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
P38831 UniProt NPD GO	YHS5_YEAST	Hypothetical 11.9 kDa protein in NDT80-FUR1 intergenic region	0.16	-	nuc	0					101
P39999 UniProt NPD GO	YEB4_YEAST	Hypothetical 12.2 kDa protein in PMP2-VAC8 intergenic region	0.16	-	cyt	0					101
P36092 UniProt NPD GO	YKE4_YEAST	Hypothetical 12.4 kDa protein in PRI2-PHD1 intergenic region	0.16	-	mit	2 *					106
Q04329 UniProt NPD GO	YM53_YEAST	Hypothetical 14.3 kDa protein in RPL36A-VTI1 intergenic region	0.16	-	nuc	0		vacuolar membrane (sensu Fungi) [IDA]			127
P49533 UniProt NPD GO	YCF35_ODOSI	Hypothetical 14.9 kDa protein ycf35 (ORF128)	0.16	-	nuc	0	Plastid; chloroplast				128
P51350 UniProt NPD GO	YCXJ_PORPU	Hypothetical 17.4 kDa protein in groL-rps16 intergenic region (ORF148)	0.16	-	nuc	1	Plastid; chloroplast				148
P51380 UniProt NPD GO	YCF21_PORPU	Hypothetical 20.6 kDa protein ycf21 (ORF174)	0.16	-	mit	0	Plastid; chloroplast				174
P48335 UniProt NPD GO	YCXE_CYAPA	Hypothetical 21.2 kDa protein in ycf23-apcF intergenic region (ORF179)	0.16	-	cyt	0	Plastid; cyanelle				179
P38471 UniProt NPD GO	YMF29_MARPO	Hypothetical 23.5 kDa protein in COX3-NAD1 intergenic region (ORF 207)	0.16	-	nuc	0					207
O19887 UniProt NPD GO	YCF53_CYACA	Hypothetical 28.1 kDa protein ycf53	0.16	-	end	0	Plastid; chloroplast				237
P58147 UniProt NPD GO	YCY3_ASTLO	Hypothetical 32.5 kDa protein in rpl14-rpl12 intergenic region (ORF263)	0.16	-	cyt	0	Plastid				263
Q9MTN4 UniProt NPD GO	YCX4_OENHO	Hypothetical 8.4 kDa protein in ycf9-trnS intergenic region (ORF75)	0.16	-	nuc	0	Plastid; chloroplast				75
P35912 UniProt NPD GO	YCF24_GALSU	Hypothetical UPF0051 protein in atpA 3'region (ORF X) (Fragment)	0.16	-	nuc	0	Plastid; chloroplast				221
Q9W0Y2 UniProt NPD GO	YS11_DROME	Hypothetical UPF0131 protein CG2811	0.16	-	cyt	0					157
P47188 UniProt NPD GO	YJ9Z_YEAST	Hypothetical UPF0320 protein YJR162C	0.16	-	nuc	0					116
Q18964 UniProt NPD GO	YLN2_CAEEL	Hypothetical WD repeat protein D2013.2	0.16	-	cyt	0					415
Q09309 UniProt NPD GO	YQS1_CAEEL	Hypothetical WD repeat protein F21H12.1	0.16	-	cyt	0					454
P92538 UniProt NPD GO	M1040_ARATH	Hypothetical mitochondrial protein AtMg01040 (ORF107f)	0.16	-	nuc	0	Mitochondrion (Potential)				107
P34298 UniProt NPD GO	YKQ3_CAEEL	Hypothetical protein C06E1.3	0.16	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				397
Q10095 UniProt NPD GO	YAOG_SCHPO	Hypothetical protein C11D3.16c in chromosome I	0.16	-	cyt	0					131
O13689 UniProt NPD GO	YDYA_SCHPO	Hypothetical protein C11E3.10 in chromosome I	0.16	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				162
O13692 UniProt NPD GO	YDYD_SCHPO	Hypothetical protein C11E3.13c precursor	0.16	-	exc	0					510
O13777 UniProt NPD GO	YIU1_SCHPO	Hypothetical protein C1610.01 in chromosome I	0.16	-	nuc	0					217
