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
Q09232 UniProt NPD GO	ORAI_CAEEL	Protein orai	0.03	-	end	3	Membrane; multi-pass membrane protein (By similarity)				293
Q6TLE6 UniProt NPD GO	ORAI1_BRARE	Protein orai-1	0.03	-	end	4 *	Cell membrane; multi-pass membrane protein (By similarity)				222
Q6NZI6 UniProt NPD GO	ORAI2_XENLA	Protein orai-2	0.03	-	end	3	Membrane; multi-pass membrane protein (By similarity)				257
P59282 UniProt NPD GO	P25B_HUMAN	Protein p25-beta	0.03	-	nuc	0					170
Q74Z47 UniProt NPD GO	PPME1_ASHGO	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.03	-	mit	0					385
Q9P7D2 UniProt NPD GO	PPME1_SCHPO	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.03	-	cyt	0					341
Q874R1 UniProt NPD GO	RHO4_SCHPO	Protein rho4	0.03	-	mit	0	Membrane-bound. Associates with the septum during mitosis	barrier septum [IDA]			203
O44252 UniProt NPD GO	ROST_DROME	Protein rolling stone	0.03	-	end	6 *	Membrane; multi-pass membrane protein	membrane [IDA]			275
Q94JV4 UniProt NPD GO	SUI12_ARATH	Protein translation factor SUI1 homolog 2	0.03	-	cyt	0					113
Q9SW34 UniProt NPD GO	S61G1_ARATH	Protein transport protein SEC61 gamma-1 subunit	0.03	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				69
Q9V668 UniProt NPD GO	S61G1_DROME	Protein transport protein SEC61 gamma-1 subunit	0.03	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)	integral to endoplasmic reticulum membrane [ISS]			68
Q9VWE9 UniProt NPD GO	S61G2_DROME	Protein transport protein SEC61 gamma-2 subunit	0.03	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)	integral to endoplasmic reticulum membrane [ISS]			68
Q870W0 UniProt NPD GO	SC61A_NEUCR	Protein transport protein SEC61 subunit alpha	0.03	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				476
Q962X7 UniProt NPD GO	SC61G_BRABE	Protein transport protein SEC61 subunit gamma	0.03	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				68
Q8I7D9 UniProt NPD GO	SC61G_CIOIN	Protein transport protein SEC61 subunit gamma	0.03	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				68
P38385 UniProt NPD GO	SC61G_ORYSA	Protein transport protein SEC61 subunit gamma	0.03	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				69
Q8X0S4 UniProt NPD GO	TR112_NEUCR	Protein trm-112 (tRNA methyltransferase 112)	0.03	-	cyt	0	Cytoplasm. Nucleus (By similarity)				127
O44342 UniProt NPD GO	WBL_DROME	Protein windbeutel precursor (Erp29 homolog)	0.03	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum [IDA]		1OVN	257
Q65Z56 UniProt NPD GO	YPEL4_CERAE	Protein yippee-like 4	0.03	-	nuc	0	Nucleus; nucleolus (By similarity)				127
Q96NS1 UniProt NPD GO	YPEL4_HUMAN	Protein yippee-like 4	0.03	-	nuc	0	Nucleus; nucleolus		609725		127
Q65Z93 UniProt NPD GO	YPEL4_MOUSE	Protein yippee-like 4	0.03	-	nuc	0	Nucleus; nucleolus				127
Q5XID5 UniProt NPD GO	YPEL4_RAT	Protein yippee-like 4	0.03	-	nuc	0	Nucleus; nucleolus				127
O12947 UniProt NPD GO	ICMT_XENLA	Protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100) (Isoprenylcysteine carboxylmethyltran ...	0.03	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				288
O70281 UniProt NPD GO	TPS1_MOUSE	Protein-tyrosine sulfotransferase 1 (EC 2.8.2.20) (Tyrosylprotein sulfotransferase-1) (TPST-1)	0.03	-	cyt	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				370
P84795 UniProt NPD GO	CEKI_CAEEC	Proteinase inhibitor CeKI (Fragment)	0.03	-	cyt	0					30
P01082 UniProt NPD GO	IP2B_SOLTU	Proteinase inhibitor IIB (Fragments)	0.03	-	nuc	0	Secreted protein				40
P83579 UniProt NPD GO	IKP2_PHYSA	Proteinase inhibitor PSKP-2	0.03	-	nuc	0	Secreted protein	extracellular region [IDA]			58
Q43502 UniProt NPD GO	IP23_LYCES	Proteinase inhibitor type-2 CEVI57 precursor (Proteinase inhibitor type II CEVI57)	0.03	-	nuc	0					201
