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
P01691 UniProt NPD GO	KV10_RABIT	Ig kappa chain V region 12F2 precursor (Fragment)	0.02	-	mit	0					117
P01727 UniProt NPD GO	LV1E_MOUSE	Ig lambda-1 chain V region S43 precursor	0.02	-	exc	0					129
P83907 UniProt NPD GO	IGW3_HETFR	IgW heavy chain V region W26 (Fragment)	0.02	-	cyt	0					118
P56090 UniProt NPD GO	HIS7_CANAL	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.02	-	cyt	0					223
O94126 UniProt NPD GO	HIS7_PICJA	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.02	-	mit	0					224
Q9V8G0 UniProt NPD GO	IM03_DROME	Immune-induced peptide 3 precursor (DIM-3)	0.02	-	exc	0	Secreted protein	extracellular region [IDA]			39
Q7ZXX1 UniProt NPD GO	IGS4B_XENLA	Immunoglobulin superfamily member 4B precursor	0.02	-	end	1	Membrane; single-pass type I membrane protein (Potential)				394
P83891 UniProt NPD GO	IMPL_MOUSE	Implantin (Fragment)	0.02	-		0	Cytoplasm. Nucleus				20
O95050 UniProt NPD GO	INMT_HUMAN	Indolethylamine N-methyltransferase (EC 2.1.1.49) (Aromatic alkylamine N-methyltransferase) (Indolam ...	0.02	-	mit	0	Cytoplasm (By similarity)		604854	2A14	263
Q5RFR7 UniProt NPD GO	INMT_PONPY	Indolethylamine N-methyltransferase (EC 2.1.1.49) (Aromatic alkylamine N-methyltransferase) (Indolam ...	0.02	-	cyt	0	Cytoplasm (By similarity)				263
P19873 UniProt NPD GO	ITH5_CUCMA	Inhibitor of trypsin and hageman factor (CMTI-V)	0.02	-	cyt	0	Secreted protein			1TIN	68
Q9XYN1 UniProt NPD GO	INX2_SCHAM	Innexin inx2 (Innexin-2) (G-Inx2)	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				359
Q9V427 UniProt NPD GO	INX2_DROME	Innexin inx2 (Innexin-2) (Gap junction protein prp33) (Pas-related protein 33)	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	gap junction [IEP] integral to membrane [NAS]			367
O01393 UniProt NPD GO	UNC9_CAEEL	Innexin unc-9 (Uncoordinated protein 9)	0.02	-	end	4 *	Membrane; multi-pass membrane protein				386
O61787 UniProt NPD GO	INX16_CAEEL	Innexin-16	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				372
Q96243 UniProt NPD GO	PHT12_ARATH	Inorganic phosphate transporter 1-2 (AtPht1;2) (H(+)/Pi cotransporter)	0.02	-	end	11 *	Membrane; multi-pass membrane protein (By similarity)				524
P83777 UniProt NPD GO	IPYR_CANAL	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.02	-	cyt	0	Cytoplasm				288
Q6FRB7 UniProt NPD GO	IPYR_CANGA	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.02	-	cyt	0	Cytoplasm (By similarity)				287
Q6BWA5 UniProt NPD GO	IPYR_DEBHA	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.02	-	cyt	0	Cytoplasm (By similarity)				287
P13998 UniProt NPD GO	IPYR_KLULA	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.02	-	cyt	0	Cytoplasm				286
Q4R543 UniProt NPD GO	IPYR_MACFA	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.02	-	cyt	0	Cytoplasm (By similarity)				289
Q6MVH7 UniProt NPD GO	IPYR_NEUCR	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.02	-	cyt	0	Cytoplasm (By similarity)				290
P19117 UniProt NPD GO	IPYR_SCHPO	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.02	-	cyt	0	Cytoplasm	cytoplasm [IDA]			288
P00817 UniProt NPD GO	IPYR_YEAST	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.02	-	cyt	0	Cytoplasm	cytosol [TAS]		8PRK	286
Q9H2U2 UniProt NPD GO	IPYR2_HUMAN	Inorganic pyrophosphatase 2, mitochondrial precursor (EC 3.6.1.1) (PPase 2) (Pyrophosphatase SID6-30 ...	0.02	-	mit	0	Mitochondrion (Potential)				334
O49071 UniProt NPD GO	IMPP_MESCR	Inositol monophosphatase (EC 3.1.3.25) (IMPase) (IMP) (Inositol-1(or 4)-monophosphatase)	0.02	-	cyt	0					270
P54927 UniProt NPD GO	IMP2_LYCES	Inositol monophosphatase 2 (EC 3.1.3.25) (IMPase 2) (IMP 2) (Inositol-1(or 4)-monophosphatase 2)	0.02	-	nuc	0					265
Q8L799 UniProt NPD GO	MIOX1_ARATH	Inositol oxygenase 1 (EC 1.13.99.1) (Myo-inositol oxygenase 1) (AtMIOX1)	0.02	-	cyt	0	Cytoplasm (Probable)				311
Q96348 UniProt NPD GO	INO1_BRANA	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.02	-	cyt	0	Cytoplasm (By similarity)				510
P42802 UniProt NPD GO	INO1_CITPA	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.02	-	cyt	0	Cytoplasm (Potential)				507
Q41107 UniProt NPD GO	INO1_PHAVU	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.02	-	cyt	0	Cytoplasm (By similarity)				511
Q9S7U0 UniProt NPD GO	INO1_WHEAT	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.02	-	cyt	0	Cytoplasm (By similarity)				510
P42801 UniProt NPD GO	INO1_ARATH	Inositol-3-phosphate synthase isozyme 1 (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase 1) (MI-1-P s ...	0.02	-	cyt	0	Cytoplasm				511
Q38862 UniProt NPD GO	INO2_ARATH	Inositol-3-phosphate synthase isozyme 2 (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase 2) (MI-1-P s ...	0.02	-	cyt	0	Cytoplasm				510
P82811 UniProt NPD GO	SIX1_BUTSI	Insect toxin 1 (BsIT1) (Bs-dprIT1)	0.02	-	nuc	0	Secreted protein				61
Q5G8A8 UniProt NPD GO	SCX38_TITCO	Insect-like toxic peptide Tco 38.32-2 precursor	0.02	-	mit	0	Secreted protein				84
O76963 UniProt NPD GO	SIXI_ORTSC	Insecticidal toxin OsI-1	0.02	-	nuc	0	Secreted protein				64
P61504 UniProt NPD GO	SIT_SEGFL	Insectotoxin SIT	0.02	-	nuc	0	Secreted protein				35
P01338 UniProt NPD GO	INS2_BATSP	Insulin 2 [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				50
P01339 UniProt NPD GO	INS2_THUTH	Insulin 2 [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				51
P01314 UniProt NPD GO	INS_BALBO	Insulin [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				51
P67973 UniProt NPD GO	INS_BALPH	Insulin [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				51
P01320 UniProt NPD GO	INS_CAMDR	Insulin [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				51
P69047 UniProt NPD GO	INS_CHRDO	Insulin [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				51
P69046 UniProt NPD GO	INS_LOPPI	Insulin [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				51
P67968 UniProt NPD GO	INS_MELGA	Insulin [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				51
P07453 UniProt NPD GO	INS_MYOSC	Insulin [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				50
P67974 UniProt NPD GO	INS_PHYCA	Insulin [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				51
P67971 UniProt NPD GO	INS_SAISC	Insulin [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				51
P67969 UniProt NPD GO	INS_STRCA	Insulin [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				51

You are viewing entries 84051 to 84100 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.