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
P70105 UniProt NPD GO	MCP_CAVPO	Membrane cofactor protein precursor (CD46 antigen)	0.12	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				379
O43462 UniProt NPD GO	MBTP2_HUMAN	Membrane-bound transcription factor site 2 protease (EC 3.4.24.85) (S2P endopeptidase) (Site-2 prote ...	0.12	-	end	6 *	Membrane; multi-pass membrane protein (Probable)	integral to membrane [TAS]	300294		519
Q99N07 UniProt NPD GO	M4A6D_MOUSE	Membrane-spanning 4-domains subfamily A member 6D (CD20 antigen-like 8)	0.12	-	end	4 *	Membrane; multi-pass membrane protein				247
Q01416 UniProt NPD GO	MSA1_SARMU	Merozoite 31 kDa surface antigen precursor	0.12	-	end	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)				280
Q9TRZ7 UniProt NPD GO	TIMP2_RABIT	Metalloproteinase inhibitor 2 (TIMP-2) (Tissue inhibitor of metalloproteinases 2)	0.12	-	nuc	0	Secreted protein				194
P16368 UniProt NPD GO	TIMP2_BOVIN	Metalloproteinase inhibitor 2 precursor (TIMP-2) (Tissue inhibitor of metalloproteinases 2) (Collage ...	0.12	-	exc	0	Secreted protein			1BUV	220
Q99727 UniProt NPD GO	TIMP4_HUMAN	Metalloproteinase inhibitor 4 precursor (TIMP-4) (Tissue inhibitor of metalloproteinases 4)	0.12	-	exc	0	Secreted protein	extracellular region [NAS]	601915		224
Q800D3 UniProt NPD GO	MT_GOBCO	Metallothionein (MT)	0.12	-	nuc	0					60
O13257 UniProt NPD GO	MT_LIZAU	Metallothionein (MT)	0.12	-	nuc	0					60
P25128 UniProt NPD GO	MT_NOEBA	Metallothionein (MT)	0.12	-	nuc	0					60
P52728 UniProt NPD GO	MT_ZOAVI	Metallothionein (MT)	0.12	-	nuc	0					60
P52721 UniProt NPD GO	MTA_THECR	Metallothionein A (MT-A)	0.12	-	nuc	0					60
O93609 UniProt NPD GO	MTA_PAGBE	Metallothionein A (MT-A) (MT-I)	0.12	-	nuc	0					60
Q8AWG1 UniProt NPD GO	MTB_CARCW	Metallothionein B (MT-B)	0.12	-	nuc	0					60
P52724 UniProt NPD GO	MTB_CHAAC	Metallothionein B (MT-B)	0.12	-	nuc	0					60
P04731 UniProt NPD GO	MT1A_HUMAN	Metallothionein-1A (MT-1A) (Metallothionein-IA) (MT-IA)	0.12	-	nuc	0		cytoplasm [NAS]	156350		61
P18055 UniProt NPD GO	MT2A_RABIT	Metallothionein-2A (MT-2A) (Metallothionein-IIA) (MT-IIA)	0.12	-	nuc	0				2MRB	62
P80290 UniProt NPD GO	MT2C_RABIT	Metallothionein-2C (MT-2C) (Metallothionein-IIC) (MT-IIC)	0.12	-	nuc	0					62
Q499X9 UniProt NPD GO	SYMM_MOUSE	Methionyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.10) (Methionine--tRNA ligase 2) (Mitoch ...	0.12	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				586
Q9U5P2 UniProt NPD GO	ALL5_LEPDS	Mite allergen Lep d 5 (Fragment)	0.12	-	nuc	0					110
P82922 UniProt NPD GO	RT29_BOVIN	Mitochondrial 28S ribosomal protein S29 (S29mt) (MRP-S29) (Fragments)	0.12	-	cyt	0	Mitochondrion				122
Q05492 UniProt NPD GO	RM05_OENBE	Mitochondrial 60S ribosomal protein L5	0.12	-	cyt	0	Mitochondrion				192
O21255 UniProt NPD GO	RM06_RECAM	Mitochondrial 60S ribosomal protein L6	0.12	-	mit	0	Mitochondrion				185
Q5HZI9 UniProt NPD GO	MCAR1_MOUSE	Mitochondrial carrier triple repeat 1	0.12	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				298
Q9DAM5 UniProt NPD GO	DNC_MOUSE	Mitochondrial deoxynucleotide carrier (Solute carrier family 25 member 19)	0.12	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				318
Q9H936 UniProt NPD GO	GHC1_HUMAN	Mitochondrial glutamate carrier 1 (GC-1) (Glutamate/H(+) symporter 1) (Solute carrier family 25 memb ...	0.12	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial inner membrane [IDA]	609304		323
Q9D6M3 UniProt NPD GO	GHC1_MOUSE	Mitochondrial glutamate carrier 1 (GC-1) (Glutamate/H(+) symporter 1) (Solute carrier family 25 memb ...	0.12	-	end	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial inner membrane [ISS] mitochondrion [IDA]			323
