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
P22911 UniProt NPD GO	DH16B_ORYSA	Dehydrin Rab16B	0.25	-	nuc	0					164
Q570Q8 UniProt NPD GO	DDPS5_ARATH	Dehydrodolichyl diphosphate synthase 5 (EC 2.5.1.-) (Dedol-PP synthase 5)	0.25	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				302
Q5NVG2 UniProt NPD GO	DHRS8_PONPY	Dehydrogenase/reductase SDR family member 8 precursor (EC 1.1.1.-) (17-beta-hydroxysteroid dehydroge ...	0.25	-	mit	0	Secreted protein (Potential)				300
O88516 UniProt NPD GO	DLL3_MOUSE	Delta-like protein 3 precursor (Drosophila Delta homolog 3) (M-Delta-3)	0.25	-	exc	1	Membrane; single-pass type I membrane protein (Probable)				592
Q16854 UniProt NPD GO	DGUOK_HUMAN	Deoxyguanosine kinase, mitochondrial precursor (EC 2.7.1.113) (dGK)	0.25	-	mit	0	Mitochondrion	mitochondrion [TAS]	251880	1JAG	277
Q2QDF1 UniProt NPD GO	DNSL1_CERAE	Deoxyribonuclease I-like 1 precursor (EC 3.1.21.-) (DNase I-like 1) (DNase X)	0.25	-	exc	0	Endoplasmic reticulum (By similarity)				302
P18359 UniProt NPD GO	DEST_CHICK	Destrin (Actin-depolymerizing factor) (ADF)	0.25	+	cyt	0					164
Q9UBP4 UniProt NPD GO	DKK3_HUMAN	Dickkopf-related protein 3 precursor (Dkk-3) (Dickkopf-3) (hDkk-3)	0.25	-	exc	0	Secreted protein	extracellular space [TAS]	605416		350
Q6CLC9 UniProt NPD GO	DPH1_KLULA	Diphthamide biosynthesis protein 1	0.25	-	nuc	0	Cytoplasm (By similarity)				422
P31985 UniProt NPD GO	DISI_CROVE	Disintegrin cereberin (Platelet aggregation activation inhibitor)	0.25	-	nuc	0	Secreted protein				72
Q10661 UniProt NPD GO	DPY30_CAEEL	Dosage compensation protein dpy-30 (Protein dumpy-30)	0.25	+	nuc	0	Nucleus	nucleus [IDA]			123
P70611 UniProt NPD GO	DOC2A_RAT	Double C2-like domain-containing protein alpha (Doc2-alpha)	0.25	-	nuc	0	Synaptic vesicle; synaptic vesicle membrane; peripheral membrane protein (By similarity)				403
Q9UN19 UniProt NPD GO	DAPP1_HUMAN	Dual adapter for phosphotyrosine and 3-phosphotyrosine and 3-phosphoinositide (hDAPP1) (B cell adapt ...	0.25	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Membrane-associated after cell stimulation leading ...		605768	1FB8	280
Q566R7 UniProt NPD GO	DUS22_BRARE	Dual specificity protein phosphatase 22 (EC 3.1.3.48) (EC 3.1.3.16)	0.25	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				183
Q8R180 UniProt NPD GO	ERO1A_MOUSE	ERO1-like protein alpha precursor (EC 1.8.4.-) (ERO1-Lalpha) (Oxidoreductin-1-Lalpha) (Endoplasmic o ...	0.25	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				464
O75355 UniProt NPD GO	ENP3_HUMAN	Ectonucleoside triphosphate diphosphohydrolase 3 (EC 3.6.1.5) (NTPDase3) (Ecto-ATP diphosphohydrolas ...	0.25	-	end	2 *	Membrane; multi-pass membrane protein (Potential)		603161		529
Q9NJH0 UniProt NPD GO	EF1G_DROME	Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma)	0.25	-	nuc	0					431
P15112 UniProt NPD GO	EF2_DICDI	Elongation factor 2 (EF-2)	0.25	-	nuc	0	Cytoplasm				830
O14460 UniProt NPD GO	EF2_SCHPO	Elongation factor 2 (EF-2)	0.25	-	cyt	0	Cytoplasm (By similarity)				842
Q63961 UniProt NPD GO	EGLN_MOUSE	Endoglin precursor (Cell surface MJ7/18 antigen)	0.25	-	end	1	Membrane; single-pass type I membrane protein				653
Q9R0H2 UniProt NPD GO	MUCEN_MOUSE	Endomucin precursor (Endomucin-1/2)	0.25	-	end	1	Membrane; single-pass type I membrane protein (Potential)	external side of plasma membrane [ISS] integral to membrane [TAS] plasma membrane [ISS]			261
Q4R520 UniProt NPD GO	ENPL_MACFA	Endoplasmin precursor (Heat shock protein 90 kDa beta member 1)	0.25	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				804
Q5R6F7 UniProt NPD GO	ENPL_PONPY	Endoplasmin precursor (Heat shock protein 90 kDa beta member 1)	0.25	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				804
P14625 UniProt NPD GO	ENPL_HUMAN	Endoplasmin precursor (Heat shock protein 90 kDa beta member 1) (94 kDa glucose-regulated protein) ( ...	0.25	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	cytosol [IDA] endoplasmic reticulum [TAS] endoplasmic reticulum lumen [IEP] endoplasmic reticulum membrane [IEP] microsome [IEP] perinuclear region [IDA]	191175		803
Q6FUA5 UniProt NPD GO	YSH1_CANGA	Endoribonuclease YSH1 (EC 3.1.27.-) (mRNA 3'-end-processing protein YSH1)	0.25	-	cyt	0	Nucleus (By similarity)				771
