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
Q8WKK9 UniProt NPD GO	MATK_MARSC	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				508
Q6PSC6 UniProt NPD GO	MATK_PHAVU	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				513
Q8HQT1 UniProt NPD GO	MATK_PINAT	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q9MV60 UniProt NPD GO	MATK_PINBN	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
P24685 UniProt NPD GO	MATK_PINCO	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q7YMF8 UniProt NPD GO	MATK_PINCU	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HQS8 UniProt NPD GO	MATK_PINEC	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HQT6 UniProt NPD GO	MATK_PINEG	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HW57 UniProt NPD GO	MATK_PINEL	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HQQ8 UniProt NPD GO	MATK_PINHA	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HQS7 UniProt NPD GO	MATK_PINPA	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HQQ3 UniProt NPD GO	MATK_PINPI	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HQT2 UniProt NPD GO	MATK_PINPN	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HQT9 UniProt NPD GO	MATK_PINPO	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HQQ6 UniProt NPD GO	MATK_PINPS	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HQT0 UniProt NPD GO	MATK_PINRA	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HQS2 UniProt NPD GO	MATK_PINRE	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				513
Q8HQT4 UniProt NPD GO	MATK_PINRI	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HQQ4 UniProt NPD GO	MATK_PINRO	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8HQT5 UniProt NPD GO	MATK_PINTA	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q7YMG2 UniProt NPD GO	MATK_PINUN	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8WKA5 UniProt NPD GO	MATK_PINVI	Maturase K (Intron maturase)	0.74	-	nuc	0	Plastid; chloroplast				515
Q8WJP3 UniProt NPD GO	MATK_PRUDU	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				506
Q7JD61 UniProt NPD GO	MATK_ROSAC	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				503
O79977 UniProt NPD GO	MATK_ROSCL	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				503
Q7JF34 UniProt NPD GO	MATK_ROSCN	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				503
O78253 UniProt NPD GO	MATK_ROSRU	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				503
O78256 UniProt NPD GO	MATK_ROSST	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				505
P58271 UniProt NPD GO	MATK_WHEAT	Maturase K (Intron maturase)	0.74	-	cyt	0	Plastid; chloroplast				511
Q08014 UniProt NPD GO	MEDB_GIALA	Median body protein	0.74	-	nuc	0	Median body				857
P32645 UniProt NPD GO	ISC10_YEAST	Meiosis-specific protein ISC10	0.74	-	nuc	0					267
Q5UAK0 UniProt NPD GO	MIER1_MOUSE	Mesoderm induction early response protein 1 (Mi-er1)	0.74	+	exc	0	Nucleus (By similarity)				556
Q9R190 UniProt NPD GO	MTA2_MOUSE	Metastasis-associated protein MTA2 (Metastasis-associated 1-like 1)	0.74	-	nuc	0	Nucleus	chromatin remodeling complex [IPI] nucleus [IDA] NuRD complex [IDA]			668
O94776 UniProt NPD GO	MTA2_HUMAN	Metastasis-associated protein MTA2 (Metastasis-associated 1-like 1) (MTA1-L1 protein) (p53 target pr ...	0.74	-	nuc	0	Nucleus (By similarity)	histone deacetylase complex [TAS]	603947		668
Q9QYR6 UniProt NPD GO	MAP1A_MOUSE	Microtubule-associated protein 1A (MAP 1A) (Fragment)	0.74	+	nuc	0		cytosol [IDA]			1021
Q06820 UniProt NPD GO	MDM36_YEAST	Mitochondrial distribution and morphology protein 36	0.74	-	nuc	0					579
P15755 UniProt NPD GO	RT12_PARTE	Mitochondrial ribosomal protein S12	0.74	-	nuc	0	Mitochondrion				139
O22040 UniProt NPD GO	ANP1_ARATH	Mitogen-activated protein kinase kinase kinase ANP1 (EC 2.7.11.25) (Arabidopsis NPK1-related kinase ...	0.74	-	nuc	0					666
Q12851 UniProt NPD GO	M4K2_HUMAN	Mitogen-activated protein kinase kinase kinase kinase 2 (EC 2.7.11.1) (MAPK/ERK kinase kinase kinase ...	0.74	-	cyt	0	Cytoplasm (By similarity). Cell membrane; basolateral cell membrane; peripheral membrane protein (By ...	Golgi membrane [TAS] soluble fraction [TAS]	603166		819
Q10107 UniProt NPD GO	MRA1_SCHPO	Multicopy suppressor of ras1 (Suppressor protein mra1)	0.74	-	nuc	0	Nucleus; nucleolus (By similarity)	nuclear microtubule [IDA]			359
P08911 UniProt NPD GO	ACM5_RAT	Muscarinic acetylcholine receptor M5	0.74	-	end	7 *	Membrane; multi-pass membrane protein				531
P12979 UniProt NPD GO	MYOG_MOUSE	Myogenin (MYOD1-related protein)	0.74	+	nuc	0	Nucleus	nucleus [TAS]			224
Q7LFX5 UniProt NPD GO	ST4S6_HUMAN	N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase (EC 2.8.2.33) (GalNAc4S-6ST) (B-cell RAG-associ ...	0.74	-	mit	1	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable). A small fraction m ...		608277		561
Q69ZN6 UniProt NPD GO	GNPTA_MOUSE	N-acetylglucosamine-1-phosphotransferase subunits alpha/beta precursor (EC 2.7.8.17) (GlcNAc-1-phosp ...	0.74	-	mit	2 *	Subunit alpha: Golgi apparatus; Golgi membrane; single-pass type I membrane protein (By similarity). ...				1235
P59046 UniProt NPD GO	NAL12_HUMAN	NACHT, LRR and PYD-containing protein 12 (PYRIN-containing APAF1-like protein 7) (Monarch-1) (Regula ...	0.74	-	nuc	0	Cytoplasm	cytoplasm [IDA]	609648		1061
Q8MJ87 UniProt NPD GO	NUB1_BOVIN	NEDD8 ultimate buster 1 (Fragment)	0.74	+	nuc	0	Nucleus (By similarity). Predominantly (By similarity)				221
Q80UM3 UniProt NPD GO	NARG1_MOUSE	NMDA receptor-regulated protein 1 (N-terminal acetyltransferase 1) (Protein Tubedown-1)	0.74	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Mainly cytoplasmic, nuclear in some cases (By si ...	cytoplasm [IDA]			865
Q9Y2A7 UniProt NPD GO	NCKP1_HUMAN	Nck-associated protein 1 (NAP 1) (p125Nap1) (Membrane-associated protein HEM-2)	0.74	-	cyt	0			604891		1128
P55161 UniProt NPD GO	NCKP1_RAT	Nck-associated protein 1 (NAP 1) (p125Nap1) (Membrane-associated protein HEM-2)	0.74	-	cyt	0					1128
P28660 UniProt NPD GO	NCKP1_MOUSE	Nck-associated protein 1 (NAP 1) (p125Nap1) (Membrane-associated protein HEM-2) (Brain protein H19) ...	0.74	-	cyt	0	Cytoplasm. At the interface between the lamellipodial actin meshwork and the membrane	lamellipodium [IDA]			1128

You are viewing entries 11901 to 11950 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.