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
Q06375 UniProt NPD GO	PYRF_PICAN	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.06	-	cyt	0					263
P43230 UniProt NPD GO	PYRF_RHINI	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.06	-	cyt	0					265
Q71HN5 UniProt NPD GO	PYRF_RHIOR	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.06	-	cyt	0					265
P32431 UniProt NPD GO	PYRF_RHIRA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.06	-	cyt	0					265
P15188 UniProt NPD GO	PYRF_USTMA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.06	-	cyt	0					298
Q8BG16 UniProt NPD GO	S6A15_MOUSE	Orphan sodium- and chloride-dependent neurotransmitter transporter NTT73 (Orphan transporter v7-3) ( ...	0.06	-	end	12	Membrane; multi-pass membrane protein				729
Q08469 UniProt NPD GO	S6A15_RAT	Orphan sodium- and chloride-dependent neurotransmitter transporter NTT73 (Orphan transporter v7-3) ( ...	0.06	-	end	12	Membrane; multi-pass membrane protein				729
Q800Y1 UniProt NPD GO	OSTC_ARGRE	Osteocalcin precursor (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.06	-	exc	0	Secreted protein	extracellular matrix [IDA]		1VZM	97
P02820 UniProt NPD GO	OSTC_BOVIN	Osteocalcin precursor (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.06	-	exc	0	Secreted protein	extracellular region [ISS]		1Q3M	100
P02818 UniProt NPD GO	OSTC_HUMAN	Osteocalcin precursor (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.06	-	exc	0	Secreted protein	extracellular region [NAS]	112260		100
Q8K560 UniProt NPD GO	OTOSP_RAT	Otospiralin precursor	0.06	-	exc	0	Secreted protein (Probable)				89
Q6V115 UniProt NPD GO	OVAL_COTCO	Ovalbumin	0.06	-	nuc	0	Secreted protein (By similarity)				382
Q60557 UniProt NPD GO	OVGP1_MESAU	Oviduct-specific glycoprotein precursor (Oviductal glycoprotein) (Oviductin) (Estrogen-dependent ovi ...	0.06	-	cyt	0	Secretory granules				671
P56410 UniProt NPD GO	TRFE_ANAPL	Ovotransferrin	0.06	-	mit	0	Secreted protein			1OVB	686
P83504 UniProt NPD GO	PSBO_BRARA	Oxygen-evolving enhancer protein 1, chloroplast (OEE1) (Fragment)	0.06	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				31
O49079 UniProt NPD GO	PSBO_FRIAG	Oxygen-evolving enhancer protein 1, chloroplast precursor (OEE1) (33 kDa subunit of oxygen evolving ...	0.06	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				329
P23322 UniProt NPD GO	PSBO_LYCES	Oxygen-evolving enhancer protein 1, chloroplast precursor (OEE1) (33 kDa subunit of oxygen evolving ...	0.06	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				329
P23321 UniProt NPD GO	PSBO1_ARATH	Oxygen-evolving enhancer protein 1-1, chloroplast precursor (OEE1) (33 kDa subunit of oxygen evolvin ...	0.06	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				332
O49080 UniProt NPD GO	PSBP_FRIAG	Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving ...	0.06	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				264
Q7DM39 UniProt NPD GO	PSBP1_TOBAC	Oxygen-evolving enhancer protein 2-1, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolvin ...	0.06	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				268
P21129 UniProt NPD GO	P3_MOUSE	P3 protein (Solute carrier family 10 member 3)	0.06	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				473
P52944 UniProt NPD GO	PDLI1_RAT	PDZ and LIM domain protein 1 (Elfin) (LIM domain protein CLP-36) (C-terminal LIM domain protein 1)	0.06	-	nuc	0	Cytoplasm (By similarity). Associates with the actin stress fibers (By similarity)				326
Q5RCF7 UniProt NPD GO	PDZD1_PONPY	PDZ domain-containing protein 1 (Na(+)/H(+) exchanger regulatory factor 3) (Sodium-hydrogen exchange ...	0.06	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with pe ...				519
Q9Z2H7 UniProt NPD GO	GIPC2_MOUSE	PDZ domain-containing protein GIPC2 (SemaF cytoplasmic domain-associated protein 2) (SEMCAP-2)	0.06	-	cyt	0	Cytoplasm (Probable)				314
