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
P34467 UniProt NPD GO	YMF7_CAEEL	Hypothetical protein F55H2.7	0.88	-	nuc	0					379
Q09424 UniProt NPD GO	YRO7_CAEEL	Hypothetical protein R07G3.7	0.88	-	nuc	0					366
P34578 UniProt NPD GO	YNX5_CAEEL	Hypothetical protein T20G5.5 in chromosome III	0.88	-	vac	2 *					1234
O14079 UniProt NPD GO	YEAE_SCHPO	Hypothetical protein UNK4.14 in chromosome I	0.88	-	nuc	0					520
P34675 UniProt NPD GO	YO25_CAEEL	Hypothetical protein ZK688.5	0.88	-	nuc	0					1620
Q5DU25 UniProt NPD GO	IQEC2_MOUSE	IQ motif and Sec7 domain-containing protein 2	0.88	-	nuc	0	Cytoplasm (Potential)				1478
P15975 UniProt NPD GO	UBP53_MOUSE	Inactive ubiquitin carboxyl-terminal hydrolase 53 (Ubiquitin-specific peptidase 53) (Per-hexamer rep ...	0.88	-	nuc	0					1069
P35568 UniProt NPD GO	IRS1_HUMAN	Insulin receptor substrate 1 (IRS-1)	0.88	-	nuc	0		cytoplasm [ISS] microsome [ISS] nucleus [ISS]	125853	1QQG	1242
Q9XTN2 UniProt NPD GO	IRS1_DROME	Insulin receptor substrate 1 (Protein Chico) (dIRS)	0.88	-	nuc	0		cytoplasm [ISS] microsome [ISS] nucleus [ISS]			968
P42161 UniProt NPD GO	IFNG_CANFA	Interferon gamma precursor (IFN-gamma)	0.88	-	exc	0	Secreted protein				166
Q25BC0 UniProt NPD GO	IFNG_VULVU	Interferon gamma precursor (IFN-gamma)	0.88	-	exc	0	Secreted protein (By similarity)				166
Q62240 UniProt NPD GO	JAD1D_MOUSE	Jumonji/ARID domain-containing protein 1D (SmcY protein) (Histocompatibility Y antigen) (H-Y)	0.88	+	nuc	0					1548
Q6VAB6 UniProt NPD GO	KSR2_HUMAN	Kinase suppressor of ras-2 (hKSR2)	0.88	+	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				829
Q07970 UniProt NPD GO	ATK1_ARATH	Kinesin-1 (Kinesin-like protein A)	0.88	-	nuc	0					793
O81635 UniProt NPD GO	ATK4_ARATH	Kinesin-4 (Kinesin-like protein D)	0.88	-	nuc	0					987
O60333 UniProt NPD GO	KIF1B_HUMAN	Kinesin-like protein KIF1B (Klp)	0.88	-	nuc	0	Cytoplasmic vesicle (By similarity). Predominantly found on the vesicle- and tubule-like structures ...	cytoplasmic vesicle membrane [ISS] microtubule associated complex [ISS]	605995		1816
O00139 UniProt NPD GO	KIF2_HUMAN	Kinesin-like protein KIF2 (Kinesin-2) (HK2)	0.88	-	nuc	0			602591		679
Q91637 UniProt NPD GO	KIF2_XENLA	Kinesin-like protein KIF2 (Kinesin-related protein XKIF2)	0.88	+	nuc	0					682
Q05404 UniProt NPD GO	MYCLA_XENLA	L-myc A protein (L-myc 1 protein)	0.88	-	nuc	0	Nucleus (Potential)				344
P36198 UniProt NPD GO	LHX2_RAT	LIM/homeobox protein Lhx2 (Homeobox protein LH-2)	0.88	-	nuc	0	Nucleus (Probable)				426
P13648 UniProt NPD GO	LMNA_CHICK	Lamin-A	0.88	-	mit	0	Nucleus				657
Q9H400 UniProt NPD GO	LIME1_HUMAN	Lck-interacting transmembrane adapter 1 (Lck-interacting membrane protein) (Lck-interacting molecule ...	0.88	-	nuc	1 *	Cell membrane; single-pass type III membrane protein. Present in lipid rafts. Recruited to the immun ...		609809		295
Q9EQR5 UniProt NPD GO	LIME1_MOUSE	Lck-interacting transmembrane adapter 1 (Lck-interacting molecule)	0.88	-	mit	1 *	Cell membrane; single-pass type III membrane protein. Present in lipid rafts. Recruited to the immun ...				269
Q86VH5 UniProt NPD GO	LRTM3_HUMAN	Leucine-rich repeat transmembrane neuronal protein 3 precursor	0.88	-	nuc	2 *	Membrane; single-pass type I membrane protein (Potential)				581
Q9BGP6 UniProt NPD GO	LRTM3_MACFA	Leucine-rich repeat transmembrane neuronal protein 3 precursor	0.88	-	nuc	2 *	Membrane; single-pass type I membrane protein (Potential)				581
Q505F5 UniProt NPD GO	LRC47_MOUSE	Leucine-rich repeat-containing protein 47	0.88	+	nuc	0					581
Q8NEP3 UniProt NPD GO	LRC50_HUMAN	Leucine-rich repeat-containing protein 50	0.88	-	nuc	0					725
