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
O93450 UniProt NPD GO	MTA_PARCR	Metallothionein A (MT-A) (MT-I)	0.10	-	nuc	0					60
P17511 UniProt NPD GO	MT1_CAEEL	Metallothionein-1 (MT-1) (Metallothionein-I) (MT-I)	0.10	-	nuc	0					74
P11957 UniProt NPD GO	MT1A_RABIT	Metallothionein-1A (MT-1A) (Metallothionein-IA) (MT-IA)	0.10	-	nuc	0					61
P07438 UniProt NPD GO	MT1B_HUMAN	Metallothionein-1B (MT-1B) (Metallothionein-IB) (MT-IB)	0.10	-	nuc	0		cytoplasm [NAS]	156349		61
Q7ZSY6 UniProt NPD GO	MT2_BRARE	Metallothionein-2 (MT-2)	0.10	-	nuc	0					60
P67981 UniProt NPD GO	MT2_CRIGR	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.10	-	nuc	0					61
P68041 UniProt NPD GO	MT2_CRILO	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.10	-	nuc	0					61
Q9I9I0 UniProt NPD GO	MT2_CYPCA	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.10	-	nuc	0					60
P80289 UniProt NPD GO	MT2B_RABIT	Metallothionein-2B (MT-2B) (Metallothionein-IIB) (MT-IIB)	0.10	-	nuc	0					61
P25713 UniProt NPD GO	MT3_HUMAN	Metallothionein-3 (MT-3) (Metallothionein-III) (MT-III) (Growth inhibitory factor) (GIF) (GIFB)	0.10	-	nuc	0		synaptic vesicle [ISS]	139255	2FJ5	68
P55942 UniProt NPD GO	MT1H_BOVIN	Metallothionein-I, hippocampal (MT-1)	0.10	-	nuc	0					61
P55943 UniProt NPD GO	MT2H_BOVIN	Metallothionein-II, hippocampal (MT-2)	0.10	-	nuc	0					61
Q9D1I5 UniProt NPD GO	MCEE_MOUSE	Methylmalonyl-CoA epimerase, mitochondrial precursor (EC 5.1.99.1) (DL-methylmalonyl-CoA racemase)	0.10	-	mit	0	Mitochondrion (Probable)	mitochondrion [IDA]			178
Q9BQA1 UniProt NPD GO	MEP50_HUMAN	Methylosome protein 50 (MEP50 protein) (WD repeat protein 77)	0.10	-	mit	0					342
Q99J09 UniProt NPD GO	MEP50_MOUSE	Methylosome protein 50 (MEP50 protein) (WD repeat protein 77)	0.10	-	mit	0					342
P07277 UniProt NPD GO	KIME_YEAST	Mevalonate kinase (EC 2.7.1.36) (MK) (MvK)	0.10	-	mit	0	Cytoplasm				443
Q9D1H9 UniProt NPD GO	MFAP4_MOUSE	Microfibril-associated glycoprotein 4 precursor	0.10	-	vac	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				257
Q9CPU4 UniProt NPD GO	MGST3_MOUSE	Microsomal glutathione S-transferase 3 (EC 2.5.1.18) (Microsomal GST-3) (Microsomal GST-III)	0.10	-	nuc	4 *	Microsome; microsomal membrane; multi-pass membrane protein (Potential)				153
Q3ZBD9 UniProt NPD GO	MARE1_BOVIN	Microtubule-associated protein RP/EB family member 1 (APC-binding protein EB1) (End-binding protein ...	0.10	-	cyt	0	Cytoplasm (By similarity). Associated with the microtubule network at the growing distal tip of micr ...				267
P21741 UniProt NPD GO	MK_HUMAN	Midkine precursor (MK) (Neurite outgrowth-promoting protein) (Midgestation and kidney protein) (Amph ...	0.10	+	nuc	1 *	Secreted protein		162096	1MKN	143
P34394 UniProt NPD GO	MPS4_CAEEL	MinK-related peptide, potassium channel accessory subunit protein 4	0.10	-	nuc	1 *					91
P23635 UniProt NPD GO	PP2A1_SCHPO	Minor serine/threonine-protein phosphatase PP2A-1 catalytic subunit (EC 3.1.3.16)	0.10	-	cyt	0					309
P82915 UniProt NPD GO	RT16_BOVIN	Mitochondrial 28S ribosomal protein S16 (S16mt) (MRP-S16) (Fragments)	0.10	-		0	Mitochondrion				20
Q99N95 UniProt NPD GO	RM03_MOUSE	Mitochondrial 39S ribosomal protein L3 (L3mt) (MRP-L3)	0.10	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IDA] mitochondrion [IDA]			348
Q4RGM4 UniProt NPD GO	RM33_TETNG	Mitochondrial 39S ribosomal protein L33 (L33mt)	0.10	-	mit	1 *	Mitochondrion (By similarity)				65
P38127 UniProt NPD GO	RIM2_YEAST	Mitochondrial carrier protein RIM2	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			377
Q9H1U9 UniProt NPD GO	MCAR1_HUMAN	Mitochondrial carrier triple repeat 1	0.10	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				297
Q5IS35 UniProt NPD GO	DNC_MACFA	Mitochondrial deoxynucleotide carrier (Solute carrier family 25 member 19)	0.10	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				320
