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
P20941 UniProt NPD GO	PHOS_HUMAN	Phosducin (PHD) (33 kDa phototransducing protein) (MEKA protein)	0.34	-	cyt	0	Outer and inner segments of the rod cells		171490		246
Q9DBX2 UniProt NPD GO	PHLP_MOUSE	Phosducin-like protein (PHLP)	0.34	-	cyt	0					301
Q63737 UniProt NPD GO	PHLP_RAT	Phosducin-like protein (PHLP)	0.34	-	nuc	0					301
P42338 UniProt NPD GO	PK3CB_HUMAN	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta isoform (EC 2.7.1.153) (PI3-ki ...	0.34	-	cyt	0			602925		1070
P84742 UniProt NPD GO	PBL1F_EUGGR	Photoactivated adenylate cyclase subunit beta-like protein 1224-5/1F	0.34	-	cyt	0	Flagellum. Paraxonemal body. And paraxonemal bodies (PABs)	flagellum [IDA]			859
P46486 UniProt NPD GO	PSAF_FLATR	Photosystem I reaction center subunit III, chloroplast precursor (Light-harvesting complex I 17 kDa ...	0.34	-	nuc	1	Plastid; chloroplast; chloroplast thylakoid lumen				232
Q41046 UniProt NPD GO	PHY_PINSY	Phytochrome	0.34	-	nuc	0					1131
P06593 UniProt NPD GO	PHYA3_AVESA	Phytochrome A type 3 (AP3)	0.34	-	nuc	0					1128
P06595 UniProt NPD GO	PHYA5_AVESA	Phytochrome A type 5 (AP5) (Fragment)	0.34	-	mit	0					494
P93526 UniProt NPD GO	PHYA_SORBI	Phytochrome a	0.34	-	mit	0					1131
P37295 UniProt NPD GO	PSY_NEUCR	Phytoene synthase (EC 2.5.1.-) (Albino-2 protein)	0.34	+	end	6 *	Membrane; multi-pass membrane protein				602
P13589 UniProt NPD GO	PACA_RAT	Pituitary adenylate cyclase-activating polypeptide precursor (PACAP) [Contains: PACAP-related peptid ...	0.34	-	nuc	0	Secreted protein				175
P28877 UniProt NPD GO	PMA1_CANAL	Plasma membrane ATPase 1 (EC 3.6.3.6) (Proton pump 1)	0.34	+	end	8	Cell membrane; multi-pass membrane protein				895
P14725 UniProt NPD GO	LAV1_PHYPO	Plasmodial-specific protein LAV1-2	0.34	-	nuc	0				1IJ6	355
O08770 UniProt NPD GO	GPV_RAT	Platelet glycoprotein V precursor (GPV) (CD42D antigen)	0.34	-	end	1	Membrane; single-pass type I membrane protein				567
Q94A18 UniProt NPD GO	PDR1_ARATH	Pleiotropic drug resistance protein 1	0.34	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1416
Q949G3 UniProt NPD GO	PDR1_NICPL	Pleiotropic drug resistance protein 1 (NpPDR1)	0.34	-	end	13	Cell membrane; multi-pass membrane protein				1436
Q8S628 UniProt NPD GO	PDR13_ORYSA	Pleiotropic drug resistance protein 13	0.34	+	end	13	Membrane; multi-pass membrane protein (By similarity)				1441
Q2KID6 UniProt NPD GO	PLRG1_BOVIN	Pleiotropic regulator 1	0.34	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				513
Q6UX71 UniProt NPD GO	PXDC2_HUMAN	Plexin domain-containing protein 2 precursor (Tumor endothelial marker 7-related protein)	0.34	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)		606827		529
P43212 UniProt NPD GO	PGLR2_CRYJA	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase) (Major pollen allergen Cry j 2) (Cry j II ...	0.34	-	nuc	0	Or: Secreted protein (Potential). Or: Plastid; amyloplast (Potential)				514
Q6NZI2 UniProt NPD GO	PTRF_HUMAN	Polymerase I and transcript release factor (PTRF protein)	0.34	-	nuc	0	Cell membrane; caveola. Found at the surface of the caveolae. Cell membrane. Microsome. Cytoplasm; c ...		603198		390
Q95ZJ1 UniProt NPD GO	GALT5_CAEEL	Polypeptide N-acetylgalactosaminyltransferase 5 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.34	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				626
Q00438 UniProt NPD GO	PTBP1_RAT	Polypyrimidine tract-binding protein 1 (PTB) (Heterogeneous nuclear ribonucleoprotein I) (hnRNP I) ( ...	0.34	-	nuc	0	Nucleus				555
Q9HBU9 UniProt NPD GO	POPD2_HUMAN	Popeye domain-containing protein 2 (Popeye protein 2)	0.34	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]	605823		364
Q6CT60 UniProt NPD GO	HEM3_KLULA	Porphobilinogen deaminase (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyri ...	0.34	-	nuc	0					327
