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
P53193 UniProt NPD GO	JAC1_YEAST	J-type co-chaperone JAC1, mitochondrial precursor (J-type accessory chaperone 1)	0.36	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			184
P38199 UniProt NPD GO	YBD2_YEAST	KH domain-containing protein YBL032W	0.36	-	nuc	0		cytoplasm [IDA] nuclear chromosome, telomeric region [IDA]			381
Q6TDP3 UniProt NPD GO	KLH17_MOUSE	Kelch-like protein 17 (Actinfilin)	0.36	-	cyt	0	Postsynaptic density (By similarity)				640
Q8K430 UniProt NPD GO	KLH17_RAT	Kelch-like protein 17 (Actinfilin)	0.36	-	cyt	0	Postsynaptic density				640
P02440 UniProt NPD GO	KRB2C_SHEEP	Keratin, high-sulfur matrix protein, B2C	0.36	-	nuc	0					151
P08730 UniProt NPD GO	K1C13_MOUSE	Keratin, type I cytoskeletal 13 (Cytokeratin-13) (CK-13) (Keratin-13) (K13) (47 kDa cytokeratin)	0.36	-	nuc	0					437
P08728 UniProt NPD GO	K1C19_BOVIN	Keratin, type I cytoskeletal 19 (Cytokeratin-19) (CK-19) (Keratin-19) (K19)	0.36	-	mit	0					399
P19001 UniProt NPD GO	K1C19_MOUSE	Keratin, type I cytoskeletal 19 (Cytokeratin-19) (CK-19) (Keratin-19) (K19)	0.36	-	mit	0		sarcolemma [IDA] Z disc [IDA]			403
P51856 UniProt NPD GO	K1C19_POTTR	Keratin, type I cytoskeletal 19 (Cytokeratin-19) (CK-19) (Keratin-19) (K19)	0.36	-	nuc	0					401
P05781 UniProt NPD GO	K1C4_XENLA	Keratin, type I cytoskeletal 47 kDa	0.36	-	nuc	0					419
Q7Z794 UniProt NPD GO	K2C1B_HUMAN	Keratin, type II cytoskeletal 1b	0.36	+	cyt	0					576
P15241 UniProt NPD GO	K2M2_SHEEP	Keratin, type II microfibrillar, component 7C	0.36	-	nuc	0					491
Q07627 UniProt NPD GO	KRA11_HUMAN	Keratin-associated protein 1-1 (Keratin-associated protein 1.1) (High sulfur keratin-associated prot ...	0.36	-	nuc	0		extracellular region [NAS]	608819		177
P60371 UniProt NPD GO	KR106_HUMAN	Keratin-associated protein 10-6 (Keratin-associated protein 10.6) (High sulfur keratin-associated pr ...	0.36	-	nuc	0					365
Q8IUC1 UniProt NPD GO	KR111_HUMAN	Keratin-associated protein 11-1 (High sulfur keratin-associated protein 11.1)	0.36	-	mit	0					163
Q52LG2 UniProt NPD GO	KR132_HUMAN	Keratin-associated protein 13-2	0.36	-	nuc	0					175
P20826 UniProt NPD GO	SCF_MOUSE	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF) (Hemato ...	0.36	-	cyt	1	Isoform 1, isoform 2: Cell membrane; single-pass type I membrane protein (By similarity). Processed ...	extracellular space [IDA] integral to membrane [IDA] plasma membrane [IDA]			273
P14151 UniProt NPD GO	LYAM1_HUMAN	L-selectin precursor (Lymph node homing receptor) (Leukocyte adhesion molecule 1) (LAM-1) (Leukocyte ...	0.36	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	153240	1KJB	372
Q8BP74 UniProt NPD GO	PSTK_MOUSE	L-seryl-tRNA(Ser/Sec) kinase (EC 2.7.1.-) (Phosphoseryl-tRNA(Ser/Sec) kinase)	0.36	+	mit	0					267
Q8LBW3 UniProt NPD GO	LBD12_ARATH	LOB domain-containing protein 12	0.36	-	nuc	0					193
Q02401 UniProt NPD GO	LPH_RAT	Lactase-phlorizin hydrolase precursor (Lactase-glycosylceramidase) [Includes: Lactase (EC 3.2.1.108) ...	0.36	-	nuc	1	Cell membrane; single-pass type I membrane protein. Brush border	brush border [IDA]			1928
P02788 UniProt NPD GO	TRFL_HUMAN	Lactotransferrin precursor (EC 3.4.21.-) (Lactoferrin) (Talalactoferrin alfa) [Contains: Kaliocin-1; ...	0.36	-	exc	0	Secreted protein		150210	2DP4	710
Q5T753 UniProt NPD GO	LCE1E_HUMAN	Late cornified envelope protein 1E (Late envelope protein 5)	0.36	-	mit	0					118
Q29144 UniProt NPD GO	LLP_TRIVU	Late lactation protein precursor (LLP)	0.36	-	exc	0	Secreted protein				176
Q1XG29 UniProt NPD GO	LEP_URSTH	Leptin precursor (Obesity factor)	0.36	-	exc	0	Secreted protein (Probable)				167
Q62959 UniProt NPD GO	LEPR_RAT	Leptin receptor precursor (LEP-R) (OB receptor) (OB-R) (CD295 antigen)	0.36	-	nuc	3 *	Cell membrane; single-pass type I membrane protein. Isoform E: Secreted protein (Probable)				1162
Q8K3W2 UniProt NPD GO	LRC10_MOUSE	Leucine-rich repeat-containing protein 10 (Heart-restricted leucine-rich repeat protein)	0.36	-	nuc	0	Nucleus	cytoskeleton [IDA] mitochondrion [IDA] nucleus [IDA]			274
Q68F79 UniProt NPD GO	LRC8E_XENTR	Leucine-rich repeat-containing protein 8E	0.36	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				806
