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
Q4V8I1 UniProt NPD GO	EPCR_RAT	Endothelial protein C receptor precursor (Endothelial cell protein C receptor) (Activated protein C ...	0.21	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				241
Q9UNN8 UniProt NPD GO	EPCR_HUMAN	Endothelial protein C receptor precursor (Endothelial cell protein C receptor) (Activated protein C ...	0.21	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600646	1LQV	238
Q22640 UniProt NPD GO	ERH_CAEEL	Enhancer of rudimentary homolog	0.21	-	nuc	0					103
P80030 UniProt NPD GO	FABI_BRANA	Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplast precursor (EC 1.3.1.9) (NADH-dependent en ...	0.21	-	mit	0	Plastid; chloroplast			1ENP	385
Q9TTQ4 UniProt NPD GO	CCL11_HORSE	Eotaxin precursor (Small inducible cytokine A11) (CCL11)	0.21	-	mit	0	Secreted protein				100
P80325 UniProt NPD GO	CCL11_CAVPO	Eotaxin precursor (Small inducible cytokine A11) (CCL11) (Eosinophil chemotactic protein)	0.21	-	exc	0	Secreted protein				96
P51671 UniProt NPD GO	CCL11_HUMAN	Eotaxin precursor (Small inducible cytokine A11) (CCL11) (Eosinophil chemotactic protein)	0.21	-	mit	1 *	Secreted protein		601156	2EOT	97
Q9UF33 UniProt NPD GO	EPHA6_HUMAN	Ephrin type-A receptor 6 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EHK-2) (EPH homol ...	0.21	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		600066		1035
Q90344 UniProt NPD GO	EPHB2_COTJA	Ephrin type-B receptor 2 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor QEK5)	0.21	-	end	1	Membrane; single-pass type I membrane protein				987
P48617 UniProt NPD GO	EPO_BOVIN	Erythropoietin precursor	0.21	-	end	1 *	Secreted protein				192
P33708 UniProt NPD GO	EPO_FELCA	Erythropoietin precursor	0.21	-	nuc	1 *	Secreted protein				192
Q9NVF9 UniProt NPD GO	EKI2_HUMAN	Ethanolamine kinase 2 (EC 2.7.1.82) (EKI 2) (Ethanolamine kinase-like protein)	0.21	-	nuc	0			609859		394
Q9UBQ5 UniProt NPD GO	IF3C_HUMAN	Eukaryotic translation initiation factor 3 subunit 12 (eIF-3 p25) (eIF-3 p28) (eIF3k) (Muscle-specif ...	0.21	-	cyt	0	Nucleus. Cytoplasm		609596	1RZ4	218
P48598 UniProt NPD GO	IF4E_DROME	Eukaryotic translation initiation factor 4E (eIF4E) (eIF-4E) (mRNA cap-binding protein) (eIF-4F 25 k ...	0.21	-	nuc	0		cytoplasm [IDA] eukaryotic translation initiation factor 4F... [NAS]			259
Q5E997 UniProt NPD GO	CAZA2_BOVIN	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.21	-	nuc	0					285
Q75DS4 UniProt NPD GO	CAPZA_ASHGO	F-actin capping protein subunit alpha	0.21	-	cyt	0					261
Q5RE08 UniProt NPD GO	FBX22_PONPY	F-box only protein 22	0.21	-	cyt	0					403
Q2YDD1 UniProt NPD GO	FR1OP_BOVIN	FGFR1 oncogene partner	0.21	-	nuc	0	Centrosome. Associated with gamma-tubulin (By similarity)				399
Q61576 UniProt NPD GO	FKB10_MOUSE	FK506-binding protein 10 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rota ...	0.21	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum lumen				581
Q9N4V0 UniProt NPD GO	FLP18_CAEEL	FMRFamide-like neuropeptide 18 precursor [Contains: SVPGVLRF-amide 1; SVPGVLRF-amide 2; SVPGVLRF-ami ...	0.21	-	exc	0	Secreted protein	extracellular region [IC]			208
Q96LA5 UniProt NPD GO	FCRL2_HUMAN	Fc receptor-like protein 2 precursor (SH2 domain-containing phosphatase anchor protein 1) (Fc recept ...	0.21	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)		606509		508
P25915 UniProt NPD GO	FRIH_RABIT	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit) (Fragment)	0.21	-	nuc	0					164
P49948 UniProt NPD GO	FRIH2_XENLA	Ferritin heavy chain 2 (EC 1.16.3.1) (XL2-17)	0.21	-	cyt	0					176
P29391 UniProt NPD GO	FRIL1_MOUSE	Ferritin light chain 1 (Ferritin L subunit 1)	0.21	-	cyt	0				1LB3	182
P22087 UniProt NPD GO	FBRL_HUMAN	Fibrillarin (34 kDa nucleolar scleroderma antigen)	0.21	+	cyt	0	Nucleus; nucleolus. Fibrillar region of the nucleolus		134795		321
