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
Q91ZM9 UniProt NPD GO	DOK5_MOUSE	Docking protein 5 (Downstream of tyrosine kinase 5) (Protein dok-5)	0.46	-	nuc	0					306
P70610 UniProt NPD GO	DOC2B_RAT	Double C2-like domain-containing protein beta (Doc2-beta)	0.46	-	nuc	0	Membrane; peripheral membrane protein				412
Q91447 UniProt NPD GO	MP2K1_SERCA	Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) (MAP kinase kinase 1) (MAPK ...	0.46	-	nuc	0					388
O93248 UniProt NPD GO	OPA1_ONCMA	Dynamin-like 120 kDa protein, mitochondrial precursor (120 kDa G protein expressed in motor neurons) ...	0.46	-	mit	0	Mitochondrion (By similarity)	dendrite [ISS] mitochondrial crista [ISS] mitochondrial intermembrane space [ISS] mitochondrial outer membrane [ISS]			971
P33730 UniProt NPD GO	LYAM2_CANFA	E-selectin precursor (Endothelial leukocyte adhesion molecule 1) (ELAM-1) (Leukocyte-endothelial cel ...	0.46	+	exc	1	Membrane; single-pass type I membrane protein				611
Q96C19 UniProt NPD GO	EFHD2_HUMAN	EF-hand domain-containing protein 2 (Swiprosin-1)	0.46	-	cyt	0					240
Q8K482 UniProt NPD GO	EMIL2_MOUSE	EMILIN-2 precursor (Elastin microfibril interface-located protein 2) (Elastin microfibril interfacer ...	0.46	-	nuc	0	Secreted protein; extracellular space; extracellular matrix. Found mainly at the interface between a ...				1074
P61552 UniProt NPD GO	EFCB_PAPAN	ERV-BabFcenv provirus ancestral Env polyprotein precursor (Envelope polyprotein) (BabFcenv) [Include ...	0.46	-	end	1 *					579
Q93YW0 UniProt NPD GO	EXEC1_ARATH	EXECUTER1 protein, chloroplast precursor	0.46	-	mit	0	Plastid; chloroplast				684
Q05215 UniProt NPD GO	EGR4_HUMAN	Early growth response protein 4 (EGR-4) (AT133)	0.46	-	nuc	0	Nucleus (Probable)		128992		486
Q9HC35 UniProt NPD GO	EMAL4_HUMAN	Echinoderm microtubule-associated protein-like 4 (EMAP-4) (Restrictedly overexpressed proliferation- ...	0.46	-	nuc	0	Cytoplasm	cytoplasm [NAS]	607442		981
Q04119 UniProt NPD GO	PPN1_YEAST	Endopolyphosphatase precursor (EC 3.6.1.10) (EC 3.6.1.11) (Exopolyphosphatase) (Phosphate metabolism ...	0.46	+	cyt	1 *	Vacuole; vacuolar membrane; single-pass type II membrane protein	vacuolar membrane [IDA]			674
Q9SP32 UniProt NPD GO	DICER_ARATH	Endoribonuclease Dicer homolog (EC 3.1.26.-) (Protein CARPEL FACTORY) (Protein SHORT INTEGUMENTS 1) ...	0.46	+	nuc	0	Nucleus (Potential)				1909
P13207 UniProt NPD GO	EDN3_RAT	Endothelin-3 precursor (ET-3) (Preproendothelin-3) (PPET3)	0.46	-	nuc	0	Secreted protein				167
Q10711 UniProt NPD GO	ECE2_BOVIN	Endothelin-converting enzyme 2 (EC 3.4.24.71) (ECE-2)	0.46	-	mit	1	Membrane; single-pass type II membrane protein	cytoplasmic vesicle membrane [ISS]			787
P97426 UniProt NPD GO	ECP1_MOUSE	Eosinophil cationic protein 1 precursor (EC 3.1.27.-) (ECP 1) (Ribonuclease 3-1) (RNase 3-1) (Eosino ...	0.46	-	exc	1 *	Matrix of eosinophil's large specific granule (By similarity)				155
P09759 UniProt NPD GO	EPHB1_RAT	Ephrin type-B receptor 1 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EPH-2) (ELK)	0.46	-	end	1	Membrane; single-pass type I membrane protein				984
Q91736 UniProt NPD GO	EPB1B_XENLA	Ephrin type-B receptor 1-B (EC 2.7.10.1) (Tyrosine-protein kinase receptor XELK) (Fragment)	0.46	-	nuc	1	Membrane; single-pass type I membrane protein				902
O35393 UniProt NPD GO	EFNB3_MOUSE	Ephrin-B3 precursor	0.46	-	end	2 *	Membrane; single-pass type I membrane protein				340
Q01279 UniProt NPD GO	EGFR_MOUSE	Epidermal growth factor receptor precursor (EC 2.7.10.1)	0.46	-	exc	2	Membrane; single-pass type I membrane protein	basolateral plasma membrane [IDA] endocytic vesicle [IDA] intracellular [IDA]			1210
O75822 UniProt NPD GO	IF31_HUMAN	Eukaryotic translation initiation factor 3 subunit 1 (eIF-3 alpha) (eIF3 p35) (eIF3j)	0.46	-	cyt	0		eukaryotic translation initiation factor 3 ... [TAS]	603910		258
Q91WK2 UniProt NPD GO	IF33_MOUSE	Eukaryotic translation initiation factor 3 subunit 3 (eIF-3 gamma) (eIF3 p40 subunit) (eIF3h)	0.46	-	nuc	0					352
Q60876 UniProt NPD GO	4EBP1_MOUSE	Eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) (eIF4E-binding protein 1) (Ph ...	0.46	-	nuc	0		cytoplasm [IC]			116
Q921I9 UniProt NPD GO	EXOS4_MOUSE	Exosome complex exonuclease RRP41 (EC 3.1.13.-) (Ribosomal RNA-processing protein 41) (Exosome compo ...	0.46	+	cyt	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				244
