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
Q9D0F3 UniProt NPD GO	LMAN1_MOUSE	ERGIC-53 protein precursor (ER-Golgi intermediate compartment 53 kDa protein) (Lectin, mannose-bindi ...	0.35	-	cyt	1	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...	ER-Golgi intermediate compartment [IDA] Golgi apparatus [IDA] sarcomere [IDA]			517
P26641 UniProt NPD GO	EF1G_HUMAN	Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma)	0.35	-	cyt	0		intracellular [NAS]	130593	1PBU	436
Q6TY21 UniProt NPD GO	EPA2B_XENLA	Embryonic polyadenylate-binding protein 2-B (Embryonic poly(A)-binding protein 2-B) (Embryonic poly( ...	0.35	-	nuc	0	Cytoplasm	cytoplasm [IDA]			218
Q12168 UniProt NPD GO	ENG2_YEAST	Endo-1,3(4)-beta-glucanase 2 (EC 3.2.1.6) (Endo-1,4-beta-glucanase 2) (Endo-1,3-beta-glucanase 2) (L ...	0.35	-	nuc	0	Cytoplasm	intracellular [TAS]			779
P17813 UniProt NPD GO	EGLN_HUMAN	Endoglin precursor (CD105 antigen)	0.35	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	187300		658
Q6R2P8 UniProt NPD GO	NEIL2_MOUSE	Endonuclease VIII-like 2 (EC 3.2.2.-) (EC 4.2.99.18) (Nei-like 2) (DNA glycosylase/AP lyase Neil2) ( ...	0.35	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] spindle microtubule [IDA]			328
Q38802 UniProt NPD GO	KSA_ARATH	Ent-kaurene synthase A, chloroplast precursor (EC 5.5.1.13) (Ent-copalyl diphosphate synthase) (KSA) ...	0.35	-	mit	0	Plastid; chloroplast	chloroplast [TAS]			802
P12724 UniProt NPD GO	ECP_HUMAN	Eosinophil cationic protein precursor (EC 3.1.27.-) (ECP) (Ribonuclease 3) (RNase 3)	0.35	-	exc	0	Matrix of eosinophil's large specific granule	extracellular region [TAS] soluble fraction [TAS]	131398	1QMT	160
P47781 UniProt NPD GO	ECP_PONPY	Eosinophil cationic protein precursor (EC 3.1.27.-) (ECP) (Ribonuclease 3) (RNase 3)	0.35	-	mit	1 *	Matrix of eosinophil's large specific granule				160
Q9TTS6 UniProt NPD GO	CCL11_BOVIN	Eotaxin precursor (Small inducible cytokine A11) (CCL11)	0.35	-	mit	0	Secreted protein				97
Q91845 UniProt NPD GO	EPA4A_XENLA	Ephrin type-A receptor 4-A precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor SEK-1) (xSEK-1) ...	0.35	-	end	1 *	Membrane; single-pass type I membrane protein				986
Q91694 UniProt NPD GO	EPA4B_XENLA	Ephrin type-A receptor 4-B precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor PAG) (Pagliacci ...	0.35	-	end	1 *	Membrane; single-pass type I membrane protein				985
O08644 UniProt NPD GO	EPHB6_MOUSE	Ephrin type-B receptor 6 precursor (Tyrosine-protein kinase-defective receptor EPH-6) (MEP)	0.35	-	end	2 *	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2, isoform 3: Secreted protei ...				1014
O73612 UniProt NPD GO	EFNB1_CHICK	Ephrin-B1 precursor (CEK5 ligand) (CEL5-L)	0.35	-	end	1	Membrane; single-pass type I membrane protein				334
Q9DA01 UniProt NPD GO	EPPI_MOUSE	Eppin precursor (Epididymal protease inhibitor) (Serine protease inhibitor-like with Kunitz and WAP ...	0.35	-	exc	0	Secreted protein (Potential)	acrosome [IDA] cytoplasm [IDA]			134
