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
P07752 UniProt NPD GO	ALF_TRYBB	Fructose-bisphosphate aldolase, glycosomal (EC 4.1.2.13)	0.11	-	cyt	0	Glycosome			1F2J	371
P35795 UniProt NPD GO	SC14_SCHCO	Fruiting body protein SC14 precursor	0.11	-	exc	0	Secreted protein. Associated with the fruiting bodies				214
Q9I926 UniProt NPD GO	FUCL6_ANGJA	Fucolectin-6 precursor	0.11	-	cyt	1 *	Secreted protein	extracellular space [IDA]			186
P83120 UniProt NPD GO	MTH_DROSI	G-protein coupled receptor Mth precursor (Protein methuselah)	0.11	-	end	7	Membrane; multi-pass membrane protein (Potential)				515
Q95NQ0 UniProt NPD GO	MTH2_DROSI	G-protein coupled receptor Mth2 precursor (Protein methuselah-2)	0.11	-	end	7	Membrane; multi-pass membrane protein (Potential)				536
P30650 UniProt NPD GO	ZK643_CAEEL	G-protein coupled receptor ZK643.3	0.11	-	end	6	Membrane; multi-pass membrane protein (Potential)				480
P14635 UniProt NPD GO	CCNB1_HUMAN	G2/mitotic-specific cyclin-B1	0.11	-	mit	0			123836		433
P24860 UniProt NPD GO	CCNB1_MOUSE	G2/mitotic-specific cyclin-B1	0.11	-	mit	0		nucleus [IDA]			430
Q00420 UniProt NPD GO	GABP2_MOUSE	GA-binding protein beta chain (GABP subunit beta-2) (GABP-2) (GABP subunit beta-1) (GABPB-1)	0.11	-	cyt	0				1AWC	383
P32837 UniProt NPD GO	UGA4_YEAST	GABA-specific permease (GABA-specific transport protein)	0.11	-	end	11	Membrane; multi-pass membrane protein	vacuolar membrane (sensu Fungi) [IDA]			571
Q5AXD1 UniProt NPD GO	MCD4_EMENI	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-)	0.11	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				930
P36051 UniProt NPD GO	MCD4_YEAST	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-) (Morphogenesis checkpoint dependent protein 4) ...	0.11	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	cell wall (sensu Fungi) [IDA] endoplasmic reticulum [IDA] vacuole (sensu Fungi) [IDA]			919
Q2U9J2 UniProt NPD GO	GPI7_ASPOR	GPI ethanolamine phosphate transferase 2 (EC 2.-.-.-) (Glycosylphosphatidylinositol-anchor biosynthe ...	0.11	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				852
Q9BPQ5 UniProt NPD GO	PIGM_TRYBB	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Phosphatidylinositol- ...	0.11	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				430
Q09712 UniProt NPD GO	GPI18_SCHPO	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.11	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				426
Q6CDD0 UniProt NPD GO	SMP3_YARLI	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV)	0.11	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				510
P79735 UniProt NPD GO	RAN_BRARE	GTP-binding nuclear protein Ran (GTPase Ran)	0.11	+	cyt	0	Nucleus (By similarity)				215
Q7ZZX9 UniProt NPD GO	RAN_CARAU	GTP-binding nuclear protein Ran (GTPase Ran)	0.11	+	cyt	0	Nucleus (By similarity)				215
Q9YGC0 UniProt NPD GO	RAN_SALSA	GTP-binding nuclear protein Ran (GTPase Ran)	0.11	+	cyt	0	Nucleus (By similarity)				215
P38542 UniProt NPD GO	RAN_BRUMA	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.11	+	cyt	0	Nucleus (By similarity)				215
O17915 UniProt NPD GO	RAN_CAEEL	GTP-binding nuclear protein ran-1	0.11	+	cyt	0	Nucleus. At interphase, ran-1 is localized to the nucleus and the nuclear envelope. At prometaphase, ...				215
Q9UIJ7 UniProt NPD GO	KAD3_HUMAN	GTP:AMP phosphotransferase mitochondrial (EC 2.7.4.10) (Adenylate kinase 3) (AK3) (Adenylate kinase ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [ISS]		1ZD8	226
Q5F352 UniProt NPD GO	RASN_CHICK	GTPase NRas precursor (Transforming protein N-Ras)	0.11	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Golgi apparatus; Golgi membrane; lipi ...				189