Q3T0V7 UniProt NPD GO	EDF1_BOVIN	Endothelial differentiation-related factor 1 (EDF-1)	0.25	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Also nuclear upon binding to NR5A1 and treatment ...				148
O60869 UniProt NPD GO	EDF1_HUMAN	Endothelial differentiation-related factor 1 (EDF-1) (Multiprotein-bridging factor 1) (MBF1)	0.25	-	nuc	0	Cytoplasm. Nucleus. Also nuclear upon binding to NR5A1 and treatment of cells with TPA or forskolin	cytoplasm [IDA] intracellular [TAS] nucleus [IDA]	605107	1X57	148
P29320 UniProt NPD GO	EPHA3_HUMAN	Ephrin type-A receptor 3 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor ETK1) (HEK) (HEK4 ...	0.25	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	integral to plasma membrane [TAS]	179611		983
P54761 UniProt NPD GO	EPHB4_MOUSE	Ephrin type-B receptor 4 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor MDK-2) (Developme ...	0.25	-	end	1	Membrane; single-pass type I membrane protein				987
P46058 UniProt NPD GO	EDSP_CYNPY	Epidermal differentiation-specific protein	0.25	-	cyt	0					335
P81439 UniProt NPD GO	EQST_ACTEQ	Equistatin	0.25	-	nuc	0	Secreted protein				199
Q9V3A6 UniProt NPD GO	ERO1L_DROME	Ero1-like protein precursor (EC 1.8.4.-) (Endoplasmic oxidoreductin-1-like protein)	0.25	-	gol	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...	endoplasmic reticulum [ISS]			483
P27639 UniProt NPD GO	IF4A_CAEEL	Eukaryotic initiation factor 4A (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A) (eIF-4A)	0.25	-	cyt	0					402
P48024 UniProt NPD GO	EIF1_MOUSE	Eukaryotic translation initiation factor 1 (eIF1) (Protein translation factor SUI1 homolog)	0.25	-	cyt	0					113
P05198 UniProt NPD GO	IF2A_HUMAN	Eukaryotic translation initiation factor 2 subunit 1 (Eukaryotic translation initiation factor 2 sub ...	0.25	-	cyt	0		polysome [TAS]	603907	1Q8K	314
P41374 UniProt NPD GO	IF2A_DROME	Eukaryotic translation initiation factor 2 subunit alpha (eIF-2-alpha)	0.25	-	nuc	0					341
O36041 UniProt NPD GO	IF2G_SPIVO	Eukaryotic translation initiation factor 2 subunit gamma (eIF-2-gamma) (Fragment)	0.25	-	nuc	0					210
O60516 UniProt NPD GO	4EBP3_HUMAN	Eukaryotic translation initiation factor 4E-binding protein 3 (4E-BP3) (eIF4E-binding protein 3)	0.25	-	nuc	0		eukaryotic translation initiation factor 4F... [NAS]	603483		100
Q22918 UniProt NPD GO	IF5_CAEEL	Eukaryotic translation initiation factor 5 (eIF-5)	0.25	-	nuc	0		eukaryotic translation initiation factor 2B... [NAS]			436
Q13868 UniProt NPD GO	EXOS2_HUMAN	Exosome complex exonuclease RRP4 (EC 3.1.13.-) (Ribosomal RNA-processing protein 4) (Exosome compone ...	0.25	-	cyt	0		cytoplasm [TAS] nucleus [TAS]	602238		293
P06599 UniProt NPD GO	EXTN_DAUCA	Extensin precursor	0.25	-	exc	0	Secreted protein; extracellular space; extracellular matrix				306
Q96KX2 UniProt NPD GO	CAZA3_HUMAN	F-actin capping protein alpha-3 subunit (CapZ alpha-3) (CP-alpha-3) (Germ cell-specific protein 3)	0.25	-	nuc	0			608722		299
Q9N0C8 UniProt NPD GO	FBX27_MACFA	F-box only protein 27	0.25	-	mit	0					280
Q9NRD1 UniProt NPD GO	FBX6_HUMAN	F-box only protein 6 (F-box/G-domain protein 2)	0.25	-	cyt	0			605647		293
Q9QXW2 UniProt NPD GO	FBXW5_MOUSE	F-box/WD repeat protein 5 (F-box and WD-40 domain protein 5)	0.25	-	nuc	0					573
Q6FKI2 UniProt NPD GO	POB3_CANGA	FACT complex subunit POB3 (Facilitates chromatin transcription complex subunit POB3)	0.25	+	cyt	0	Nucleus (By similarity)				543
Q6C7V4 UniProt NPD GO	POB3_YARLI	FACT complex subunit POB3 (Facilitates chromatin transcription complex subunit POB3)	0.25	-	mit	0	Nucleus (By similarity)				544
Q12331 UniProt NPD GO	YFAS1_YEAST	FAS1 domain-containing protein YDR262W precursor	0.25	-	exc	0	Vacuole	vacuole (sensu Fungi) [IDA]			272
Q4R7V3 UniProt NPD GO	FR1OP_MACFA	FGFR1 oncogene partner	0.25	-	nuc	0	Centrosome. Associated with gamma-tubulin (By similarity)				379
P45878 UniProt NPD GO	FKBP2_MOUSE	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.25	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Probable)				140

You are viewing entries 45151 to 45200 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.