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
O17319 UniProt NPD GO	HM24_CAEBR	Homeobox protein ceh-24	0.84	-	nuc	0	Nucleus (By similarity)				297
O14529 UniProt NPD GO	CUTL2_HUMAN	Homeobox protein cut-like 2 (Homeobox protein Cux-2) (Cut-like 2)	0.84	+	nuc	0	Nucleus (By similarity)	nucleus [NAS]		1X2L	1424
P70298 UniProt NPD GO	CUTL2_MOUSE	Homeobox protein cut-like 2 (Homeobox protein Cux-2) (Cut-like 2)	0.84	+	nuc	0	Nucleus	nucleus [IDA]			1426
P31533 UniProt NPD GO	HME2B_BRARE	Homeobox protein engrailed-2b (Zf-En-1) (Eng3)	0.84	+	nuc	0	Nucleus				261
Q02283 UniProt NPD GO	HAT5_ARATH	Homeobox-leucine zipper protein HAT5 (HD-ZIP protein 5) (HD-ZIP protein ATHB-1)	0.84	+	nuc	0	Nucleus				272
Q8BUK6 UniProt NPD GO	HOOK3_MOUSE	Hook homolog 3	0.84	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus (By similarity). Associates with the Golgi complex. Enric ...				718
Q9U1N0 UniProt NPD GO	HRP65_CHITE	Hrp65 protein (Ct-Hrp65)	0.84	-	nuc	0	Isoform 1: Nucleus. Isoform 2, isoform 3: Cytoplasm. Cytoplasmic (isoform 2), cytoplasmic actin fibe ...	cytoplasm [IDA] nucleus [IDA]			535
P51112 UniProt NPD GO	HD_FUGRU	Huntingtin (Huntington disease protein homolog) (HD protein)	0.84	-	end	0	Cytoplasm (By similarity). Nucleus (By similarity)				3148
Q90W33 UniProt NPD GO	HIC2_BRARE	Hypermethylated in cancer 2 protein	0.84	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]			560
P50084 UniProt NPD GO	YG4V_YEAST	Hypothetical 15.8 kDa protein in SMI1-PHO81 intergenic region	0.84	-	nuc	0					137
P53328 UniProt NPD GO	YG5P_YEAST	Hypothetical 17.9 kDa protein in YTA7-TAF145 intergenic region	0.84	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			152
P47022 UniProt NPD GO	YJL8_YEAST	Hypothetical 25.6 kDa protein in POS18-PHO86 intergenic region	0.84	+	nuc	0	Membrane; multi-pass membrane protein (Potential)				219
P47129 UniProt NPD GO	YJ53_YEAST	Hypothetical 35.5 kDa protein in MIR1-STE18 intergenic region	0.84	-	nuc	0					309
P38848 UniProt NPD GO	YHV0_YEAST	Hypothetical 66.1 kDa protein in IMP3-SPO12 intergenic region	0.84	+	end	2	Membrane; multi-pass membrane protein (Potential)	peroxisomal membrane [IDA]			579
P38338 UniProt NPD GO	YB9F_YEAST	Hypothetical 80.4 kDa protein in POP4-SHM1 intergenic region	0.84	-	cyt	0					688
Q03824 UniProt NPD GO	YM37_YEAST	Hypothetical 81.5 kDa protein in HLJ1-SMP2 intergenic region	0.84	-	nuc	0		cytoplasm [IDA]			705
Q09868 UniProt NPD GO	YAG3_SCHPO	Hypothetical RNA-binding protein C12G12.03 in chromosome I	0.84	-	nuc	0		cytoplasm [IDA]			576
Q11114 UniProt NPD GO	YX07_CAEEL	Hypothetical protein C03B1.7	0.84	-	nuc	0					818
Q10491 UniProt NPD GO	YDG1_SCHPO	Hypothetical protein C26F1.01 in chromosome I	0.84	-	nuc	0					928
O13681 UniProt NPD GO	YJ13_SCHPO	Hypothetical protein C737.03c in chromosome III	0.84	-	nuc	6	Membrane; multi-pass membrane protein (Potential)				615
Q9XVA4 UniProt NPD GO	YS0I_CAEEL	Hypothetical protein F08G2.4	0.84	+	nuc	0					171
P34390 UniProt NPD GO	YLS5_CAEEL	Hypothetical protein F09G8.5	0.84	-	end	1 *					484
Q9NEU5 UniProt NPD GO	GSCR2_CAEEL	Hypothetical protein Y39B6A.33 in chromosome V	0.84	+	nuc	0					438
P34648 UniProt NPD GO	YOT2_CAEEL	Hypothetical protein ZK632.2	0.84	-	nuc	0					710
Q4WI16 UniProt NPD GO	TIM50_ASPFU	Import inner membrane translocase subunit tim50, mitochondrial precursor	0.84	+	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				501