P79737 UniProt NPD GO	RASN_BRARE	GTPase NRas precursor (Transforming protein N-Ras) (ZRas-B1)	0.11	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Golgi apparatus; Golgi membrane; lipi ...				188
P13181 UniProt NPD GO	GAL2_YEAST	Galactose transporter (Galactose permease)	0.11	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [NAS]			574
Q9Z144 UniProt NPD GO	LEG2_RAT	Galectin-2	0.11	-	nuc	0					130
P47953 UniProt NPD GO	LEG3_CRILO	Galectin-3 (Galactose-specific lectin 3) (Mac-2 antigen) (IgE-binding protein) (35 kDa lectin) (Carb ...	0.11	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). May be secreted by a non-classical secretory pat ...				244
P38552 UniProt NPD GO	LEG4_RAT	Galectin-4 (Lactose-binding lectin 4) (L-36 lactose-binding protein) (L36LBP)	0.11	-	cyt	0					324
P46157 UniProt NPD GO	GLL1A_CHICK	Gallinacin-1 alpha precursor (Gal-1 alpha) (Antimicrobial peptide CHP2) (Chicken heterophil peptide ...	0.11	-	end	0	Cytoplasmic granule				65
P46156 UniProt NPD GO	GLL1_CHICK	Gallinacin-1 precursor (Beta-defensin 1)	0.11	-	end	0	Cytoplasmic granule				65
Q5YKI7 UniProt NPD GO	GGNB1_HUMAN	Gametogenetin-binding protein 1	0.11	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Golgi apparatus (By similarity)		609495		109
P15431 UniProt NPD GO	GBRB1_RAT	Gamma-aminobutyric-acid receptor subunit beta-1 precursor (GABA(A) receptor)	0.11	-	mit	4	Membrane; multi-pass membrane protein				474
Q99JP7 UniProt NPD GO	GGT4_MOUSE	Gamma-glutamyltransferase 4 precursor (EC 2.3.2.2) (Gamma-glutamyltranspeptidase 4) (Gamma-glutamylt ...	0.11	-	end	1	Membrane; single-pass type II membrane protein (By similarity)				662
P07314 UniProt NPD GO	GGT1_RAT	Gamma-glutamyltranspeptidase 1 precursor (EC 2.3.2.2) (Gamma-glutamyltransferase 1) (GGT 1) (CD224 a ...	0.11	-	end	1 *	Membrane; single-pass type II membrane protein				568
P29414 UniProt NPD GO	CXA3_RAT	Gap junction alpha-3 protein (Connexin-46) (Cx46)	0.11	-	end	3 *	Membrane; multi-pass membrane protein	gap junction [IDA]			415
O95452 UniProt NPD GO	CXB6_HUMAN	Gap junction beta-6 protein (Connexin-30) (Cx30)	0.11	-	end	4 *	Membrane; multi-pass membrane protein		604418		261
Q9GMY4 UniProt NPD GO	PEPC_SORUN	Gastricsin precursor (EC 3.4.23.3) (Pepsinogen C)	0.11	-	vac	0	Secreted protein				389
P18737 UniProt NPD GO	ZG8_XENLA	Gastrula zinc finger protein XLCGF8.2DB (Fragment)	0.11	-	nuc	0	Nucleus (Potential)				196
Q9V931 UniProt NPD GO	OB57C_DROME	General odorant-binding protein 57c precursor	0.11	-	nuc	0					149
P16222 UniProt NPD GO	GLBL_LAMSP	Giant hemoglobin linker AV-1 chain	0.11	-	nuc	0					224
Q9XFR9 UniProt NPD GO	G2OX2_ARATH	Gibberellin 2-beta-dioxygenase 2 (EC 1.14.11.13) (Gibberellin 2-beta-hydroxylase 2) (Gibberellin 2-o ...	0.11	-	cyt	0					341
P02215 UniProt NPD GO	GLB_CERRH	Globin (Myoglobin)	0.11	-	mit	0					151
P02209 UniProt NPD GO	GLB3_MYXGL	Globin-3 (Hemoglobin III)	0.11	-	nuc	0					148
P24076 UniProt NPD GO	BGIA_MOMCH	Glu S.griseus protease inhibitor (BGIA)	0.11	-	cyt	0	Secreted protein				68
P68954 UniProt NPD GO	GLUC_ALLMI	Glucagon	0.11	-	nuc	0	Secreted protein				29
P68952 UniProt NPD GO	GLUC_ANAPL	Glucagon	0.11	-	nuc	0	Secreted protein				29
P68953 UniProt NPD GO	GLUC_STRCA	Glucagon	0.11	-	nuc	0	Secreted protein				29
P68955 UniProt NPD GO	GLUC_TRASC	Glucagon	0.11	-	nuc	0	Secreted protein				29
P15438 UniProt NPD GO	GLUC_RANCA	Glucagon precursor [Contains: Glucagon; Glucagon-36 (Oxyntomodulin); Glucagon-like peptide 1; Glucag ...	0.11	-	cyt	0	Secreted protein				103
Q875R9 UniProt NPD GO	EXG_SACKL	Glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.11	-	exc	0	Secreted protein (Potential)				439

You are viewing entries 62701 to 62750 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.