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
Q15269 UniProt NPD GO	PWP2_HUMAN	Periodic tryptophan protein 2 homolog	0.28	-	mit	0	Nucleus; nucleolus		601475		919
Q9C270 UniProt NPD GO	PWP2_NEUCR	Periodic tryptophan protein 2 homolog	0.28	-	cyt	0					899
Q9SZB9 UniProt NPD GO	PER47_ARATH	Peroxidase 47 precursor (EC 1.11.1.7) (Atperox P47) (ATP32)	0.28	-	end	1 *	Secreted protein (By similarity)				314
P80679 UniProt NPD GO	PERA2_ARMRU	Peroxidase A2 (EC 1.11.1.7)	0.28	-	nuc	0				1PA2	305
P00433 UniProt NPD GO	PER1A_ARMRU	Peroxidase C1A precursor (EC 1.11.1.7)	0.28	-	exc	0	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...			7ATJ	353
O75521 UniProt NPD GO	PECI_HUMAN	Peroxisomal 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) (Dodecenoyl-CoA isomerase) (Delta(3),delta(2) ...	0.28	-	mit	0	Peroxisome; peroxisomal matrix	peroxisome [TAS]	608024	2F6Q	359
Q60415 UniProt NPD GO	PEX19_CRIGR	Peroxisomal biogenesis factor 19 (Peroxin-19) (Peroxisomal farnesylated protein)	0.28	-	nuc	0	Cytoplasm (By similarity). Mainly (By similarity). Peroxisome; peroxisomal membrane; lipid-anchor; c ...				299
P45817 UniProt NPD GO	PEX9_YARLI	Peroxisomal biogenesis factor 9 (Peroxin-9) (Peroxisomal protein PAY2)	0.28	-	end	1	Peroxisome; peroxisomal membrane; multi-pass membrane protein (Potential)				404
O75192 UniProt NPD GO	PX11A_HUMAN	Peroxisomal membrane protein 11A (Peroxin-11A) (Peroxisomal biogenesis factor 11A) (PEX11alpha) (Pex ...	0.28	-	cyt	1	Peroxisome; peroxisomal membrane; multi-pass membrane protein	integral to peroxisomal membrane [TAS]	603866		247
O96011 UniProt NPD GO	PX11B_HUMAN	Peroxisomal membrane protein 11B (Peroxin-11B) (Peroxisomal biogenesis factor 11B) (PEX11beta) (Pex1 ...	0.28	-	nuc	1	Peroxisome	peroxisome [IDA]	603867		259
O00623 UniProt NPD GO	PEX12_HUMAN	Peroxisome assembly protein 12 (Peroxin-12) (Peroxisome assembly factor 3) (PAF-3)	0.28	-	cyt	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein	integral to peroxisomal membrane [TAS]	601758		359
Q04593 UniProt NPD GO	PAL2_PEA	Phenylalanine ammonia-lyase 2 (EC 4.3.1.5)	0.28	-	nuc	0	Cytoplasm (Probable)				724
O74787 UniProt NPD GO	CHO2_SCHPO	Phosphatidylethanolamine N-methyltransferase (EC 2.1.1.17) (PEAMT)	0.28	-	end	10					905
Q9VI75 UniProt NPD GO	PICA_DROME	Phosphatidylinositol-binding clathrin assembly protein LAP (Like-AP180)	0.28	-	nuc	0	Cell membrane. Clathrin-coated areas of the plasma membrane. Golgi apparatus. Colocalized with clath ...	coated pit [IDA] synaptic vesicle [TAS]		1HX8	468
Q9FR44 UniProt NPD GO	PEAM1_ARATH	Phosphoethanolamine N-methyltransferase 1 (EC 2.1.1.103) (PEAMT 1) (AtNMT1)	0.28	-	cyt	0	Cytoplasm (Probable)				491
Q76L33 UniProt NPD GO	PCYAB_ASTLO	Photoactivated adenylate cyclase subunit beta (EC 4.6.1.1) (Photoactivated adenylyl cyclase beta sub ...	0.28	-	mit	0	Flagellum	flagellum [IDA]			860
P56311 UniProt NPD GO	YCF3_CHLVU	Photosystem I assembly protein ycf3	0.28	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
Q9TL02 UniProt NPD GO	YCF3_NEPOL	Photosystem I assembly protein ycf3 (RF3)	0.28	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				171
P12355 UniProt NPD GO	PSAF_SPIOL	Photosystem I reaction center subunit III, chloroplast precursor (Light-harvesting complex I 17 kDa ...	0.28	-	mit	1	Plastid; chloroplast; chloroplast thylakoid lumen				231
P33529 UniProt NPD GO	PHY_MOUSC	Phytochrome	0.28	-	mit	0					1124
Q01549 UniProt NPD GO	PHY1_SELMA	Phytochrome 1	0.28	-	mit	0					1134
P37271 UniProt NPD GO	PSY_ARATH	Phytoene synthase, chloroplast precursor (EC 2.5.1.-)	0.28	-	cyt	0	Plastid; chloroplast				422
P41535 UniProt NPD GO	PACA_PIG	Pituitary adenylate cyclase-activating polypeptide precursor (PACAP) [Contains: PACAP-related peptid ...	0.28	-	nuc	1 *	Secreted protein				176
Q98SH2 UniProt NPD GO	AT2B1_CHICK	Plasma membrane calcium-transporting ATPase 1 (EC 3.6.3.8) (PMCA1) (Plasma membrane calcium pump iso ...	0.28	-	nuc	2 *	Cell membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [NAS]			214
P06172 UniProt NPD GO	RETBP_XENLA	Plasma retinol-binding protein precursor (PRBP)	0.28	-	exc	0	Secreted protein				197
