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
P31755 UniProt NPD GO	OCH1_YEAST	Initiation-specific alpha-1,6-mannosyltransferase (EC 2.4.1.232)	0.73	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	Golgi cis cisterna [IDA]			480
Q8WN96 UniProt NPD GO	ITPR2_BOVIN	Inositol 1,4,5-trisphosphate receptor type 2 (Type 2 inositol 1,4,5-trisphosphate receptor) (Type 2 ...	0.73	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Secretory vesicl ...				2701
P70227 UniProt NPD GO	ITPR3_MOUSE	Inositol 1,4,5-trisphosphate receptor type 3 (Type 3 inositol 1,4,5-trisphosphate receptor) (Type 3 ...	0.73	+	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				2670
Q63269 UniProt NPD GO	ITPR3_RAT	Inositol 1,4,5-trisphosphate receptor type 3 (Type 3 inositol 1,4,5-trisphosphate receptor) (Type 3 ...	0.73	+	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				2670
Q8R071 UniProt NPD GO	IP3KA_MOUSE	Inositol-trisphosphate 3-kinase A (EC 2.7.1.127) (Inositol 1,4,5-trisphosphate 3-kinase A) (IP3K A) ...	0.73	-	nuc	0					459
Q9Y4H2 UniProt NPD GO	IRS2_HUMAN	Insulin receptor substrate 2 (IRS-2)	0.73	+	nuc	0			600797		1338
P42162 UniProt NPD GO	IFNG_CERTO	Interferon gamma precursor (IFN-gamma)	0.73	-	exc	0	Secreted protein				165
P01579 UniProt NPD GO	IFNG_HUMAN	Interferon gamma precursor (IFN-gamma) (Immune interferon)	0.73	-	exc	0	Secreted protein		147570	1HIG	166
Q91192 UniProt NPD GO	MX_ONCMY	Interferon-induced GTP-binding protein Mx	0.73	-	cyt	0					621
P18588 UniProt NPD GO	MX1_RAT	Interferon-induced GTP-binding protein Mx1	0.73	+	nuc	0	Nucleus				652
P23731 UniProt NPD GO	IFEB_ASCSU	Intermediate filament protein B (IF-B)	0.73	-	nuc	0	Cytoplasm				589
Q9ET77 UniProt NPD GO	JPH3_MOUSE	Junctophilin-3 (Junctophilin type 3) (JP-3)	0.73	-	nuc	1	Cell membrane; peripheral membrane protein. Endoplasmic reticulum; endoplasmic reticulum membrane; s ...	integral to membrane [TAS] microsome [IDA]			744
Q8BX46 UniProt NPD GO	LBXCO_MOUSE	Ladybird homeobox corepressor 1 (Transcriptional corepressor Corl1)	0.73	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			964
P29536 UniProt NPD GO	LMD1_HUMAN	Leiomodin-1 (Leiomodin, muscle form) (64 kDa autoantigen D1) (64 kDa autoantigen 1D) (64 kDa autoant ...	0.73	-	nuc	0	Cytoplasm. Cytoskeleton	membrane fraction [TAS]	602715		572
Q4R6X9 UniProt NPD GO	LRC48_MACFA	Leucine-rich repeat-containing protein 48	0.73	-	cyt	0					523
Q6UXM1 UniProt NPD GO	LRIG3_HUMAN	Leucine-rich repeats and immunoglobulin-like domains protein 3 precursor (LIG-3)	0.73	-	exc	1	Membrane; single-pass type I membrane protein (Potential)		608870		1119
Q14114 UniProt NPD GO	LRP8_HUMAN	Low-density lipoprotein receptor-related protein 8 precursor (Apolipoprotein E receptor 2)	0.73	-	exc	2 *	Cell membrane; single-pass type I membrane protein (By similarity). Secreted protein (By similarity) ...	integral to membrane [IC] plasma membrane [NAS]	602600		963
Q6Q9I2 UniProt NPD GO	MAD15_ORYSA	MADS-box transcription factor 15 (OsMADS15) (Protein APETALA1-like A) (FDRMADS3) (RMADS215)	0.73	-	nuc	0	Nucleus (Probable)				267
Q9HGP0 UniProt NPD GO	PVG4_SCHPO	MADS-box transcription factor pvg4 (Pyruvylated Gal-beta-1,3-epitope synthesis protein 4) (PvGal syn ...	0.73	-	nuc	0	Nucleus				372
Q96JB8 UniProt NPD GO	MPP4_HUMAN	MAGUK p55 subfamily member 4 (Discs large homolog 6) (Amyotrophic lateral sclerosis 2 chromosomal re ...	0.73	-	cyt	0	Cytoplasm. Detected at the outer limiting membrane (OLM) and in the outer plexiform layer (OPL) of t ...		606575		637
