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
P0C0V5 UniProt NPD GO	DPH4_EMENI	Diphthamide biosynthesis protein 4	0.02	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				188
Q6CIZ1 UniProt NPD GO	DPH5_KLULA	Diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.02	-	cyt	0	Cytoplasm (By similarity)				298
Q01783 UniProt NPD GO	D230_PEA	Disease resistance response protein 230 precursor	0.02	-	vac	0					72
Q01784 UniProt NPD GO	DR39_PEA	Disease resistance response protein 39 precursor	0.02	-	exc	1 *					74
Q2KIN1 UniProt NPD GO	DPM2_BOVIN	Dolichol phosphate-mannose biosynthesis regulatory protein	0.02	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				83
O94777 UniProt NPD GO	DPM2_HUMAN	Dolichol phosphate-mannose biosynthesis regulatory protein	0.02	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [TAS] glycosylphosphatidylinositol-N-acetylglucos... [TAS] mannosyltransferase complex [TAS]	603564		83
Q9D1Q4 UniProt NPD GO	DPM3_MOUSE	Dolichol-phosphate mannosyltransferase subunit 3 (Dolichol-phosphate mannose synthase subunit 3) (Do ...	0.02	-	exc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS] mannosyltransferase complex [ISS]			92
P39656 UniProt NPD GO	OST48_HUMAN	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit precursor (EC 2.4.1.11 ...	0.02	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	oligosaccharyl transferase complex [TAS]	602202		439
O54734 UniProt NPD GO	OST48_MOUSE	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit precursor (EC 2.4.1.11 ...	0.02	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	oligosaccharyl transferase complex [ISS]			441
P46964 UniProt NPD GO	OST2_YEAST	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 (EC 2.4.1.119) (Oligosac ...	0.02	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	oligosaccharyl transferase complex [IPI]			129
Q03723 UniProt NPD GO	OST6_YEAST	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 (EC 2.4.1.119) (Oligosac ...	0.02	-	vac	4	Membrane; multi-pass membrane protein (Potential)	oligosaccharyl transferase complex [IPI]			332
Q9JLY7 UniProt NPD GO	DUS14_MOUSE	Dual specificity protein phosphatase 14 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinas ...	0.02	-	mit	0					198
Q95LF4 UniProt NPD GO	DUFFY_CEBAP	Duffy antigen/chemokine receptor (CD234 antigen)	0.02	-	end	7	Membrane; multi-pass membrane protein				336
Q95LF7 UniProt NPD GO	DUFFY_SAGIM	Duffy antigen/chemokine receptor (CD234 antigen)	0.02	-	end	7	Membrane; multi-pass membrane protein				336
Q9BTE1 UniProt NPD GO	DCTN5_HUMAN	Dynactin subunit 5 (Dynactin subunit p25)	0.02	-	cyt	0					182
Q9QZB9 UniProt NPD GO	DCTN5_MOUSE	Dynactin subunit 5 (Dynactin subunit p25)	0.02	-	cyt	0					182
Q5R559 UniProt NPD GO	DCTN5_PONPY	Dynactin subunit 5 (Dynactin subunit p25)	0.02	-	cyt	0					182
Q94524 UniProt NPD GO	DYLT_DROME	Dynein light chain Tctex-type (TCTEX-1 protein homolog)	0.02	-	cyt	0				1YGT	111
Q76NM1 UniProt NPD GO	ERD2_PLAF7	ER lumen protein retaining receptor	0.02	-	end	4 *	Membrane; multi-pass membrane protein				221
P33948 UniProt NPD GO	ERD2_PLAFA	ER lumen protein retaining receptor	0.02	-	end	4 *	Membrane; multi-pass membrane protein				221
O43731 UniProt NPD GO	ERD23_HUMAN	ER lumen protein retaining receptor 3 (KDEL receptor 3) (KDEL endoplasmic reticulum protein retentio ...	0.02	-	nuc	5 *	Membrane; multi-pass membrane protein				214
Q8R1L4 UniProt NPD GO	ERD23_MOUSE	ER lumen protein retaining receptor 3 (KDEL receptor 3) (KDEL endoplasmic reticulum protein retentio ...	0.02	-	end	5 *	Membrane; multi-pass membrane protein				214
O24369 UniProt NPD GO	NO40_SESRO	Early nodulin 40	0.02	-		0					12
