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
Q8IVH4 UniProt NPD GO	MMAA_HUMAN	Methylmalonic aciduria type A protein, mitochondrial precursor	0.69	-	cyt	0	Mitochondrion (Probable)		607481		418
P55156 UniProt NPD GO	MTP_BOVIN	Microsomal triglyceride transfer protein large subunit precursor (Fragment)	0.69	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				887
P22199 UniProt NPD GO	MCR_RAT	Mineralocorticoid receptor (MR)	0.69	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Endoplasmic reticulum; endoplasmic reticulum mem ...				981
Q08179 UniProt NPD GO	MDM38_YEAST	Mitochondrial distribution and morphology protein 38, mitochondrial precursor	0.69	-	nuc	1	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			573
P07213 UniProt NPD GO	TOM70_YEAST	Mitochondrial import receptor subunit TOM70 (70 kDa mitochondrial outer membrane protein) (Transloca ...	0.69	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	integral to mitochondrial outer membrane [IDA] mitochondrial outer membrane translocase co... [TAS]		2GW1	617
P23231 UniProt NPD GO	TOM70_NEUCR	Mitochondrial precursor proteins import receptor (72 kDa mitochondrial outer membrane protein) (Mito ...	0.69	-	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				624
P15759 UniProt NPD GO	RT14_PARTE	Mitochondrial ribosomal protein S14	0.69	-	nuc	0	Mitochondrion				102
Q13201 UniProt NPD GO	MMRN1_HUMAN	Multimerin-1 precursor (Endothelial cell multimerin 1) (EMILIN-4) (Elastin microfibril interface loc ...	0.69	-	nuc	0			601456		1228
Q6FXP4 UniProt NPD GO	MRD1_CANGA	Multiple RNA-binding domain-containing protein 1	0.69	-	nuc	0	Nucleus (By similarity)				861
P28665 UniProt NPD GO	MUG1_MOUSE	Murinoglobulin-1 precursor (MuG1)	0.69	-	mit	0	Secreted protein				1476
Q17107 UniProt NPD GO	AV71_ACAVI	Muscle cell intermediate filament protein AV71 (Fragment)	0.69	-	nuc	0					394
Q23405 UniProt NPD GO	HIM14_CAEEL	MutS protein homolog him-14	0.69	-	mit	0	Nucleus				842
P01103 UniProt NPD GO	MYB_CHICK	Myb proto-oncogene protein (C-myb)	0.69	+	nuc	0	Nucleus			1POM	641
P49812 UniProt NPD GO	MYOG_PIG	Myogenin	0.69	+	nuc	0	Nucleus				224
Q63379 UniProt NPD GO	MYCN_RAT	N-myc proto-oncogene protein	0.69	+	nuc	0	Nucleus				462
Q61976 UniProt NPD GO	MYCN_MARMO	N-myc proto-oncogene protein (N-myc1)	0.69	+	nuc	0	Nucleus				460
Q98902 UniProt NPD GO	L1CAM_FUGRU	Neural cell adhesion molecule L1 precursor (N-CAM L1) (L1-CAM)	0.69	-	nuc	1	Membrane; single-pass type I membrane protein				1277
P19527 UniProt NPD GO	NFL_RAT	Neurofilament triplet L protein (68 kDa neurofilament protein) (Neurofilament light polypeptide) (NF ...	0.69	-	nuc	0		neurofilament [NAS]			541
P35001 UniProt NPD GO	NEUM_CHICK	Neuromodulin (Axonal membrane protein GAP-43) (Growth-associated protein 43)	0.69	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic surface of growth cone and ...	cytosol [IDA] synaptosome [IDA]			246
Q64387 UniProt NPD GO	PNOC_MOUSE	Nociceptin precursor (N23K/N27K) [Contains: Neuropeptide 1; Nociceptin (Orphanin FQ) (PPNOC); Neurop ...	0.69	-	exc	0	Secreted protein				187
Q14934 UniProt NPD GO	NFAC4_HUMAN	Nuclear factor of activated T-cells, cytoplasmic 4 (NF-ATc4) (NFATc4) (T cell transcription factor N ...	0.69	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic for the phosphorylated form and nuclear after activation that is con ...		602699		902
O44960 UniProt NPD GO	NHR64_CAEEL	Nuclear hormone receptor family member nhr-64	0.69	-	nuc	0	Nucleus (Potential)				412
Q9XVV3 UniProt NPD GO	NHR67_CAEEL	Nuclear hormone receptor family member nhr-67	0.69	-	nuc	0	Nucleus (Potential)				416
O02235 UniProt NPD GO	NHR89_CAEEL	Nuclear hormone receptor family member nhr-89	0.69	-	nuc	0	Nucleus (Potential)				310
Q06066 UniProt NPD GO	YBOX1_CHICK	Nuclease sensitive element-binding protein 1 (Y-box-binding protein 1) (Y-box transcription factor)	0.69	+	nuc	0	Cytoplasm. Nucleus. Shuttles between nucleus and cytoplasm. Predominantly cytoplasmic in proliferati ...				321
