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
O02775 UniProt NPD GO	EAP_BOVIN	Enteric beta-defensin precursor	0.11	-	mit	0	Secreted protein				64
P54754 UniProt NPD GO	EPHB3_MOUSE	Ephrin type-B receptor 3 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor MDK-5) (Developme ...	0.11	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]			993
P52804 UniProt NPD GO	EFNA5_CHICK	Ephrin-A5 precursor (EPH-related receptor tyrosine kinase ligand 7) (LERK-7) (RAGS protein)	0.11	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	anchored to plasma membrane [ISS] extracellular space [ISS]			228
Q2NKU9 UniProt NPD GO	EMP2_BOVIN	Epithelial membrane protein 2 (EMP-2)	0.11	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				167
P34913 UniProt NPD GO	HYES_HUMAN	Epoxide hydrolase 2 (EC 3.3.2.3) (Soluble epoxide hydrolase) (SEH) (Epoxide hydratase) (Cytosolic ep ...	0.11	-	mit	0	Cytoplasm. Peroxisome	cytosol [NAS] soluble fraction [NAS]	132811	1ZD5	555
P34914 UniProt NPD GO	HYES_MOUSE	Epoxide hydrolase 2 (EC 3.3.2.3) (Soluble epoxide hydrolase) (SEH) (Epoxide hydratase) (Cytosolic ep ...	0.11	-	mit	0	Cytoplasm. Peroxisome			1EK2	554
Q91V76 UniProt NPD GO	CK054_MOUSE	Ester hydrolase C11orf54 homolog (EC 3.1.-.-)	0.11	-	cyt	0	Nucleus (By similarity)				315
Q5U2Q3 UniProt NPD GO	CK054_RAT	Ester hydrolase C11orf54 homolog (EC 3.1.-.-)	0.11	-	cyt	0	Nucleus (By similarity)				315
P25726 UniProt NPD GO	EST5B_DROPS	Esterase-5B precursor (EC 3.1.1.1) (Est-5B) (Carboxylic-ester hydrolase 5B) (Carboxylesterase-5B)	0.11	-	exc	0	Secreted protein				545
Q9ZPQ3 UniProt NPD GO	GEK1_ARATH	Ethanol tolerance protein GEKO1	0.11	-	cyt	0					317
Q9SSY6 UniProt NPD GO	ETR1_CUCSA	Ethylene receptor (EC 2.7.13.3) (CS-ETR1)	0.11	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				740
Q9BMM0 UniProt NPD GO	ERF1_STYLE	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.11	-	cyt	0	Cytoplasm				445
Q9NAX8 UniProt NPD GO	ERF1_TRYBB	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.11	-	cyt	0	Cytoplasm (By similarity)				452
Q95L46 UniProt NPD GO	IF4G2_BOVIN	Eukaryotic translation initiation factor 4 gamma 2 (eIF-4-gamma 2) (eIF-4G 2) (eIF4G 2) (p97) (Fragm ...	0.11	-	nuc	0					136
Q9N0T5 UniProt NPD GO	IF4E_BOVIN	Eukaryotic translation initiation factor 4E (eIF4E) (eIF-4E) (mRNA cap-binding protein)	0.11	-	cyt	0					217
Q9DFS6 UniProt NPD GO	IF4EA_BRARE	Eukaryotic translation initiation factor 4E-1A (eIF4E-1A) (mRNA cap-binding protein)	0.11	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			215
P38672 UniProt NPD GO	IF5A_NEUCR	Eukaryotic translation initiation factor 5A (eIF-5A) (eIF-4D)	0.11	-	cyt	0					163
P07987 UniProt NPD GO	GUX2_TRIRE	Exoglucanase 2 precursor (EC 3.2.1.91) (Exoglucanase II) (Exocellobiohydrolase II) (CBHII) (1,4-beta ...	0.11	-	exc	0	Secreted protein			3CBH	471
O62714 UniProt NPD GO	CASR_PIG	Extracellular calcium-sensing receptor (CaSR) (Parathyroid Cell calcium-sensing receptor) (Fragments ...	0.11	-	end	3 *	Membrane; multi-pass membrane protein (By similarity)				208
Q9YH98 UniProt NPD GO	EYA4_CHICK	Eyes absent homolog 4 (EC 3.1.3.48) (Fragment)	0.11	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				119
Q8BHJ5 UniProt NPD GO	TBL1R_MOUSE	F-box-like/WD repeat protein TBL1XR1 (Transducin beta-like 1X-related protein 1) (Nuclear receptor c ...	0.11	-	cyt	0	Nucleus (By similarity)				514
Q5R941 UniProt NPD GO	FKB14_PONPY	FK506-binding protein 14 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rota ...	0.11	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				211
Q9NWM8 UniProt NPD GO	FKB14_HUMAN	FK506-binding protein 14 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rota ...	0.11	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				211
P20080 UniProt NPD GO	FKB1A_NEUCR	FK506-binding protein 1A (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (EC 5.2.1.8)	0.11	-	cyt	0	Cytoplasm				120
