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
Q28385 UniProt NPD GO	IL1A_HORSE	Interleukin-1 alpha precursor (IL-1 alpha)	0.60	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				270
Q9UHF5 UniProt NPD GO	IL17B_HUMAN	Interleukin-17B precursor (IL-17B) (Cytokine-like protein Zcyto7) (Neuronal interleukin-17-related f ...	0.60	-	nuc	0	Secreted protein		604627		180
P01590 UniProt NPD GO	IL2RA_MOUSE	Interleukin-2 receptor alpha chain precursor (IL-2 receptor alpha subunit) (IL-2-RA) (IL2-RA) (p55) ...	0.60	-	exc	1	Membrane; single-pass type I membrane protein				268
Q6FPL6 UniProt NPD GO	JHD1_CANGA	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.60	+	cyt	0	Nucleus (By similarity)				403
Q6BJY4 UniProt NPD GO	SMI2_DEBHA	KNR4/SMI1 homolog 2	0.60	-	nuc	0					590
O08876 UniProt NPD GO	KLF10_RAT	Krueppel-like factor 10 (Transforming growth factor-beta-inducible early growth response protein 1) ...	0.60	-	nuc	0	Nucleus (By similarity)				480
P30836 UniProt NPD GO	LYAM1_RAT	L-selectin precursor (Lymph node homing receptor) (Leukocyte adhesion molecule 1) (LAM-1) (Lymphocyt ...	0.60	-	nuc	1	Membrane; single-pass type I membrane protein				372
P48742 UniProt NPD GO	LHX1_HUMAN	LIM/homeobox protein Lhx1 (LIM homeobox protein 1) (Homeobox protein Lim-1)	0.60	+	nuc	0	Nucleus (Probable)		601999		406
O88706 UniProt NPD GO	LHX6_MOUSE	LIM/homeobox protein Lhx6	0.60	-	nuc	0	Nucleus (Probable)				361
Q61001 UniProt NPD GO	LAMA5_MOUSE	Laminin alpha-5 chain precursor	0.60	-	exc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basement membrane [IDA]			3718
P24309 UniProt NPD GO	DBR1_YEAST	Lariat debranching enzyme (EC 3.1.-.-)	0.60	-	nuc	0		nucleus [IC]			405
P07795 UniProt NPD GO	H2BL2_PSAMI	Late histone H2B.2.2	0.60	+	nuc	0	Nucleus				123
P16890 UniProt NPD GO	H2BL4_STRPU	Late histone H2B.L4 (Fragment)	0.60	+	nuc	0	Nucleus				107
Q9NS15 UniProt NPD GO	LTBP3_HUMAN	Latent-transforming growth factor beta-binding protein 3 precursor (LTBP-3)	0.60	-	nuc	1 *	Secreted protein (By similarity). Secretion occurs after coexpression with TGFB1 and requires comple ...		602090		1302
Q8BHA1 UniProt NPD GO	LRC24_MOUSE	Leucine-rich repeat-containing protein 24 precursor	0.60	+	end	1 *	Membrane; single-pass membrane protein (Potential)				521
Q8R2U7 UniProt NPD GO	LRC42_MOUSE	Leucine-rich repeat-containing protein 42	0.60	-	nuc	0					421
Q96JA1 UniProt NPD GO	LRIG1_HUMAN	Leucine-rich repeats and immunoglobulin-like domains protein 1 precursor (LIG-1)	0.60	-	nuc	1	Membrane; single-pass type I membrane protein		608868		1093
P16150 UniProt NPD GO	LEUK_HUMAN	Leukosialin precursor (Leukocyte sialoglycoprotein) (Sialophorin) (Galactoglycoprotein) (GALGP) (CD4 ...	0.60	-	exc	1	Membrane; single-pass type I membrane protein	extracellular space [IDA] integral to plasma membrane [TAS]	182160		400
P48100 UniProt NPD GO	CHLN_CYAPA	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.60	+	cyt	0	Plastid; cyanelle				460
Q5SW96 UniProt NPD GO	ARH_HUMAN	Low density lipoprotein receptor adapter protein 1 (Autosomal recessive hypercholesterolemia protein ...	0.60	-	nuc	0	Cytoplasm	basal plasma membrane [IDA] cytosol [IDA] early endosome [IDA]	603813	2G30	308
Q07954 UniProt NPD GO	LRP1_HUMAN	Low-density lipoprotein receptor-related protein 1 precursor (LRP) (Alpha-2-macroglobulin receptor) ...	0.60	-	exc	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Cytoplasm (By si ...	integral to plasma membrane [TAS] membrane fraction [TAS]	107770	1J8E	4544
O75074 UniProt NPD GO	LRP3_HUMAN	Low-density lipoprotein receptor-related protein 3 precursor (hLRp105)	0.60	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [TAS]	603159		770
O88204 UniProt NPD GO	LRP3_RAT	Low-density lipoprotein receptor-related protein 3 precursor (rLRp105)	0.60	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				770
