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
Q8L9V6 UniProt NPD GO	DOF11_ARATH	Dof zinc finger protein DOF1.1 (AtDOF1.1) (OBF-binding protein 2)	0.39	-	nuc	0	Nucleus (Probable)				331
Q9FM03 UniProt NPD GO	DOF56_ARATH	Dof zinc finger protein DOF5.6 (AtDOF5.6)	0.39	-	nuc	0	Nucleus (Probable)				372
O60762 UniProt NPD GO	DPM1_HUMAN	Dolichol-phosphate mannosyltransferase (EC 2.4.1.83) (Dolichol-phosphate mannose synthase) (Dolichyl ...	0.39	-	nuc	0	Endoplasmic reticulum	endoplasmic reticulum membrane [TAS] mannosyltransferase complex [TAS]	608799		260
Q90321 UniProt NPD GO	MP2K2_CYPCA	Dual specificity mitogen-activated protein kinase kinase 2 (EC 2.7.12.2) (MAP kinase kinase 2) (MAPK ...	0.39	-	cyt	0					397
P59900 UniProt NPD GO	EMIL3_MOUSE	EMILIN-3 precursor (EMILIN-5) (Elastin microfibril interface located protein 5) (Elastin microfibril ...	0.39	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity). Ref.3: Cytoplasm	cytoplasm [IDA]			758
Q8VCD3 UniProt NPD GO	LMA1L_MOUSE	ERGIC-53-like protein precursor (ERGIC53-like protein) (Lectin, mannose-binding 1-like) (LMAN1-like ...	0.39	-	mit	0	Membrane; single-pass type I membrane protein (Potential)				374
P41971 UniProt NPD GO	ELK3_MOUSE	ETS domain-containing protein Elk-3 (ETS-related protein NET) (ETS-related protein ERP)	0.39	-	nuc	0	Nucleus	nucleus [IDA]			409
Q6PCB8 UniProt NPD GO	EMB_HUMAN	Embigin precursor	0.39	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				327
P46520 UniProt NPD GO	EMP1_ORYSA	Embryonic abundant protein 1	0.39	-	nuc	0					95
P52406 UniProt NPD GO	CHI4_SOLTU	Endochitinase 4 precursor (EC 3.2.1.14) (Fragment)	0.39	-	nuc	0	Vacuole (By similarity). Vacuolar and protoplast (By similarity)				302
P08252 UniProt NPD GO	CHI1_TOBAC	Endochitinase A precursor (EC 3.2.1.14) (CHN-A)	0.39	-	exc	0	Vacuole. Vacuolar and protoplast				329
P24091 UniProt NPD GO	CHI2_TOBAC	Endochitinase B precursor (EC 3.2.1.14) (CHN-B)	0.39	-	exc	0	Vacuole. Vacuolar and protoplast				324
Q75BB5 UniProt NPD GO	ERO1_ASHGO	Endoplasmic oxidoreductin-1 precursor (EC 1.8.4.-)	0.39	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				546
Q7YTU4 UniProt NPD GO	ERO1_CAEEL	Endoplasmic oxidoreductin-1 precursor (EC 1.8.4.-)	0.39	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				478
O18750 UniProt NPD GO	ENPL_RABIT	Endoplasmin (Heat shock protein 90 kDa beta member 1) (94 kDa glucose-regulated protein) (GRP94) (Fr ...	0.39	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				716
P42891 UniProt NPD GO	ECE1_BOVIN	Endothelin-converting enzyme 1 (EC 3.4.24.71) (ECE-1)	0.39	-	mit	1	Membrane; single-pass type II membrane protein				754
P42892 UniProt NPD GO	ECE1_HUMAN	Endothelin-converting enzyme 1 (EC 3.4.24.71) (ECE-1)	0.39	-	mit	1	Membrane; single-pass type II membrane protein	integral to membrane [TAS] membrane fraction [TAS]	600423		770
P97435 UniProt NPD GO	ENTK_MOUSE	Enteropeptidase (EC 3.4.21.9) (Enterokinase) [Contains: Enteropeptidase non-catalytic heavy chain; E ...	0.39	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)				1069
P52796 UniProt NPD GO	EFNB1_RAT	Ephrin-B1 precursor (EPH-related receptor tyrosine kinase ligand 2) (LERK-2) (ELK ligand) (ELK-L)	0.39	-	mit	1	Membrane; single-pass type I membrane protein	synapse [IDA]			345
Q810Z1 UniProt NPD GO	LCN10_MOUSE	Epididymal-specific lipocalin-10 precursor	0.39	+	mit	0	Secreted protein (By similarity)				182
Q9Y2E5 UniProt NPD GO	MA2B2_HUMAN	Epididymis-specific alpha-mannosidase precursor (EC 3.2.1.24) (Mannosidase alpha class 2B member 2)	0.39	-	mit	0	Secreted protein (Potential)				1009
O80340 UniProt NPD GO	ERF4_ARATH	Ethylene-responsive transcription factor 4 (Ethylene-responsive element-binding factor 4) (Related t ...	0.39	-	nuc	0	Nucleus (Probable)				222
P41382 UniProt NPD GO	IF410_TOBAC	Eukaryotic initiation factor 4A-10 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-10) (eIF-4A-10)	0.39	-	cyt	0					413
Q40467 UniProt NPD GO	IF414_TOBAC	Eukaryotic initiation factor 4A-14 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-14) (eIF-4A-14)	0.39	-	cyt	0					413
P41379 UniProt NPD GO	IF4A2_NICPL	Eukaryotic initiation factor 4A-2 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-2) (eIF-4A-2)	0.39	-	cyt	0					413
