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
Q9DA79 UniProt NPD GO	DPEP3_MOUSE	Dipeptidase 3 precursor (EC 3.4.13.19) (Membrane-bound dipeptidase 3) (MBD-3)	0.27	-	mit	0	Membrane; lipid-anchor; GPI-anchor	membrane fraction [IDA]			493
P32377 UniProt NPD GO	ERG19_YEAST	Diphosphomevalonate decarboxylase (EC 4.1.1.33) (Mevalonate pyrophosphate decarboxylase) (Mevalonate ...	0.27	-	cyt	0				1FI4	396
Q6BMF6 UniProt NPD GO	DPH2_DEBHA	Diphthamide biosynthesis protein 2	0.27	-	nuc	0	Cytoplasm (By similarity)				588
Q39088 UniProt NPD GO	DOF34_ARATH	Dof zinc finger protein DOF3.4 (AtDOF3.4) (OBF-binding protein 1)	0.27	-	nuc	0	Nucleus (Probable)				253
Q7TNF0 UniProt NPD GO	DOC2A_MOUSE	Double C2-like domain-containing protein alpha (Doc2-alpha)	0.27	-	nuc	0	Synaptic vesicle; synaptic vesicle membrane; peripheral membrane protein (By similarity)				405
P49592 UniProt NPD GO	DR1_ARATH	Dr1 protein homolog	0.27	-	nuc	0	Nucleus (By similarity)				159
P52564 UniProt NPD GO	MP2K6_HUMAN	Dual specificity mitogen-activated protein kinase kinase 6 (EC 2.7.12.2) (MAP kinase kinase 6) (MAPK ...	0.27	-	cyt	0			601254		334
Q24324 UniProt NPD GO	DSOR1_DROME	Dual specificity mitogen-activated protein kinase kinase dSOR1 (EC 2.7.12.2) (Downstream of RAF) (MA ...	0.27	-	cyt	0					396
P28562 UniProt NPD GO	DUS1_HUMAN	Dual specificity protein phosphatase 1 (EC 3.1.3.48) (EC 3.1.3.16) (MAP kinase phosphatase 1) (MKP-1 ...	0.27	-	cyt	0			600714		367
Q8BKD6 UniProt NPD GO	IBRD2_MOUSE	E3 ubiquitin ligase IBRDC2 (EC 6.3.2.-) (IBR domain-containing protein 2)	0.27	-	nuc	1					301
P32249 UniProt NPD GO	EBI2_HUMAN	EBV-induced G-protein coupled receptor 2 (EBI2)	0.27	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	605741		361
O43854 UniProt NPD GO	EDIL3_HUMAN	EGF-like repeat and discoidin I-like domain-containing protein 3 precursor (EGF-like repeats and dis ...	0.27	-	exc	0	Secreted protein		606018		480
Q8VEH5 UniProt NPD GO	EPMIP_MOUSE	EPM2A-interacting protein 1 (Laforin-interacting protein)	0.27	-	cyt	0	Endoplasmic reticulum (By similarity)				606
P61561 UniProt NPD GO	ENW1_GORGO	ERV-W1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (ERVWE1 envelope protein) ...	0.27	-	end	1	TM: Cell membrane; single-pass type I membrane protein. SU: Cell membrane; peripheral membrane prote ...				538
Q04406 UniProt NPD GO	EMI1_YEAST	Early meiotic induction protein 1	0.27	-	nuc	0					187
P57776 UniProt NPD GO	EF1D_MOUSE	Elongation factor 1-delta (EF-1-delta)	0.27	-	nuc	0					280
Q969S9 UniProt NPD GO	EFG2_HUMAN	Elongation factor G 2, mitochondrial precursor (mEF-G 2) (Elongation factor G2)	0.27	-	mit	0	Mitochondrion (By similarity)		606544		779
Q9TM32 UniProt NPD GO	EFTS_CYACA	Elongation factor Ts (EF-Ts)	0.27	-	nuc	0	Plastid; chloroplast				208
P18905 UniProt NPD GO	EFTU_COLOB	Elongation factor Tu (EF-Tu)	0.27	-	mit	0	Plastid; chloroplast				415
P42935 UniProt NPD GO	ELP2_YEAST	Elongator complex protein 2 (Gamma-toxin target 2)	0.27	-	mit	0	Cytoplasm. Nucleus	transcription elongation factor complex [IDA]			788
Q804A5 UniProt NPD GO	EPA2A_XENLA	Embryonic polyadenylate-binding protein 2-A (Embryonic poly(A)-binding protein 2-A) (Embryonic poly( ...	0.27	-	nuc	0	Cytoplasm	cytoplasm [IDA]			218
Q09023 UniProt NPD GO	CHI2_BRANA	Endochitinase CH25 precursor (EC 3.2.1.14)	0.27	-	exc	0					322
P16061 UniProt NPD GO	CHI8_POPTR	Endochitinase WIN8 precursor (EC 3.2.1.14)	0.27	-	exc	0					316
P29029 UniProt NPD GO	CHIT_YEAST	Endochitinase precursor (EC 3.2.1.14) (Soluble cell wall protein 2)	0.27	-	exc	0	Secreted protein. Cell wall; peripheral membrane protein. Most of the enzyme is secreted, but a sign ...	cell wall (sensu Fungi) [TAS] endoplasmic reticulum [IDA] extracellular region [IDA] nuclear envelope [IDA]			562
Q7M4F3 UniProt NPD GO	CUD2_SCHGR	Endocuticle structural glycoprotein SgAbd-2	0.27	-	nuc	0					135
Q12714 UniProt NPD GO	GUN1_TRILO	Endoglucanase EG-1 precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase)	0.27	-	nuc	0	Secreted protein				463
