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
O49347 UniProt NPD GO	PSBY_ARATH	Photosystem II core complex proteins psbY, chloroplast precursor (L-arginine-metabolizing enzyme) (L ...	0.18	-	end	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				189
Q92561 UniProt NPD GO	PHYIP_HUMAN	Phytanoyl-CoA hydroxylase-interacting protein (Phytanoyl-CoA hydroxylase-associated protein 1) (PAHX ...	0.18	-	cyt	0			608511		330
Q8K0S0 UniProt NPD GO	PHYIP_MOUSE	Phytanoyl-CoA hydroxylase-interacting protein (Phytanoyl-CoA hydroxylase-associated protein 1) (PAHX ...	0.18	-	cyt	0					330
P32215 UniProt NPD GO	PACR_RAT	Pituitary adenylate cyclase-activating polypeptide type IA receptor precursor (PACAP type IA recepto ...	0.18	-	end	7	Membrane; multi-pass membrane protein				523
Q9JHK0 UniProt NPD GO	PRLPM_MOUSE	Placental prolactin-like protein M precursor (PRL-like protein M) (PLP-M)	0.18	-	nuc	0	Secreted protein (By similarity)				228
P23220 UniProt NPD GO	AT2B1_PIG	Plasma membrane calcium-transporting ATPase 1 (EC 3.6.3.8) (PMCA1) (Plasma membrane calcium pump iso ...	0.18	-	end	7	Cell membrane; multi-pass membrane protein				1220
Q02325 UniProt NPD GO	PRGB_HUMAN	Plasminogen-related protein B precursor	0.18	-	mit	0	Secreted protein		173340		96
P30066 UniProt NPD GO	RK16_EPIVI	Plastid 50S ribosomal protein L16	0.18	-	nuc	0	Plastid				135
P19179 UniProt NPD GO	PLSI_CHICK	Plastin-1 (Fimbrin)	0.18	-	cyt	0	Cytoplasm				630
Q9JLB9 UniProt NPD GO	PVRL3_MOUSE	Poliovirus receptor-related protein 3 precursor (Cell adhesion molecule nectin-3) (Nectin-3) (CDw113 ...	0.18	-	end	1	Membrane; single-pass membrane protein (Potential)	cell-cell adherens junction [IDA]			549
Q7M1E7 UniProt NPD GO	PGLR2_CHAOB	Polygalacturonase precursor (PG) (EC 3.2.1.15) (Pectinase) (Major pollen allergen Cha o 2)	0.18	-	nuc	0	Secreted protein				514
Q08304 UniProt NPD GO	PPOB_LYCES	Polyphenol oxidase B, chloroplast precursor (EC 1.10.3.1) (PPO) (Catechol oxidase)	0.18	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				596
Q9M7J9 UniProt NPD GO	POT8_ARATH	Potassium transporter 8 (AtPOT8) (AtHAK8)	0.18	-	end	13 *	Cell membrane; multi-pass membrane protein (Potential)				781
O35173 UniProt NPD GO	KCNS1_MOUSE	Potassium voltage-gated channel subfamily S member 1 (Voltage-gated potassium channel subunit Kv9.1) ...	0.18	-	end	3	Cell membrane; multi-pass membrane protein. Membrane; multi-pass membrane protein. May not reach the ...	plasma membrane [ISS] voltage-gated potassium channel complex [ISS]			497
Q9UTB8 UniProt NPD GO	INI1_SCHPO	Pre-mRNA-splicing factor ini1	0.18	-	nuc	0	Nucleus	nucleus [IDA]			117
Q06672 UniProt NPD GO	TSR2_YEAST	Pre-rRNA-processing protein TSR2 (20S rRNA accumulation protein 2)	0.18	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			205
Q8HYI9 UniProt NPD GO	PFD5_BOVIN	Prefoldin subunit 5	0.18	-	cyt	0					154
Q5RAY0 UniProt NPD GO	PFD5_PONPY	Prefoldin subunit 5	0.18	-	cyt	0					154
Q99471 UniProt NPD GO	PFD5_HUMAN	Prefoldin subunit 5 (C-myc-binding protein Mm-1) (Myc modulator 1)	0.18	-	cyt	0		cytoplasm [TAS] nucleus [TAS]	604899		154
Q38885 UniProt NPD GO	SECY_ARATH	Preprotein translocase secY subunit, chloroplast precursor (CpSecY)	0.18	-	end	6	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				551
Q01608 UniProt NPD GO	SPE4_CAEEL	Presenilin spe-4	0.18	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				465
Q9EPH0 UniProt NPD GO	S26A5_RAT	Prestin (Solute carrier family 26 member 5)	0.18	-	end	10	Integral membrane protein; lateral wall of outer hair cells	lateral plasma membrane [IDA]			744
Q10071 UniProt NPD GO	STE24_SCHPO	Probable CAAX prenyl protease 1 (EC 3.4.24.84) (Prenyl protein-specific endoprotease 1) (PPSEP 1)	0.18	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				474
Q17684 UniProt NPD GO	RPB6_CAEEL	Probable DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide (EC 2.7.7.6) (RPB6)	0.18	-	cyt	0	Nucleus (By similarity)				137
