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
P62990 UniProt NPD GO	UBIQ_BOVIN	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus			2FIF	76
Q865C5 UniProt NPD GO	UBIQ_CAMDR	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P61862 UniProt NPD GO	UBIQ_CANAL	Ubiquitin	0.20	-	nuc	0	Cytoplasm. Nucleus				76
P63049 UniProt NPD GO	UBIQ_CANFA	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P62977 UniProt NPD GO	UBIQ_CAVPO	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P68197 UniProt NPD GO	UBIQ_CERCA	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
P62973 UniProt NPD GO	UBIQ_CHICK	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P62976 UniProt NPD GO	UBIQ_CRIGR	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P61863 UniProt NPD GO	UBIQ_CRYNE	Ubiquitin	0.20	-	nuc	0	Cytoplasm. Nucleus				76
P68198 UniProt NPD GO	UBIQ_DROME	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
P46574 UniProt NPD GO	UBIQ_EIMBO	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
P23324 UniProt NPD GO	UBIQ_EUPEU	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
P63051 UniProt NPD GO	UBIQ_FELCA	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
Q867C2 UniProt NPD GO	UBIQ_GORGO	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
Q8MKD1 UniProt NPD GO	UBIQ_HORSE	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P62988 UniProt NPD GO	UBIQ_HUMAN	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus	nucleus [IC]	191321	2GBN	76
P68199 UniProt NPD GO	UBIQ_ICTPU	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
Q9Y848 UniProt NPD GO	UBIQ_KLULA	Ubiquitin	0.20	-	nuc	0	Cytoplasm. Nucleus				76
P68196 UniProt NPD GO	UBIQ_MANSE	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
P62991 UniProt NPD GO	UBIQ_MOUSE	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P68204 UniProt NPD GO	UBIQ_OPHHA	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
Q867C3 UniProt NPD GO	UBIQ_PANTR	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)			2GBM	76
P62974 UniProt NPD GO	UBIQ_PIG	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
P68201 UniProt NPD GO	UBIQ_PLUXY	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
Q867C4 UniProt NPD GO	UBIQ_PONPY	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P62975 UniProt NPD GO	UBIQ_RABIT	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
P62989 UniProt NPD GO	UBIQ_RAT	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
P0C014 UniProt NPD GO	UBIQ_SCHPO	Ubiquitin	0.20	-	nuc	0	Cytoplasm. Nucleus				76
O46543 UniProt NPD GO	UBIQ_SHEEP	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P68195 UniProt NPD GO	UBIQ_SPOFR	Ubiquitin	0.20	-	cyt	0	Cytoplasm. Nucleus				76
P62972 UniProt NPD GO	UBIQ_XENLA	Ubiquitin	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P61864 UniProt NPD GO	UBIQ_YEAST	Ubiquitin	0.20	-	nuc	0	Cytoplasm. Nucleus	cytosolic large ribosomal subunit (sensu Eu... [TAS]		2G3Q	76
Q9CR14 UniProt NPD GO	FANCL_MOUSE	Ubiquitin ligase protein FANCL (EC 6.3.2.-) (Fanconi anemia group L protein homolog) (Proliferation ...	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nuclear envelope [IPI] nucleus [IPI]			375
Q8SWD4 UniProt NPD GO	UBIQ_ENCCU	Ubiquitin precursor	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				77
P70711 UniProt NPD GO	UB2D4_RAT	Ubiquitin-conjugating enzyme E2 D4 (EC 6.3.2.19) (Ubiquitin-protein ligase D4) (Ubiquitin carrier pr ...	0.20	-	nuc	0					147
Q1RML1 UniProt NPD GO	UBE2S_BOVIN	Ubiquitin-conjugating enzyme E2 S (EC 6.3.2.19) (Ubiquitin-protein ligase S) (Ubiquitin carrier prot ...	0.20	-	cyt	0					223
Q9BVV8 UniProt NPD GO	CS024_HUMAN	Uncharacterized protein C19orf24	0.20	-	nuc	0					132
Q96KT0 UniProt NPD GO	CH012_HUMAN	Uncharacterized protein C8orf12	0.20	-	nuc	0					104
P25574 UniProt NPD GO	YCE5_YEAST	Uncharacterized protein YCL045C	0.20	-	end	2 *		endoplasmic reticulum [IDA]			760
P42937 UniProt NPD GO	YG4E_YEAST	Uncharacterized protein YGR203W	0.20	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			148
P38793 UniProt NPD GO	YHN0_YEAST	Uncharacterized protein YHR070W	0.20	-	mit	0		cytoplasm [IDA] nucleus [IDA]			499
P38885 UniProt NPD GO	YHZ9_YEAST	Uncharacterized protein YHR199C	0.20	-	mit	0		mitochondrion [IDA]			310
P40506 UniProt NPD GO	YII3_YEAST	Uncharacterized protein YIL083C	0.20	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			365
P36059 UniProt NPD GO	YKP1_YEAST	Uncharacterized protein YKL151C	0.20	-	cyt	0		cytoplasm [IDA]			337
Q07986 UniProt NPD GO	YL036_YEAST	Uncharacterized protein YLR036C	0.20	-	nuc	3 *	Membrane; multi-pass membrane protein (Potential)				203
P39535 UniProt NPD GO	YJT8_YEAST	Uncharacterized transporter YJL198W	0.20	-	end	12	Membrane; multi-pass membrane protein (Potential)				881
Q9S9T7 UniProt NPD GO	VP281_ARATH	VPS28 protein homolog 1	0.20	-	nuc	0					209
P48413 UniProt NPD GO	VATB_CYACA	Vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B subunit)	0.20	-	cyt	0					500
P54648 UniProt NPD GO	VATC_DICDI	Vacuolar ATP synthase subunit C (EC 3.6.3.14) (V-ATPase C subunit) (Vacuolar proton pump C subunit)	0.20	-	cyt	0					368
Q5R422 UniProt NPD GO	VPP1_PONPY	Vacuolar proton translocating ATPase 116 kDa subunit a isoform 1 (V-ATPase 116 kDa isoform a1)	0.20	-	end	7	Integral membrane protein. Coated vesicle (By similarity)				837

You are viewing entries 51351 to 51400 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.