Q6P4Y6 UniProt NPD GO	IRS1_XENTR	Insulin receptor substrate 1 (IRS-1)	0.84	-	nuc	0		cytoplasm [ISS] microsome [ISS] nucleus [ISS]			654
Q866Y6 UniProt NPD GO	IFNG_BOSIN	Interferon gamma precursor (IFN-gamma)	0.84	-	exc	1 *	Secreted protein (By similarity)				166
P07353 UniProt NPD GO	IFNG_BOVIN	Interferon gamma precursor (IFN-gamma)	0.84	-	exc	1 *	Secreted protein			1RFB	166
Q8SPW9 UniProt NPD GO	IFNG_BUBBU	Interferon gamma precursor (IFN-gamma)	0.84	-	exc	1 *	Secreted protein (By similarity)				166
Q865W6 UniProt NPD GO	IFNG_CAMBA	Interferon gamma precursor (IFN-gamma)	0.84	-	exc	0	Secreted protein (By similarity)				166
P17773 UniProt NPD GO	IFNG_SHEEP	Interferon gamma precursor (IFN-gamma)	0.84	-	exc	1 *	Secreted protein				166
Q6DTM3 UniProt NPD GO	AHI1_RAT	Jouberin (Abelson helper integration site 1 protein homolog) (AHI-1)	0.84	+	nuc	0					1047
P46865 UniProt NPD GO	KINL_LEICH	Kinesin-like protein K39 (Fragment)	0.84	-	nuc	0					955
Q12756 UniProt NPD GO	KIF1A_HUMAN	Kinesin-like protein KIF1A (Axonal transporter of synaptic vesicles)	0.84	-	nuc	0			601255		1690
P40460 UniProt NPD GO	NDC80_YEAST	Kinetochore protein NDC80 (Protein TID3)	0.84	-	nuc	0	Nucleus. Associated with kinetochores	condensed nuclear chromosome kinetochore [IDA] Ndc80 complex [IDA]			691
P34341 UniProt NPD GO	KLE2_CAEEL	Kleisin, abnormal closure, protein 2	0.84	+	cyt	0	Nucleus. Localised to condensing chromosomes exclusively around metaphase				821
Q15345 UniProt NPD GO	LRC41_HUMAN	Leucine-rich repeat-containing protein 41 (Protein Muf1)	0.84	-	nuc	0					843
P25823 UniProt NPD GO	TUD_DROME	Maternal protein tudor	0.84	-	nuc	0		mitochondrion [TAS] polar granule [TAS]			2515
P22017 UniProt NPD GO	B3_USTMA	Mating-type locus allele B3 protein	0.84	-	nuc	0	Nucleus				410
Q86Z42 UniProt NPD GO	MTAL2_CANGA	Mating-type-like protein ALPHA2 (MTL1alpha2 protein)	0.84	-	nuc	0	Nucleus (By similarity)				186
O93470 UniProt NPD GO	MMP21_XENLA	Matrix metalloproteinase-21 precursor (EC 3.4.24.-) (MMP-21) (xMMP)	0.84	+	nuc	0	Secreted protein (Potential)				604
Q5GGS4 UniProt NPD GO	MATK_CHIAL	Maturase K (Intron maturase)	0.84	-	cyt	0	Plastid; chloroplast				505
Q85ZU5 UniProt NPD GO	MATK_HORJU	Maturase K (Intron maturase)	0.84	-	cyt	0	Plastid; chloroplast				511
Q85ZU4 UniProt NPD GO	MATK_HORLE	Maturase K (Intron maturase)	0.84	-	cyt	0	Plastid; chloroplast				511
Q85BR7 UniProt NPD GO	MATK_HORML	Maturase K (Intron maturase)	0.84	-	cyt	0	Plastid; chloroplast				511
Q85ZS9 UniProt NPD GO	MATK_HORSA	Maturase K (Intron maturase)	0.84	-	cyt	0	Plastid; chloroplast				511
Q9TIC1 UniProt NPD GO	MATK_PHRAU	Maturase K (Intron maturase)	0.84	+	cyt	0	Plastid; chloroplast				513
Q9TIQ5 UniProt NPD GO	MATK_VERTH	Maturase K (Intron maturase)	0.84	-	cyt	0	Plastid; chloroplast				509
O08609 UniProt NPD GO	MLX_MOUSE	Max-like protein X (Max-like bHLHZip protein) (BigMax protein) (Protein Mlx) (Transcription factor-l ...	0.84	-	nuc	0	Isoform Alpha, isoform Beta: Cytoplasm (By similarity). Predominantly. Isoform Gamma: Nucleus (By si ...	cytoplasm [IDA] nucleus [IDA]			298
Q9UTJ3 UniProt NPD GO	MEU1_SCHPO	Meiotic expression up-regulated protein 1/2	0.84	-	nuc	0					776

You are viewing entries 7001 to 7050 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.