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
P28431 UniProt NPD GO	RBL_MORAL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				459
Q32625 UniProt NPD GO	RBL_MORRU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P28432 UniProt NPD GO	RBL_MYRCE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
O20241 UniProt NPD GO	RBL_NANDO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P28433 UniProt NPD GO	RBL_NELCA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
Q05800 UniProt NPD GO	RBL_NELLU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				394
P28434 UniProt NPD GO	RBL_NEPAL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
Q32686 UniProt NPD GO	RBL_NICPH	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				469
Q32699 UniProt NPD GO	RBL_NOLSP	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				468
Q32668 UniProt NPD GO	RBL_NOTFE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				441
Q05801 UniProt NPD GO	RBL_NUPVA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				394
Q05802 UniProt NPD GO	RBL_NYMOD	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				394
Q36610 UniProt NPD GO	RBL_ONYJA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				414
Q9XQJ6 UniProt NPD GO	RBL_PACAQ	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				469
O98668 UniProt NPD GO	RBL_PANJS	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				468
Q32770 UniProt NPD GO	RBL_PELAN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				441
P28439 UniProt NPD GO	RBL_PELHO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				463
P28440 UniProt NPD GO	RBL_PINCA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P28441 UniProt NPD GO	RBL_PLAOC	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P28442 UniProt NPD GO	RBL_PLAVR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P28443 UniProt NPD GO	RBL_POLCR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P28444 UniProt NPD GO	RBL_PROLU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P28445 UniProt NPD GO	RBL_PRUDO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				459
P28446 UniProt NPD GO	RBL_QUIIN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P36485 UniProt NPD GO	RBL_SALDI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				468
P28452 UniProt NPD GO	RBL_SAXIN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				459
P25835 UniProt NPD GO	RBL_SCHTR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	mit	0	Plastid; chloroplast				471
P28453 UniProt NPD GO	RBL_SCUBO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				467
P28454 UniProt NPD GO	RBL_SECDI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P28455 UniProt NPD GO	RBL_SEDRU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				450
P36487 UniProt NPD GO	RBL_SESIN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				443
P25837 UniProt NPD GO	RBL_SILGA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
Q33101 UniProt NPD GO	RBL_SOLGR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				468
P36488 UniProt NPD GO	RBL_SPIMR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				416
P36489 UniProt NPD GO	RBL_STRNX	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				471
Q05993 UniProt NPD GO	RBL_SYMAL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				441
Q37282 UniProt NPD GO	RBL_TABHE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				469
P93869 UniProt NPD GO	RBL_TAMIN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				455
P28456 UniProt NPD GO	RBL_TASIN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				467
O98671 UniProt NPD GO	RBL_TECST	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				468
P28457 UniProt NPD GO	RBL_THEPO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P28458 UniProt NPD GO	RBL_TROAR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P48717 UniProt NPD GO	RBL_TROMA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
Q33245 UniProt NPD GO	RBL_ULMAL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
Q05803 UniProt NPD GO	RBL_VICCZ	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				394
P27067 UniProt NPD GO	RBL_VIGSI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-		0	Plastid; chloroplast				16
P48719 UniProt NPD GO	RBL_WELMI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				444
P24671 UniProt NPD GO	RBL_ABIMA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475
P25826 UniProt NPD GO	RBL_ALLPR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				480
Q70XZ5 UniProt NPD GO	RBL_AMBTC	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	cyt	0	Plastid; chloroplast				475

You are viewing entries 97801 to 97850 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.