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
P08258 UniProt NPD GO	HBA_MANSP	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin) (Hemoglobin alpha-I/II ...	0.03	-	cyt	0					141
P19002 UniProt NPD GO	HBA_MACNE	Hemoglobin subunit alpha-1/2/3 (Hemoglobin alpha-1/2/3 chain) (Alpha-1/2/3-globin)	0.03	-	cyt	0					141
P01978 UniProt NPD GO	HBA2_TACAC	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.03	-	cyt	0					141
Q9TSN9 UniProt NPD GO	HBA3_BUBBU	Hemoglobin subunit alpha-3 (Hemoglobin alpha-3 chain) (Alpha-3-globin) (IIalpha3)	0.03	-	cyt	0					141
P21767 UniProt NPD GO	HBA_MACFA	Hemoglobin subunit alpha-A/Q/R/T (Hemoglobin alpha-A/Q/R/T chain) (Alpha-A/Q/R/T-globin)	0.03	-	cyt	0					141
P01939 UniProt NPD GO	HBA2_GALCR	Hemoglobin subunit alpha-B (Hemoglobin alpha-B chain) (Alpha-B-globin) (Alpha-II)	0.03	-	cyt	0					141
P18982 UniProt NPD GO	HBB_AILFU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
Q6WN26 UniProt NPD GO	HBB_AOTAZ	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02035 UniProt NPD GO	HBB_AOTTR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68047 UniProt NPD GO	HBB_ARCGA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
Q6WN22 UniProt NPD GO	HBB_ATEPA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P09422 UniProt NPD GO	HBB_BISBO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					145
P02072 UniProt NPD GO	HBB_BOSMU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					145
Q6WN21 UniProt NPD GO	HBB_CALGO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
Q6WN20 UniProt NPD GO	HBB_CALTO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68230 UniProt NPD GO	HBB_CAMBA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68231 UniProt NPD GO	HBB_CAMDR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P19885 UniProt NPD GO	HBB_COLPO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P11754 UniProt NPD GO	HBB_CYNSP	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P56692 UniProt NPD GO	HBB_DASAK	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0				1CG8	141
P02087 UniProt NPD GO	HBB_DASNO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P24292 UniProt NPD GO	HBB_ECHTE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02053 UniProt NPD GO	HBB_EULFU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P19016 UniProt NPD GO	HBB_HIPAM	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68226 UniProt NPD GO	HBB_LAMGL	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68229 UniProt NPD GO	HBB_LAMGU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68228 UniProt NPD GO	HBB_LAMPA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68227 UniProt NPD GO	HBB_LAMVI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02138 UniProt NPD GO	HBB_LEPPA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					147
P02048 UniProt NPD GO	HBB_LORTA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P10893 UniProt NPD GO	HBB_LUTLU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68223 UniProt NPD GO	HBB_MACFA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68222 UniProt NPD GO	HBB_MACFU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P24660 UniProt NPD GO	HBB_MACGG	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02026 UniProt NPD GO	HBB_MACMU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68225 UniProt NPD GO	HBB_MACNE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68224 UniProt NPD GO	HBB_MACSP	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68053 UniProt NPD GO	HBB_MARFO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P15449 UniProt NPD GO	HBB_MELCA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02055 UniProt NPD GO	HBB_MELME	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P23602 UniProt NPD GO	HBB_MUSLU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68044 UniProt NPD GO	HBB_MUSPF	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68045 UniProt NPD GO	HBB_MUSPU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02049 UniProt NPD GO	HBB_NYCCO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68046 UniProt NPD GO	HBB_ODORO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02076 UniProt NPD GO	HBB_OVIMU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					145
P02030 UniProt NPD GO	HBB_PAPCY	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
Q6WN27 UniProt NPD GO	HBB_PITPI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P14391 UniProt NPD GO	HBB_PTEAL	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68052 UniProt NPD GO	HBB_PTEBR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146

You are viewing entries 80151 to 80200 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.