elongation factor 1-alpha, somatic form (EF-1-alpha-S)	0.11	-	cyt	0	Cytoplasm				462
P29522 UniProt NPD GO	EF1B2_BOMMO	Elongation factor 1-beta'	0.11	-	cyt	0					221
O13430 UniProt NPD GO	EF2_CANAL	Elongation factor 2 (EF-2)	0.11	-	cyt	0	Cytoplasm				842
Q43467 UniProt NPD GO	EFTU1_SOYBN	Elongation factor Tu, chloroplast precursor (EF-Tu)	0.11	-	mit	0	Plastid; chloroplast				479
Q40863 UniProt NPD GO	EMB8_PICGL	Embryogenesis-associated protein EMB8	0.11	-	nuc	0					457
Q06562 UniProt NPD GO	XYN1_COCCA	Endo-1,4-beta-xylanase I precursor (EC 3.2.1.8) (Xylanase I) (1,4-beta-D-xylan xylanohydrolase 1)	0.11	-	exc	0	Secreted protein				221
Q12647 UniProt NPD GO	GUNB_NEOPA	Endoglucanase B precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase B) (Cellulase B)	0.11	-	cyt	0					473
Q5KMQ3 UniProt NPD GO	ERV25_CRYNE	Endoplasmic reticulum vesicle protein 25 precursor	0.11	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				213
Q28105 UniProt NPD GO	EPCR_BOVIN	Endothelial protein C receptor precursor (Endothelial cell protein C receptor) (Activated protein C ...	0.11	-	end	1	Membrane; single-pass type I membrane protein				241
Q6BTB1 UniProt NPD GO	ENO1_DEBHA	Enolase 1 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 1) (2-phospho-D-glycerate hydro-lyase 1)	0.11	-	nuc	0	Cytoplasm (By similarity)				439
Q5R646 UniProt NPD GO	ECHM_PONPY	Enoyl-CoA hydratase, mitochondrial precursor (EC 4.2.1.17) (Short chain enoyl-CoA hydratase) (SCEH) ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				290

You are viewing entries 62601 to 62650 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.