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
O08746 UniProt NPD GO	MATN2_MOUSE	Matrilin-2 precursor	0.72	-	nuc	0	Secreted protein	extracellular matrix (sensu Metazoa) [IDA]			956
Q6E4Q3 UniProt NPD GO	MATK_ACAFA	Maturase K (Intron maturase)	0.72	-	cyt	0	Plastid; chloroplast				509
Q9GHG8 UniProt NPD GO	MATK_ACOGR	Maturase K (Intron maturase)	0.72	-	nuc	0	Plastid; chloroplast				511
Q9GF63 UniProt NPD GO	MATK_ARAAL	Maturase K (Intron maturase)	0.72	-	mit	0	Plastid; chloroplast				506
Q7YKQ9 UniProt NPD GO	MATK_AVIGE	Maturase K (Intron maturase)	0.72	-	nuc	0	Plastid; chloroplast				506
O47143 UniProt NPD GO	MATK_CALVU	Maturase K (Intron maturase)	0.72	-	nuc	0	Plastid; chloroplast				506
Q8WJR3 UniProt NPD GO	MATK_CERBE	Maturase K (Intron maturase)	0.72	-	cyt	0	Plastid; chloroplast				503
Q8MA04 UniProt NPD GO	MATK_CHAGL	Maturase K (Intron maturase)	0.72	+	nuc	0	Plastid; chloroplast				508
Q7YMX0 UniProt NPD GO	MATK_CLEFL	Maturase K (Intron maturase)	0.72	-	cyt	0	Plastid; chloroplast				509
Q7YMV6 UniProt NPD GO	MATK_CLELI	Maturase K (Intron maturase)	0.72	-	cyt	0	Plastid; chloroplast				509
Q7YMX3 UniProt NPD GO	MATK_CLETE	Maturase K (Intron maturase)	0.72	-	cyt	0	Plastid; chloroplast				509
Q9MUY2 UniProt NPD GO	MATK_DANSP	Maturase K (Intron maturase)	0.72	+	cyt	0	Plastid; chloroplast				513
Q3HT77 UniProt NPD GO	MATK_EHRAN	Maturase K (Intron maturase)	0.72	-	cyt	0	Plastid; chloroplast				502
Q8MCR6 UniProt NPD GO	MATK_LENCU	Maturase K (Intron maturase)	0.72	-	cyt	0	Plastid; chloroplast				507
Q52ZT5 UniProt NPD GO	MATK_MACIN	Maturase K (Intron maturase)	0.72	-	cyt	0	Plastid; chloroplast				509
Q95ED6 UniProt NPD GO	MATK_MAIPO	Maturase K (Intron maturase)	0.72	-	nuc	0	Plastid; chloroplast				511
Q9MUZ7 UniProt NPD GO	MATK_NARST	Maturase K (Intron maturase)	0.72	+	cyt	0	Plastid; chloroplast				511
Q95DR2 UniProt NPD GO	MATK_NICPA	Maturase K (Intron maturase)	0.72	-	cyt	0	Plastid; chloroplast				509
Q9AVL5 UniProt NPD GO	MATK_PANGI	Maturase K (Intron maturase)	0.72	-	cyt	0	Plastid; chloroplast				503
Q8WJP1 UniProt NPD GO	MATK_PRUPE	Maturase K (Intron maturase)	0.72	-	cyt	0	Plastid; chloroplast				506
Q95F35 UniProt NPD GO	MATK_SPAPE	Maturase K (Intron maturase)	0.72	+	cyt	0	Plastid; chloroplast				513
Q8MCJ5 UniProt NPD GO	MATK_VICSA	Maturase K (Intron maturase)	0.72	-	nuc	0	Plastid; chloroplast				503
Q8N9U0 UniProt NPD GO	TAC2N_HUMAN	Membrane targeting tandem C2 domain-containing protein 1 (Tandem C2 protein in nucleus) (Tac2-N)	0.72	-	nuc	0	Nucleus (By similarity)				490
P82675 UniProt NPD GO	RT05_HUMAN	Mitochondrial 28S ribosomal protein S5 (S5mt) (MRP-S5)	0.72	+	mit	0	Mitochondrion				430
Q4P4Y2 UniProt NPD GO	MG101_USTMA	Mitochondrial genome maintenance protein MGM101, mitochondrial precursor	0.72	+	mit	0	Mitochondrion. Associated with the mitochondrial nucleoid structure (By similarity)				331
P16547 UniProt NPD GO	OM45_YEAST	Mitochondrial outer membrane 45 kDa protein	0.72	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane	integral to mitochondrial outer membrane [IDA] mitochondrial outer membrane [IDA]			393
Q08622 UniProt NPD GO	FMP38_YEAST	Mitochondrial protein FMP38 (Found in mitochondrial proteome protein 38)	0.72	-	nuc	0	Mitochondrion	mitochondrion [IDA]			556
P23351 UniProt NPD GO	RMS5_NEUCR	Mitochondrial ribosomal protein S5	0.72	+	nuc	0	Mitochondrion				426
