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
Q864G9 UniProt NPD GO	MSHR_CEBAL	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.03	-	end	7 *	Membrane; multi-pass membrane protein				316
P41589 UniProt NPD GO	MLA_ANOCA	Melanotropin alpha (Alpha-MSH)	0.03	-		0					13
P61281 UniProt NPD GO	MLA_CAMDR	Melanotropin alpha (Alpha-MSH)	0.03	-		0	Secreted protein				13
P61280 UniProt NPD GO	MLA_HORSE	Melanotropin alpha (Alpha-MSH)	0.03	-		0	Secreted protein				13
P01206 UniProt NPD GO	MLB_SCYCA	Melanotropin beta (Beta-MSH)	0.03	-		0	Secreted protein				18
P51047 UniProt NPD GO	MR1A2_BRARE	Melatonin receptor type 1A Z1.4 (MEL-1A-R) (Fragment)	0.03	-	end	3 *	Membrane; multi-pass membrane protein				152
Q13585 UniProt NPD GO	MTR1L_HUMAN	Melatonin-related receptor (G protein-coupled receptor 50) (H9)	0.03	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	300207		613
Q6P1A2 UniProt NPD GO	MBOA5_HUMAN	Membrane bound O-acyltransferase domain-containing protein 5 (EC 2.3.-.-) (O-acyltransferase domain- ...	0.03	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				487
Q5FVN0 UniProt NPD GO	MBOA5_RAT	Membrane bound O-acyltransferase domain-containing protein 5 (EC 2.3.-.-) (O-acyltransferase domain- ...	0.03	+	end	9 *	Membrane; multi-pass membrane protein (Potential)				487
Q91V01 UniProt NPD GO	MBOA5_MOUSE	Membrane bound O-acyltransferase domain-containing protein 5 (EC 2.3.-.-) (O-acyltransferase domain- ...	0.03	+	end	7 *	Membrane; multi-pass membrane protein (Potential)				487
Q80ZE5 UniProt NPD GO	MPRB_MOUSE	Membrane progestin receptor beta (mPR beta) (Progestin and adipoQ receptor family member VIII)	0.03	-	end	6	Membrane; multi-pass membrane protein (By similarity)				354
P29523 UniProt NPD GO	PPB_BOMMO	Membrane-bound alkaline phosphatase precursor (EC 3.1.3.1) (M-ALP)	0.03	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				547
Q96HJ5 UniProt NPD GO	MS4A3_HUMAN	Membrane-spanning 4-domains subfamily A member 3 (Hematopoietic-specific transmembrane 4 protein) (H ...	0.03	-	end	4 *	Intracellular membrane; perinuclear region; multi-pass membrane protein (By similarity). Located in ...		606498		214
Q12067 UniProt NPD GO	ATX2_YEAST	Metal homeostasis factor ATX2	0.03	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi membrane [IDA]			313
Q8H1G3 UniProt NPD GO	MTPC4_ARATH	Metal tolerance protein C4 (AtMTPc4)	0.03	-	mit	4	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				457
Q9SNV9 UniProt NPD GO	NRAM3_ARATH	Metal transporter Nramp3 (AtNramp3)	0.03	-	end	11	Membrane; multi-pass membrane protein (Probable)				509
P48032 UniProt NPD GO	TIMP3_RAT	Metalloproteinase inhibitor 3 precursor (TIMP-3) (Tissue inhibitor of metalloproteinases 3)	0.03	-	mit	0	Secreted protein; extracellular space; extracellular matrix				211
O73746 UniProt NPD GO	TIMP3_XENLA	Metalloproteinase inhibitor 3 precursor (TIMP-3) (Tissue inhibitor of metalloproteinases 3)	0.03	-	mit	0	Secreted protein; extracellular space; extracellular matrix				214
P61873 UniProt NPD GO	MT1_DROAN	Metallothionein-1 (MT-1)	0.03	-	nuc	0					40
P04357 UniProt NPD GO	MT1_DROME	Metallothionein-1 (MT-1)	0.03	-	nuc	0					40
P61874 UniProt NPD GO	MT1_DROSI	Metallothionein-1 (MT-1)	0.03	-	nuc	0					40
Q26497 UniProt NPD GO	MTA_SPHGR	Metallothionein-A (MTA) (Fragment)	0.03	-	nuc	0					67
Q39511 UniProt NPD GO	MT1_CASGL	Metallothionein-like protein 1 (MT-1)	0.03	-	nuc	0					71
O24528 UniProt NPD GO	MT1_FESRU	Metallothionein-like protein 1 (MT-1)	0.03	-	nuc	0					70
Q40854 UniProt NPD GO	MT3_PICGL	Metallothionein-like protein EMB30	0.03	-	nuc	0					60
P93433 UniProt NPD GO	MT22_ORYSA	Metallothionein-like protein type 2	0.03	-	nuc	0					84
Q43515 UniProt NPD GO	MT2Z_LYCES	Metallothionein-like protein type 2	0.03	-	nuc	0					84
