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
P25511 UniProt NPD GO	ORNB_PLAOR	Ornatin-B	0.08	-	nuc	0	Secreted protein				52
P25514 UniProt NPD GO	ORNE_PLAOR	Ornatin-E	0.08	-	nuc	0	Secreted protein				50
P11803 UniProt NPD GO	OTC_EMENI	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.08	-	mit	0	Mitochondrion; mitochondrial matrix				359
Q9UQW9 UniProt NPD GO	DCOR_SCHPO	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.08	-	cyt	0					432
P14964 UniProt NPD GO	PYRF_SCHCO	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.08	-	cyt	0					278
P35211 UniProt NPD GO	ORYZ_ASPFL	Oryzin precursor (EC 3.4.21.63) (Alkaline proteinase) (ALP) (Elastase) (Elastinolytic serine protein ...	0.08	-	exc	1 *	Secreted protein				403
P83491 UniProt NPD GO	OLPA_HEVBR	Osmotin-like protein (Thaumatin-like protein) (Fragments)	0.08	-	cyt	0					39
Q9ERC5 UniProt NPD GO	OTOF_RAT	Otoferlin (Fer-1-like protein 2) (Fragment)	0.08	-	cyt	0	Membrane; single-pass type II membrane protein (By similarity)				266
O73860 UniProt NPD GO	OVAL_MELGA	Ovalbumin	0.08	-	cyt	0	Secreted protein (By similarity)				385
P83687 UniProt NPD GO	PSBP_EUGGR	Oxygen-evolving enhancer protein 2 (OEE2) (23 kDa subunit of oxygen evolving system of photosystem I ...	0.08	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex	chloroplast [IDA]			30
Q40407 UniProt NPD GO	PSBP_NARPS	Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving ...	0.08	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				265
P93566 UniProt NPD GO	PSBP_SOLTU	Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving ...	0.08	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				260
Q04127 UniProt NPD GO	PSBP3_TOBAC	Oxygen-evolving enhancer protein 2-3, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolvin ...	0.08	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				266
P51582 UniProt NPD GO	P2RY4_HUMAN	P2Y purinoceptor 4 (P2Y4) (Uridine nucleotide receptor) (UNR) (P2P)	0.08	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	300038		365
Q12055 UniProt NPD GO	FAP7_YEAST	POS9-activating factor FAP7	0.08	-	cyt	0	Nucleus	cytoplasm [IMP] nucleus [IDA]			197
Q39190 UniProt NPD GO	PRL2_ARATH	PP1/PP2A phosphatases pleiotropic regulator PRL2	0.08	-	cyt	0					479
Q2KHX3 UniProt NPD GO	PRAF2_BOVIN	PRA1 family protein 2	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				178
Q4R4I9 UniProt NPD GO	PRAF2_MACFA	PRA1 family protein 2	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				178
Q9JIG8 UniProt NPD GO	PRAF2_MOUSE	PRA1 family protein 2	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				178
Q75D19 UniProt NPD GO	PFA5_ASHGO	Palmitoyltransferase PFA5 (EC 2.3.1.-) (Protein fatty acyltransferase 5)	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				359
Q6FXC6 UniProt NPD GO	SWF1_CANGA	Palmitoyltransferase SWF1 (EC 2.3.1.-)	0.08	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				330
Q9NYG2 UniProt NPD GO	ZDHC3_HUMAN	Palmitoyltransferase ZDHHC3 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 3) (DHHC-3) (Zi ...	0.08	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				327
Q91WU6 UniProt NPD GO	ZDHC7_MOUSE	Palmitoyltransferase ZDHHC7 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 7) (DHHC-7) (GA ...	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				308
Q923G5 UniProt NPD GO	ZDHC7_RAT	Palmitoyltransferase ZDHHC7 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 7) (DHHC-7) (Se ...	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				308
Q7Z8U2 UniProt NPD GO	AKR1_ASPOR	Palmitoyltransferase akr1 (EC 2.3.1.-) (Ankyrin repeat-containing protein akr1)	0.08	-	end	5	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				737
