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
Q864G4 UniProt NPD GO	MSHR_ALOSA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864K2 UniProt NPD GO	MSHR_CERAE	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	4 *	Membrane; multi-pass membrane protein				317
Q864J9 UniProt NPD GO	MSHR_CERMI	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	6 *	Membrane; multi-pass membrane protein				317
P55167 UniProt NPD GO	MSHR_CHICK	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein				314
Q864F6 UniProt NPD GO	MSHR_EULFU	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864F5 UniProt NPD GO	MSHR_HAPGR	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein				317
P79166 UniProt NPD GO	MSHR_HORSE	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein				317
Q01726 UniProt NPD GO	MSHR_HUMAN	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	155555		317
Q9TUK4 UniProt NPD GO	MSHR_PANTR	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	4 *	Membrane; multi-pass membrane protein				317
Q864I9 UniProt NPD GO	MSHR_PRECO	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	8 *	Membrane; multi-pass membrane protein				317
Q864H1 UniProt NPD GO	MSHR_SAGMI	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864H2 UniProt NPD GO	MSHR_SAGOE	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.07	-	end	4 *	Membrane; multi-pass membrane protein				317
P43355 UniProt NPD GO	MAGA1_HUMAN	Melanoma-associated antigen 1 (MAGE-1 antigen) (Antigen MZ2-E)	0.07	-	mit	0	Cytoplasm	plasma membrane [TAS]	300016	1W72	309
O97490 UniProt NPD GO	TRFM_RABIT	Melanotransferrin precursor (Membrane-bound transferrin-like protein p97) (CD228 antigen)	0.07	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				736
O02781 UniProt NPD GO	MTR1A_PIG	Melatonin receptor type 1A (Mel-1A-R) (Mel1a melatonin receptor) (Fragment)	0.07	-	end	3 *	Membrane; multi-pass membrane protein				154
P51050 UniProt NPD GO	MTR1B_CHICK	Melatonin receptor type 1B (MEL-1B-R) (Fragment)	0.07	-	end	6 *	Membrane; multi-pass membrane protein				289
P79138 UniProt NPD GO	MCP_CERAE	Membrane cofactor protein precursor (CD46 antigen)	0.07	-	cyt	1	Acrosome; acrosomal inner membrane; single-pass type I membrane protein (By similarity). Inner acros ...				369
O19124 UniProt NPD GO	MCP_SAGMY	Membrane cofactor protein precursor (CD46 antigen) (Fragment)	0.07	-	mit	0	Acrosome; acrosomal inner membrane; single-pass type I membrane protein (By similarity). Inner acros ...				285
P11655 UniProt NPD GO	SEC12_YEAST	Membrane glycoprotein SEC12	0.07	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	integral to endoplasmic reticulum membrane [IDA] integral to membrane of membrane fraction [IDA]			471
Q86WK9 UniProt NPD GO	MPRA_HUMAN	Membrane progestin receptor alpha (mPR alpha) (Progestin and adipoQ receptor family member VII)	0.07	-	end	6	Membrane; multi-pass membrane protein		607779		346
P31422 UniProt NPD GO	MGR3_RAT	Metabotropic glutamate receptor 3 precursor (mGluR3)	0.07	-	end	6	Membrane; multi-pass membrane protein				879
