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
P97519 UniProt NPD GO	HMGCL_RAT	Hydroxymethylglutaryl-CoA lyase, mitochondrial precursor (EC 4.1.3.4) (HMG-CoA lyase) (HL) (3-hydrox ...	0.05	-	mit	0	Mitochondrion; mitochondrial matrix				325
P23228 UniProt NPD GO	HMCS1_CHICK	Hydroxymethylglutaryl-CoA synthase, cytoplasmic (EC 2.3.3.10) (HMG-CoA synthase) (3-hydroxy-3-methyl ...	0.05	-	cyt	0	Cytoplasm				522
Q01581 UniProt NPD GO	HMCS1_HUMAN	Hydroxymethylglutaryl-CoA synthase, cytoplasmic (EC 2.3.3.10) (HMG-CoA synthase) (3-hydroxy-3-methyl ...	0.05	-	cyt	0	Cytoplasm	cytoplasm [TAS] soluble fraction [TAS]	142940		520
Q5R7Z9 UniProt NPD GO	HMCS1_PONPY	Hydroxymethylglutaryl-CoA synthase, cytoplasmic (EC 2.3.3.10) (HMG-CoA synthase) (3-hydroxy-3-methyl ...	0.05	-	cyt	0	Cytoplasm (By similarity)				520
P05721 UniProt NPD GO	YCX2_CHLPY	Hypothetical 11.9 kDa protein in 16S-23S DNA spacer	0.05	-	cyt	0	Plastid; chloroplast				103
P38458 UniProt NPD GO	YMF14_MARPO	Hypothetical 12.5 kDa protein in COX2-COX3 intergenic region (ORF 109)	0.05	-	mit	1 *					109
P38327 UniProt NPD GO	YB82_YEAST	Hypothetical 12.7 kDa protein in MCX1-PBP2 intergenic region	0.05	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				119
P48326 UniProt NPD GO	YCF50_CYAPA	Hypothetical 12.7 kDa protein ycf50 (ORF108)	0.05	-	cyt	0	Plastid; cyanelle				108
P53151 UniProt NPD GO	YGI8_YEAST	Hypothetical 14.2 kDa protein in MFAL2-MAD1 intergenic region	0.05	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)				121
P36109 UniProt NPD GO	YKZ2_YEAST	Hypothetical 14.3 kDa protein in FOX2-YPT52 intergenic region	0.05	-	mit	2 *					125
Q31673 UniProt NPD GO	YCX2_ASTLO	Hypothetical 15.6 kDa protein in rps12-trnP intergenic region (ORF125a)	0.05	-	end	4 *	Plastid				125
P50943 UniProt NPD GO	YNK5_YEAST	Hypothetical 16.2 kDa protein in CYB5-LEU4 intergenic region	0.05	-	mit	1 *	Membrane; multi-pass membrane protein (Potential)				142
P40538 UniProt NPD GO	YIC9_YEAST	Hypothetical 16.6 kDa protein in SSM4-IRR1 intergenic region	0.05	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				142
P50083 UniProt NPD GO	YG4T_YEAST	Hypothetical 21.9 kDa protein in PET54-DIE2 intergenic region	0.05	-	cyt	1 *					199
P43614 UniProt NPD GO	YFL2_YEAST	Hypothetical 23.6 kDa protein in SAP155-YMR31 intergenic region	0.05	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				200
P47155 UniProt NPD GO	YJ88_YEAST	Hypothetical 23.6 kDa protein in STE24-ATP2 intergenic region	0.05	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			203
P39541 UniProt NPD GO	YJT5_YEAST	Hypothetical 25.4 kDa protein in UBP12-CDC6 intergenic region	0.05	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				233
P31605 UniProt NPD GO	YCF23_CYAPA	Hypothetical 26.6 kDa protein ycf23	0.05	-	nuc	0	Plastid; cyanelle				243
P53929 UniProt NPD GO	YNK8_YEAST	Hypothetical 30.7 kDa protein in CYB5-LEU4 intergenic region	0.05	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			270
P53912 UniProt NPD GO	YNN4_YEAST	Hypothetical 41.2 kDa protein in FPR1-TOM22 intergenic region	0.05	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			376
P42946 UniProt NPD GO	YJK8_YEAST	Hypothetical 41.5 kDa protein in GZF3-IME2 intergenic region	0.05	-	end	10	Membrane; multi-pass membrane protein (Potential)				383