P80250 UniProt NPD GO	PMCH_RAT	Palmitoyl-CoA hydrolase (EC 3.1.2.2) (Long-chain fatty-acyl-CoA hydrolase) (Fragment)	0.06	-	nuc	0	Microsome				64
Q6FJ70 UniProt NPD GO	AKR1_CANGA	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.06	-	end	6	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				763
Q8R173 UniProt NPD GO	ZDHC3_MOUSE	Palmitoyltransferase ZDHHC3 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 3) (DHHC-3) (Go ...	0.06	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi apparatus [IDA]			299
P83053 UniProt NPD GO	AMYP_STRCA	Pancreatic alpha-amylase (EC 3.2.1.1) (PA) (1,4-alpha-D-glucan glucanohydrolase)	0.06	-	pox	0	Secreted protein; extracellular space				497
P41337 UniProt NPD GO	PAHO_LARAR	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.06	-	cyt	0	Secreted protein				36
P06857 UniProt NPD GO	LIPR1_CANFA	Pancreatic lipase-related protein 1 precursor (EC 3.1.1.3)	0.06	-	end	0	Secreted protein			1RP1	467
P54316 UniProt NPD GO	LIPR1_RAT	Pancreatic lipase-related protein 1 precursor (EC 3.1.1.3)	0.06	-	exc	0	Secreted protein (Potential)				473
P09655 UniProt NPD GO	IPK1_RAT	Pancreatic secretory trypsin inhibitor I precursor (PSTI-I) (Cholecystokinin-releasing peptide) (Mon ...	0.06	-	exc	0	Secreted protein				79
Q96H96 UniProt NPD GO	COQ2_HUMAN	Para-hydroxybenzoate--polyprenyltransferase, mitochondrial precursor (EC 2.5.1.-) (PHB:polyprenyltra ...	0.06	-	end	6	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Probable)		609825		371
O46166 UniProt NPD GO	TXI1_TEGAG	Paralytic insecticidal toxin 1 precursor (TaITX-1)	0.06	-	exc	0	Secreted protein				68
O46168 UniProt NPD GO	TXI3_TEGAG	Paralytic insecticidal toxin 3 precursor (TaITX-3)	0.06	-	exc	0	Secreted protein				68
P80059 UniProt NPD GO	PMD1_LOCMI	Pars intercerebralis major peptide D1 (PMP-D1)	0.06	-	nuc	0	Secreted protein				54
Q566B3 UniProt NPD GO	PBURS_ANOGA	Partner of bursicon precursor (Bursicon subunit beta)	0.06	-	exc	1 *	Secreted protein (By similarity)				153
P02625 UniProt NPD GO	PRVA_RAT	Parvalbumin alpha	0.06	-	cyt	0				1XVJ	109
Q9LD79 UniProt NPD GO	PRR3_JUNVI	Pathogenesis-related protein precursor (Putative major pollen allergen Jun v 3) (Fragment)	0.06	-	cyt	0					110
Q42608 UniProt NPD GO	PME_BRACM	Pectinesterase (EC 3.1.1.11) (Pectin methylesterase) (PE) (Fragment)	0.06	-	nuc	0					571
Q12535 UniProt NPD GO	PME_ASPAC	Pectinesterase precursor (EC 3.1.1.11) (Pectin methylesterase) (PE)	0.06	-	cyt	0					331
P81060 UniProt NPD GO	PEN3C_PENVA	Penaeidin-3c precursor (Pen-3c) (P3-c)	0.06	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				81
Q963C9 UniProt NPD GO	PEN3E_PENVA	Penaeidin-3e precursor (Pen-3e)	0.06	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				82
P20139 UniProt NPD GO	PEP1_THUTO	Pepsin-1 precursor (EC 3.4.23.-) (Fragment)	0.06	-	cyt	0					58
P0C174 UniProt NPD GO	SCKP1_TITSE	Peptide TsPep1	0.06	-	nuc	0	Secreted protein				29
Q76CL2 UniProt NPD GO	PYY_ANGJA	Peptide YY precursor	0.06	-	exc	1 *	Secreted protein (By similarity)				97
P82694 UniProt NPD GO	PH1_PERAM	Peptide hormone 1 (Pea-SKNacid)	0.06	-		0					18
Q96LB9 UniProt NPD GO	PGRP3_HUMAN	Peptidoglycan recognition protein I-alpha precursor (Peptidoglycan recognition protein intermediate ...	0.06	-	mit	0	Membrane; peripheral membrane protein (Potential)	intracellular [NAS] membrane [NAS]	608197	1TWQ	341
Q9VS97 UniProt NPD GO	PGPSD_DROME	Peptidoglycan-recognition protein-SD precursor	0.06	-	cyt	0	Secreted protein (Probable)	extracellular region [IDA]			186
Q70PR8 UniProt NPD GO	PGPSD_DROSI	Peptidoglycan-recognition protein-SD precursor	0.06	-	cyt	0	Secreted protein (By similarity)	extracellular region [ISS]			186

You are viewing entries 72701 to 72750 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.