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
P28411 UniProt NPD GO	RBL_DRORE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
Q37328 UniProt NPD GO	RBL_EPHSI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				444
Q32223 UniProt NPD GO	RBL_EPHTW	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
Q33443 UniProt NPD GO	RBL_EREMA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P28413 UniProt NPD GO	RBL_ERICA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				467
Q33438 UniProt NPD GO	RBL_ERYCG	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P28415 UniProt NPD GO	RBL_EUCUL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	mit	0	Plastid; chloroplast				465
Q05799 UniProt NPD GO	RBL_EURFE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				394
P48703 UniProt NPD GO	RBL_FRAAN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P28416 UniProt NPD GO	RBL_GAREL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				459
P28417 UniProt NPD GO	RBL_GERGR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				463
P28418 UniProt NPD GO	RBL_GEUCH	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				459
P48704 UniProt NPD GO	RBL_GINBI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				444
P93906 UniProt NPD GO	RBL_GLAGU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				458
O98890 UniProt NPD GO	RBL_HALCL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				460
Q33528 UniProt NPD GO	RBL_HALRB	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				469
P28420 UniProt NPD GO	RBL_HARGR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P28421 UniProt NPD GO	RBL_HEDHE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P28423 UniProt NPD GO	RBL_HEUMI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				459
P28424 UniProt NPD GO	RBL_HUMBA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P28425 UniProt NPD GO	RBL_HYDVI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				467
P28426 UniProt NPD GO	RBL_ILECR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P92463 UniProt NPD GO	RBL_ISOTA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P28427 UniProt NPD GO	RBL_JASSU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				467
P28428 UniProt NPD GO	RBL_JUSOD	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
O98664 UniProt NPD GO	RBL_KIGAF	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				470
P28429 UniProt NPD GO	RBL_LOBSP	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P69572 UniProt NPD GO	RBL_LUPAA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69573 UniProt NPD GO	RBL_LUPAB	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69574 UniProt NPD GO	RBL_LUPAE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P92397 UniProt NPD GO	RBL_LUPAL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69575 UniProt NPD GO	RBL_LUPAN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69576 UniProt NPD GO	RBL_LUPAR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69577 UniProt NPD GO	RBL_LUPAT	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69578 UniProt NPD GO	RBL_LUPAU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69579 UniProt NPD GO	RBL_LUPCO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69580 UniProt NPD GO	RBL_LUPDI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69581 UniProt NPD GO	RBL_LUPHI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69582 UniProt NPD GO	RBL_LUPLA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69583 UniProt NPD GO	RBL_LUPLU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69584 UniProt NPD GO	RBL_LUPMC	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69585 UniProt NPD GO	RBL_LUPMU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P92407 UniProt NPD GO	RBL_LUPNA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69586 UniProt NPD GO	RBL_LUPNO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69587 UniProt NPD GO	RBL_LUPPA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69588 UniProt NPD GO	RBL_LUPPE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69589 UniProt NPD GO	RBL_LUPPI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69590 UniProt NPD GO	RBL_LUPPO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P69591 UniProt NPD GO	RBL_LUPPR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P28430 UniProt NPD GO	RBL_MANZA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465

You are viewing entries 97751 to 97800 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.