Q9Y5Y3 UniProt NPD GO	GPR45_HUMAN	Probable G-protein coupled receptor 45 (PSP24-alpha) (PSP24-1)	0.18	-	vac	7 *	Membrane; multi-pass membrane protein		604838		372
Q9BZJ6 UniProt NPD GO	GPR63_HUMAN	Probable G-protein coupled receptor 63 (PSP24-beta) (PSP24-2)	0.18	-	end	7	Membrane; multi-pass membrane protein	membrane [NAS]	606915		419
Q9VS77 UniProt NPD GO	MTH6_DROME	Probable G-protein coupled receptor Mth-like 6 precursor (Protein methuselah-like 6)	0.18	-	end	7	Membrane; multi-pass membrane protein (Potential)				480
Q09638 UniProt NPD GO	YR13_CAEEL	Probable G-protein coupled receptor T27D1.3	0.18	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				356
P43084 UniProt NPD GO	EBP1_CANAL	Probable NADPH dehydrogenase (EC 1.6.99.1) (Estrogen-binding protein) (EBP)	0.18	-	cyt	0					406
Q9BLB6 UniProt NPD GO	RU2A_CAEEL	Probable U2 small nuclear ribonucleoprotein A' (U2 snRNP-A') (Spliceosome-associated protein 1)	0.18	-	nuc	0	Nucleus (Potential)				253
P91167 UniProt NPD GO	ARPC5_CAEEL	Probable actin-related protein 2/3 complex subunit 5 (ARP2/3 complex 16 kDa subunit) (p16-ARC)	0.18	-	mit	0					146
O13914 UniProt NPD GO	SYAC_SCHPO	Probable alanyl-tRNA synthetase, cytoplasmic (EC 6.1.1.7) (Alanine--tRNA ligase) (AlaRS)	0.18	-	cyt	0	Cytoplasm (Potential)				959
O14154 UniProt NPD GO	AMY3_SCHPO	Probable alpha-amylase meu30 precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (Mei4-depe ...	0.18	-	mit	0					513
P40884 UniProt NPD GO	MALX1_YEAST	Probable alpha-glucosidase YJL216C (EC 3.2.1.20) (Maltase)	0.18	-	cyt	0					581
O64817 UniProt NPD GO	CSK23_ARATH	Probable casein kinase II subunit alpha (EC 2.7.11.1) (CK II)	0.18	-	cyt	0					333
Q8L481 UniProt NPD GO	HKT3_ORYSA	Probable cation transporter HKT3 (OsHKT3)	0.18	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				509
Q8L4K5 UniProt NPD GO	HKT9_ORYSA	Probable cation transporter HKT9 (OsHKT9)	0.18	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				509
O74767 UniProt NPD GO	COPE_SCHPO	Probable coatomer subunit epsilon (Epsilon-coat protein) (Epsilon-COP)	0.18	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				288
O22682 UniProt NPD GO	CYSK4_ARATH	Probable cysteine synthase, chloroplast precursor (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-ac ...	0.18	-	nuc	0	Plastid; chloroplast (Potential)				404
Q9V770 UniProt NPD GO	C6A17_DROME	Probable cytochrome P450 6a17 (EC 1.14.-.-) (CYPVIA17)	0.18	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				501
Q940K0 UniProt NPD GO	DRL15_ARATH	Probable disease resistance protein At1g61180	0.18	-	cyt	0					889
Q9VKX7 UniProt NPD GO	ALG6_DROME	Probable dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl-P-G ...	0.18	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				475
O13775 UniProt NPD GO	SYEC_SCHPO	Probable glutamyl-tRNA synthetase, cytoplasmic (EC 6.1.1.17) (Glutamate--tRNA ligase) (GluRS)	0.18	-	cyt	0	Cytoplasm (By similarity)				716
Q9LZ46 UniProt NPD GO	H2A4_ARATH	Probable histone H2A.4 (HTA12)	0.18	-	nuc	0	Nucleus (By similarity)				153
Q94E96 UniProt NPD GO	H2A5_ORYSA	Probable histone H2A.5	0.18	-	cyt	0	Nucleus (By similarity)				159
Q8NBV4 UniProt NPD GO	PPAC3_HUMAN	Probable lipid phosphate phosphatase PPAPDC3 (EC 3.1.3.-) (Phosphatidic acid phosphatase type 2 doma ...	0.18	-	end	3	Membrane; multi-pass membrane protein (Potential)				271
O59730 UniProt NPD GO	AMPM1_SCHPO	Probable methionine aminopeptidase 1 (EC 3.4.11.18) (MetAP 1) (MAP 1) (Peptidase M 1)	0.18	-	nuc	0					379
Q09836 UniProt NPD GO	ATP10_SCHPO	Probable mitochondrial ATPase complex subunit atp1Q09836part1	0.18	-	mit	0	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				267
P15722 UniProt NPD GO	PEL59_LYCES	Probable pectate lyase P59 precursor (EC 4.2.2.2)	0.18	-	mit	1 *					449
P43590 UniProt NPD GO	YFH6_YEAST	Probable peptidase YFR006W (EC 3.4.-.-)	0.18	-	nuc	1 *		cytoplasm [IDA]			535

You are viewing entries 53451 to 53500 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.