Q9HC21 UniProt NPD GO	DNC_HUMAN	Mitochondrial deoxynucleotide carrier (Solute carrier family 25 member 19) (Mitochondrial uncoupling ...	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [NAS]	607196		320
Q6FJZ5 UniProt NPD GO	PPT2_CANGA	Mitochondrial holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) (Mitochondrial holo-ACP synthase) (4 ...	0.10	-	cyt	0	Mitochondrion (By similarity)				152
Q759W7 UniProt NPD GO	TIM10_ASHGO	Mitochondrial import inner membrane translocase subunit TIM10	0.10	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				89
Q6DI06 UniProt NPD GO	TIM10_BRARE	Mitochondrial import inner membrane translocase subunit Tim10	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				88
Q4QR62 UniProt NPD GO	TI10A_XENLA	Mitochondrial import inner membrane translocase subunit Tim10 A	0.10	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				93
Q9Z0V8 UniProt NPD GO	TI17A_MOUSE	Mitochondrial import inner membrane translocase subunit Tim17-A (Inner membrane preprotein transloca ...	0.10	-	mit	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				171
P62077 UniProt NPD GO	TIM8B_MOUSE	Mitochondrial import inner membrane translocase subunit Tim8 B (Deafness dystonia protein 2 homolog) ...	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...	mitochondrion [IDA]			83
P62078 UniProt NPD GO	TIM8B_RAT	Mitochondrial import inner membrane translocase subunit Tim8 B (Deafness dystonia protein 2 homolog) ...	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				83
P80967 UniProt NPD GO	TOM5_YEAST	Mitochondrial import receptor subunit TOM5 (Translocase of outer membrane 5 kDa subunit)	0.10	-	cyt	1 *	Mitochondrion; mitochondrial outer membrane; single-pass membrane protein (Potential). Outer membran ...	mitochondrial outer membrane translocase co... [IPI]			50
Q9BKU4 UniProt NPD GO	PHB1_CAEEL	Mitochondrial prohibitin complex protein 1 (Prohibitin-1)	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane				275
P53721 UniProt NPD GO	YN89_YEAST	Mitochondrial protein YNR018W	0.10	-	nuc	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrion [IDA]			224
Q9Y829 UniProt NPD GO	MTF1_SACDO	Mitochondrial replication protein MTF1 (Mitochondrial transcription factor mtTFB)	0.10	-	cyt	0	Mitochondrion (By similarity)				340
Q287T7 UniProt NPD GO	MFRN1_BRARE	Mitoferrin-1 (Mitochondrial iron transporter 1) (Solute carrier family 25 member 37) (Protein frasca ...	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				332
Q9DAJ4 UniProt NPD GO	MORG1_MOUSE	Mitogen-activated protein kinase organizer 1 (MAPK organizer 1)	0.10	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Partially (By similarity)				315
P07223 UniProt NPD GO	MPI1_LYMST	Molluscan insulin-related peptide 1 precursor (MIP I) [Contains: Molluscan insulin-related peptide 1 ...	0.10	-	exc	1 *	Secretory granules				123
P53985 UniProt NPD GO	MOT1_HUMAN	Monocarboxylate transporter 1 (MCT 1)	0.10	-	end	11 *	Cell membrane; multi-pass membrane protein	integral to membrane [TAS] membrane fraction [TAS]	600682		500
O15427 UniProt NPD GO	MOT4_HUMAN	Monocarboxylate transporter 4 (MCT 4) (MCT 3)	0.10	-	end	12 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	603877		465
O15403 UniProt NPD GO	MOT7_HUMAN	Monocarboxylate transporter 7 (MCT 7) (MCT 6)	0.10	-	end	12 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	603880		523
O43193 UniProt NPD GO	MTLR_HUMAN	Motilin receptor (G-protein coupled receptor 38)	0.10	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602885		412
Q9MYW9 UniProt NPD GO	OPRM_MACMU	Mu-type opioid receptor (MOR-1)	0.10	-	end	7	Membrane; multi-pass membrane protein				400
Q95247 UniProt NPD GO	OPRM_PIG	Mu-type opioid receptor (MOR-1)	0.10	-	end	7	Membrane; multi-pass membrane protein				401
O35682 UniProt NPD GO	MYADM_MOUSE	Myeloid-associated differentiation marker (Myeloid up-regulated protein)	0.10	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				320

You are viewing entries 64701 to 64750 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.