Q2KJC8 UniProt NPD GO	FKBP9_BOVIN	FK506-binding protein 9 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.11	-	end	0	Endoplasmic reticulum (By similarity)				574
P83318 UniProt NPD GO	FAR3_PENMO	FMRFamide-like neuropeptide FLP3 (AQPSMRLRF-amide)	0.11	-		0	Secreted protein				9
P83278 UniProt NPD GO	FAR5_MACRS	FMRFamide-like neuropeptide FLP5 (DRTPALRLRF-amide)	0.11	-		0	Secreted protein				10
Q08906 UniProt NPD GO	FIT2_YEAST	Facilitator of iron transport 2 precursor	0.11	-	nuc	0	Cell wall; lipid-anchor; GPI-anchor	cell wall (sensu Fungi) [IDA]			153
Q08907 UniProt NPD GO	FIT3_YEAST	Facilitator of iron transport 3 precursor	0.11	-	exc	0	Cell wall; lipid-anchor; GPI-anchor	cell wall (sensu Fungi) [IDA]			204
P80049 UniProt NPD GO	FABPL_GINCI	Fatty acid-binding protein, liver (L-FABP)	0.11	-	nuc	0	Cytoplasm				132
P02449 UniProt NPD GO	KRFT_DRONO	Feather keratin (F-ker)	0.11	-	nuc	0					102
Q9PRI5 UniProt NPD GO	KRF1_COLLI	Feather keratin Cos1-1/Cos1-3/Cos2-1 (F-ker)	0.11	-	nuc	0					100
Q9UPI3 UniProt NPD GO	FLVC2_HUMAN	Feline leukemia virus subgroup C receptor-related protein 2 (Calcium-chelate transporter) (CCT)	0.11	-	end	12	Cell membrane; multi-pass membrane protein				526
P53991 UniProt NPD GO	FENR_CHLRE	Ferredoxin--NADP reductase, chloroplast precursor (EC 1.18.1.2) (FNR)	0.11	-	mit	0	Plastid; chloroplast; chloroplast stroma. Stromal side of the thylakoid membrane in the vicinity of ...				354
O46415 UniProt NPD GO	FRIL_BOVIN	Ferritin light chain (Ferritin L subunit)	0.11	-	cyt	0					174
Q5R538 UniProt NPD GO	FRIL_PONPY	Ferritin light chain (Ferritin L subunit)	0.11	-	cyt	0					174
Q22053 UniProt NPD GO	FBRL_CAEEL	Fibrillarin	0.11	+	mit	0	Nucleus; nucleolus (By similarity). Fibrillar region of the nucleolus (By similarity)				352
Q8SR42 UniProt NPD GO	FBRL_ENCCU	Fibrillarin	0.11	-	cyt	0	Nucleus; nucleolus (By similarity). Fibrillar region of the nucleolus (By similarity)				291
Q9HE26 UniProt NPD GO	FBRL_NEUCR	Fibrillarin	0.11	+	cyt	0	Nucleus; nucleolus (By similarity). Fibrillar region of the nucleolus (By similarity)				323
P48804 UniProt NPD GO	FGF4_CHICK	Fibroblast growth factor 4 precursor (FGF-4) (HBGF-4)	0.11	-	exc	0					194
P48806 UniProt NPD GO	FGF4B_XENLA	Fibroblast growth factor 4-II precursor (FGF-4-II) (HBGF-4-II) (Embryonic fibroblast growth factor I ...	0.11	-	exc	1 *	Secreted protein (Probable)				192
P21802 UniProt NPD GO	FGFR2_HUMAN	Fibroblast growth factor receptor 2 precursor (EC 2.7.10.1) (FGFR-2) (Keratinocyte growth factor rec ...	0.11	-	end	1	Cell membrane; single-pass type I membrane protein. Isoform 14, isoform 19: Secreted protein	integral to membrane [NAS] membrane [NAS]	101200	2FDB	821
P21803 UniProt NPD GO	FGFR2_MOUSE	Fibroblast growth factor receptor 2 precursor (EC 2.7.10.1) (FGFR-2) (Keratinocyte growth factor rec ...	0.11	-	end	1	Membrane; single-pass type I membrane protein	nucleus [IDA]			821
Q9FKI0 UniProt NPD GO	FIMB2_ARATH	Fimbrin-like protein 2	0.11	-	cyt	0	Cytoplasm (By similarity)				687
P41440 UniProt NPD GO	S19A1_HUMAN	Folate transporter 1 (Solute carrier family 19 member 1) (Placental folate transporter) (FOLT) (Redu ...	0.11	-	end	11	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	600424		591
Q95179 UniProt NPD GO	FSHR_EQUAS	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.11	-	end	7	Membrane; multi-pass membrane protein				687
Q76JU9 UniProt NPD GO	FFAR1_MOUSE	Free fatty acid receptor 1 (G-protein coupled receptor 40)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				300
O14843 UniProt NPD GO	FFAR3_HUMAN	Free fatty acid receptor 3 (G-protein coupled receptor 41)	0.11	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603821		346
P09202 UniProt NPD GO	F16P_SCHPO	Fructose-1,6-bisphosphatase (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase) (FBPase)	0.11	-	nuc	0					347
P53447 UniProt NPD GO	ALDOB_SPAAU	Fructose-bisphosphate aldolase B (EC 4.1.2.13) (Liver-type aldolase)	0.11	-	cyt	0					363

You are viewing entries 62651 to 62700 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.