P49835 UniProt NPD GO	YCX9_ODOSI	Hypothetical 5.4 kDa protein in trnK-psbC intergenic region (ORF44)	0.05	-	mit	0	Plastid; chloroplast				44
P40441 UniProt NPD GO	YIR0_YEAST	Hypothetical 50.8 kDa protein in SDL1 5'region	0.05	-	end	10 *	Membrane; multi-pass membrane protein (Probable)				457
Q9MTP8 UniProt NPD GO	YCX1_OENHO	Hypothetical 9.5 kDa protein in rbcL-atpB intergenic region (ORF82a)	0.05	-	nuc	0	Plastid; chloroplast				82
P48409 UniProt NPD GO	YCF20_GALSU	Hypothetical 9.5 kDa protein ycf20	0.05	-	mit	3 *	Plastid; chloroplast				83
Q8TGK7 UniProt NPD GO	YAG8_YEAST	Hypothetical UPF0320 protein YAL068W-A	0.05	-	cyt	0					84
O14293 UniProt NPD GO	YF19_SCHPO	Hypothetical aldehyde dehydrogenase-like protein C9E9.09c (EC 1.2.1.-)	0.05	-	cyt	0					503
Q10917 UniProt NPD GO	YT13_CAEEL	Hypothetical protein B0252.3 in chromosome II	0.05	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				484
Q10927 UniProt NPD GO	YWR4_CAEEL	Hypothetical protein B0302.4	0.05	-	cyt	0					31
P34317 UniProt NPD GO	YKT6_CAEEL	Hypothetical protein C07A9.6 precursor	0.05	-	end	0					507
P87133 UniProt NPD GO	YFK6_SCHPO	Hypothetical protein C167.06c in chromosome I	0.05	-	mit	0					121
Q09253 UniProt NPD GO	YQ5A_CAEEL	Hypothetical protein C16C10.10	0.05	-	mit	0					281
Q10300 UniProt NPD GO	YD46_SCHPO	Hypothetical protein C22H10.06c in chromosome I	0.05	-	mit	0					93
Q10177 UniProt NPD GO	YAV8_SCHPO	Hypothetical protein C27F1.08 in chromosome I	0.05	-	end	11	Membrane; multi-pass membrane protein (Potential)				521
P34354 UniProt NPD GO	YK89_CAEEL	Hypothetical protein C30A5.9	0.05	-	cyt	0					66
Q09832 UniProt NPD GO	YAD6_SCHPO	Hypothetical protein C4G8.06c in chromosome I	0.05	-	cyt	0					418
O14197 UniProt NPD GO	YDQ4_SCHPO	Hypothetical protein C5D6.04 in chromosome I	0.05	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				452
Q09678 UniProt NPD GO	YA07_SCHPO	Hypothetical protein C5H10.07 in chromosome I	0.05	-	cyt	0					89
Q9VH95 UniProt NPD GO	YC17_DROME	Hypothetical protein CG16817	0.05	-	mit	0					184
Q9VV43 UniProt NPD GO	Y4893_DROME	Hypothetical protein CG4893	0.05	-	nuc	0					192
Q5FC78 UniProt NPD GO	YQV8_CAEEL	Hypothetical protein F27E5.8	0.05	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				349
P34438 UniProt NPD GO	YL58_CAEEL	Hypothetical protein F44E2.8	0.05	-	cyt	0					242
O45731 UniProt NPD GO	YFC7_CAEEL	Hypothetical protein T02E1.7 in chromosome I	0.05	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				269
Q10004 UniProt NPD GO	YRS8_CAEEL	Hypothetical protein T05H10.8	0.05	-	nuc	0					377
Q10015 UniProt NPD GO	YR02_CAEEL	Hypothetical protein T25E4.2	0.05	-	end	3	Membrane; multi-pass membrane protein (Potential)				471
Q09380 UniProt NPD GO	YS64_CAEEL	Hypothetical protein ZK675.4	0.05	-	mit	0					196
O74838 UniProt NPD GO	WTF10_SCHPO	Hypothetical protein wtf10	0.05	-	end	4	Membrane; multi-pass membrane protein (Potential)				258
Q8NIP8 UniProt NPD GO	WTF12_SCHPO	Hypothetical protein wtf12	0.05	-	end	2	Membrane; multi-pass membrane protein (Potential)				197
P93312 UniProt NPD GO	YMF16_ARATH	Hypothetical tatC-like protein ymf16 (ORFX)	0.05	-	end	6 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				280
Q03263 UniProt NPD GO	YM8M_YEAST	Hypothetical transport protein YMR279C	0.05	-	end	13	Membrane; multi-pass membrane protein (Potential)				540

You are viewing entries 74651 to 74700 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.