Q92328 UniProt NPD GO	MDM12_YEAST	Mitochondrial inheritance component MDM12	0.12	-	mit	0	Mitochondrion; mitochondrial outer membrane	mitochondrial outer membrane [TAS]			271
P46762 UniProt NPD GO	RT19_ACACA	Mitochondrial ribosomal protein S19	0.12	-	nuc	0	Mitochondrion				78
Q7T292 UniProt NPD GO	MFRN2_BRARE	Mitoferrin-2 (Mitochondrial iron transporter 2) (Solute carrier family 25 member 28)	0.12	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				376
Q39025 UniProt NPD GO	MPK5_ARATH	Mitogen-activated protein kinase 5 (EC 2.7.11.24) (MAP kinase 5) (AtMPK5)	0.12	-	cyt	0					376
P59941 UniProt NPD GO	SIRT6_MOUSE	Mono-ADP-ribosyltransferase sirtuin-6 (EC 2.4.2.31) (SIR2-like protein 6)	0.12	-	cyt	0	Nucleus. Predominantly	nucleus [IDA]			334
P28291 UniProt NPD GO	MCPA_BOVIN	Monocyte chemotactic protein 1A precursor (MCP-1A) (MCP-1) (Acidic seminal fluid protein)	0.12	-	exc	0					99
Q95122 UniProt NPD GO	CD14_BOVIN	Monocyte differentiation antigen CD14 precursor (Myeloid cell-specific leucine-rich glycoprotein)	0.12	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				373
Q8BGG6 UniProt NPD GO	MSPD3_MOUSE	Motile sperm domain-containing protein 3	0.12	-	end	2	Membrane; multi-pass membrane protein (Potential)				235
P21449 UniProt NPD GO	MDR2_CRIGR	Multidrug resistance protein 2 (EC 3.6.3.44) (P-glycoprotein 2)	0.12	-	end	11 *	Membrane; multi-pass membrane protein				1276
O80725 UniProt NPD GO	MDR4_ARATH	Multidrug resistance protein 4 (P-glycoprotein 4)	0.12	-	end	9	Cell membrane; multi-pass membrane protein. Non-polar distribution in apical cells. Apical (bottom) ...	membrane [IDA]			1286
Q00748 UniProt NPD GO	MDR65_DROME	Multidrug resistance protein homolog 65 (EC 3.6.3.44) (P-glycoprotein 65)	0.12	-	end	11 *	Membrane; multi-pass membrane protein				1302
P60236 UniProt NPD GO	NXM14_DENAN	Muscarinic m1-toxin4 (Fragment)	0.12	-	nuc	0	Secreted protein				40
P20024 UniProt NPD GO	MYB1_MAIZE	Myb-related protein Zm1	0.12	-	nuc	0	Nucleus (Probable)				340
Q6VBQ5 UniProt NPD GO	MYADM_RAT	Myeloid-associated differentiation marker (Myeloid up-regulated protein)	0.12	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				318
Q06580 UniProt NPD GO	MLC2_YEAST	Myosin light chain 2 (MYO1 light chain 2) (Myosin-1 light chain) (Calmodulin-like myosin light chain ...	0.12	-	cyt	0	Bud neck. Forms a ring at the bud neck in a MYO1-dependent manner	contractile ring (sensu Saccharomyces) [IDA]			163
O02827 UniProt NPD GO	MYLK_SHEEP	Myosin light chain kinase, smooth muscle (EC 2.7.11.18) (MLCK) (Telokin) (Fragment)	0.12	+	mit	0					438
P02609 UniProt NPD GO	MLRS_CHICK	Myosin regulatory light chain 2, skeletal muscle isoform (G2) (DTNB) (MLC-2) (LC2f)	0.12	+	cyt	0				2MYS	168
P04113 UniProt NPD GO	MLRA_PATYE	Myosin regulatory light chain A, smooth adductor muscle	0.12	-	cyt	0					161
P08052 UniProt NPD GO	MLR_TODPA	Myosin regulatory light chain LC-2, mantle muscle (RLC)	0.12	-	nuc	0					153
P29738 UniProt NPD GO	MYR2_SINAL	Myrosinase MB2 (EC 3.2.1.147) (Sinigrinase) (Thioglucosidase) (Fragment)	0.12	-	cyt	0	Vacuole				243
P13997 UniProt NPD GO	TRPF_KLULA	N-(5'-phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) (PRAI)	0.12	-	cyt	0					210
P17560 UniProt NPD GO	RENBP_PIG	N-acylglucosamine 2-epimerase (EC 5.1.3.8) (GlcNAc 2-epimerase) (N-acetyl-D-glucosamine 2-epimerase) ...	0.12	-	mit	0				1FP3	402
Q8NFW8 UniProt NPD GO	NEUA_HUMAN	N-acylneuraminate cytidylyltransferase (EC 2.7.7.43) (CMP-N-acetylneuraminic acid synthetase) (CMP-N ...	0.12	-	mit	0	Nucleus		603316		434

You are viewing entries 61451 to 61500 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.