P35550 UniProt NPD GO	FBRL_MOUSE	Fibrillarin (Nucleolar protein 1)	0.21	+	cyt	0	Nucleus; nucleolus. Fibrillar region of the nucleolus	Cajal body [IDA] nucleolus [IDA]			327
P22509 UniProt NPD GO	FBRL_RAT	Fibrillarin (Nucleolar protein 1)	0.21	+	cyt	0	Nucleus; nucleolus. Fibrillar region of the nucleolus	dense fibrillar component [IDA]			327
Q96581 UniProt NPD GO	C75A4_GENTR	Flavonoid 3',5'-hydroxylase (EC 1.14.13.88) (F3'5'H) (Cytochrome P450 75A4)	0.21	-	mit	0					516
Q62866 UniProt NPD GO	S19A1_RAT	Folate transporter 1 (Solute carrier family 19 member 1) (Reduced folate carrier 1) (RFC1) (RFC-1)	0.21	-	end	12 *	Membrane; multi-pass membrane protein (Probable)	plasma membrane [IDA]			512
Q7ZTV5 UniProt NPD GO	FSHR_CAIMO	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.21	-	end	7	Membrane; multi-pass membrane protein				693
P23945 UniProt NPD GO	FSHR_HUMAN	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.21	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	136435	1XWD	695
P32212 UniProt NPD GO	FSHR_MACFA	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.21	-	end	7	Membrane; multi-pass membrane protein				695
Q76JQ2 UniProt NPD GO	FLCN_RAT	Folliculin (Birt-Hogg-Dube syndrome protein homolog)	0.21	-	cyt	0					579
Q9VVX3 UniProt NPD GO	FRIZ2_DROME	Frizzled-2 precursor (dFz2)	0.21	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			694
Q9H479 UniProt NPD GO	FN3K_HUMAN	Fructosamine-3-kinase (EC 2.7.1.-)	0.21	-	cyt	0			608425		309
P07341 UniProt NPD GO	ALDOB_CHICK	Fructose-bisphosphate aldolase B (EC 4.1.2.13) (Liver-type aldolase)	0.21	-	nuc	0					363
Q9NQ84 UniProt NPD GO	GPC5C_HUMAN	G-protein coupled receptor family C group 5 member C precursor (Retinoic acid-induced gene 3 protein ...	0.21	-	end	8 *	Cell membrane; multi-pass membrane protein. Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi ...	integral to plasma membrane [TAS]	605949		441
O93229 UniProt NPD GO	CCNB2_RANJA	G2/mitotic-specific cyclin-B2	0.21	-	mit	0					392
Q2UTP0 UniProt NPD GO	SMP3_ASPOR	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV)	0.21	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				543
Q96S52 UniProt NPD GO	PIGS_HUMAN	GPI transamidase component PIG-S (Phosphatidylinositol-glycan biosynthesis class S protein)	0.21	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	GPI-anchor transamidase complex [TAS]			554
Q03515 UniProt NPD GO	NAR1_RABIT	GPI-linked NAD(P)(+)--arginine ADP-ribosyltransferase 1 precursor (EC 2.4.2.31) (Mono(ADP-ribosyl)tr ...	0.21	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum membrane; lipid-anchor; GPI-anchor				327
Q05915 UniProt NPD GO	GCH1_MOUSE	GTP cyclohydrolase I precursor (EC 3.5.4.16) (GTP-CH-I)	0.21	-	cyt	0					241
P22288 UniProt NPD GO	GCH1_RAT	GTP cyclohydrolase I precursor (EC 3.5.4.16) (GTP-CH-I)	0.21	-	cyt	0				1WPL	241
P38545 UniProt NPD GO	RAN_PLAFA	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.21	-	cyt	0	Nucleus (By similarity)				214
P41919 UniProt NPD GO	RANB1_TOBAC	GTP-binding nuclear protein Ran-B1	0.21	-	cyt	0	Nucleus (By similarity)				221
P17608 UniProt NPD GO	RYH1_SCHPO	GTP-binding protein ryh1	0.21	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201
P21963 UniProt NPD GO	LECG_CROAT	Galactose-specific lectin (RSL)	0.21	-	cyt	0	Secreted protein			1MUQ	135
Q90W78 UniProt NPD GO	GALE_KASSE	Galensin precursor	0.21	-	exc	0	Secreted protein				72
P02531 UniProt NPD GO	CRG2_RANTE	Gamma crystallin 2 (Gamma crystallin II) (Fragment)	0.21	-	nuc	0					169
P60521 UniProt NPD GO	GBRL2_MOUSE	Gamma-aminobutyric acid receptor-associated protein-like 2 (GABA(A) receptor-associated protein-like ...	0.21	-	cyt	0	Golgi apparatus (By similarity)	Golgi apparatus [IDA] Golgi membrane [IDA]			117

You are viewing entries 49451 to 49500 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.