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
Q9MSV2 UniProt NPD GO	MATK_CUNLA	Maturase K (Intron maturase)	0.68	+	mit	0	Plastid; chloroplast				508
Q646R8 UniProt NPD GO	MATK_CUPAN	Maturase K (Intron maturase)	0.68	-	nuc	0	Plastid; chloroplast				507
Q9MV47 UniProt NPD GO	MATK_CYCPA	Maturase K (Intron maturase)	0.68	+	nuc	0	Plastid; chloroplast				519
Q6J9Z4 UniProt NPD GO	MATK_CYPCL	Maturase K (Intron maturase)	0.68	-	nuc	0	Plastid; chloroplast				516
Q95GJ0 UniProt NPD GO	MATK_GAUPR	Maturase K (Intron maturase)	0.68	-	nuc	0	Plastid; chloroplast				506
Q8MCR8 UniProt NPD GO	MATK_LATTI	Maturase K (Intron maturase)	0.68	-	nuc	0	Plastid; chloroplast				506
Q8MCR7 UniProt NPD GO	MATK_LATVE	Maturase K (Intron maturase)	0.68	-	nuc	0	Plastid; chloroplast				503
Q8GVB5 UniProt NPD GO	MATK_LEUAE	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				520
O98370 UniProt NPD GO	MATK_LIQFO	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				503
P48190 UniProt NPD GO	MATK_MAIZE	Maturase K (Intron maturase)	0.68	+	cyt	0	Plastid; chloroplast				513
Q70D04 UniProt NPD GO	MATK_MANOF	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				511
Q9MUZ2 UniProt NPD GO	MATK_MELAL	Maturase K (Intron maturase)	0.68	+	cyt	0	Plastid; chloroplast				511
Q95GT2 UniProt NPD GO	MATK_NEPAL	Maturase K (Intron maturase)	0.68	-	nuc	0	Plastid; chloroplast				504
Q94Q55 UniProt NPD GO	MATK_NEPGR	Maturase K (Intron maturase)	0.68	-	nuc	0	Plastid; chloroplast				504
Q95GQ8 UniProt NPD GO	MATK_NEPMI	Maturase K (Intron maturase)	0.68	-	nuc	0	Plastid; chloroplast				504
Q70D38 UniProt NPD GO	MATK_NICAC	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				509
Q95DP2 UniProt NPD GO	MATK_NICBE	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				509
Q94Q76 UniProt NPD GO	MATK_NICPL	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				509
Q76MT0 UniProt NPD GO	MATK_NICSY	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				509
Q6BDJ4 UniProt NPD GO	MATK_PINCE	Maturase K (Intron maturase)	0.68	-	nuc	0	Plastid; chloroplast				515
Q3MKB9 UniProt NPD GO	MATK_POROL	Maturase K (Intron maturase)	0.68	-	nuc	0	Plastid; chloroplast				509
Q8WJN5 UniProt NPD GO	MATK_RUBUR	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				503
Q5YJU0 UniProt NPD GO	MATK_SOPJA	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				506
Q9GF35 UniProt NPD GO	MATK_THLAR	Maturase K (Intron maturase)	0.68	-	mit	0	Plastid; chloroplast				504
P12176 UniProt NPD GO	MATK_TOBAC	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				509
Q09094 UniProt NPD GO	REC15_SCHPO	Meiotic recombination protein rec15	0.68	-	nuc	0					180
Q09728 UniProt NPD GO	CUF1_SCHPO	Metal-binding regulatory protein cuf1	0.68	-	nuc	0	Nucleus (Potential)				411
Q9VFL5 UniProt NPD GO	SYMM_DROME	Methionyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.10) (Mitochondrial methionine--tRNA lig ...	0.68	+	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial matrix [ISS]			582
P08235 UniProt NPD GO	MCR_HUMAN	Mineralocorticoid receptor (MR)	0.68	+	nuc	0	Cytoplasm. Nucleus. Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane prote ...		177735	2AB2	984
