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
P01934 UniProt NPD GO	HBA3_GORGO	Hemoglobin subunit alpha-3 (Hemoglobin alpha-2 chain) (Alpha-3-globin)	0.02	-	cyt	0					141
P01935 UniProt NPD GO	HBA3_PANTR	Hemoglobin subunit alpha-3 (Hemoglobin alpha-2 chain) (Alpha-3-globin)	0.02	-	cyt	0					141
P02011 UniProt NPD GO	HBA3_RANCA	Hemoglobin subunit alpha-3 (Hemoglobin alpha-3 chain) (Alpha-3-globin) (Hemoglobin alpha-III chain, ...	0.02	-	cyt	0					141
P06637 UniProt NPD GO	HBA4_XENLA	Hemoglobin subunit alpha-4 (Hemoglobin alpha-4 chain) (Alpha-4-globin) (Alpha-T4)	0.02	-	cyt	0					141
Q9XSK1 UniProt NPD GO	HBA4_BUBBU	Hemoglobin subunit alpha-4 (Hemoglobin alpha-4 chain) (Alpha-4-globin) (IIalpha4)	0.02	-	cyt	0					141
P04442 UniProt NPD GO	HBAD_ANAPL	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.02	-	cyt	0					141
P15164 UniProt NPD GO	HBAD_APUAP	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.02	-	cyt	0					141
P84791 UniProt NPD GO	HBAD_AYTFU	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.02	-	cyt	0		hemoglobin complex [IDA]			141
P04240 UniProt NPD GO	HBAD_BRACA	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.02	-	cyt	0					141
P02003 UniProt NPD GO	HBAD_CAIMO	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.02	-	cyt	0					141
P02005 UniProt NPD GO	HBAD_CHRPI	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.02	-	cyt	0					141
P30892 UniProt NPD GO	HBAD_COTJA	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.02	-	cyt	0					141
Q9DF25 UniProt NPD GO	HBAD_GEOCR	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.02	-	cyt	0					141
P10062 UniProt NPD GO	HBAD_SPHPU	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.02	-	cyt	0					141
P09423 UniProt NPD GO	HBA_BISBO	Hemoglobin subunit alpha-I/II (Hemoglobin alpha-I/II chain) (Alpha-I/II-globin)	0.02	-	cyt	0					141
P18983 UniProt NPD GO	HBB_AILME	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P02073 UniProt NPD GO	HBB_ALCAA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					145
Q6WN29 UniProt NPD GO	HBB_ALOBE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P68234 UniProt NPD GO	HBB_ATEBE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P68232 UniProt NPD GO	HBB_ATEGE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P67819 UniProt NPD GO	HBB_BOSGF	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					145
P02070 UniProt NPD GO	HBB_BOVIN	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0				1HDA	145
P67820 UniProt NPD GO	HBB_BUBBU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					145
P18985 UniProt NPD GO	HBB_CALAR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
Q6WN28 UniProt NPD GO	HBB_CALJA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P02140 UniProt NPD GO	HBB_CARAU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					147
Q10733 UniProt NPD GO	HBB_CARCR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	nuc	0					146
P02040 UniProt NPD GO	HBB_CEBAL	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P67821 UniProt NPD GO	HBB_CEBAP	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P67822 UniProt NPD GO	HBB_CEBCA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P02066 UniProt NPD GO	HBB_CERSI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P02031 UniProt NPD GO	HBB_CERTO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P02033 UniProt NPD GO	HBB_COLBA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P67823 UniProt NPD GO	HBB_EQUHE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P67824 UniProt NPD GO	HBB_EQUZE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
O13077 UniProt NPD GO	HBB_GADMO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P02024 UniProt NPD GO	HBB_GORGO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
Q7M3C2 UniProt NPD GO	HBB_HAPGR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P02062 UniProt NPD GO	HBB_HORSE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0				2MHB	146
P68871 UniProt NPD GO	HBB_HUMAN	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0		hemoglobin complex [TAS]	141900	6HBW	146
P02025 UniProt NPD GO	HBB_HYLLA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
Q6WN25 UniProt NPD GO	HBB_LAGLA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P19646 UniProt NPD GO	HBB_PAGLA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P68872 UniProt NPD GO	HBB_PANPA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P68873 UniProt NPD GO	HBB_PANTR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P09907 UniProt NPD GO	HBB_RHIUN	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P02036 UniProt NPD GO	HBB_SAISC	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P02075 UniProt NPD GO	HBB_SHEEP	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					145
P28781 UniProt NPD GO	HBB_TAPGE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P02051 UniProt NPD GO	HBB_TARBA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146

You are viewing entries 83801 to 83850 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.