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
Q45XJ0 UniProt NPD GO	HBD_LOXAF	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.01	-	cyt	0					146
Q45XI8 UniProt NPD GO	HBD_TRIMA	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.01	-	cyt	0					146
Q45XI4 UniProt NPD GO	HBD_DENDR	Hemoglobin subunit deltaH (Hemoglobin deltaH chain) (DeltaH-globin)	0.01	-	cyt	0					146
Q45XI5 UniProt NPD GO	HBD_HETBR	Hemoglobin subunit deltaH (Hemoglobin deltaH chain) (DeltaH-globin)	0.01	-	cyt	0					146
Q45XI6 UniProt NPD GO	HBD_PROCA	Hemoglobin subunit deltaH (Hemoglobin deltaH chain) (DeltaH-globin)	0.01	-	cyt	0					146
P68017 UniProt NPD GO	HBE_ALOBE	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68018 UniProt NPD GO	HBE_ALOSE	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68016 UniProt NPD GO	HBE_AOTAZ	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P51438 UniProt NPD GO	HBE_ATEBE	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68019 UniProt NPD GO	HBE_ATEGE	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68020 UniProt NPD GO	HBE_BRAAR	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
Q45XH3 UniProt NPD GO	HBE_BRATR	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68021 UniProt NPD GO	HBE_CACCA	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68024 UniProt NPD GO	HBE_CALGO	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68026 UniProt NPD GO	HBE_CALJA	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68022 UniProt NPD GO	HBE_CALMO	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68023 UniProt NPD GO	HBE_CALTO	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
Q28220 UniProt NPD GO	HBE_CEBAL	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
Q7JFR7 UniProt NPD GO	HBE_CEBKA	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
Q29415 UniProt NPD GO	HBE_CEBOL	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68027 UniProt NPD GO	HBE_CEBPY	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
Q28338 UniProt NPD GO	HBE_CHEME	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P02128 UniProt NPD GO	HBE_CHICK	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68025 UniProt NPD GO	HBE_CHISA	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
Q28356 UniProt NPD GO	HBE_DAUMA	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P08223 UniProt NPD GO	HBE_EULFU	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P19759 UniProt NPD GO	HBE_GALCR	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
Q6LDH0 UniProt NPD GO	HBE_GORGO	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P02100 UniProt NPD GO	HBE_HUMAN	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0		hemoglobin complex [TAS]	142100	1A9W	146
Q95190 UniProt NPD GO	HBE_HYLSY	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P51440 UniProt NPD GO	HBE_LAGLA	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P51441 UniProt NPD GO	HBE_LEORO	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P81042 UniProt NPD GO	HBE_MACEU	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	nuc	0					146
Q28507 UniProt NPD GO	HBE_MACMU	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
Q28496 UniProt NPD GO	HBE_MICMU	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
Q28775 UniProt NPD GO	HBE_PANPA	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
Q6LDH1 UniProt NPD GO	HBE_PANTR	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P02101 UniProt NPD GO	HBE_PIG	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P18994 UniProt NPD GO	HBE_PONPY	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
Q95238 UniProt NPD GO	HBE_PROVE	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P51443 UniProt NPD GO	HBE_SAGMI	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68029 UniProt NPD GO	HBE_SAIBB	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P68028 UniProt NPD GO	HBE_SAISC	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P18435 UniProt NPD GO	HBE_TARSY	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.01	-	cyt	0					146
P02103 UniProt NPD GO	HBE_RABIT	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin) (Beta-4 globin)	0.01	-	cyt	0					146
O13071 UniProt NPD GO	HBE_CALGE	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin) (Fragment)	0.01	-	cyt	0					141
Q28931 UniProt NPD GO	HBE_SMICR	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin) (Hemoglobin embryonic beta ch ...	0.01	-	cyt	0					146
P02102 UniProt NPD GO	HBE1_CAPHI	Hemoglobin subunit epsilon-1 (Hemoglobin epsilon-1 chain) (Epsilon-1-globin) (Hemoglobin epsilon-I c ...	0.01	-	cyt	0					146
P06642 UniProt NPD GO	HBE2_BOVIN	Hemoglobin subunit epsilon-2 (Hemoglobin epsilon-2 chain) (Epsilon-2-globin)	0.01	-	cyt	0					146
P02105 UniProt NPD GO	HBE2_CAPHI	Hemoglobin subunit epsilon-2 (Hemoglobin epsilon-2 chain) (Epsilon-2-globin) (Hemoglobin epsilon-II ...	0.01	-	cyt	0					146

You are viewing entries 88901 to 88950 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.