P55961 UniProt NPD GO	NO40_VICSA	Early nodulin 40	0.02	-		0					13
Q9SK27 UniProt NPD GO	ENL1_ARATH	Early nodulin-like protein 1 precursor (Phytocyanin-like protein)	0.02	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			176
Q9ER31 UniProt NPD GO	ENP6_RAT	Ectonucleoside triphosphate diphosphohydrolase 6 (EC 3.6.1.6) (NTPDase6) (CD39 antigen-like 2)	0.02	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein. Secreted protein. But also oc ...	Golgi apparatus [IDA]			455
Q9EQG7 UniProt NPD GO	ENPP5_MOUSE	Ectonucleotide pyrophosphatase/phosphodiesterase 5 precursor (EC 3.1.-.-) (E-NPP5) (NPP-5)	0.02	-	nuc	1	Secreted protein (Potential)				477
P84039 UniProt NPD GO	ENPP5_RAT	Ectonucleotide pyrophosphatase/phosphodiesterase 5 precursor (EC 3.1.-.-) (E-NPP5) (NPP-5)	0.02	-	end	1	Membrane	plasma membrane [IDA]			477
P16264 UniProt NPD GO	SPER_STRPU	Egg peptide speract receptor precursor	0.02	-	end	1	Membrane; single-pass type I membrane protein				532
P10296 UniProt NPD GO	IELI_MOMCH	Elastase inhibitor 4 (Elastase inhibitor IV) (MCEI-IV) [Contains: Elastase inhibitor 3 (Elastase inh ...	0.02	-	nuc	0	Secreted protein				31
Q5R1M5 UniProt NPD GO	ELA1_FELCA	Elastase-1 precursor (EC 3.4.21.36)	0.02	-	exc	0	Secreted protein				266
O19023 UniProt NPD GO	ELA3B_MACMU	Elastase-3B precursor (EC 3.4.21.70) (Elastase IIIB) (Protease E) (Fragment)	0.02	-	cyt	0					257
P82099 UniProt NPD GO	EI03_LITRU	Electrin-3	0.02	-		0	Secreted protein				5
Q2KJE4 UniProt NPD GO	ETFA_BOVIN	Electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				333
P13804 UniProt NPD GO	ETFA_HUMAN	Electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [TAS] mitochondrion [TAS]	231680	2A1U	333
Q8HXY0 UniProt NPD GO	ETFA_MACFA	Electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				333
Q99LC5 UniProt NPD GO	ETFA_MOUSE	Electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	electron transfer flavoprotein complex (sen... [TAS] mitochondrion [IDA]			333
Q5RC31 UniProt NPD GO	ETFA_PONPY	Electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				333
P13803 UniProt NPD GO	ETFA_RAT	Electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix				333
P84788 UniProt NPD GO	VSP1_TRIEL	Elegaxobin-1 (EC 3.4.21.-) (Elegaxobin I)	0.02	-	cyt	0	Secreted protein	extracellular region [IDA]			233
Q7GC09 UniProt NPD GO	ERG1_ORYSA	Elicitor-responsive protein 1 (Fungal elicitor immediate early-responsive gene 1 protein) (FIERG1) ( ...	0.02	-	cyt	0	Cytoplasm. Partially translocated to plasma membrane upon elicitor treatment				159
Q7F9X0 UniProt NPD GO	ERG3_ORYSA	Elicitor-responsive protein 3 (16 kDa phloem protein) (RPP16)	0.02	-	cyt	0					144
Q5E983 UniProt NPD GO	EF1B_BOVIN	Elongation factor 1-beta (EF-1-beta)	0.02	-	cyt	0					224
Q9YGQ1 UniProt NPD GO	EF1B_CHICK	Elongation factor 1-beta (EF-1-beta)	0.02	-	cyt	0					224
P24534 UniProt NPD GO	EF1B_HUMAN	Elongation factor 1-beta (EF-1-beta)	0.02	-	cyt	0		eukaryotic translation elongation factor 1 ... [NAS]	600655	1B64	224
P34826 UniProt NPD GO	EF1B_RABIT	Elongation factor 1-beta (EF-1-beta)	0.02	-	cyt	0					224
Q9SCX3 UniProt NPD GO	EF1B2_ARATH	Elongation factor 1-beta 2 (EF-1-beta 2) (Elongation factor 1B-alpha 2) (eEF-1B alpha 2) (Elongation ...	0.02	-	cyt	0	Cell membrane; peripheral membrane protein (Potential)				224
Q9TLV8 UniProt NPD GO	EFTU_CYACA	Elongation factor Tu (EF-Tu)	0.02	-	mit	0	Plastid; chloroplast				410
P50373 UniProt NPD GO	EFTU_CYCME	Elongation factor Tu (EF-Tu)	0.02	-	cyt	0	Plastid; chloroplast				409
Q9MUP0 UniProt NPD GO	EFTU_MESVI	Elongation factor Tu (EF-Tu)	0.02	-	cyt	0	Plastid; chloroplast				410

You are viewing entries 83351 to 83400 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.