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
P83113 UniProt NPD GO	HBA2_TELPE	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin) (Fragment)	0.00	-	cyt	0					137
P18981 UniProt NPD GO	HBA2_VAREX	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin) (Hemoglobin alpha-II chain)	0.00	-	cyt	0					141
P10784 UniProt NPD GO	HBA2_TRICR	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin) (Hemoglobin alpha-minor chain ...	0.00	-	cyt	0					141
P07431 UniProt NPD GO	HBA2_XENBO	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin) (Hemoglobin alpha-minor chain ...	0.00	-	cyt	0					141
Q9TSN8 UniProt NPD GO	HBA2_BUBBU	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin) (Ialpha2)	0.00	-	cyt	0					141
P06636 UniProt NPD GO	HBA3_XENLA	Hemoglobin subunit alpha-3 (Hemoglobin alpha-2 chain) (Alpha-3-globin) (Alpha-T3)	0.00	-	cyt	0					141
P08850 UniProt NPD GO	HBA_ACCGE	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P07417 UniProt NPD GO	HBA_AEGMO	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P22740 UniProt NPD GO	HBA_ANAPE	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01986 UniProt NPD GO	HBA_ANAPL	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01988 UniProt NPD GO	HBA_ANAPP	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01989 UniProt NPD GO	HBA_ANSAN	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0				1FAW	141
P01990 UniProt NPD GO	HBA_ANSIN	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0				1HV4	141
P01985 UniProt NPD GO	HBA_ANSSE	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P15162 UniProt NPD GO	HBA_APUAP	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01993 UniProt NPD GO	HBA_AQUCH	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01996 UniProt NPD GO	HBA_ARAAR	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P84790 UniProt NPD GO	HBA_AYTFU	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0		hemoglobin complex [IDA]			141
P01991 UniProt NPD GO	HBA_BRACA	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01987 UniProt NPD GO	HBA_CAIMO	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
Q10732 UniProt NPD GO	HBA_CARCR	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01994 UniProt NPD GO	HBA_CHICK	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P07034 UniProt NPD GO	HBA_CHLME	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P13273 UniProt NPD GO	HBA_CHRPI	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01983 UniProt NPD GO	HBA_CICCI	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P21871 UniProt NPD GO	HBA_COLLI	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	mit	0					141
P24589 UniProt NPD GO	HBA_COTJA	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01992 UniProt NPD GO	HBA_CYGOL	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P0C0U6 UniProt NPD GO	HBA_DRYCE	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P19789 UniProt NPD GO	HBA_EUDSC	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P22741 UniProt NPD GO	HBA_FRAPO	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P08260 UniProt NPD GO	HBA_LARRI	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P81023 UniProt NPD GO	HBA_MELGA	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P07407 UniProt NPD GO	HBA_PASMO	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P10780 UniProt NPD GO	HBA_PHACA	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01995 UniProt NPD GO	HBA_PHACO	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0				1OPV	141
P01984 UniProt NPD GO	HBA_PHORU	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01982 UniProt NPD GO	HBA_RHEAM	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P10059 UniProt NPD GO	HBA_SPHPU	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01981 UniProt NPD GO	HBA_STRCA	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
Q7LZC3 UniProt NPD GO	HBA_STROE	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P01997 UniProt NPD GO	HBA_STUVU	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P19832 UniProt NPD GO	HBA_TRIOC	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P14522 UniProt NPD GO	HBA_TURME	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P07404 UniProt NPD GO	HBA_VULGR	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.00	-	cyt	0					141
P14259 UniProt NPD GO	HBA1_GALCR	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin) (Alpha-I)	0.00	-	cyt	0					141
P08256 UniProt NPD GO	HBA_GYPRU	Hemoglobin subunit alpha-A/A' (Hemoglobin alpha-A/A' chain) (Alpha-A/A'-globin)	0.00	-	cyt	0					141
P51465 UniProt NPD GO	HBAB_RANCA	Hemoglobin subunit alpha-B (Hemoglobin alpha-B chain) (Alpha-B-globin)	0.00	-	cyt	0					141
Q9PVM3 UniProt NPD GO	HBAB_SERQU	Hemoglobin subunit alpha-B (Hemoglobin alpha-B chain) (Alpha-B-globin)	0.00	-	nuc	0					143
P55267 UniProt NPD GO	HBAC_RANCA	Hemoglobin subunit alpha-C (Hemoglobin alpha-C chain) (Alpha-C-globin)	0.00	-	cyt	0					141

You are viewing entries 95051 to 95100 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.