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
Q43083 UniProt NPD GO	H4_PYRSA	Histone H4	0.31	-	cyt	0	Nucleus (By similarity)				102
P27996 UniProt NPD GO	H4_SOLST	Histone H4	0.31	-	cyt	0	Nucleus (By similarity)				102
Q9UBN7 UniProt NPD GO	HDAC6_HUMAN	Histone deacetylase 6 (HD6)	0.31	+	cyt	0	Nucleus. Cytoplasm. It is mainly cytoplasmic, where it is associated with microtubules	cytoplasm [ISS] histone deacetylase complex [IDA] microtubule [IDA] nucleus [NAS]	300272		1215
Q9VEX9 UniProt NPD GO	SAP18_DROME	Histone deacetylase complex subunit SAP18 (Sin3-associated polypeptide, 18 kDa) (Bicoid-interacting ...	0.31	-	nuc	0	Nucleus				150
O64827 UniProt NPD GO	SUVR5_ARATH	Histone-lysine N-methyltransferase SUVR5 (EC 2.1.1.43) (Suppressor of variegation 3-9-related protei ...	0.31	-	nuc	0	Nucleus (By similarity). Associates with euchromatic regions (By similarity)				203
Q9HBU1 UniProt NPD GO	BARX1_HUMAN	Homeobox protein BarH-like 1	0.31	+	nuc	0	Nucleus (Probable)	nuclear chromosome [NAS]	603260		225
Q8SUB7 UniProt NPD GO	HD1_ENCCU	Homeobox protein HD-1 (EcHD-1)	0.31	-	nuc	0	Nucleus (Potential)				157
P31534 UniProt NPD GO	HMEN_LAMPL	Homeobox protein engrailed-like (EN) (Fragment)	0.31	+	nuc	0	Nucleus (Probable)				60
P31535 UniProt NPD GO	HMENA_MYXGL	Homeobox protein engrailed-like A (EN-A) (Fragment)	0.31	+	nuc	0	Nucleus (Probable)				60
P31536 UniProt NPD GO	HMENB_MYXGL	Homeobox protein engrailed-like B (EN-B) (Fragment)	0.31	+	nuc	0	Nucleus (Probable)				60
P51611 UniProt NPD GO	HCFC1_MESAU	Host cell factor (HCF) (HCF-1) (C1 factor) (VP16 accessory protein) (VCAF) [Contains: HCF N-terminal ...	0.31	-	nuc	0	Nucleus				2090
O24495 UniProt NPD GO	GLO2M_ARATH	Hydroxyacylglutathione hydrolase 1, mitochondrial precursor (EC 3.1.2.6) (Glyoxalase II) (Glx II)	0.31	-	mit	0	Mitochondrion				331
P47105 UniProt NPD GO	YJ07_YEAST	Hypothetical 14.4 kDa protein in HUL4-GEF1 intergenic region	0.31	-	nuc	0					127
Q9MTM7 UniProt NPD GO	YCX8_OENHO	Hypothetical 15.0 kDa protein in psbM-petN intergenic region (ORF125)	0.31	-	mit	0	Plastid; chloroplast				125
P53936 UniProt NPD GO	YNI9_YEAST	Hypothetical 17.1 kDa protein RHO2-TOP2 intergenic region	0.31	-	mit	1 *					158
Q9MTP2 UniProt NPD GO	YCX2_OENHO	Hypothetical 17.5 kDa protein in trnF-trnL intergenic region (ORF151)	0.31	-	nuc	2 *	Plastid; chloroplast				151
P36090 UniProt NPD GO	YKE7_YEAST	Hypothetical 58.9 kDa protein in ELM1-PRI2 intergenic region	0.31	-	cyt	0	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			516
P15606 UniProt NPD GO	YM05_PARTE	Hypothetical 8.3 kDa protein (ORF5)	0.31	-	nuc	0					70
P08747 UniProt NPD GO	YMC3_OENBE	Hypothetical 9.2 kDa protein in COXIII region	0.31	-	nuc	0					79
Q9SUB1 UniProt NPD GO	DOF42_ARATH	Hypothetical Dof zinc finger protein DOF4.2 (AtDOF4.2)	0.31	-	nuc	0	Nucleus (Probable)				194
Q23256 UniProt NPD GO	YH92_CAEEL	Hypothetical WD repeat protein ZC302.2	0.31	-	nuc	0					501
P14587 UniProt NPD GO	YDH1_PLAFS	Hypothetical protein 5' to Asp-rich and His-rich proteins (Fragment)	0.31	-	nuc	0					77
Q10933 UniProt NPD GO	YT24_CAEEL	Hypothetical protein B0304.4	0.31	-	nuc	0					128
