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
P98074 UniProt NPD GO	ENTK_PIG	Enteropeptidase precursor (EC 3.4.21.9) (Enterokinase) [Contains: Enteropeptidase non-catalytic mini ...	0.37	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)				1034
P47779 UniProt NPD GO	ECP_MACFA	Eosinophil cationic protein precursor (EC 3.1.27.-) (ECP) (Ribonuclease 3) (RNase 3)	0.37	-	exc	0	Matrix of eosinophil's large specific granule				160
P29322 UniProt NPD GO	EPHA8_HUMAN	Ephrin type-A receptor 8 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EEK) (EPH- and EL ...	0.37	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS] plasma membrane [TAS]	176945	1X5L	1005
P35683 UniProt NPD GO	IF4A_ORYSA	Eukaryotic initiation factor 4A (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A) (eIF-4A)	0.37	-	cyt	0					414
Q40466 UniProt NPD GO	IF413_TOBAC	Eukaryotic initiation factor 4A-13 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-13) (eIF-4A-13) (F ...	0.37	-	cyt	0					355
Q40468 UniProt NPD GO	IF415_TOBAC	Eukaryotic initiation factor 4A-15 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-15) (eIF-4A-15)	0.37	-	cyt	0					413
Q9CAI7 UniProt NPD GO	IF4A3_ARATH	Eukaryotic initiation factor 4A-3 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-3) (eIF-4A-3) (DEAD ...	0.37	-	cyt	0	Cytoplasm (By similarity)	cell wall (sensu Magnoliophyta) [IDA]			414
P33279 UniProt NPD GO	E2AK1_RABIT	Eukaryotic translation initiation factor 2-alpha kinase 1 (EC 2.7.11.1) (Heme-regulated eukaryotic i ...	0.37	-	nuc	0		cytoplasm [ISS]			626
Q93063 UniProt NPD GO	EXT2_HUMAN	Exostosin-2 (EC 2.4.1.224) (EC 2.4.1.225) (Glucuronosyl-N-acetylglucosaminyl-proteoglycan/N-acetylgl ...	0.37	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	endoplasmic reticulum [TAS] endoplasmic reticulum membrane [TAS] Golgi apparatus [TAS]	608210		718
O43592 UniProt NPD GO	XPOT_HUMAN	Exportin-T (tRNA exportin) (Exportin(tRNA))	0.37	-	cyt	0	Nucleus. Cytoplasm. Nuclear, once bound to tRNA and Ran the complex translocates to the cytoplasm. S ...		603180		962
Q02202 UniProt NPD GO	ECM9_YEAST	Extracellular matrix protein 9	0.37	-	cyt	0					377
Q9JMJ2 UniProt NPD GO	FBXW4_MOUSE	F-box/WD repeat protein 4 (F-box and WD-40 domain protein 4) (Hagoromo protein)	0.37	-	mit	0					410
Q6FK71 UniProt NPD GO	FKBP4_CANGA	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.37	+	cyt	0	Nucleus; nucleolus (By similarity)				398
Q96AE4 UniProt NPD GO	FUBP1_HUMAN	Far upstream element-binding protein 1 (FUSE-binding protein 1) (FBP) (DNA helicase V) (HDH V)	0.37	-	nuc	0	Nucleus (Probable)		603444	1J4W	643
Q920E5 UniProt NPD GO	FPPS_MOUSE	Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) (Choleste ...	0.37	-	cyt	0	Cytoplasm (By similarity)				353
Q9GZV9 UniProt NPD GO	FGF23_HUMAN	Fibroblast growth factor 23 precursor (FGF-23) (Tumor-derived hypophosphatemia-inducing factor)	0.37	-	mit	0	Secreted protein	extracellular space [NAS]	605380		251
Q7T2H2 UniProt NPD GO	FGRL1_CHICK	Fibroblast growth factor receptor-like 1 precursor	0.37	-	exc	1	Cell membrane; single-pass type I membrane protein (By similarity)				487
Q14512 UniProt NPD GO	FGFP1_HUMAN	Fibroblast growth factor-binding protein 1 precursor (FGF-binding protein 1) (FGF-BP1) (FGFBP-1) (FG ...	0.37	-	nuc	0	Secreted protein; extracellular space. Extracellular and plasma membrane-associated. Colocalizes wit ...	extracellular space [TAS]	607737		234
Q8BX90 UniProt NPD GO	FNDC3_MOUSE	Fibronectin type-III domain-containing protein 3a	0.37	-	mit	1					1134
Q8MJJ9 UniProt NPD GO	FBLN1_CERAE	Fibulin-1 (Fragment)	0.37	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				598
O73775 UniProt NPD GO	FBLN1_CHICK	Fibulin-1 precursor	0.37	-	exc	0	Secreted protein; extracellular space; extracellular matrix				704
Q9WVH9 UniProt NPD GO	FBLN5_MOUSE	Fibulin-5 precursor (FIBL-5) (Developmental arteries and neural crest EGF-like protein) (Dance)	0.37	-	exc	0	Secreted protein				448
P02702 UniProt NPD GO	FOLR1_BOVIN	Folate receptor alpha precursor (FR-alpha) (Folate receptor 1) (Folate-binding protein 1) (Milk fola ...	0.37	-	exc	0					241