Q4JM28 UniProt NPD GO	MCR_SAIBB	Mineralocorticoid receptor (MR)	0.68	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic and nuclear in the absence of ligand ...				982
Q9D9F8 UniProt NPD GO	MIPO1_MOUSE	Mirror-image polydactyly gene 1 protein homolog	0.68	-	nuc	0					279
Q6B860 UniProt NPD GO	RT14_BOVIN	Mitochondrial 28S ribosomal protein S14 (S14mt) (MRP-S14)	0.68	+	nuc	0	Mitochondrion (By similarity)				128
P82920 UniProt NPD GO	RT21_BOVIN	Mitochondrial 28S ribosomal protein S21 (S21mt) (MRP-S21)	0.68	-	nuc	0	Mitochondrion				87
Q5RFN3 UniProt NPD GO	MTFR1_PONPY	Mitochondrial fission regulator 1	0.68	-	mit	0	Mitochondrion (By similarity)				333
Q15390 UniProt NPD GO	MTFR1_HUMAN	Mitochondrial fission regulator 1 (Chondrocyte protein with a poly-proline region)	0.68	-	mit	0	Mitochondrion (By similarity)	plasma membrane [IDA]			333
P60096 UniProt NPD GO	RT12_MAGGA	Mitochondrial ribosomal protein S12	0.68	-	nuc	0	Mitochondrion				125
P60097 UniProt NPD GO	RT12_MAGSO	Mitochondrial ribosomal protein S12	0.68	-	nuc	0	Mitochondrion				125
P49387 UniProt NPD GO	RT14_BRANA	Mitochondrial ribosomal protein S14	0.68	-	nuc	0	Mitochondrion				100
Q9C5C0 UniProt NPD GO	MPK18_ARATH	Mitogen-activated protein kinase 18 (EC 2.7.11.24) (MAP kinase 18) (AtMPK18)	0.68	-	nuc	0					603
Q99759 UniProt NPD GO	M3K3_HUMAN	Mitogen-activated protein kinase kinase kinase 3 (EC 2.7.11.25) (MAPK/ERK kinase kinase 3) (MEK kina ...	0.68	-	nuc	0			602539	2C60	626
Q92918 UniProt NPD GO	M4K1_HUMAN	Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) (MAPK/ERK kinase kinase kinase ...	0.68	-	nuc	0			601983		833
P13568 UniProt NPD GO	MDR_PLAFF	Multidrug resistance protein (EC 3.6.3.44) (Chloroquine resistance protein)	0.68	-	end	11	Membrane; multi-pass membrane protein				1419
Q5IS53 UniProt NPD GO	ACM5_PANTR	Muscarinic acetylcholine receptor M5	0.68	-	end	7 *	Membrane; multi-pass membrane protein				532
Q5IS98 UniProt NPD GO	ACM5_SAIBB	Muscarinic acetylcholine receptor M5	0.68	-	end	7 *	Membrane; multi-pass membrane protein				532
Q94250 UniProt NPD GO	MBL_CAEEL	Muscleblind-like protein	0.68	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			284
P41218 UniProt NPD GO	MNDA_HUMAN	Myeloid cell nuclear differentiation antigen	0.68	-	nuc	0	Nucleus. Cytoplasm. Uniformly distributed throughout the interphase cell nucleus. Associates with ch ...		159553	2DBG	407
Q32KY3 UniProt NPD GO	MLF1_BOVIN	Myeloid leukemia factor 1 (Myelodysplasia-myeloid leukemia factor 1)	0.68	-	nuc	0	Cytoplasm. Nucleus (By similarity)				270
O00936 UniProt NPD GO	MYOB_TOXGO	Myosin B/C (MyoB/C) (TgM-B)	0.68	-	mit	0	Cytoplasm. Isoform MyoB is cytoplasmic while isoform MyoC is concentrated at the anterior and poster ...				1171
Q5R6F6 UniProt NPD GO	MTMR7_PONPY	Myotubularin-related protein 7 (EC 3.1.3.-)	0.68	-	nuc	0					660
Q86W25 UniProt NPD GO	NAL13_HUMAN	NACHT, LRR and PYD-containing protein 13 (Nucleotide-binding oligomerization domain protein 14)	0.68	-	nuc	0			609660		1043

You are viewing entries 14801 to 14850 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.