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
P30307 UniProt NPD GO	MPIP3_HUMAN	M-phase inducer phosphatase 3 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25C)	0.71	-	nuc	0	Nucleus	intracellular [NAS]	157680		473
Q6VAM4 UniProt NPD GO	MAD23_ORYSA	MADS-box transcription factor 23 (OsMADS23)	0.71	-	nuc	0	Nucleus (Probable)				159
P49136 UniProt NPD GO	MAPK2_CRILO	MAP kinase-activated protein kinase 2 (EC 2.7.11.1) (MAPK-activated protein kinase 2) (MAPKAP kinase ...	0.71	-	nuc	0					329
Q8IW41 UniProt NPD GO	MAPK5_HUMAN	MAP kinase-activated protein kinase 5 (EC 2.7.11.1) (MAPK-activated protein kinase 5) (MAPKAP kinase ...	0.71	+	nuc	0	Cytoplasm (Probable). Nucleus. Also observed in the nucleus		606723		473
Q9D7G9 UniProt NPD GO	MISS_MOUSE	MAPK-interacting and spindle-stabilizing protein (Mitogen-activated protein kinase 1-interacting pro ...	0.71	+	nuc	0	Cytoplasm. Spindle. Colocalizes with the spindle at discrete sites during the second meiotic divisio ...				263
P50540 UniProt NPD GO	MXI1_MOUSE	MAX-interacting protein 1 (Protein MXI1)	0.71	-	nuc	0	Nucleus	nucleus [IDA]			228
O09015 UniProt NPD GO	MXI1_RAT	MAX-interacting protein 1 (Protein MXI1)	0.71	-	nuc	0	Nucleus				228
Q707Y0 UniProt NPD GO	MTAL2_YARLI	Mating-type protein ALPHA2 (MATB2 transcription factor)	0.71	-	cyt	0	Nucleus (By similarity)				367
Q85FP0 UniProt NPD GO	MATK_ADICA	Maturase K (Intron maturase)	0.71	+	nuc	0	Plastid; chloroplast				500
Q5YK47 UniProt NPD GO	MATK_ALBJU	Maturase K (Intron maturase)	0.71	-	cyt	0	Plastid; chloroplast				499
Q9GF32 UniProt NPD GO	MATK_ALLPE	Maturase K (Intron maturase)	0.71	-	mit	0	Plastid; chloroplast				504
Q71ML5 UniProt NPD GO	MATK_ARCUU	Maturase K (Intron maturase)	0.71	-	cyt	0	Plastid; chloroplast				506
Q5VH50 UniProt NPD GO	MATK_BATMA	Maturase K (Intron maturase)	0.71	-	mit	0	Plastid; chloroplast				499
Q5VH41 UniProt NPD GO	MATK_CAPHA	Maturase K (Intron maturase)	0.71	-	nuc	0	Plastid; chloroplast				504
Q9TKP0 UniProt NPD GO	MATK_CARAB	Maturase K (Intron maturase)	0.71	-	cyt	0	Plastid; chloroplast				503
Q8MEY2 UniProt NPD GO	MATK_DIOED	Maturase K (Intron maturase)	0.71	-	nuc	0	Plastid; chloroplast				505
Q5J2U8 UniProt NPD GO	MATK_DROLU	Maturase K (Intron maturase)	0.71	-	cyt	0	Plastid; chloroplast				514
Q8WJQ6 UniProt NPD GO	MATK_FRAVE	Maturase K (Intron maturase)	0.71	-	cyt	0	Plastid; chloroplast				500
Q8WH60 UniProt NPD GO	MATK_HEDHE	Maturase K (Intron maturase)	0.71	-	cyt	0	Plastid; chloroplast				505
Q8WHM0 UniProt NPD GO	MATK_LEMAE	Maturase K (Intron maturase)	0.71	-	nuc	0	Plastid; chloroplast				512
Q95DQ5 UniProt NPD GO	MATK_NICGU	Maturase K (Intron maturase)	0.71	-	cyt	0	Plastid; chloroplast				509
Q8WKL8 UniProt NPD GO	MATK_POPNI	Maturase K (Intron maturase)	0.71	-	nuc	0	Plastid; chloroplast				510
Q8WI35 UniProt NPD GO	MATK_PSINU	Maturase K (Intron maturase)	0.71	-	nuc	0	Plastid; chloroplast				503
Q9GF29 UniProt NPD GO	MATK_SISIR	Maturase K (Intron maturase)	0.71	-	cyt	0	Plastid; chloroplast				502
Q5VH43 UniProt NPD GO	MATK_STAPI	Maturase K (Intron maturase)	0.71	-	mit	0	Plastid; chloroplast				502
Q8WIT2 UniProt NPD GO	MATK_STEPS	Maturase K (Intron maturase)	0.71	-	cyt	0	Plastid; chloroplast				508
Q8IH24 UniProt NPD GO	MED31_DROME	Mediator of RNA polymerase II transcription subunit 31 (Mediator complex subunit 31) (Protein SOH1) ...	0.71	-	nuc	0	Nucleus (Potential)	mediator complex [IDA]			204
Q08818 UniProt NPD GO	MSC6_YEAST	Meiotic sister-chromatid recombination protein 6, mitochondrial precursor	0.71	-	mit	0	Mitochondrion	mitochondrion [IDA]			692