Q9Y6I3 UniProt NPD GO	EPN1_HUMAN	Epsin-1 (EPS-15-interacting protein 1) (EH domain-binding mitotic phosphoprotein)	0.35	-	mit	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity). Nucleus (By s ...		607262	1INZ	551
Q92080 UniProt NPD GO	NARE_CHICK	Erythroblast NAD(P)(+)--arginine ADP-ribosyltransferase precursor (EC 2.4.2.31) (Mono(ADP-ribosyl)tr ...	0.35	-	mit	0					300
O02494 UniProt NPD GO	IF4A_CRYPV	Eukaryotic initiation factor 4A (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A) (eIF-4A)	0.35	-	cyt	0					405
P29562 UniProt NPD GO	IF4A1_RABIT	Eukaryotic initiation factor 4A-I (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-1) (eIF4A-I) (eIF-4 ...	0.35	-	cyt	0					398
Q9Z1D1 UniProt NPD GO	IF34_MOUSE	Eukaryotic translation initiation factor 3 subunit 4 (eIF-3 delta) (eIF3 p44) (eIF-3 RNA-binding sub ...	0.35	-	nuc	0					320
Q28619 UniProt NPD GO	NHERF_RABIT	Ezrin-radixin-moesin-binding phosphoprotein 50 (EBP50) (Na(+)/H(+) exchange regulatory cofactor NHE- ...	0.35	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity). Colocalizes with actin in mi ...				357
Q91W61 UniProt NPD GO	FBX37_MOUSE	F-box only protein 37 (F-box/LRR-repeat protein 15)	0.35	-	cyt	0					296
Q6PDJ6 UniProt NPD GO	FBX42_MOUSE	F-box only protein 42	0.35	-	nuc	0					717
Q9UF56 UniProt NPD GO	FXL17_HUMAN	F-box/LRR-repeat protein 17 (F-box and leucine-rich repeat protein 17) (F-box only protein 13) (Frag ...	0.35	-	cyt	0			609083		370
Q09855 UniProt NPD GO	POF11_SCHPO	F-box/WD repeat protein pof11	0.35	-	cyt	0					506
Q756X6 UniProt NPD GO	POB3_ASHGO	FACT complex subunit POB3 (Facilitates chromatin transcription complex subunit POB3)	0.35	+	cyt	0	Nucleus (By similarity)				542
P38913 UniProt NPD GO	FAD1_YEAST	FAD synthetase (EC 2.7.7.2) (FMN adenylyltransferase) (FAD pyrophosphorylase) (Flavin adenine dinucl ...	0.35	-	cyt	0	Cytoplasm	cytoplasm [IDA]			306
Q4V7C1 UniProt NPD GO	FR1OP_RAT	FGFR1 oncogene partner	0.35	-	nuc	0	Centrosome. Associated with gamma-tubulin (By similarity)				399
Q9TUX7 UniProt NPD GO	NPFF_BOVIN	FMRFamide-related peptides precursor [Contains: Neuropeptide SF (NPSF); Neuropeptide FF (NPFF); Neur ...	0.35	-	exc	0	Secreted protein				115
P15278 UniProt NPD GO	FAS3_DROME	Fasciclin-3 precursor (Fasciclin III) (FAS III)	0.35	-	end	1	Membrane; single-pass type I membrane protein	basolateral plasma membrane [NAS] lateral plasma membrane [TAS] plasma membrane [TAS] septate junction [TAS]			508
Q920A9 UniProt NPD GO	FCRL_MOUSE	Fc receptor-like and mucin-like 1 precursor (Fc receptor homolog expressed in B-cells) (Fc receptor- ...	0.35	-	exc	0	Secreted protein (Probable). Cytoplasm (By similarity)				352
P19132 UniProt NPD GO	FRIH_RAT	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit)	0.35	-	nuc	0		plasma membrane [ISS]			181
P02676 UniProt NPD GO	FIBB_BOVIN	Fibrinogen beta chain precursor [Contains: Fibrinopeptide B]	0.35	-	nuc	0	Secreted protein			1JY3	468