Q05932 UniProt NPD GO	FOLC_HUMAN	Folylpolyglutamate synthase, mitochondrial precursor (EC 6.3.2.17) (Folylpoly-gamma-glutamate synthe ...	0.37	-	mit	0	Mitochondrion. Cytoplasm	cytoplasm [TAS] cytosol [TAS] mitochondrion [TAS]	136510		587
O70433 UniProt NPD GO	FHL2_MOUSE	Four and a half LIM domains protein 2 (FHL-2) (Skeletal muscle LIM-protein 3) (SLIM 3)	0.37	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [IDA]			279
O35115 UniProt NPD GO	FHL2_RAT	Four and a half LIM domains protein 2 (FHL-2) (Skeletal muscle LIM-protein 3) (SLIM 3) (LIM-domain p ...	0.37	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				279
P46275 UniProt NPD GO	F16P1_PEA	Fructose-1,6-bisphosphatase, chloroplast precursor (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phos ...	0.37	-	nuc	0	Plastid; chloroplast; chloroplast stroma			1DCU	407
Q13065 UniProt NPD GO	GAGE1_HUMAN	G antigen 1 (GAGE-1) (MZ2-F antigen)	0.37	-	nuc	0			604243		138
O60269 UniProt NPD GO	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth 2 (GRIN2)	0.37	-	nuc	0					458
P79960 UniProt NPD GO	APJ_XENLA	G-protein coupled receptor APJ homolog (Angiotensin receptor-related protein) (XAngio1) (Mesenchyme- ...	0.37	-	end	7 *	Membrane; multi-pass membrane protein				353
Q3MHH5 UniProt NPD GO	CCND3_BOVIN	G1/S-specific cyclin-D3	0.37	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				292
P25011 UniProt NPD GO	CCNB1_SOYBN	G2/mitotic-specific cyclin S13-6 (B-like cyclin)	0.37	-	cyt	0					454
Q06546 UniProt NPD GO	GABPA_HUMAN	GA-binding protein alpha chain (GABP-subunit alpha) (Transcription factor E4TF1-60) (Nuclear respira ...	0.37	-	cyt	0	Nucleus	nucleus [TAS]	600609		454
P55042 UniProt NPD GO	RAD_HUMAN	GTP-binding protein RAD (RAS associated with diabetes) (RAD1)	0.37	-	cyt	0			179503	2GJS	308
Q03740 UniProt NPD GO	CRGE_MOUSE	Gamma crystallin E	0.37	-	cyt	0					173
P02528 UniProt NPD GO	CRGE_RAT	Gamma crystallin E (Gamma crystallin 3-1) (Gamma-2)	0.37	-	cyt	0				1ZIR	173
P10068 UniProt NPD GO	CRGF_RAT	Gamma crystallin F (Gamma crystallin 4-1)	0.37	-	cyt	0					173
P48648 UniProt NPD GO	CRGM1_CHICO	Gamma crystallin M1 (Gamma-M1)	0.37	-	nuc	0					174
P20158 UniProt NPD GO	THG1_WHEAT	Gamma-1 purothionin	0.37	-	nuc	0				1GPS	47
P21548 UniProt NPD GO	GBRG2_CHICK	Gamma-aminobutyric-acid receptor gamma-2 subunit precursor (GABA(A) receptor)	0.37	-	end	4 *	Membrane; multi-pass membrane protein				474
P28228 UniProt NPD GO	CXA7_CANFA	Gap junction alpha-7 protein (Connexin-45) (Cx45)	0.37	-	end	4 *	Membrane; multi-pass membrane protein				396
P36383 UniProt NPD GO	CXA7_HUMAN	Gap junction alpha-7 protein (Connexin-45) (Cx45)	0.37	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [TAS]			396
P69998 UniProt NPD GO	CXA9_RAJER	Gap junction alpha-9 protein (Connexin-35) (Cx35)	0.37	-	end	4 *	Membrane; multi-pass membrane protein				302
P69999 UniProt NPD GO	CXA9_RAJOC	Gap junction alpha-9 protein (Connexin-35) (Cx35)	0.37	-	end	4 *	Membrane; multi-pass membrane protein				302
Q9EST1 UniProt NPD GO	GSDM1_MOUSE	Gasdermin	0.37	-	cyt	0		cytoplasm [IDA]			446
O14091 UniProt NPD GO	SUT1_SCHPO	General alpha-glucoside permease	0.37	-	end	12 *	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS]			553
Q9JHK4 UniProt NPD GO	PGTA_MOUSE	Geranylgeranyl transferase type-2 alpha subunit (EC 2.5.1.60) (Geranylgeranyl transferase type II al ...	0.37	-	nuc	0					567
Q8N5D6 UniProt NPD GO	GBGT1_HUMAN	Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (EC 2.4.1.-) (Forssman glycolipid synthetase ...	0.37	-	end	1 *	Membrane; single-pass type II membrane protein (Potential)		606074		347
Q06210 UniProt NPD GO	GFPT1_HUMAN	Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (EC 2.6.1.16) (Hexosephosphate am ...	0.37	-	nuc	0			138292		698
Q9NFN6 UniProt NPD GO	GSH1_ONCVO	Glutamate--cysteine ligase (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamma-ECS) (GCS)	0.37	+	mit	0					652

You are viewing entries 34151 to 34200 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.