P32906 UniProt NPD GO	MNS1_YEAST	Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (EC 3.2.1.113) (ER alpha-1,2-ma ...	0.27	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein	endoplasmic reticulum [IDA]		1G6I	549
Q9NQZ8 UniProt NPD GO	ZNF71_HUMAN	Endothelial zinc finger protein induced by tumor necrosis factor alpha (Zinc finger protein 71) (ZNF ...	0.27	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	194545		489
P29319 UniProt NPD GO	EPHA3_MOUSE	Ephrin type-A receptor 3 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor ETK1) (MEK4)	0.27	-	end	1	Isoform Long: Cell membrane; single-pass type I membrane protein. Isoform Short: Secreted protein				983
Q03137 UniProt NPD GO	EPHA4_MOUSE	Ephrin type-A receptor 4 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor SEK) (MPK-3)	0.27	-	end	1	Membrane; single-pass type I membrane protein			1B0X	986
Q60872 UniProt NPD GO	IF1A_MOUSE	Eukaryotic translation initiation factor 1A (eIF-1A) (eIF-4C)	0.27	-	nuc	0					143
Q6VV72 UniProt NPD GO	IF1A_RAT	Eukaryotic translation initiation factor 1A (eIF-1A) (eIF-4C) (Liver regeneration-related protein LR ...	0.27	-	nuc	0					143
P47813 UniProt NPD GO	IF1AX_HUMAN	Eukaryotic translation initiation factor 1A, X-chromosomal (eIF-1A X isoform) (eIF-4C)	0.27	-	nuc	0			300186	1D7Q	143
Q8BMJ3 UniProt NPD GO	IF1AX_MOUSE	Eukaryotic translation initiation factor 1A, X-chromosomal (eIF-1A X isoform) (eIF-4C)	0.27	-	nuc	0					143
Q5RA42 UniProt NPD GO	IF1AX_PONPY	Eukaryotic translation initiation factor 1A, X-chromosomal (eIF-1A X isoform) (eIF-4C)	0.27	-	nuc	0					143
O14602 UniProt NPD GO	IF1AY_HUMAN	Eukaryotic translation initiation factor 1A, Y-chromosomal (eIF-1A Y isoform) (eIF-4C)	0.27	-	nuc	0			400014		143
Q10339 UniProt NPD GO	EXO70_SCHPO	Exocyst complex component exo70	0.27	-	cyt	0		cell cortex of cell tip [IDA] exocyst [IDA]			615
Q9CRT8 UniProt NPD GO	XPOT_MOUSE	Exportin-T (tRNA exportin) (Exportin(tRNA)) (Fragment)	0.27	-	cyt	0	Nucleus. Cytoplasm. Nuclear; once bound to tRNA and Ran the complex translocates to the cytoplasm. S ...				397
P13127 UniProt NPD GO	CAZA1_CHICK	F-actin capping protein alpha-1 subunit (CapZ 36/32) (Beta-actinin subunit I)	0.27	-	cyt	0	CapZ is located at the Z line in chicken muscle			1IZN	286
P13021 UniProt NPD GO	CAPZB_DICDI	F-actin capping protein subunit beta (CAP32)	0.27	-	nuc	0					272
P14315 UniProt NPD GO	CAPZB_CHICK	F-actin capping protein subunit beta isoforms 1 and 2 (CapZ 36/32) (CapZ B1 and B2) (Beta-actinin su ...	0.27	-	nuc	0				1IZN	276
Q80UW2 UniProt NPD GO	FBX2_MOUSE	F-box only protein 2	0.27	-	cyt	0		cytosol [TAS]		1UMI	297
Q6DIA9 UniProt NPD GO	FBX27_MOUSE	F-box only protein 27	0.27	-	cyt	0					280
Q96CD0 UniProt NPD GO	FBXL8_HUMAN	F-box/LRR-repeat protein 8 (F-box and leucine-rich repeat protein 8) (F-box protein FBL8)	0.27	-	cyt	0			609077		374
Q6BHU6 UniProt NPD GO	YFAS1_DEBHA	FAS1 domain-containing protein DEHA0G16764g precursor	0.27	-	exc	0	Vacuole (By similarity)				293
Q9BXM9 UniProt NPD GO	FSD1L_HUMAN	FSD1-like protein (FSD1 N-terminal-like protein) (Coiled-coil domain-containing protein 10)	0.27	-	nuc	0			609829		145
Q7L513 UniProt NPD GO	FCRL_HUMAN	Fc receptor-like and mucin-like 1 precursor (Fc receptor homolog expressed in B-cells) (Fc receptor- ...	0.27	-	mit	1 *	Secreted protein (Probable). Cytoplasm		606891		359
Q08908 UniProt NPD GO	FRE5_YEAST	Ferric reductase transmembrane component 5 precursor (EC 1.16.1.7) (Ferric-chelate reductase 5)	0.27	-	end	6	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			694
P09528 UniProt NPD GO	FRIH_MOUSE	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit)	0.27	-	nuc	0		plasma membrane [ISS]			181
Q498D6 UniProt NPD GO	FGFR4_RAT	Fibroblast growth factor receptor 4 precursor (EC 2.7.10.1) (FGFR-4)	0.27	-	end	0	Membrane; single-pass type I membrane protein (By similarity)				800

You are viewing entries 43151 to 43200 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.