P07947 UniProt NPD GO	YES_HUMAN	Proto-oncogene tyrosine-protein kinase Yes (EC 2.7.10.2) (p61-Yes) (c-Yes)	0.03	-	nuc	0	Cytoplasm; cytosol. In epithelial cells infected with Neisseria gonorrhoeae, forms aggregates beneat ...		164880		542
Q924A5 UniProt NPD GO	S36A1_RAT	Proton-coupled amino acid transporter 1 (Proton/amino acid transporter 1) (Solute carrier family 36 ...	0.03	-	end	11	Cell membrane; multi-pass membrane protein. Lysosome; lysosomal membrane; multi-pass membrane protei ...	lysosome [IDA] plasma membrane [IDA]			475
P56602 UniProt NPD GO	PPOX_BOVIN	Protoporphyrinogen oxidase (EC 1.3.3.4) (PPO) (Fragments)	0.03	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				28
P29264 UniProt NPD GO	PH2_PRUSE	Prunasin beta-glucosidase IIA (EC 3.2.1.118) (Prunasin hydrolase isozyme IIA) (PH IIA) (Fragment)	0.03	-		0					16
P84847 UniProt NPD GO	PHCY_NECPU	Pseudohemocyanin (Fragment)	0.03	-		0					12
P61458 UniProt NPD GO	PHS_MOUSE	Pterin-4-alpha-carbinolamine dehydratase (EC 4.2.1.96) (PHS) (4-alpha-hydroxy-tetrahydropterin dehyd ...	0.03	-	cyt	0	Cytoplasm. Nucleus. Cytoplasmic and/or nuclear	nucleus [IPI]			103
O73930 UniProt NPD GO	PHS_CHICK	Pterin-4-alpha-carbinolamine dehydratase (EC 4.2.1.96) (PHS) (4-alpha-hydroxy-tetrahydropterin dehyd ...	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic and/or nuclear (By similarity)				103
Q91901 UniProt NPD GO	PHS_XENLA	Pterin-4-alpha-carbinolamine dehydratase (EC 4.2.1.96) (PHS) (4-alpha-hydroxy-tetrahydropterin dehyd ...	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic and/or nuclear (By similarity)				103
O42658 UniProt NPD GO	PHS_SCHPO	Pterin-4-alpha-carbinolamine dehydratase (EC 4.2.1.96) (PHS) (4-alpha-hydroxy-tetrahydropterin dehyd ...	0.03	-	mit	0	Inner spore wall	spore wall (sensu Fungi) [IDA]			96
P08427 UniProt NPD GO	SFTPA_RAT	Pulmonary surfactant-associated protein A precursor (SP-A) (PSP-A) (PSAP)	0.03	-	end	0	Secreted protein; extracellular space			1R14	248
P22398 UniProt NPD GO	PSPC_RABIT	Pulmonary surfactant-associated protein C precursor (SP-C) (Pulmonary surfactant-associated proteoli ...	0.03	-	gol	1 *	Secreted protein; extracellular space				188
P55859 UniProt NPD GO	PNPH_BOVIN	Purine nucleoside phosphorylase (EC 2.4.2.1) (Inosine phosphorylase) (PNP)	0.03	-	cyt	0				4PNP	289
P23492 UniProt NPD GO	PNPH_MOUSE	Purine nucleoside phosphorylase (EC 2.4.2.1) (Inosine phosphorylase) (PNP)	0.03	-	cyt	0					289
Q11087 UniProt NPD GO	PLC12_CAEEL	Putative 1-acyl-sn-glycerol-3-phosphate acyltransferase acl-12 (EC 2.3.1.51) (1-AGP acyltransferase) ...	0.03	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)				391
Q22267 UniProt NPD GO	PLC2_CAEEL	Putative 1-acyl-sn-glycerol-3-phosphate acyltransferase acl-2 (EC 2.3.1.51) (1-AGP acyltransferase) ...	0.03	-	nuc	3 *	Membrane; multi-pass membrane protein (Potential)				282
P84729 UniProt NPD GO	BAS1_PINST	Putative 2-cys peroxiredoxin BAS1 (EC 1.11.1.15) (Thiol-specific antioxidant protein) (PS13) (Fragme ...	0.03	-	cyt	0	Plastid; chloroplast (By similarity)				56
P34539 UniProt NPD GO	ATP5E_CAEEL	Putative ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14)	0.03	-	mit	0	Mitochondrion				54
Q9W141 UniProt NPD GO	ATPK_DROME	Putative ATP synthase f chain, mitochondrial (EC 3.6.3.14)	0.03	-	cyt	1					107
P43538 UniProt NPD GO	YFG6_YEAST	Putative ATP-dependent helicase YFL066C (EC 3.6.1.-)	0.03	-	nuc	0					392
Q9LMU0 UniProt NPD GO	FCL2_ARATH	Putative GDP-L-fucose synthase 2 (EC 1.1.1.271) (GDP-4-keto-6-deoxy-D-mannose-3, 5-epimerase-4-reduc ...	0.03	-	cyt	0					328
P84724 UniProt NPD GO	PS8_PINST	Putative H+-ATPase I subunit PS8 (Fragments)	0.03	-		0					20
Q60YI3 UniProt NPD GO	NOLA2_CAEBR	Putative H/ACA ribonucleoprotein complex subunit 2-like protein	0.03	+	cyt	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			163

You are viewing entries 81401 to 81450 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.