P48053 UniProt NPD GO	YPD1_CAEEL	Hypothetical protein C05D11.1 in chromosome III	0.31	-	cyt	0					995
Q17851 UniProt NPD GO	YAVK_CAEEL	Hypothetical protein C09B9.3 in chromosome IV	0.31	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				884
O42901 UniProt NPD GO	YBA9_SCHPO	Hypothetical protein C119.09c in chromosome II	0.31	-	mit	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				186
Q09234 UniProt NPD GO	YQ41_CAEEL	Hypothetical protein C13B9.1	0.31	-	mit	0					143
O13733 UniProt NPD GO	YDOD_SCHPO	Hypothetical protein C15A10.13 in chromosome I	0.31	-	nuc	0					637
Q10098 UniProt NPD GO	YAP1_SCHPO	Hypothetical protein C15F9.01c in chromosome I	0.31	-	nuc	0					227
O74728 UniProt NPD GO	YH93_SCHPO	Hypothetical protein C1709.03 in chromosome II	0.31	-	nuc	1					398
Q09800 UniProt NPD GO	YAA7_SCHPO	Hypothetical protein C22G7.07c in chromosome I	0.31	-	cyt	0					413
Q09266 UniProt NPD GO	YQD6_CAEEL	Hypothetical protein C32D5.6	0.31	-	cyt	0					578
Q8SVF8 UniProt NPD GO	Y604_ENCCU	Hypothetical protein ECU06_0040	0.31	-	cyt	0					477
Q8SV57 UniProt NPD GO	Y6G8_ENCCU	Hypothetical protein ECU06_1680	0.31	-	cyt	0					458
Q8ST30 UniProt NPD GO	Y7I9_ENCCU	Hypothetical protein ECU07_1890/ECU10_0010	0.31	-	cyt	0					433
Q19981 UniProt NPD GO	YC81_CAEEL	Hypothetical protein F33C8.1 precursor	0.31	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1271
Q9UT00 UniProt NPD GO	YKH3_SCHPO	Hypothetical protein PYUK71.03c in chromosome I	0.31	-	nuc	1					1225
P34626 UniProt NPD GO	YOJ3_CAEEL	Hypothetical protein ZK353.3	0.31	-	nuc	0					164
P34658 UniProt NPD GO	YOUB_CAEEL	Hypothetical protein ZK637.12	0.31	-	nuc	0					246
Q6ENI8 UniProt NPD GO	YCF70_ORYNI	Hypothetical protein ycf70 (ORF89)	0.31	-	mit	1 *	Plastid; chloroplast				89
O81641 UniProt NPD GO	ILL3_ARATH	IAA-amino acid hydrolase ILR1-like 3 precursor (EC 3.5.1.-)	0.31	-	exc	0					428
P34047 UniProt NPD GO	HIS7A_ARATH	Imidazoleglycerol-phosphate dehydratase 1 (EC 4.2.1.19) (IGPD 1)	0.31	-	nuc	0				2F1D	270
O77755 UniProt NPD GO	INHA_TRIVU	Inhibin alpha chain precursor	0.31	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			361
P27093 UniProt NPD GO	INHBB_CHICK	Inhibin beta B chain precursor (Activin beta-B chain)	0.31	-	exc	1 *	Secreted protein (By similarity)	extracellular region [ISS]			391
Q9SKD3 UniProt NPD GO	OXA1L_ARATH	Inner membrane protein OXA1-like, mitochondrial precursor	0.31	-	end	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				431
P25297 UniProt NPD GO	PHO84_YEAST	Inorganic phosphate transporter PHO84	0.31	-	end	9	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			587
Q6UXB1 UniProt NPD GO	IGFL3_HUMAN	Insulin growth factor-like family member 3 precursor	0.31	-	mit	0	Secreted protein (Probable)				125
Q90325 UniProt NPD GO	IGF1A_CYPCA	Insulin-like growth factor I, adult form precursor	0.31	-	nuc	0	Secreted protein				161
P16501 UniProt NPD GO	IGF1A_XENLA	Insulin-like growth factor I-A precursor (IGF-IA) (xIGF-1) (IGF-I') (Somatomedin)	0.31	-	nuc	1 *	Secreted protein				153
P10764 UniProt NPD GO	IGF2_SHEEP	Insulin-like growth factor II precursor (IGF-II)	0.31	-	exc	0	Secreted protein				179

You are viewing entries 39501 to 39550 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.