Q5F334 UniProt NPD GO	LRC59_CHICK	Leucine-rich repeat-containing protein 59	0.88	+	nuc	0	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				339
Q6ZPI3 UniProt NPD GO	LCOR_MOUSE	Ligand-dependent corepressor (LCoR) (Mblk1-related protein 2)	0.88	-	nuc	0	Nucleus (By similarity)	nucleus [IC]			433
Q7TNN8 UniProt NPD GO	LPIN3_MUSSP	Lipin-3	0.88	+	nuc	0	Nucleus (Potential)				847
Q9BQK8 UniProt NPD GO	LPIN3_HUMAN	Lipin-3 (Lipin 3-like)	0.88	+	nuc	0	Nucleus (Potential)		605520		851
Q91Z80 UniProt NPD GO	LIPA4_RAT	Liprin-alpha-4 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-4 ...	0.88	-	nuc	0	Cytoplasm (By similarity). Cell surface (By similarity). Colocalizes with PTPRF at the cell surface ...				1043
Q867Z4 UniProt NPD GO	LOLA4_DROME	Longitudinals lacking protein, isoforms F/I/K/T	0.88	-	nuc	0	Nucleus	nucleus [IDA]			970
P34078 UniProt NPD GO	LTV1_YEAST	Low-temperature viability protein LTV1	0.88	-	mit	0		cytoplasm [IDA]			463
P28048 UniProt NPD GO	LAA_XENLA	Lupus La protein homolog A (La ribonucleoprotein A) (La autoantigen homolog A)	0.88	-	nuc	0	Nucleus (Probable)				428
Q8CDB0 UniProt NPD GO	MKNK2_MOUSE	MAP kinase-interacting serine/threonine-protein kinase 2 (EC 2.7.11.1) (MAP kinase signal-integratin ...	0.88	-	nuc	0					459
Q5U2N4 UniProt NPD GO	MKNK2_RAT	MAP kinase-interacting serine/threonine-protein kinase 2 (EC 2.7.11.1) (MAP kinase signal-integratin ...	0.88	-	nuc	0					459
Q24617 UniProt NPD GO	EXU2_DROPS	Maternal protein exuperantia 2	0.88	+	nuc	0					477
Q766U5 UniProt NPD GO	MATK_AVIMR	Maturase K (Intron maturase)	0.88	-	cyt	0	Plastid; chloroplast				509
Q49U13 UniProt NPD GO	MATK_EQUAR	Maturase K (Intron maturase)	0.88	-	cyt	0	Plastid; chloroplast				476
Q6YXN6 UniProt NPD GO	MATK_PHYPA	Maturase K (Intron maturase)	0.88	+	cyt	0	Plastid; chloroplast				505
O15151 UniProt NPD GO	MDM4_HUMAN	Mdm4 protein (p53-binding protein Mdm4) (Mdm2-like p53-binding protein) (Mdmx protein) (Double minut ...	0.88	-	nuc	0	Nucleus	nucleus [NAS]	602704	2CR8	490
P23624 UniProt NPD GO	SPO13_YEAST	Meiosis-specific protein SPO13 (Sporulation-specific protein 13)	0.88	-	nuc	0		condensed nuclear chromosome, pericentric r... [IDA] nucleus [IDA]			291
O18209 UniProt NPD GO	PMYT1_CAEEL	Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (EC 2.7.11.1) (Myt1 kina ...	0.88	-	nuc	1	Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity)				677
P21192 UniProt NPD GO	ACE2_YEAST	Metallothionein expression activator	0.88	-	nuc	0	Nucleus	cytosol [IDA] nucleus [IDA]			770
Q5RFW2 UniProt NPD GO	TAB2_BRARE	Mitogen-activated protein kinase kinase kinase 7-interacting protein 2 homolog	0.88	-	nuc	0					711
Q9Y6D9 UniProt NPD GO	MD1L1_HUMAN	Mitotic spindle assembly checkpoint protein MAD1 (Mitotic arrest deficient-like protein 1) (MAD1-lik ...	0.88	-	nuc	0	Nucleus. From the beginning to the end of mitosis, it is seen to move from a diffusely nuclear distr ...	centrosome [NAS] spindle [NAS]	602686	1GO4	718
P26041 UniProt NPD GO	MOES_MOUSE	Moesin (Membrane-organizing extension spike protein)	0.88	-	nuc	0	Cytoplasm. Phosphorylated form is enriched in microvilli-like structures at apical membrane	apical plasma membrane [IDA] basolateral plasma membrane [IDA] uropod [IDA]			576
O35763 UniProt NPD GO	MOES_RAT	Moesin (Membrane-organizing extension spike protein)	0.88	-	nuc	0	Cytoplasm (By similarity). Phosphorylated form is enriched in microvilli-like structures at apical m ...	internal side of plasma membrane [IDA]			576
Q4PC17 UniProt NPD GO	MRD1_USTMA	Multiple RNA-binding domain-containing protein 1	0.88	+	nuc	0	Nucleus (By similarity)				858

You are viewing entries 5151 to 5200 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.