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
P56494 UniProt NPD GO	OXYR_MACMU	Oxytocin receptor (OT-R)	0.14	-	end	7 *	Membrane; multi-pass membrane protein				389
P97926 UniProt NPD GO	OXYR_MOUSE	Oxytocin receptor (OT-R)	0.14	-	end	7 *	Membrane; multi-pass membrane protein				388
P01176 UniProt NPD GO	NEU1_HORSE	Oxytocin-neurophysin 1 precursor (OT-NPI) [Contains: Oxytocin (Ocytocin); Neurophysin 1] (Fragment)	0.14	-	nuc	0	Secreted protein			1XY2	105
Q96G91 UniProt NPD GO	P2Y11_HUMAN	P2Y purinoceptor 11 (P2Y11)	0.14	-	end	5 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602697		374
Q9BE53 UniProt NPD GO	P2Y13_MACFA	P2Y purinoceptor 13 (P2Y13) (G-protein coupled receptor 86) (Fragment)	0.14	-	end	5 *	Membrane; multi-pass membrane protein				245
Q99PE4 UniProt NPD GO	P2RY4_MERUN	P2Y purinoceptor 4 (P2Y4) (Fragment)	0.14	-	end	2 *	Membrane; multi-pass membrane protein				135
P09084 UniProt NPD GO	PAX1_MOUSE	Paired box protein Pax-1	0.14	-	nuc	0	Nucleus	transcription factor complex [TAS]			361
P47236 UniProt NPD GO	PAX1_CHICK	Paired box protein Pax-1 (Fragment)	0.14	-	nuc	0	Nucleus				203
Q2VL58 UniProt NPD GO	PAX9_CALJA	Paired box protein Pax-9	0.14	-	nuc	0	Nucleus				341
Q2YFS1 UniProt NPD GO	PILB2_MOUSE	Paired immunoglobulin-like type 2 receptor beta 2 precursor (Activating receptor PILR-beta-2)	0.14	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				225
Q75AW7 UniProt NPD GO	PFA3_ASHGO	Palmitoyltransferase PFA3 (EC 2.3.1.-) (Protein fatty acyltransferase 3)	0.14	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				325
Q75CB4 UniProt NPD GO	PFA4_ASHGO	Palmitoyltransferase PFA4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.14	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				375
Q58DA8 UniProt NPD GO	ZDHC9_BOVIN	Palmitoyltransferase ZDHHC9 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 9) (DHHC-9) (DH ...	0.14	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				363
P59268 UniProt NPD GO	ZDHC9_MOUSE	Palmitoyltransferase ZDHHC9 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 9) (DHHC-9) (DH ...	0.14	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				364
P37999 UniProt NPD GO	PAHO_CERSI	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.14	-	nuc	0	Secreted protein				36
P80024 UniProt NPD GO	PMY_PETMA	Pancreatic polypeptide MY (PMY)	0.14	-	nuc	0	Secreted protein				36
P60570 UniProt NPD GO	PANX1_RAT	Pannexin-1	0.14	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	gap junction [IMP]			426
Q923S8 UniProt NPD GO	PANK4_RAT	Pantothenate kinase 4 (EC 2.7.1.33) (Pantothenic acid kinase 4) (rPanK4)	0.14	-	cyt	0	Cytoplasm (Probable)				773
O43000 UniProt NPD GO	LIZ1_SCHPO	Pantothenate transporter liz1	0.14	-	end	10 *	Cell membrane; multi-pass membrane protein	plasma membrane [TAS]			514
Q03431 UniProt NPD GO	PTHR1_HUMAN	Parathyroid hormone/parathyroid hormone-related peptide receptor precursor (PTH/PTHr receptor) (PTH/ ...	0.14	-	end	7	Membrane; multi-pass membrane protein	cytoplasm [TAS] integral to plasma membrane [TAS] nucleus [TAS]	156400	1ET3	593
P50133 UniProt NPD GO	PTHR1_PIG	Parathyroid hormone/parathyroid hormone-related peptide receptor precursor (PTH/PTHr receptor) (PTH/ ...	0.14	-	end	7	Membrane; multi-pass membrane protein				585
P83947 UniProt NPD GO	PME1_FICAW	Pectinesterase precursor (EC 3.1.1.11) (Pectin methylesterase) (PE)	0.14	-	cyt	1 *					545
Q9GMY7 UniProt NPD GO	PEPA_RHIFE	Pepsin A precursor (EC 3.4.23.1)	0.14	-	exc	0	Secreted protein				386
Q9GMY8 UniProt NPD GO	PEPA_SORUN	Pepsin A precursor (EC 3.4.23.1)	0.14	-	exc	0	Secreted protein				387
P27677 UniProt NPD GO	PEPA2_MACFU	Pepsin A-2/A-3 precursor (EC 3.4.23.1) (Pepsin III-2/III-1)	0.14	-	exc	0	Secreted protein				388
