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
P68944 UniProt NPD GO	HBB_BRACA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	nuc	0					146
P14260 UniProt NPD GO	HBB_CAIMO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P60524 UniProt NPD GO	HBB_CANFA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P60525 UniProt NPD GO	HBB_CANLA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P82113 UniProt NPD GO	HBB_CATMA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	nuc	0					146
P02095 UniProt NPD GO	HBB_CAVPO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02112 UniProt NPD GO	HBB_CHICK	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0		hemoglobin complex [ISS]		1HBR	146
P07036 UniProt NPD GO	HBB_CHLME	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P60526 UniProt NPD GO	HBB_CHRBR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0				1FHJ	146
P13274 UniProt NPD GO	HBB_CHRPI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02125 UniProt NPD GO	HBB_CICCI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	nuc	0					146
P11342 UniProt NPD GO	HBB_COLLI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	mit	0				1N1R	146
P30893 UniProt NPD GO	HBB_COTJA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P18986 UniProt NPD GO	HBB_CROCR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P20855 UniProt NPD GO	HBB_CTEGU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P68945 UniProt NPD GO	HBB_CYGOL	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	nuc	0					146
O13164 UniProt NPD GO	HBB_DECMA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					147
P14521 UniProt NPD GO	HBB_ELEEL	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					147
P02084 UniProt NPD GO	HBB_ELEMA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02059 UniProt NPD GO	HBB_ERIEU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P10058 UniProt NPD GO	HBB_EUDCR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	mit	0					146
P22742 UniProt NPD GO	HBB_FRAPO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
Q98905 UniProt NPD GO	HBB_GEOCR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P83123 UniProt NPD GO	HBB_GEONI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P29625 UniProt NPD GO	HBB_GYMAC	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P68063 UniProt NPD GO	HBB_GYPRU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02143 UniProt NPD GO	HBB_HETPO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					141
P23741 UniProt NPD GO	HBB_LATCH	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P56251 UniProt NPD GO	HBB_LEIXA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0				1SPG	147
P02054 UniProt NPD GO	HBB_LEMCA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P21667 UniProt NPD GO	HBB_LEMVA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P08535 UniProt NPD GO	HBB_LEPEU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P15166 UniProt NPD GO	HBB_LEPWE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P16418 UniProt NPD GO	HBB_LIOMI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02085 UniProt NPD GO	HBB_LOXAF	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P41328 UniProt NPD GO	HBB_LYNLY	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P09840 UniProt NPD GO	HBB_MACCA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P08853 UniProt NPD GO	HBB_MARMA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P11752 UniProt NPD GO	HBB_MEGLY	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
O09232 UniProt NPD GO	HBB_MELAE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
O13078 UniProt NPD GO	HBB_MERMR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P18707 UniProt NPD GO	HBB_MESBR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P41332 UniProt NPD GO	HBB_MICGA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P11758 UniProt NPD GO	HBB_MYOVE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P26916 UniProt NPD GO	HBB_NASNA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P29628 UniProt NPD GO	HBB_NOTAN	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P16309 UniProt NPD GO	HBB_NOTCO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
Q98TS0 UniProt NPD GO	HBB_ONCNE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					147
P02093 UniProt NPD GO	HBB_ONDZI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02111 UniProt NPD GO	HBB_ORNAN	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146

You are viewing entries 88751 to 88800 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.