Q40469 UniProt NPD GO	IF4A6_TOBAC	Eukaryotic initiation factor 4A-6 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-6) (eIF-4A-6) (Frag ...	0.39	-	nuc	0					253
Q40471 UniProt NPD GO	IF4A9_TOBAC	Eukaryotic initiation factor 4A-9 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-9) (eIF-4A-9)	0.39	-	cyt	0					413
P55884 UniProt NPD GO	IF39_HUMAN	Eukaryotic translation initiation factor 3 subunit 9 (eIF-3 eta) (eIF3 p116) (eIF3 p110) (eIF3b) (Pr ...	0.39	-	cyt	0		eukaryotic translation initiation factor 3 ... [TAS]	603917		814
P38792 UniProt NPD GO	RRP4_YEAST	Exosome complex exonuclease RRP4 (EC 3.1.13.-) (Ribosomal RNA-processing protein 4)	0.39	-	nuc	0	Nucleus (Potential)	cytoplasmic exosome (RNase complex) [IDA] nuclear exosome (RNase complex) [IDA]			359
O09164 UniProt NPD GO	SODE_MOUSE	Extracellular superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1) (EC-SOD)	0.39	-	end	0	Secreted protein; extracellular space	extracellular space [IDA]			251
O08575 UniProt NPD GO	EYA2_MOUSE	Eyes absent homolog 2 (EC 3.1.3.48)	0.39	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			532
P13517 UniProt NPD GO	CAPZB_YEAST	F-actin capping protein subunit beta	0.39	-	nuc	0	Found at cortical actin spots at the site of bud emergence and at the tips of growing buds and shmoo ...	actin cortical patch [IDA] actin filament [IPI] F-actin capping protein complex [IDA]			287
Q9D417 UniProt NPD GO	FBX24_MOUSE	F-box only protein 24	0.39	-	cyt	0					589
Q8BH16 UniProt NPD GO	FBXL2_MOUSE	F-box/LRR-repeat protein 2 (F-box and leucine-rich repeat protein 2)	0.39	-	nuc	0					423
Q4WC84 UniProt NPD GO	YFAS1_ASPFU	FAS1 domain-containing protein Afu8g05360 precursor	0.39	-	mit	1 *	Vacuole (By similarity)				234
Q5KIJ5 UniProt NPD GO	FKBP4_CRYNE	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.39	-	mit	0	Nucleus; nucleolus (By similarity)				405
Q9HCQ7 UniProt NPD GO	RFRP_HUMAN	FMRFamide-related peptides precursor [Contains: Neuropeptide NPSF (Neuropeptide RFRP-1); Neuropeptid ...	0.39	-	exc	0	Secreted protein	membrane [NAS]			196
Q6NVD0 UniProt NPD GO	FREM2_MOUSE	FRAS1-related extracellular matrix protein 2 precursor (ECM3 homolog) (NV domain-containing protein ...	0.39	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				3160
Q91837 UniProt NPD GO	FASC_XENLA	Fascin	0.39	-	cyt	0					483
Q9UUG0 UniProt NPD GO	FAS1_SCHPO	Fatty acid synthase subunit beta (EC 2.3.1.86) [Includes: 3-hydroxypalmitoyl-[acyl-carrier-protein] ...	0.39	-	cyt	0		fatty acid synthase complex [IDA]			2073
Q3B8P2 UniProt NPD GO	FCRL_RAT	Fc receptor-like and mucin-like 1 precursor	0.39	-	nuc	0	Secreted protein (Probable). Cytoplasm (By similarity)				347
Q9D5H4 UniProt NPD GO	FTMT_MOUSE	Ferritin, mitochondrial precursor (EC 1.16.3.1)	0.39	-	mit	0	Mitochondrion (By similarity)	mitochondrion [TAS]			237
P07589 UniProt NPD GO	FINC_BOVIN	Fibronectin (FN)	0.39	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				2265
P02751 UniProt NPD GO	FINC_HUMAN	Fibronectin precursor (FN) (Cold-insoluble globulin) (CIG)	0.39	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	ER-Golgi intermediate compartment [IDA] extracellular matrix (sensu Metazoa) [NAS] extracellular region [NAS]	135600	2FNB	2386
Q5EA62 UniProt NPD GO	FBLN5_BOVIN	Fibulin-5 precursor (FIBL-5)	0.39	-	exc	0	Secreted protein (By similarity)				448
Q9UBX5 UniProt NPD GO	FBLN5_HUMAN	Fibulin-5 precursor (FIBL-5) (Developmental arteries and neural crest EGF-like protein) (Dance) (Uri ...	0.39	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS] soluble fraction [TAS]	608895		448
O61492 UniProt NPD GO	FLOT2_DROME	Flotillin-2	0.39	-	cyt	0	Membrane (By similarity). In neuronal cells; associated with GPI-anchored cell-adhesion molecules (B ...	flotillin complex [NAS]			438
Q2KHP9 UniProt NPD GO	FMR1B_XENLA	Fragile X mental retardation protein 1 homolog-B (Protein FMR-1-B) (FMRP-B) (XFMR1-B)	0.39	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				564
Q61089 UniProt NPD GO	FZD6_MOUSE	Frizzled-6 precursor (Fz-6) (mFz6)	0.39	-	end	7	Membrane; multi-pass membrane protein	apical part of cell [IDA]			709
P46023 UniProt NPD GO	GR101_LYMST	G-protein coupled receptor GRL101 precursor	0.39	-	end	7	Membrane; multi-pass membrane protein				1115

You are viewing entries 32551 to 32600 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.