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
P01923 UniProt NPD GO	HBA_GORGO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P69905 UniProt NPD GO	HBA_HUMAN	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0			141800	6HBW	141
P01938 UniProt NPD GO	HBA_LORTA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P63107 UniProt NPD GO	HBA_MACFU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P63108 UniProt NPD GO	HBA_MACMU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P11751 UniProt NPD GO	HBA_MEGLY	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	mit	1					141
P01937 UniProt NPD GO	HBA_NYCCO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P69906 UniProt NPD GO	HBA_PANPA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P69907 UniProt NPD GO	HBA_PANTR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P09904 UniProt NPD GO	HBA_PHYCA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01965 UniProt NPD GO	HBA_PIG	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0				2PGH	141
Q862A7 UniProt NPD GO	HBA_PIPAB	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					142
P06635 UniProt NPD GO	HBA_PONPY	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01957 UniProt NPD GO	HBA_PROHA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					142
P14389 UniProt NPD GO	HBA_PTEAL	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P21379 UniProt NPD GO	HBA_RANTA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P09906 UniProt NPD GO	HBA_RHIUN	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01929 UniProt NPD GO	HBA_SAGFU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
Q7M3B6 UniProt NPD GO	HBA_SAGMY	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P67818 UniProt NPD GO	HBA_SAGOE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01924 UniProt NPD GO	HBA_SEMEN	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P01950 UniProt NPD GO	HBA_SUNMU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P04237 UniProt NPD GO	HBA_TRAST	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					140
P68235 UniProt NPD GO	HBA_URSMA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P68237 UniProt NPD GO	HBA_URSML	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
P68236 UniProt NPD GO	HBA_URSTH	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.02	-	cyt	0					141
Q1AGS5 UniProt NPD GO	HBA1_ARCGL	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.02	-	cyt	0					142
Q1AGS9 UniProt NPD GO	HBA1_BORSA	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.02	-	cyt	0					142
Q9XSN3 UniProt NPD GO	HBA1_EQUBU	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.02	-	cyt	0					141
Q9XSN2 UniProt NPD GO	HBA1_EQUGR	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.02	-	cyt	0					141
P84609 UniProt NPD GO	HBA1_GADMO	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.02	-	mit	0					142
Q9TS35 UniProt NPD GO	HBA1_HYLLA	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.02	-	cyt	0					141
P01977 UniProt NPD GO	HBA1_TACAC	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.02	-	cyt	0					141
P11755 UniProt NPD GO	HBA1_TADBR	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.02	-	cyt	0					141
P06639 UniProt NPD GO	HBA1_PLEWA	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin) (Hemoglobin alpha-major chain ...	0.02	-	cyt	0					141
P68239 UniProt NPD GO	HBA_AMMLE	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.02	-	cyt	0					141
P68238 UniProt NPD GO	HBA_CAPHI	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.02	-	cyt	0					141
P01961 UniProt NPD GO	HBA_EQUHE	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.02	-	cyt	0					141
P07402 UniProt NPD GO	HBA_MACSP	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.02	-	cyt	0					141
P68240 UniProt NPD GO	HBA_SHEEP	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.02	-	cyt	0					141
P24659 UniProt NPD GO	HBA_MACGG	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin) (Hemoglobin alpha-I/II ...	0.02	-	cyt	0					141
P21766 UniProt NPD GO	HBA_MACAS	Hemoglobin subunit alpha-1/2/3 (Hemoglobin alpha-1/2/3 chain) (Alpha-1/2/3-globin)	0.02	-	cyt	0					141
Q1AGS4 UniProt NPD GO	HBA2_ARCGL	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.02	-	mit	0					142
P01968 UniProt NPD GO	HBA2_BOSMU	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.02	-	cyt	0					141
Q9TVA3 UniProt NPD GO	HBA2_EQUBU	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.02	-	cyt	0					141
Q7JFN6 UniProt NPD GO	HBA2_EQUGR	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.02	-	cyt	0					141
O42425 UniProt NPD GO	HBA2_GADMO	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.02	-	cyt	0					142
Q9TS34 UniProt NPD GO	HBA2_HYLLA	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.02	-	cyt	0					141
P41330 UniProt NPD GO	HBA2_ARCGA	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin) (Hemoglobin alpha-II chain)	0.02	-	cyt	0					141
P02013 UniProt NPD GO	HBA2_XENLA	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin) (Hemoglobin alpha-minor chain ...	0.02	-	cyt	0					141

You are viewing entries 83751 to 83800 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.