O24058 UniProt NPD GO	MT2_MALDO	Metallothionein-like protein type 2	0.03	-	nuc	0					79
Q40410 UniProt NPD GO	MT2_NICPL	Metallothionein-like protein type 2	0.03	-	nuc	0					74
P53582 UniProt NPD GO	AMPM1_HUMAN	Methionine aminopeptidase 1 (EC 3.4.11.18) (MetAP 1) (MAP 1) (Peptidase M 1)	0.03	-	cyt	0		cytoplasm [TAS]		2GZ5	386
Q8BP48 UniProt NPD GO	AMPM1_MOUSE	Methionine aminopeptidase 1 (EC 3.4.11.18) (MetAP 1) (MAP 1) (Peptidase M 1)	0.03	-	cyt	0		cytoplasm [ISS]			386
Q9NZV6 UniProt NPD GO	MSRX_HUMAN	Methionine-R-sulfoxide reductase (EC 1.8.4.-) (Selenoprotein X 1)	0.03	-	nuc	0			606216		116
P16455 UniProt NPD GO	MGMT_HUMAN	Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) (6-O-methylguanine-DNA methyltransf ...	0.03	-	cyt	0	Nucleus	nucleus [TAS]	156569	1YFH	207
Q02046 UniProt NPD GO	MTD1_YEAST	Methylenetetrahydrofolate dehydrogenase [NAD+] (EC 1.5.1.15)	0.03	-	cyt	0	Cytoplasm	cytosol [IDA]		1EE9	320
Q10258 UniProt NPD GO	MTHR1_SCHPO	Methylenetetrahydrofolate reductase 1 (EC 1.5.1.20)	0.03	-	cyt	0					603
P11495 UniProt NPD GO	TXMET_METSE	Metridin	0.03	-	nuc	0	Secreted protein. Found in nematocyst				36
P46086 UniProt NPD GO	KIME_ARATH	Mevalonate kinase (EC 2.7.1.36) (MK)	0.03	-	mit	0	Cytoplasm (Potential)				378
P13679 UniProt NPD GO	SPC21_CANFA	Microsomal signal peptidase 21 kDa subunit (EC 3.4.-.-) (SPase 21 kDa subunit) (SPC21) (SEC11-like 3 ...	0.03	-	mit	1 *	Microsome; microsomal membrane; single-pass type II membrane protein				191
Q9BY50 UniProt NPD GO	SPC21_HUMAN	Microsomal signal peptidase 21 kDa subunit (EC 3.4.-.-) (SPase 21 kDa subunit) (SPC21) (SEC11-like 3 ...	0.03	+	mit	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				191
Q9D8V7 UniProt NPD GO	SPC21_MOUSE	Microsomal signal peptidase 21 kDa subunit (EC 3.4.-.-) (SPase 21 kDa subunit) (SPC21) (SEC11-like 3 ...	0.03	-	mit	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				191
Q5RC30 UniProt NPD GO	SPC21_PONPY	Microsomal signal peptidase 21 kDa subunit (EC 3.4.-.-) (SPase 21 kDa subunit) (SPC21) (SEC11-like 3 ...	0.03	+	mit	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				191
Q9WTR7 UniProt NPD GO	SPC21_RAT	Microsomal signal peptidase 21 kDa subunit (EC 3.4.-.-) (SPase 21 kDa subunit) (SPC21) (SEC11-like 3 ...	0.03	-	mit	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				191
P19616 UniProt NPD GO	VITM_MANSE	Microvitellogenin precursor	0.03	-	exc	0					249
Q9NPA3 UniProt NPD GO	M1IP1_HUMAN	Mid1-interacting protein 1 (Gastrulation-specific G12-like protein) (Mid1-interacting G12-like prote ...	0.03	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Associated with microtubules (By similarity)	microtubule cytoskeleton [ISS]			183
P82456 UniProt NPD GO	TRI18_MUSCR	Midline-1 (Tripartite motif-containing protein 18) (Fragment)	0.03	-	cyt	0	Cytoplasm (By similarity). Microtubule-associated (By similarity)				108
P42058 UniProt NPD GO	ALTA7_ALTAL	Minor allergen Alt a 7 (Alt a VII)	0.03	-	cyt	0	Cytoplasm (Probable)				204
Q8TCT9 UniProt NPD GO	HM13_HUMAN	Minor histocompatibility antigen H13 (EC 3.4.99.-) (Signal peptide peptidase) (Presenilin-like prote ...	0.03	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)		607106		377
P49275 UniProt NPD GO	DERF3_DERFA	Mite allergen Der f 3 precursor (EC 3.4.21.-) (Der f III)	0.03	-	exc	0	Secreted protein				259
P22292 UniProt NPD GO	M2OM_BOVIN	Mitochondrial 2-oxoglutarate/malate carrier protein (OGCP) (Solute carrier family 25 member 11)	0.03	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				313
Q9CR62 UniProt NPD GO	M2OM_MOUSE	Mitochondrial 2-oxoglutarate/malate carrier protein (OGCP) (Solute carrier family 25 member 11)	0.03	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			313

You are viewing entries 80551 to 80600 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.