O74384 UniProt NPD GO	ERFB_SCHPO	Palmitoyltransferase erf2 (EC 2.3.1.-) (DHHC cysteine-rich domain-containing protein erf2) (Ras prot ...	0.08	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				350
Q92778 UniProt NPD GO	PBCG_MESAU	Pancreatic beta cell growth factor precursor (Islet neogenesis-associated protein)	0.08	-	mit	0	Secreted protein (By similarity)	extracellular region [NAS]			175
P54315 UniProt NPD GO	LIPR1_HUMAN	Pancreatic lipase-related protein 1 precursor (EC 3.1.1.3)	0.08	-	cyt	0	Secreted protein (Potential)	extracellular region [TAS]	604422		467
P00591 UniProt NPD GO	LIPP_PIG	Pancreatic triacylglycerol lipase (EC 3.1.1.3) (Pancreatic lipase) (PL)	0.08	-	cyt	0	Secreted protein			1ETH	450
Q5REE3 UniProt NPD GO	PANX1_PONPY	Pannexin-1	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				426
P51434 UniProt NPD GO	PRVA_CAVPO	Parvalbumin alpha (Fragment)	0.08	-	cyt	0					95
P32938 UniProt NPD GO	PR1C_HORVU	Pathogenesis-related protein 1C precursor	0.08	-	exc	1 *					173
P29062 UniProt NPD GO	PR4A_TOBAC	Pathogenesis-related protein PR-4A precursor	0.08	-	exc	1 *					147
P29063 UniProt NPD GO	PR4B_TOBAC	Pathogenesis-related protein PR-4B precursor	0.08	-	exc	1 *					147
P13046 UniProt NPD GO	PRR1_TOBAC	Pathogenesis-related protein R major form precursor (Thaumatin-like protein E22)	0.08	-	nuc	0	Vacuole				226
P40972 UniProt NPD GO	PEL_TOBAC	Pectate lyase precursor (EC 4.2.2.2)	0.08	-	mit	1 *					397
P81058 UniProt NPD GO	PEN3A_PENVA	Penaeidin-3a precursor (Pen-3a) (P3-a)	0.08	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...			1UEO	82
Q962A8 UniProt NPD GO	PEN3L_LITSE	Penaeidin-3l precursor (Pen-3l)	0.08	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				75
P08566 UniProt NPD GO	ARO1_YEAST	Pentafunctional AROM polypeptide [Includes: 3-dehydroquinate synthase (EC 4.2.3.4); 3-dehydroquinate ...	0.08	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1588
P26022 UniProt NPD GO	PTX3_HUMAN	Pentraxin-related protein PTX3 precursor (Pentaxin-related protein PTX3) (Tumor necrosis factor-indu ...	0.08	-	exc	0	Secreted protein	extracellular region [TAS]	602492		381
P48759 UniProt NPD GO	PTX3_MOUSE	Pentraxin-related protein PTX3 precursor (Pentaxin-related protein PTX3) (Tumor necrosis factor-indu ...	0.08	-	exc	0	Secreted protein				381
Q8SQ41 UniProt NPD GO	PEPB_CANFA	Pepsin B precursor (EC 3.4.23.2)	0.08	-	mit	0	Secreted protein				390
P19021 UniProt NPD GO	AMD_HUMAN	Peptidyl-glycine alpha-amidating monooxygenase precursor (EC 1.14.17.3) (PAM)	0.08	-	end	1	Isoform 1, isoform 2: Membrane; single-pass type I membrane protein. Isoform 3 and isoform 4: Secret ...	secretory granule [NAS]	170270		973
P25334 UniProt NPD GO	CYPR_YEAST	Peptidyl-prolyl cis-trans isomerase CPR4 precursor (EC 5.2.1.8) (PPIase) (Rotamase)	0.08	-	end	0	Secreted protein				318
Q9V3G3 UniProt NPD GO	PPIE_DROME	Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8) (PPIase E) (Rotamase E) (Cyclophilin E) (Cyclophi ...	0.08	-	cyt	0	Nucleus (By similarity)				300
Q26288 UniProt NPD GO	PER_DROER	Period circadian protein (Fragment)	0.08	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				110
P84714 UniProt NPD GO	PER_CYNSC	Peroxidase (EC 1.11.1.7) (Fragments)	0.08	-	cyt	0					43
Q96511 UniProt NPD GO	PER69_ARATH	Peroxidase 69 precursor (EC 1.11.1.7) (Atperox P69) (ATP3a)	0.08	-	end	1 *	Secreted protein (By similarity)				331
Q02567 UniProt NPD GO	PEM1_PHACH	Peroxidase manganese-dependent 1 precursor (EC 1.11.1.13) (Peroxidase manganese-dependent I) (MnP-1) ...	0.08	-	exc	0	Secreted protein			1YZR	378
Q99P30 UniProt NPD GO	NUDT7_MOUSE	Peroxisomal coenzyme A diphosphatase NUDT7 (EC 3.6.1.-) (Nucleoside diphosphate-linked moiety X moti ...	0.08	-	mit	0	Peroxisome	peroxisome [IDA]			236

You are viewing entries 68601 to 68650 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.