Q14149 UniProt NPD GO	MORC3_HUMAN	MORC family CW-type zinc finger 3 (Zinc finger CW-type coiled-coil domain protein 3)	0.73	-	nuc	0					939
Q6T264 UniProt NPD GO	MAML1_MOUSE	Mastermind-like protein 1 (Mam-1)	0.73	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nuclear, in a punctate manner	nucleus [IDA]			1020
Q8MDD1 UniProt NPD GO	MATK_ACTCU	Maturase K (Intron maturase)	0.73	-	nuc	0	Plastid; chloroplast				503
Q9MUZ3 UniProt NPD GO	MATK_BROIN	Maturase K (Intron maturase)	0.73	-	cyt	0	Plastid; chloroplast				511
Q9GF55 UniProt NPD GO	MATK_CARAN	Maturase K (Intron maturase)	0.73	-	mit	0	Plastid; chloroplast				504
Q7YMV7 UniProt NPD GO	MATK_CLELA	Maturase K (Intron maturase)	0.73	-	cyt	0	Plastid; chloroplast				509
Q7YMV1 UniProt NPD GO	MATK_CLEVI	Maturase K (Intron maturase)	0.73	-	cyt	0	Plastid; chloroplast				509
Q8WIU9 UniProt NPD GO	MATK_GORLA	Maturase K (Intron maturase)	0.73	-	cyt	0	Plastid; chloroplast				508
Q85ZV6 UniProt NPD GO	MATK_HORBU	Maturase K (Intron maturase)	0.73	-	cyt	0	Plastid; chloroplast				511
Q9TKB6 UniProt NPD GO	MATK_KUNPU	Maturase K (Intron maturase)	0.73	-	nuc	0	Plastid; chloroplast				503
Q9TIR8 UniProt NPD GO	MATK_LATCL	Maturase K (Intron maturase)	0.73	-	nuc	0	Plastid				511
Q5YJV9 UniProt NPD GO	MATK_LUPCO	Maturase K (Intron maturase)	0.73	-	cyt	0	Plastid; chloroplast				508
Q95EC9 UniProt NPD GO	MATK_MAMHA	Maturase K (Intron maturase)	0.73	-	nuc	0	Plastid; chloroplast				510
Q95GT7 UniProt NPD GO	MATK_NEPDI	Maturase K (Intron maturase)	0.73	-	nuc	0	Plastid; chloroplast				504
Q70D40 UniProt NPD GO	MATK_NICTO	Maturase K (Intron maturase)	0.73	-	cyt	0	Plastid; chloroplast				509
Q6ENJ6 UniProt NPD GO	MATK_ORYNI	Maturase K (Intron maturase)	0.73	+	cyt	0	Plastid; chloroplast				511
P12175 UniProt NPD GO	MATK_ORYSA	Maturase K (Intron maturase)	0.73	+	cyt	0	Plastid; chloroplast				511
Q9AVL4 UniProt NPD GO	MATK_PANQU	Maturase K (Intron maturase)	0.73	-	cyt	0	Plastid; chloroplast				503
Q6BDI8 UniProt NPD GO	MATK_PINCL	Maturase K (Intron maturase)	0.73	-	nuc	0	Plastid; chloroplast				515
Q8HQR1 UniProt NPD GO	MATK_PINLE	Maturase K (Intron maturase)	0.73	-	nuc	0	Plastid; chloroplast				515
Q8HQS3 UniProt NPD GO	MATK_PINPT	Maturase K (Intron maturase)	0.73	-	nuc	0	Plastid; chloroplast				515
Q6BDG8 UniProt NPD GO	MATK_PINYU	Maturase K (Intron maturase)	0.73	-	nuc	0	Plastid; chloroplast				515
Q646L1 UniProt NPD GO	MATK_PLETI	Maturase K (Intron maturase)	0.73	-	nuc	0	Plastid; chloroplast				505
O78405 UniProt NPD GO	MATK_PRICE	Maturase K (Intron maturase)	0.73	-	cyt	0	Plastid; chloroplast				504
Q12024 UniProt NPD GO	YTM1_YEAST	Microtubule-associated protein YTM1	0.73	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]			460
P29496 UniProt NPD GO	MCM5_YEAST	Minichromosome maintenance protein 5 (Cell division control protein 46)	0.73	-	nuc	0	Nucleus. Mobilized from the cytoplasm to the nucleus as mitosis is completed. Remains in the nucleus ...	cytoplasm [TAS] MCM complex [IDA] pre-replicative complex [IDA] replication fork [IDA]			775
Q99N87 UniProt NPD GO	RT05_MOUSE	Mitochondrial 28S ribosomal protein S5 (S5mt) (MRP-S5)	0.73	+	mit	0	Mitochondrion	mitochondrion [IDA]			432
P56490 UniProt NPD GO	ACM5_MACMU	Muscarinic acetylcholine receptor M5	0.73	-	end	7 *	Membrane; multi-pass membrane protein				532
P25336 UniProt NPD GO	MSH3_YEAST	MutS protein homolog 3 (Mismatch-binding protein) (MBP)	0.73	-	nuc	0		nuclear chromosome [IPI]			1047
P80074 UniProt NPD GO	MYB1_PHYPA	Myb-related protein Pp1 (Fragment)	0.73	-	nuc	1	Nucleus (Potential)				449

You are viewing entries 12351 to 12400 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.