O43909 UniProt NPD GO	EXTL3_HUMAN	Exostosin-like 3 (EC 2.4.1.223) (Glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltran ...	0.46	-	gol	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein		605744		919
O00167 UniProt NPD GO	EYA2_HUMAN	Eyes absent homolog 2 (EC 3.1.3.48)	0.46	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		601654		538
O74783 UniProt NPD GO	POF2_SCHPO	F-box/LRR-repeat protein 2 (F-box and leucine-rich repeat protein 2) (F-box protein pof2)	0.46	-	mit	0					463
O95684 UniProt NPD GO	FR1OP_HUMAN	FGFR1 oncogene partner	0.46	-	nuc	0	Centrosome. Associated with gamma-tubulin		605392	2D68	399
Q6BSE7 UniProt NPD GO	FKBP3_DEBHA	FK506-binding protein 3 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.46	+	nuc	0	Nucleus; nucleolus (By similarity)				437
Q06205 UniProt NPD GO	FKBP4_YEAST	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.46	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			392
Q8BYN5 UniProt NPD GO	FSD1L_MOUSE	FSD1-like protein (FSD1 N-terminal-like protein) (Coiled-coil domain-containing protein 10)	0.46	-	nuc	0					131
P25653 UniProt NPD GO	FIG2_YEAST	Factor-induced gene 2 precursor (Cell wall adhesin FIG2)	0.46	-	nuc	0	Periphery of the mating cells. Localized to the mating projection. May be attached to the membrane b ...	cell wall (sensu Fungi) [IDA]			1609
Q92945 UniProt NPD GO	FUBP2_HUMAN	Far upstream element-binding protein 2 (FUSE-binding protein 2) (KH type-splicing regulatory protein ...	0.46	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). A small proportion is also found in the cytoplas ...		603445		707
Q9JIX9 UniProt NPD GO	FASTK_MOUSE	Fas-activated serine/threonine kinase (EC 2.7.11.8) (FAST kinase)	0.46	-	exc	0					511
P43098 UniProt NPD GO	FAS2_CANAL	Fatty acid synthase subunit alpha (EC 2.3.1.86) [Includes: Acyl carrier; 3-oxoacyl-[acyl-carrier-pro ...	0.46	-	nuc	0					1885
Q9QX79 UniProt NPD GO	FETUB_RAT	Fetuin-B precursor (IRL685)	0.46	-	exc	0	Secreted protein (Potential)				378
Q09147 UniProt NPD GO	FGFR2_DROME	Fibroblast growth factor receptor homolog 2 precursor (EC 2.7.10.1) (Protein breathless) (dFGF-R1)	0.46	-	end	2	Membrane; single-pass type I membrane protein	plasma membrane [IC]			1052
Q28377 UniProt NPD GO	FINC_HORSE	Fibronectin (FN) (Fragment)	0.46	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				522
P41439 UniProt NPD GO	FOLR3_HUMAN	Folate receptor gamma precursor (FR-gamma) (Folate receptor 3)	0.46	-	exc	0	Secreted protein	extrinsic to membrane [TAS] membrane fraction [TAS]	602469		243
P48760 UniProt NPD GO	FOLC_MOUSE	Folylpolyglutamate synthase, mitochondrial precursor (EC 6.3.2.17) (Folylpoly-gamma-glutamate synthe ...	0.46	-	mit	0	Mitochondrion. Cytoplasm				587
P40466 UniProt NPD GO	FKH1_YEAST	Fork head protein homolog 1	0.46	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			484
Q9DG99 UniProt NPD GO	CCNB2_ORYJA	G2/mitotic-specific cyclin-B2	0.46	-	cyt	0					382
Q9JJQ0 UniProt NPD GO	PIGB_MOUSE	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Phosphatidylinosi ...	0.46	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [IDA]			542
Q8IYK8 UniProt NPD GO	REM2_HUMAN	GTP-binding protein REM 2 (Rad and Gem-like GTP-binding protein 2)	0.46	-	nuc	0	Cell membrane (By similarity)				330
P78334 UniProt NPD GO	GBRE_HUMAN	Gamma-aminobutyric-acid receptor epsilon subunit precursor (GABA(A) receptor)	0.46	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	300093		506
P24046 UniProt NPD GO	GBRR1_HUMAN	Gamma-aminobutyric-acid receptor rho-1 subunit precursor (GABA(A) receptor)	0.46	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	137161		473
P56475 UniProt NPD GO	GBRR1_MOUSE	Gamma-aminobutyric-acid receptor rho-1 subunit precursor (GABA(A) receptor)	0.46	-	end	4	Membrane; multi-pass membrane protein				474
P68259 UniProt NPD GO	GLUC_CHICK	Glucagon precursor [Contains: Glicentin-related polypeptide (GRPP); Glucagon; Glucagon-like peptide ...	0.46	-	exc	0	Secreted protein				206
Q59ZI3 UniProt NPD GO	GNT1_CANAL	Glucose N-acetyltransferase 1 (EC 2.4.1.-) (N-acetylglucosaminyltransferase)	0.46	-	cyt	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity). Vacuole; vacu ...				462
P10387 UniProt NPD GO	GLT0_WHEAT	Glutenin, high molecular weight subunit DY10 precursor	0.46	-	exc	0					648

You are viewing entries 27601 to 27650 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.