Q91XT6 UniProt NPD GO	TAC2N_MOUSE	Membrane targeting tandem C2 domain-containing protein 1 (Tandem C2 protein in nucleus) (Tac2-N)	0.71	-	nuc	0	Nucleus	nucleus [IDA]			489
Q5ZKT9 UniProt NPD GO	MIER1_CHICK	Mesoderm induction early response protein 1 (Mi-er1)	0.71	+	nuc	0	Nucleus (By similarity)				513
O14258 UniProt NPD GO	ACE2_SCHPO	Metallothionein expression activator	0.71	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			533
P53128 UniProt NPD GO	MTHR2_YEAST	Methylenetetrahydrofolate reductase 2 (EC 1.5.1.20)	0.71	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			599
P14873 UniProt NPD GO	MAP1B_MOUSE	Microtubule-associated protein 1B (MAP 1B) (MAP1.2) (MAP1(X)) [Contains: MAP1 light chain LC1]	0.71	+	nuc	0		microtubule associated complex [TAS]			2464
P15205 UniProt NPD GO	MAP1B_RAT	Microtubule-associated protein 1B (MAP 1B) (Neuraxin) [Contains: MAP1 light chain LC1]	0.71	+	nuc	0		microtubule associated complex [IDA]			2459
Q3YC04 UniProt NPD GO	MCR_AOTNA	Mineralocorticoid receptor (MR)	0.71	+	nuc	0	Cytoplasm. Nucleus. Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane prote ...				984
Q9N0W8 UniProt NPD GO	MCR_SAISC	Mineralocorticoid receptor (MR)	0.71	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic and nuclear in the absence of ligand ...				982
Q8TD10 UniProt NPD GO	MIPO1_HUMAN	Mirror-image polydactyly gene 1 protein	0.71	-	nuc	0			606850		442
O63852 UniProt NPD GO	MSHM_SARGL	Mitochondrial MutS protein homolog	0.71	-	nuc	0					982
Q4WQ82 UniProt NPD GO	TIM54_ASPFU	Mitochondrial import inner membrane translocase subunit tim54	0.71	-	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				439
Q2UJY4 UniProt NPD GO	TIM54_ASPOR	Mitochondrial import inner membrane translocase subunit tim54	0.71	+	nuc	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				445
P46754 UniProt NPD GO	RT03_ACACA	Mitochondrial ribosomal protein S3	0.71	-	mit	0	Mitochondrion				298
Q5ZCI1 UniProt NPD GO	MPK10_ORYSA	Mitogen-activated protein kinase 10 (EC 2.7.11.24) (MAP kinase 10)	0.71	-	nuc	0					611
Q8AYG3 UniProt NPD GO	MPS1_BRARE	Mitotic checkpoint serine/threonine-protein kinase Mps1 (EC 2.7.12.2) (Monopolar spindle 1) (Nightca ...	0.71	-	nuc	0					983
Q9NZB8 UniProt NPD GO	MOS1B_HUMAN	Molybdenum cofactor biosynthesis protein 1 B (MOCS1B) (Molybdenum cofactor synthesis-step 1 protein ...	0.71	-	nuc	0			603707		636
Q5R905 UniProt NPD GO	MO4L2_PONPY	Mortality factor 4-like protein 2	0.71	-	nuc	0	Nucleus (By similarity)				288
Q15014 UniProt NPD GO	MO4L2_HUMAN	Mortality factor 4-like protein 2 (MORF-related gene X protein) (Transcription factor-like protein M ...	0.71	-	nuc	0	Nucleus	nucleolus [IDA] nucleus [NAS]	300409		288
O13921 UniProt NPD GO	MSH1_SCHPO	MutS protein homolog 1	0.71	-	mit	0	Cytoplasm				941
Q15746 UniProt NPD GO	MYLK_HUMAN	Myosin light chain kinase, smooth muscle (EC 2.7.11.18) (MLCK) (Telokin) (Kinase-related protein) (K ...	0.71	+	cyt	0			600922	2CQV	1914
Q91XQ5 UniProt NPD GO	ST4S6_MOUSE	N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase (EC 2.8.2.33) (GalNAc4S-6ST) (B-cell RAG-associ ...	0.71	-	mit	1	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable). A small fraction m ...	integral to membrane [ISS]			561
Q6WV16 UniProt NPD GO	GALT6_DROME	N-acetylgalactosaminyltransferase 6 (EC 2.4.1.-) (Protein-UDP acetylgalactosaminyltransferase 6) (UD ...	0.71	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [NAS]			666

You are viewing entries 13351 to 13400 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.