Q94KU5 UniProt NPD GO	PAP3_BRACM	Plastid lipid-associated protein 3, chloroplast precursor	0.28	-	mit	0	Plastid; chloroplast				360
Q61990 UniProt NPD GO	PCBP2_MOUSE	Poly(rC)-binding protein 2 (Alpha-CP2) (Putative heterogeneous nuclear ribonucleoprotein X) (hnRNP X ...	0.28	-	nuc	0	Nucleus				362
P58823 UniProt NPD GO	PGIP3_PHAVU	Polygalacturonase inhibitor 3 precursor (Polygalacturonase-inhibiting protein) (PGIP-2) (PGIP-3)	0.28	-	exc	0	Cell wall; peripheral membrane protein				342
P26599 UniProt NPD GO	PTBP1_HUMAN	Polypyrimidine tract-binding protein 1 (PTB) (Heterogeneous nuclear ribonucleoprotein I) (hnRNP I) ( ...	0.28	-	nuc	0	Nucleus	heterogeneous nuclear ribonucleoprotein com... [TAS] nucleolus [TAS] nucleoplasm [TAS]	600693	2EVZ	531
Q9HBV1 UniProt NPD GO	POPD3_HUMAN	Popeye domain-containing protein 3 (Popeye protein 3)	0.28	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]	605824		291
Q9ES81 UniProt NPD GO	POPD3_MOUSE	Popeye domain-containing protein 3 (Popeye protein 3)	0.28	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	membrane [IDA]			291
Q64436 UniProt NPD GO	ATP4A_MOUSE	Potassium-transporting ATPase alpha chain 1 (EC 3.6.3.10) (Proton pump) (Gastric H+/K+ ATPase subuni ...	0.28	-	end	8	Membrane; multi-pass membrane protein				1032
Q4JIM4 UniProt NPD GO	PSN1_CHICK	Presenilin-1 (EC 3.4.23.-) (PS-2) [Contains: Presenilin-1 NTF subunit; Presenilin-1 CTF subunit]	0.28	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	mitochondrion [ISS]			468
Q9V7U0 UniProt NPD GO	RESIL_DROME	Pro-resilin precursor	0.28	-	exc	0		extracellular region [NAS]			620
Q92352 UniProt NPD GO	ARPC4_SCHPO	Probable ARP2/3 complex 20 kDa subunit (p20-ARC)	0.28	-	mit	0					168
Q40742 UniProt NPD GO	RAD23_ORYSA	Probable DNA repair protein RAD23 (OsRAD23)	0.28	-	nuc	0	Nucleus (Probable)				392
O94329 UniProt NPD GO	PSF2_SCHPO	Probable DNA replication complex GINS protein psf2	0.28	-	cyt	0	Nucleus (By similarity)	GINS complex [TAS] nucleus [IDA]			183
Q3T0E9 UniProt NPD GO	GPR18_BOVIN	Probable G-protein coupled receptor 18	0.28	-	end	7 *	Membrane; multi-pass membrane protein				332
O15354 UniProt NPD GO	GPR37_HUMAN	Probable G-protein coupled receptor 37 precursor (Endothelin B receptor-like protein 1) (ETBR-LP-1) ...	0.28	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602583		613
Q9CQA9 UniProt NPD GO	U334_MOUSE	Probable UPF0334 kinase-like protein C1orf57 homolog	0.28	-	cyt	0					190
Q22498 UniProt NPD GO	COPG_CAEEL	Probable coatomer subunit gamma (Gamma-coat protein) (Gamma-COP)	0.28	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				870
Q6CQ60 UniProt NPD GO	ATG4_KLULA	Probable cysteine protease ATG4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.28	-	cyt	0	Cytoplasm (By similarity)				450
Q9VMT5 UniProt NPD GO	C28D1_DROME	Probable cytochrome P450 28d1 (EC 1.14.-.-) (CYPXXVIIID1)	0.28	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				502
Q9VGB3 UniProt NPD GO	CP133_DROME	Probable cytochrome P450 313a3 (EC 1.14.-.-) (CYPCCCXIIIA3)	0.28	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				492
Q9V9L1 UniProt NPD GO	CP6W1_DROME	Probable cytochrome P450 6w1 (EC 1.14.-.-) (CYPVIW1)	0.28	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				514
Q9UNQ2 UniProt NPD GO	DIMH_HUMAN	Probable dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N',N'-adenosyl(rRNA) dim ...	0.28	-	nuc	0	Nucleus; nucleolus			1ZQ9	313
P54137 UniProt NPD GO	NTH1_CAEEL	Probable endonuclease III homolog (EC 4.2.99.18) (DNA-(Apurinic or apyrimidinic site) lyase)	0.28	-	mit	0					259
Q92253 UniProt NPD GO	RCO3_NEUCR	Probable glucose transporter rco-3	0.28	-	end	10 *	Membrane; multi-pass membrane protein				594
Q23430 UniProt NPD GO	ILB4_CAEEL	Probable insulin-like peptide beta-type 4 precursor	0.28	-	exc	0	Secreted protein (Potential)				105
Q7S8M2 UniProt NPD GO	SPC24_NEUCR	Probable kinetochore protein spc-24	0.28	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				221

You are viewing entries 42551 to 42600 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.