Q92914 UniProt NPD GO	FGF11_HUMAN	Fibroblast growth factor 11 (FGF-11) (Fibroblast growth factor homologous factor 3) (FHF-3)	0.35	-	nuc	0			601514		225
P70378 UniProt NPD GO	FGF11_MOUSE	Fibroblast growth factor 11 (FGF-11) (Fibroblast growth factor homologous factor 3) (FHF-3)	0.35	-	nuc	0	Nucleus (Probable)				225
Q9HCT0 UniProt NPD GO	FGF22_HUMAN	Fibroblast growth factor 22 precursor (FGF-22)	0.35	-	mit	0	Secreted protein (Potential)	extracellular space [NAS]	605831		170
Q7TQM3 UniProt NPD GO	FGRL1_RAT	Fibroblast growth factor receptor-like 1 precursor (FGF receptor-like protein 1)	0.35	-	exc	1	Membrane; single-pass type I membrane protein (By similarity). Predominantly localized in the plasma ...				529
Q8N441 UniProt NPD GO	FGRL1_HUMAN	Fibroblast growth factor receptor-like 1 precursor (FGF receptor-like protein 1) (Fibroblast growth ...	0.35	-	exc	1	Membrane; single-pass type I membrane protein. Predominantly localized in the plasma membrane but al ...		605830		504
Q9GKY0 UniProt NPD GO	FSTL1_MACFA	Follistatin-related protein 1 precursor (Follistatin-like 1)	0.35	-	exc	0	Secreted protein (Potential)				308
Q9ZR07 UniProt NPD GO	FRDA_ARATH	Frataxin homolog	0.35	-	mit	0					187
Q8WMU5 UniProt NPD GO	FZD6_CANFA	Frizzled-6 precursor (Fz-6)	0.35	+	end	7	Membrane; multi-pass membrane protein				712
O60353 UniProt NPD GO	FZD6_HUMAN	Frizzled-6 precursor (Fz-6) (hFz6)	0.35	+	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603409		706
P48051 UniProt NPD GO	IRK6_HUMAN	G protein-activated inward rectifier potassium channel 2 (GIRK2) (Potassium channel, inwardly rectif ...	0.35	-	end	2	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	600877		423
Q5NUL3 UniProt NPD GO	GP120_HUMAN	G-protein coupled receptor 120 (G-protein coupled receptor PGR4) (G-protein coupled receptor GT01) ( ...	0.35	-	end	7 *	Membrane; multi-pass membrane protein		609044		377
O18982 UniProt NPD GO	GPR15_CERAE	G-protein coupled receptor 15	0.35	-	end	7 *	Membrane; multi-pass membrane protein				360
P37883 UniProt NPD GO	CCNB2_MESAU	G2/mitotic-specific cyclin-B2	0.35	-	nuc	0					397
P30276 UniProt NPD GO	CCNB2_MOUSE	G2/mitotic-specific cyclin-B2	0.35	-	nuc	0					398
Q6EV56 UniProt NPD GO	OFUT2_PANTR	GDP-fucose protein O-fucosyltransferase 2 precursor (EC 2.4.1.221) (Peptide-O-fucosyltransferase) (O ...	0.35	-	exc	0	Endoplasmic reticulum (By similarity)				429
Q3MHZ7 UniProt NPD GO	GPI8_BOVIN	GPI-anchor transamidase precursor (EC 3.-.-.-) (GPI transamidase) (Phosphatidylinositol-glycan biosy ...	0.35	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	GPI-anchor transamidase complex [ISS]			395
Q07983 UniProt NPD GO	RASK_MONDO	GTPase KRas (K-Ras 2) (Ki-Ras) (c-K-ras) (c-Ki-ras)	0.35	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity)				188

You are viewing entries 35801 to 35850 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.