Q4KLN4 UniProt NPD GO	GLE1_RAT	Nucleoporin GLE1 (GLE1-like protein)	0.69	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Shuttles between the nucleus and the cytoplasm. ...				698
Q8R5M4 UniProt NPD GO	OPTN_RAT	Optineurin (FIP-2-like protein)	0.69	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Golgi apparatus (By similarity). Found in the perinuc ...				585
P54791 UniProt NPD GO	ORC4_YEAST	Origin recognition complex subunit 4 (Origin recognition complex 56 kDa subunit)	0.69	-	nuc	0	Nucleus	nuclear origin of replication recognition c... [TAS] pre-replicative complex [TAS]			529
Q4KMM3 UniProt NPD GO	OXR1_MOUSE	Oxidation resistance protein 1 (Protein C7)	0.69	-	nuc	0	Mitochondrion (By similarity). Nucleus; nucleolus (Ref.1)	nucleolus [IDA]			751
Q91XL9 UniProt NPD GO	OSBL1_MOUSE	Oxysterol-binding protein-related protein 1 (OSBP-related protein 1) (ORP-1)	0.69	-	nuc	0					950
Q8K4M9 UniProt NPD GO	OSBL1_RAT	Oxysterol-binding protein-related protein 1 (OSBP-related protein 1) (ORP-1)	0.69	-	nuc	0				1Z9O	950
Q06710 UniProt NPD GO	PAX8_HUMAN	Paired box protein Pax-8	0.69	-	nuc	0	Nucleus	nucleus [NAS]	218700		450
Q00288 UniProt NPD GO	PAX8_MOUSE	Paired box protein Pax-8	0.69	-	nuc	0	Nucleus	transcription factor complex [TAS]			457
Q9UL45 UniProt NPD GO	PLDN_HUMAN	Pallidin (Pallid protein homolog) (Syntaxin 13-interacting protein)	0.69	-	nuc	0	Cytoplasm. It can exist as a soluble protein as well as a peripheral membrane protein		604310		172
Q5BD15 UniProt NPD GO	PFA4_EMENI	Palmitoyltransferase pfa4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.69	+	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				435
Q5B433 UniProt NPD GO	PFA5_EMENI	Palmitoyltransferase pfa5 (EC 2.3.1.-) (Protein fatty acyltransferase 5)	0.69	+	nuc	4 *	Membrane; multi-pass membrane protein (Potential)				474
Q42510 UniProt NPD GO	EMB30_ARATH	Pattern formation protein EMB30	0.69	+	end	0	Cytoplasm (Probable)				1451
O75127 UniProt NPD GO	PTCD1_HUMAN	Pentatricopeptide repeat protein 1	0.69	-	mit	0					700
Q9C1E9 UniProt NPD GO	PEX6_GLOLA	Peroxisomal biogenesis factor 6 (Peroxin-6) (ClaPEX6)	0.69	-	nuc	0					1388
Q56YP2 UniProt NPD GO	PI5K1_ARATH	Phosphatidylinositol-4-phosphate 5-kinase 1 (EC 2.7.1.68) (AtPIP5K1) (1-phosphatidylinositol-4-phosp ...	0.69	-	mit	0					752
P51061 UniProt NPD GO	CAPP2_SOYBN	Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCase) (PEPC)	0.69	-	nuc	0	Cytoplasm (By similarity)				967
Q9AU12 UniProt NPD GO	CAPP_PHAVU	Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCase) (PEPC)	0.69	-	cyt	0	Cytoplasm (By similarity)				968
P29193 UniProt NPD GO	CAPP1_SACHY	Phosphoenolpyruvate carboxylase, housekeeping isozyme (EC 4.1.1.31) (PEPCase) (PEPC)	0.69	-	nuc	0	Cytoplasm				966
Q5UE93 UniProt NPD GO	PI3R6_HUMAN	Phosphoinositide 3-kinase regulatory subunit 6 (Phosphoinositide 3-kinase gamma adapter protein of 8 ...	0.69	-	cyt	0	Cytoplasm (By similarity)				754
Q9Z280 UniProt NPD GO	PLD1_MOUSE	Phospholipase D1 (EC 3.1.4.4) (PLD 1) (Choline phosphatase 1) (Phosphatidylcholine-hydrolyzing phosp ...	0.69	-	cyt	0	Cytoplasm; perinuclear region. Endoplasmic reticulum. Golgi apparatus. Endosome; late endosome				1074
P97813 UniProt NPD GO	PLD2_MOUSE	Phospholipase D2 (EC 3.1.4.4) (PLD 2) (Choline phosphatase 2) (Phosphatidylcholine-hydrolyzing phosp ...	0.69	-	mit	0	Membrane; peripheral membrane protein	plasma membrane [IDA]			933
P70498 UniProt NPD GO	PLD2_RAT	Phospholipase D2 (EC 3.1.4.4) (PLD 2) (Choline phosphatase 2) (Phosphatidylcholine-hydrolyzing phosp ...	0.69	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				933
Q9SR43 UniProt NPD GO	PFBS_ARATH	Phytochromobilin:ferredoxin oxidoreductase, chloroplast precursor (EC 1.3.7.4) (Phytochromobilin syn ...	0.69	+	mit	0	Plastid; chloroplast				329
Q9U8Q4 UniProt NPD GO	PRSN_PIERA	Pierisin (EC 2.4.2.-) (NAD--DNA ADP-ribosyltransferase) (Pierisin-1)	0.69	-	nuc	0					850
Q9JII4 UniProt NPD GO	PRLPL_RAT	Placental prolactin-like protein L precursor (PRL-like protein L) (PLP-L)	0.69	-	nuc	0	Secreted protein (By similarity)				227

You are viewing entries 14351 to 14400 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.