Q09710 UniProt NPD GO	YA33_SCHPO	Hypothetical protein C18B11.03c in chromosome I	0.16	-	cyt	1 *	Membrane; multi-pass membrane protein (Potential)				440
Q10102 UniProt NPD GO	YAQ1_SCHPO	Hypothetical protein C18G6.01c in chromosome I	0.16	-	mit	0					259
Q09476 UniProt NPD GO	YP96_CAEEL	Hypothetical protein C28H8.6 in chromosome III	0.16	-	nuc	0					256
O14017 UniProt NPD GO	YDPE_SCHPO	Hypothetical protein C29A4.14c in chromosome I	0.16	-	mit	0					346
Q18449 UniProt NPD GO	YC2L_CAEEL	Hypothetical protein C34D4.4 in chromosome IV	0.16	-	mit	3	Membrane; multi-pass membrane protein (Potential)				247
Q9USS7 UniProt NPD GO	YNB3_SCHPO	Hypothetical protein C4.03c in chromosome II	0.16	-	end	0					891
Q8ST81 UniProt NPD GO	Y602_ENCCU	Hypothetical protein ECU06_0020/ECU06_1700	0.16	-	end	7 *					280
Q8SVF2 UniProt NPD GO	Y610_ENCCU	Hypothetical protein ECU06_0100	0.16	-	end	7 *					261
Q8SU92 UniProt NPD GO	Y8I5_ENCCU	Hypothetical protein ECU10_1850	0.16	-	end	7 *					268
P34401 UniProt NPD GO	YLU7_CAEEL	Hypothetical protein F10E9.7	0.16	-	nuc	0					131
P41881 UniProt NPD GO	YPT3_CAEEL	Hypothetical protein F37A4.3	0.16	-	nuc	1					229
P52874 UniProt NPD GO	YMI4_CAEEL	Hypothetical protein F59A2.4	0.16	-	mit	0					428
P34507 UniProt NPD GO	YMV5_CAEEL	Hypothetical protein K04H4.5	0.16	-	nuc	0					251
P34679 UniProt NPD GO	YO41_CAEEL	Hypothetical protein ZK757.1	0.16	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				324
Q09383 UniProt NPD GO	YS87_CAEEL	Hypothetical protein ZK945.7	0.16	-	nuc	0					249
Q6C673 UniProt NPD GO	ISN1_YARLI	IMP-specific 5'-nucleotidase 1 (EC 3.1.3.-)	0.16	-	nuc	0					420
P20758 UniProt NPD GO	IGHA1_GORGO	Ig alpha-1 chain C region	0.16	-	nuc	0					353
P01870 UniProt NPD GO	GC_RABIT	Ig gamma chain C region	0.16	-	nuc	0					323
P01861 UniProt NPD GO	IGHG4_HUMAN	Ig gamma-4 chain C region	0.16	-	nuc	0		membrane fraction [NAS]	147130	1ADQ	327
P23085 UniProt NPD GO	HVC2_HETFR	Ig heavy chain C region (Clone 12022) (Fragment)	0.16	-	nuc	0					438
P23087 UniProt NPD GO	HVCS_HETFR	Ig heavy chain C region, secreted form (Clone 3050)	0.16	-	nuc	0					438
P18533 UniProt NPD GO	HV62_MOUSE	Ig heavy chain V region 733 precursor	0.16	-	exc	0					117
P01834 UniProt NPD GO	KAC_HUMAN	Ig kappa chain C region	0.16	-	nuc	0			147200	1MIM	106
P01837 UniProt NPD GO	KAC_MOUSE	Ig kappa chain C region	0.16	-	nuc	0				25C8	106
P01603 UniProt NPD GO	KV1K_HUMAN	Ig kappa chain V-I region Ka	0.16	-	cyt	0		extracellular region [NAS]			108
P01629 UniProt NPD GO	KV2D_MOUSE	Ig kappa chain V-II region 2S1.3	0.16	-	mit	0					112
P01626 UniProt NPD GO	KV2A_MOUSE	Ig kappa chain V-II region MOPC 167	0.16	-	nuc	0					112

You are viewing entries 55751 to 55800 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.