Q6ICY4 UniProt NPD GO	MTPC2_ARATH	Metal tolerance protein C2 (AtMTPc2)	0.07	-	end	6	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				393
Q9SAH8 UniProt NPD GO	NRAM1_ARATH	Metal transporter Nramp1 (AtNramp1)	0.07	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				532
O18842 UniProt NPD GO	MT_BALMY	Metallothionein (MT)	0.07	-	nuc	0					61
Q6XUW5 UniProt NPD GO	MT_PLEAT	Metallothionein (MT)	0.07	-	nuc	0					61
P07216 UniProt NPD GO	MT_PLEPL	Metallothionein (MT)	0.07	-	nuc	0					60
O42152 UniProt NPD GO	MT_AMBME	Metallothionein (MT) (AnMT)	0.07	-	nuc	0					60
P80249 UniProt NPD GO	MT14_MYTED	Metallothionein 10-IV (MT-10-IV)	0.07	-	nuc	0					72
P80246 UniProt NPD GO	MT10A_MYTED	Metallothionein 10-Ia (MT-10-Ia)	0.07	-	nuc	0					72
P80251 UniProt NPD GO	MT21_MYTED	Metallothionein 20-I isoforms A and B (MT-20-IA and MT-20-IB)	0.07	-	nuc	0					71
P80252 UniProt NPD GO	MT22_MYTED	Metallothionein 20-II (MT-20-II)	0.07	-	nuc	0					71
P69153 UniProt NPD GO	MT23A_MYTED	Metallothionein 20-III isoform A (MT-20-IIIA)	0.07	-	nuc	0					71
P69154 UniProt NPD GO	MT23A_MYTGA	Metallothionein 20-III isoform A (MT-20-IIIA) (MT-I)	0.07	-	nuc	0					71
P68503 UniProt NPD GO	MTA_ONCMY	Metallothionein A (MT-A)	0.07	-	nuc	0					61
P68505 UniProt NPD GO	MTA_SALAL	Metallothionein A (MT-A)	0.07	-	nuc	0					61
P68504 UniProt NPD GO	MTA_SALSA	Metallothionein A (MT-A)	0.07	-	nuc	0					61
P02803 UniProt NPD GO	MT1_RAT	Metallothionein-1 (MT-1) (Metallothionein-I) (MT-I)	0.07	-	nuc	0					61
P04732 UniProt NPD GO	MT1E_HUMAN	Metallothionein-1E (MT-1E) (Metallothionein-IE) (MT-IE)	0.07	-	nuc	0		cytoplasm [NAS]	156351		61
P80297 UniProt NPD GO	MT1X_HUMAN	Metallothionein-1X (MT-1X) (Metallothionein-IX) (MT-IX)	0.07	-	nuc	0			156359		61
P68301 UniProt NPD GO	MT2_BOVIN	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.07	-	nuc	0					61
P68302 UniProt NPD GO	MT2_SHEEP	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.07	-	nuc	0					61
P37359 UniProt NPD GO	MT3_BOVIN	Metallothionein-3 (MT-3) (Metallothionein-III) (MT-III) (Growth inhibitory factor) (GIF)	0.07	-	nuc	0		synaptic vesicle [ISS]			68
P37360 UniProt NPD GO	MT3_HORSE	Metallothionein-3 (MT-3) (Metallothionein-III) (MT-III) (Growth inhibitory factor) (GIF)	0.07	-	nuc	0		synaptic vesicle [ISS]			68
Q41669 UniProt NPD GO	MT1A_VICFA	Metallothionein-like protein 1A (MT-1A)	0.07	-	nuc	0					77
Q41670 UniProt NPD GO	MT1B_VICFA	Metallothionein-like protein 1B (MT-1B)	0.07	-	nuc	0					75
Q38804 UniProt NPD GO	MT1C_ARATH	Metallothionein-like protein 1C (MT-1C)	0.07	-	nuc	0					45
Q38805 UniProt NPD GO	MT2B_ARATH	Metallothionein-like protein 2B (MT-2B)	0.07	-	nuc	0					77
Q00369 UniProt NPD GO	MT2_COLGL	Metallothionein-like protein CAP5	0.07	-	nuc	0					27
P43402 UniProt NPD GO	MT54_BRANA	Metallothionein-like protein LSC54	0.07	-	nuc	0					45
Q24395 UniProt NPD GO	MTK_DROME	Metchnikowin precursor	0.07	-	nuc	1 *	Secreted protein	extracellular region [IDA]			52

You are viewing entries 70401 to 70450 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.