P29683 UniProt NPD GO	CHLN_CHLRE	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.36	-	nuc	0	Plastid; chloroplast				545
O44952 UniProt NPD GO	LONM_CAEEL	Lon protease homolog, mitochondrial precursor (EC 3.4.21.-)	0.36	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				971
P01130 UniProt NPD GO	LDLR_HUMAN	Low-density lipoprotein receptor precursor (LDL receptor)	0.36	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	143890	2FCW	860
P35951 UniProt NPD GO	LDLR_MOUSE	Low-density lipoprotein receptor precursor (LDL receptor)	0.36	-	exc	1	Membrane; single-pass type I membrane protein	endosome [IDA] integral to plasma membrane [ISS] plasma membrane [ISS]			864
P18627 UniProt NPD GO	LAG3_HUMAN	Lymphocyte activation gene 3 protein precursor (LAG-3) (FDC protein) (CD223 antigen)	0.36	-	nuc	1	Membrane; single-pass type I membrane protein		153337		525
P11117 UniProt NPD GO	PPAL_HUMAN	Lysosomal acid phosphatase precursor (EC 3.1.3.2) (LAP)	0.36	-	end	1 *	Lysosome	integral to membrane [TAS]	200950		423
Q8L887 UniProt NPD GO	MAD26_ORYSA	MADS-box transcription factor 26 (OsMADS26) (FDRMADS3) (RMADS220)	0.36	-	mit	0	Nucleus (Probable)				222
Q61830 UniProt NPD GO	MRC1_MOUSE	Macrophage mannose receptor 1 precursor (MMR) (CD206 antigen)	0.36	-	end	1	Membrane; single-pass type I membrane protein	cell surface [IDA]		1FWV	1456
Q17061 UniProt NPD GO	MRJP4_APIME	Major royal jelly protein 4 precursor (MRJP-4) (Bee-milk protein) (Royal jelly protein RJP57-2)	0.36	-	exc	0	Secreted protein				464
Q9BSQ5 UniProt NPD GO	CCM2_HUMAN	Malcavernin (Cerebral cavernous malformations 2 protein)	0.36	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IEP]	607929		444
Q80UM7 UniProt NPD GO	GCS1_MOUSE	Mannosyl-oligosaccharide glucosidase (EC 3.2.1.106) (Glycoprotein-processing glucosidase I) (Glucosi ...	0.36	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				834
Q58T46 UniProt NPD GO	M3H14_BOMMX	Maximins 3/H14 precursor [Contains: Maximin-3; Maximin-H14]	0.36	-	end	0	Secreted protein				144
Q9P2E8 UniProt NPD GO	MARH4_HUMAN	Membrane-associated RING finger protein 4 (Membrane-associated RING-CH protein IV) (MARCH-IV) (RING ...	0.36	-	exc	2	Membrane; multi-pass membrane protein (Potential)		608208		410
Q99320 UniProt NPD GO	MSA2_PLAF8	Merozoite surface antigen 2 precursor (MSA-2) (Allelic form 4)	0.36	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				276
O15303 UniProt NPD GO	MGR6_HUMAN	Metabotropic glutamate receptor 6 precursor (mGluR6)	0.36	-	end	6	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	604096		877
P91685 UniProt NPD GO	MGR_DROME	Metabotropic glutamate receptor precursor	0.36	-	end	7	Membrane; multi-pass membrane protein				976
P38062 UniProt NPD GO	AMPM2_RAT	Methionine aminopeptidase 2 (EC 3.4.11.18) (MetAP 2) (Peptidase M 2) (Initiation factor 2-associated ...	0.36	+	cyt	0		cytoplasm [ISS]			478
P19332 UniProt NPD GO	TAU_RAT	Microtubule-associated protein tau (Neurofibrillary tangle protein) (Paired helical filament-tau) (P ...	0.36	-	nuc	0	Cytoplasm; cytosol. Cell membrane. Mostly found in the axons of neurons, in the cytosol and in assoc ...	axon [ISS] cytosol [ISS] growth cone [ISS] microtubule associated complex [ISS] plasma membrane [ISS] tubulin [ISS]			751
Q9CQV6 UniProt NPD GO	MLP3B_MOUSE	Microtubule-associated proteins 1A/1B light chain 3B precursor (Microtubule-associated protein 1 lig ...	0.36	-	nuc	0	LC3-I: Cytoplasm. LC3-II: Intracytoplasmic membrane; lipid-anchor. LC3-II binds to the autophagic me ...				124
Q62625 UniProt NPD GO	MLP3B_RAT	Microtubule-associated proteins 1A/1B light chain 3B precursor (Microtubule-associated protein 1 lig ...	0.36	-	nuc	0	LC3-I: Cytoplasm. LC3-II: Intracytoplasmic membrane; lipid-anchor. LC3-II binds to the autophagic me ...			1UGM	141
Q7PYH1 UniProt NPD GO	RM33_ANOGA	Mitochondrial 39S ribosomal protein L33 (L33mt)	0.36	-	nuc	0	Mitochondrion (Potential)				65
Q7ZTL7 UniProt NPD GO	BCS1_XENLA	Mitochondrial chaperone BCS1 (BCS1-like protein)	0.36	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				419

You are viewing entries 35101 to 35150 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.