Q8VYX2 UniProt NPD GO	AKT1_ORYSA	Potassium channel AKT1 (OsAKT1)	0.34	+	end	5	Membrane; multi-pass membrane protein (Probable)				935
P17971 UniProt NPD GO	KCNAL_DROME	Potassium voltage-gated channel protein Shal (Shal2)	0.34	-	end	6	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]			490
Q03721 UniProt NPD GO	KCNC4_HUMAN	Potassium voltage-gated channel subfamily C member 4 (Voltage-gated potassium channel subunit Kv3.4) ...	0.34	+	end	3	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	176265	1B4I	635
Q92036 UniProt NPD GO	AT12A_BUFMA	Potassium-transporting ATPase alpha chain 2 (EC 3.6.3.10) (Proton pump) (Non-gastric H(+)/K(+) ATPas ...	0.34	+	end	8	Membrane; multi-pass membrane protein				1042
Q64392 UniProt NPD GO	AT12A_CAVPO	Potassium-transporting ATPase alpha chain 2 (EC 3.6.3.10) (Proton pump) (Non-gastric H(+)/K(+) ATPas ...	0.34	+	end	8	Membrane; multi-pass membrane protein				1033
Q99177 UniProt NPD GO	BRR1_YEAST	Pre-mRNA-splicing factor BRR1 (Bad response to refrigeration protein 1)	0.34	-	mit	0	Nucleus	small nuclear ribonucleoprotein complex [IDA]			341
Q6BU94 UniProt NPD GO	PRP46_DEBHA	Pre-mRNA-splicing factor PRP46 (Pre-mRNA-processing protein 46)	0.34	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				417
Q4PGM6 UniProt NPD GO	RSE1_USTMA	Pre-mRNA-splicing factor RSE1	0.34	-	nuc	0	Nucleus (By similarity)				1221
Q6CYA2 UniProt NPD GO	SYF1_KLULA	Pre-mRNA-splicing factor SYF1	0.34	-	cyt	0	Nucleus (By similarity)				798
Q5TJE6 UniProt NPD GO	PFD6_CANFA	Prefoldin subunit 6 (Protein Ke2)	0.34	-	nuc	0					129
O15212 UniProt NPD GO	PFD6_HUMAN	Prefoldin subunit 6 (Protein Ke2)	0.34	-	nuc	0		prefoldin complex [NAS]	605660		129
Q00968 UniProt NPD GO	EGF_PIG	Pro-epidermal growth factor precursor (EGF) [Contains: Epidermal growth factor]	0.34	-	end	1	Membrane; single-pass type I membrane protein				1214
Q96K78 UniProt NPD GO	GP128_HUMAN	Probable G-protein coupled receptor 128 precursor	0.34	-	end	8 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]			797
Q9TTQ9 UniProt NPD GO	GPR83_CANFA	Probable G-protein coupled receptor 83 precursor (Glucocorticoid-induced receptor)	0.34	+	end	7	Membrane; multi-pass membrane protein				422
O14110 UniProt NPD GO	GCST_SCHPO	Probable aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T pr ...	0.34	-	mit	0	Mitochondrion (By similarity)				387
P35315 UniProt NPD GO	ATC_TRYBB	Probable calcium-transporting ATPase (EC 3.6.3.8) (Calcium pump)	0.34	+	end	10	Integral membrane protein. May be located in the flagellar pocket of the membrane				1011
Q9SJ22 UniProt NPD GO	CESA9_ARATH	Probable cellulose synthase A catalytic subunit 9 [UDP-forming] (EC 2.4.1.12) (AtCesA-9)	0.34	-	end	6	Cell membrane; multi-pass membrane protein (Probable)				1088
Q9VFJ0 UniProt NPD GO	CP131_DROME	Probable cytochrome P450 313a1 (EC 1.14.-.-) (CYPCCCXIIIA1)	0.34	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				492
Q9V5L3 UniProt NPD GO	C49A1_DROME	Probable cytochrome P450 49a1 (EC 1.14.-.-) (CYPXLIXA1)	0.34	+	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				589
Q9W223 UniProt NPD GO	CP6D2_DROME	Probable cytochrome P450 6d2 (EC 1.14.-.-) (CYPVID2)	0.34	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				512
Q1S9I9 UniProt NPD GO	H2B1_MEDTR	Probable histone H2B.1	0.34	+	nuc	0	Nucleus (By similarity)				147
Q1SWQ1 UniProt NPD GO	H2B2_MEDTR	Probable histone H2B.2	0.34	+	nuc	0	Nucleus (By similarity)				147
O23346 UniProt NPD GO	HIS7B_ARATH	Probable imidazoleglycerol-phosphate dehydratase 2 (EC 4.2.1.19) (IGPD 2)	0.34	-	mit	0					259
Q7KUD5 UniProt NPD GO	INSL5_DROME	Probable insulin-like peptide 5 precursor (Insulin-related peptide) (DILP5) [Contains: Probable insu ...	0.34	-	exc	0	Secreted protein (Potential)	extracellular region [ISS]			108

You are viewing entries 36951 to 37000 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.)

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