Q8W4J2 UniProt NPD GO	MPK16_ARATH	Mitogen-activated protein kinase 16 (EC 2.7.11.24) (MAP kinase 16) (AtMPK16)	0.72	-	nuc	0					567
Q61084 UniProt NPD GO	M3K3_MOUSE	Mitogen-activated protein kinase kinase kinase 3 (EC 2.7.11.25) (MAPK/ERK kinase kinase 3) (MEK kina ...	0.72	-	nuc	0					626
Q9Y4K4 UniProt NPD GO	M4K5_HUMAN	Mitogen-activated protein kinase kinase kinase kinase 5 (EC 2.7.11.1) (MAPK/ERK kinase kinase kinase ...	0.72	-	nuc	0	Cytoplasm	cytoplasm [IDA]	604923		846
O59767 UniProt NPD GO	MAD3_SCHPO	Mitotic spindle checkpoint component mad3	0.72	-	nuc	0	Nucleus. Associated with the kinetochore	condensed nuclear chromosome kinetochore [IDA]			310
Q4R578 UniProt NPD GO	MO4L2_MACFA	Mortality factor 4-like protein 2	0.72	-	nuc	0	Nucleus (By similarity)				288
P27898 UniProt NPD GO	MYBP_MAIZE	Myb-related protein P	0.72	-	nuc	0	Nucleus (Probable)				399
P40791 UniProt NPD GO	MEF2_DROME	Myocyte-specific enhancer factor 2 (MADS domain transcription factor D-mef2)	0.72	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			539
Q7YS81 UniProt NPD GO	MYOG_BOVIN	Myogenin	0.72	+	nuc	0	Nucleus (By similarity)				224
P15173 UniProt NPD GO	MYOG_HUMAN	Myogenin (Myogenic factor 4) (Myf-4)	0.72	+	nuc	0	Nucleus		159980		224
O00160 UniProt NPD GO	MYO1F_HUMAN	Myosin If (Myosin-IE)	0.72	-	cyt	0		unconventional myosin [NAS]	601480		1098
Q86WG5 UniProt NPD GO	MTMRD_HUMAN	Myotubularin-related protein 13 (SET-binding factor 2)	0.72	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with membranes		607697		1849
Q8CHI9 UniProt NPD GO	ST4S6_RAT	N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase (EC 2.8.2.33) (GalNAc4S-6ST)	0.72	-	mit	1	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable). A small fraction m ...	integral to membrane [ISS]			561
Q02368 UniProt NPD GO	NDUB7_BOVIN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.72	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side				136
Q61127 UniProt NPD GO	NAB2_MOUSE	NGFI-A-binding protein 2 (EGR-1-binding protein 2)	0.72	+	nuc	0	Nucleus. Isoform 2 is not localized to the nucleus				525
P10673 UniProt NPD GO	NEUT_CANFA	Neurotensin/neuromedin N precursor [Contains: Large neuromedin N (NmN-125); Neuromedin N (NmN) (NN); ...	0.72	-	exc	0	Secreted protein. Packaged within secretory vesicles				170
O61608 UniProt NPD GO	NOS_ANOST	Nitric-oxide synthase (EC 1.14.13.39) (NOS)	0.72	-	cyt	0					1247
Q6AYI4 UniProt NPD GO	NHEJ1_RAT	Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)	0.72	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			304
P18160 UniProt NPD GO	KYK1_DICDI	Non-receptor tyrosine kinase spore lysis A (EC 2.7.10.2) (Tyrosine-protein kinase 1)	0.72	-	nuc	0					1584
Q92021 UniProt NPD GO	NF7B_XENLA	Nuclear factor 7, brain (xNF7) (xNF7-B)	0.72	-	nuc	0	Nucleus			1FRE	609
P11709 UniProt NPD GO	BIK1_YEAST	Nuclear fusion protein BIK1	0.72	-	nuc	0	Spindle pole body. Spindle. And mitotic spindle	cell cortex [IDA] condensed nuclear chromosome kinetochore [IDA] kinetochore [IDA] spindle microtubule [IDA] spindle pole body [TAS]			440
Q19345 UniProt NPD GO	NHR25_CAEEL	Nuclear hormone receptor family member nhr-25	0.72	-	nuc	0	Nucleus (Potential)				572
O16425 UniProt NPD GO	NHR57_CAEEL	Nuclear hormone receptor family member nhr-57	0.72	-	nuc	0	Nucleus (Potential)				374

You are viewing entries 12851 to 12900 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.