P27822 UniProt NPD GO	PEPA3_RABIT	Pepsin-3 precursor (EC 3.4.23.1) (Pepsin III) (Pepsin A)	0.14	-	exc	0	Secreted protein				387
Q9PT98 UniProt NPD GO	PY_DICLA	Peptide Y precursor	0.14	-	exc	1 *	Secreted protein				97
P68005 UniProt NPD GO	PYY_PIG	Peptide YY (PYY) (Peptide tyrosine tyrosine)	0.14	-	nuc	0	Secreted protein			1RUU	36
P68004 UniProt NPD GO	PYY_CANFA	Peptide YY (PYY) (Peptide tyrosine tyrosine) [Contains: Peptide YY(3-36)]	0.14	-	nuc	0	Secreted protein (By similarity)				36
P69092 UniProt NPD GO	PYY_ONCKI	Peptide YY-like (PYY)	0.14	-	nuc	0	Secreted protein				36
P69093 UniProt NPD GO	PYY_ONCMY	Peptide YY-like (PYY)	0.14	-	nuc	0	Secreted protein				36
Q9FV54 UniProt NPD GO	DEFC_LYCES	Peptide deformylase, chloroplast precursor (EC 3.5.1.88) (PDF) (Polypeptide deformylase)	0.14	-	mit	0	Plastid; chloroplast (Potential)				279
Q9FV53 UniProt NPD GO	DEFM_ARATH	Peptide deformylase, mitochondrial precursor (EC 3.5.1.88) (PDF) (Polypeptide deformylase)	0.14	-	mit	0	Mitochondrion (Potential)			1ZY1	259
P81055 UniProt NPD GO	PLMP_PLEOS	Peptidyl-Lys metalloendopeptidase (EC 3.4.24.20) (MEP) (PoMEP)	0.14	-	mit	0	Secreted protein. Binds strongly to beta-1,3-glucan and chitin, major polysaccharides constituting t ...				168
Q26548 UniProt NPD GO	PPIE_SCHMA	Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8) (PPIase E) (Rotamase E) (Cyclophilin E)	0.14	-	cyt	0	Cytoplasm (By similarity)				273
Q25109 UniProt NPD GO	PER_HIRPI	Period circadian protein (Fragment)	0.14	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				124
P17810 UniProt NPD GO	RDS_BOVIN	Peripherin (Retinal degeneration slow protein)	0.14	-	end	4 *	Membrane; multi-pass membrane protein				345
O80912 UniProt NPD GO	PER23_ARATH	Peroxidase 23 precursor (EC 1.11.1.7) (Atperox P23) (ATP34)	0.14	-	exc	0	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				349
Q9FKA4 UniProt NPD GO	PER62_ARATH	Peroxidase 62 precursor (EC 1.11.1.7) (Atperox P62) (ATP24a)	0.14	-	end	1 *	Secreted protein (By similarity)				319
Q43387 UniProt NPD GO	PER71_ARATH	Peroxidase 71 precursor (EC 1.11.1.7) (Atperox P71) (ATP15a) (ATPO2)	0.14	-	mit	0	Secreted protein (By similarity)				328
P83918 UniProt NPD GO	PEM_IRPLA	Peroxidase manganese-dependent (EC 1.11.1.13) (Fragments)	0.14	-	nuc	0					35
P78733 UniProt NPD GO	PEM3_PHACH	Peroxidase manganese-dependent H3 precursor (EC 1.11.1.13)	0.14	-	exc	0	Secreted protein				380
Q9DCN1 UniProt NPD GO	NUD12_MOUSE	Peroxisomal NADH pyrophosphatase NUDT12 (EC 3.6.1.22) (Nucleoside diphosphate-linked moiety X motif ...	0.14	+	cyt	0	Peroxisome (By similarity)				462
Q75A82 UniProt NPD GO	ANT1_ASHGO	Peroxisomal adenine nucleotide transporter 1	0.14	-	cyt	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)				340
Q9XZD5 UniProt NPD GO	CATA_TOXGO	Peroxisomal catalase (EC 1.11.1.6)	0.14	-	cyt	0	Peroxisome				502
P07820 UniProt NPD GO	CATA_CANTR	Peroxisomal catalase (EC 1.11.1.6) (PXP-9)	0.14	-	cyt	0	Peroxisome				484
Q27487 UniProt NPD GO	CATA1_CAEEL	Peroxisomal catalase 1 (EC 1.11.1.6)	0.14	-	nuc	0	Peroxisome	peroxisome [IDA]			500
P51660 UniProt NPD GO	DHB4_MOUSE	Peroxisomal multifunctional enzyme type 2 (MFE-2) (D-bifunctional protein) (DBP) (17-beta-hydroxyste ...	0.14	-	pox	0	Peroxisome (By similarity)	mitochondrion [IDA]			734
O88177 UniProt NPD GO	PEX12_RAT	Peroxisome assembly protein 12 (Peroxin-12) (Peroxisome assembly factor 3) (PAF-3)	0.14	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				359
P45726 UniProt NPD GO	PALY_CAMSI	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.14	-	nuc	0	Cytoplasm (Probable)				714

You are viewing entries 58751 to 58800 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.