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
P01975 UniProt NPD GO	HBA_MACGI	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P17689 UniProt NPD GO	HBA_MARFO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P08852 UniProt NPD GO	HBA_MARMA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P01953 UniProt NPD GO	HBA_MELME	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P01945 UniProt NPD GO	HBA_MESAU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P41331 UniProt NPD GO	HBA_MICGA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
Q8HY34 UniProt NPD GO	HBA_MONDO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
Q9YGW2 UniProt NPD GO	HBA_MUSGR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	nuc	0				1GCW	141
P11757 UniProt NPD GO	HBA_MYOVE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P01944 UniProt NPD GO	HBA_ONDZI	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P80043 UniProt NPD GO	HBA_PAGBE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0				1S5Y	142
P19645 UniProt NPD GO	HBA_PAGLA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P18975 UniProt NPD GO	HBA_PANLE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P63109 UniProt NPD GO	HBA_PANON	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P63110 UniProt NPD GO	HBA_PANPO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P18976 UniProt NPD GO	HBA_PANPS	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P10883 UniProt NPD GO	HBA_PANTS	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P09908 UniProt NPD GO	HBA_PHOVI	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P23019 UniProt NPD GO	HBA_PROCR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P83623 UniProt NPD GO	HBA_PSEUR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0		hemoglobin complex [IDA]			142
P19831 UniProt NPD GO	HBA_PSIKR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P01956 UniProt NPD GO	HBA_ROUAE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P01943 UniProt NPD GO	HBA_SPAEH	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P09420 UniProt NPD GO	HBA_SPECI	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P11750 UniProt NPD GO	HBA_SPEPA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P07403 UniProt NPD GO	HBA_SPETO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P07408 UniProt NPD GO	HBA_SQUAC	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	mit	0					141
P01951 UniProt NPD GO	HBA_TALEU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P01940 UniProt NPD GO	HBA_TARBA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P02014 UniProt NPD GO	HBA_TARGR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					142
P07428 UniProt NPD GO	HBA_XENTR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P83270 UniProt NPD GO	HBA1_ANAMI	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.00	-	cyt	0					142
P83611 UniProt NPD GO	HBA1_GOBGI	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.00	-	cyt	0		hemoglobin complex [NAS]			142
Q7M3B8 UniProt NPD GO	HBA1_HAPGR	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.00	-	cyt	0					140
P18974 UniProt NPD GO	HBA1_IGUIG	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.00	-	cyt	0					141
P29624 UniProt NPD GO	HBA1_NOTAN	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.00	-	cyt	0					142
P45718 UniProt NPD GO	HBA1_TRENE	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.00	-	cyt	0				2AA1	142
P18979 UniProt NPD GO	HBA1_UROHA	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin) (Fragment)	0.00	-	cyt	0					90
P82111 UniProt NPD GO	HBA1_CATMA	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin) (Hb 1)	0.00	-	cyt	0					141
Q9PRL9 UniProt NPD GO	HBA1_NAJNA	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin) (Hemoglobin alpha-I chain)	0.00	-	cyt	0					141
P23600 UniProt NPD GO	HBA_MUSLU	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.00	-	cyt	0					141
P20243 UniProt NPD GO	HBA_MUSPF	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.00	-	cyt	0					141
P23601 UniProt NPD GO	HBA_MUSPU	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.00	-	cyt	0					141
P01948 UniProt NPD GO	HBA_RABIT	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.00	-	cyt	0					141
P01946 UniProt NPD GO	HBA_RAT	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.00	-	cyt	0					141
P01962 UniProt NPD GO	HBA_TAPTE	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.00	-	cyt	0					141
P83613 UniProt NPD GO	HBA2_GOBGI	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.00	-	cyt	0		hemoglobin complex [NAS]			142
P62363 UniProt NPD GO	HBA2_NOTAN	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.00	-	cyt	0					141
P62387 UniProt NPD GO	HBA2_NOTCO	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.00	-	cyt	0					141
P45719 UniProt NPD GO	HBA2_TRENE	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.00	-	cyt	0					142

You are viewing entries 95001 to 95050 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.