P16235 UniProt NPD GO	LSHR_RAT	Lutropin-choriogonadotropic hormone receptor precursor (LH/CG-R) (LSH-R) (Luteinizing hormone recept ...	0.60	-	end	7	Cell membrane; multi-pass membrane protein. Secreted protein. Some isoforms may be secreted				700
P22888 UniProt NPD GO	LSHR_HUMAN	Lutropin-choriogonadotropic hormone receptor precursor (LH/CG-R) (LSH-R) (Luteinizing hormone recept ...	0.60	-	end	7	Membrane; multi-pass membrane protein	endosome [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	152790	1XUL	699
O09039 UniProt NPD GO	LNK_MOUSE	Lymphocyte-specific adapter protein Lnk (Signal transduction protein Lnk) (Lymphocyte adapter protei ...	0.60	-	nuc	0					548
Q08397 UniProt NPD GO	LOXL1_HUMAN	Lysyl oxidase homolog 1 precursor (EC 1.4.3.-) (Lysyl oxidase-like protein 1) (LOL)	0.60	-	exc	0	Secreted protein; extracellular space (Potential)	extracellular region [TAS]	153456		574
P97873 UniProt NPD GO	LOXL1_MOUSE	Lysyl oxidase homolog 1 precursor (EC 1.4.3.-) (Lysyl oxidase-like protein 1) (Lysyl oxidase 2)	0.60	-	exc	0	Secreted protein; extracellular space (Potential)				607
Q6F2U9 UniProt NPD GO	SYK_ORYSA	Lysyl-tRNA synthetase (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS)	0.60	+	cyt	0	Cytoplasm (By similarity)				602
P15180 UniProt NPD GO	SYKC_YEAST	Lysyl-tRNA synthetase, cytoplasmic (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS)	0.60	-	cyt	0	Cytoplasm	cytoplasm [TAS]			590
Q8RU31 UniProt NPD GO	MAD21_ORYSA	MADS-box transcription factor 21 (OsMADS21) (RMADS207)	0.60	-	nuc	0	Nucleus (Probable)				265
Q707Y7 UniProt NPD GO	MTAL1_PICAN	Mating-type protein ALPHA1 (MATalpha1 transcription factor)	0.60	-	nuc	0	Nucleus (By similarity)				195
Q8K3F2 UniProt NPD GO	MMP21_MOUSE	Matrix metalloproteinase-21 precursor (EC 3.4.24.-) (MMP-21)	0.60	-	exc	0	Secreted protein (Potential)				568
Q95BZ7 UniProt NPD GO	MATK_ACTDE	Maturase K (Intron maturase)	0.60	-	nuc	0	Plastid; chloroplast				504
Q8MED5 UniProt NPD GO	MATK_AMOTI	Maturase K (Intron maturase)	0.60	-	nuc	0	Plastid; chloroplast				512
Q76DY9 UniProt NPD GO	MATK_CASCR	Maturase K (Intron maturase)	0.60	-	cyt	0	Plastid; chloroplast				464
Q9GGJ6 UniProt NPD GO	MATK_HAMMO	Maturase K (Intron maturase)	0.60	-	cyt	0	Plastid; chloroplast				504
Q5GF70 UniProt NPD GO	MATK_IRIOR	Maturase K (Intron maturase)	0.60	-	cyt	0	Plastid; chloroplast				522
Q5GF63 UniProt NPD GO	MATK_IRIPS	Maturase K (Intron maturase)	0.60	-	cyt	0	Plastid; chloroplast				526
Q5GF59 UniProt NPD GO	MATK_IRITE	Maturase K (Intron maturase)	0.60	-	cyt	0	Plastid; chloroplast				522
Q7IJL0 UniProt NPD GO	MATK_LARLA	Maturase K (Intron maturase)	0.60	-	nuc	0	Plastid; chloroplast				515
Q9BBU2 UniProt NPD GO	MATK_LOTJA	Maturase K (Intron maturase)	0.60	-	mit	0	Plastid; chloroplast				508
Q9TKP8 UniProt NPD GO	MATK_LOTPU	Maturase K (Intron maturase)	0.60	-	mit	0	Plastid; chloroplast				508
Q9MST4 UniProt NPD GO	MATK_METGY	Maturase K (Intron maturase)	0.60	-	cyt	0	Plastid; chloroplast				509
Q9MV48 UniProt NPD GO	MATK_PSEMZ	Maturase K (Intron maturase)	0.60	-	nuc	0	Plastid; chloroplast				515
Q9MSS8 UniProt NPD GO	MATK_SEQSE	Maturase K (Intron maturase)	0.60	+	cyt	0	Plastid; chloroplast				509
Q8MCM7 UniProt NPD GO	MATK_TRIMI	Maturase K (Intron maturase)	0.60	-	cyt	0	Plastid; chloroplast				506
Q8WIJ9 UniProt NPD GO	MATK_VACVI	Maturase K (Intron maturase)	0.60	-	cyt	0	Plastid; chloroplast				502
Q9NXB0 UniProt NPD GO	MKS1_HUMAN	Meckel syndrome type 1 protein	0.60	-	cyt	0			609883		559
Q9H213 UniProt NPD GO	MAGH1_HUMAN	Melanoma-associated antigen H1 (MAGE-H1 antigen) (Restin) (Apoptosis-related protein 1) (APR-1)	0.60	-	nuc	1			300548		219

You are viewing entries 19101 to 19150 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.