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
P28379 UniProt NPD GO	RBL_APHSI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P28380 UniProt NPD GO	RBL_APIGR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				459
Q05984 UniProt NPD GO	RBL_APOCA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				441
P93890 UniProt NPD GO	RBL_ARIGL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				451
P43225 UniProt NPD GO	RBL_ARTBA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				416
Q9MTE7 UniProt NPD GO	RBL_AVECA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
Q05795 UniProt NPD GO	RBL_BARLO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				394
P28382 UniProt NPD GO	RBL_BARPR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
Q33162 UniProt NPD GO	RBL_BARSC	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	nuc	0	Plastid; chloroplast				456
Q31730 UniProt NPD GO	RBL_BAURU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
Q31715 UniProt NPD GO	RBL_BERBR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				470
P36481 UniProt NPD GO	RBL_BERLA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P36477 UniProt NPD GO	RBL_BOTST	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				444
P36482 UniProt NPD GO	RBL_BUDDA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				443
O19989 UniProt NPD GO	RBL_BULAR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P28385 UniProt NPD GO	RBL_BURIN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
Q31750 UniProt NPD GO	RBL_CALCA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				469
P36483 UniProt NPD GO	RBL_CALDI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				445
P28388 UniProt NPD GO	RBL_CALPL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P27063 UniProt NPD GO	RBL_CAPAN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-		0	Plastid; chloroplast				16
Q31951 UniProt NPD GO	RBL_CAPBA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				468
Q33383 UniProt NPD GO	RBL_CATSP	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				468
Q9GGX6 UniProt NPD GO	RBL_CEDAT	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				467
Q33323 UniProt NPD GO	RBL_CEPOC	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				469
Q05798 UniProt NPD GO	RBL_CERDE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				394
P28391 UniProt NPD GO	RBL_CERGU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				459
Q05987 UniProt NPD GO	RBL_CERJA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
Q32016 UniProt NPD GO	RBL_CHELA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				441
P36484 UniProt NPD GO	RBL_CHIAL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				471
P48691 UniProt NPD GO	RBL_CHOCR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	mit	0	Plastid; chloroplast				467
P48692 UniProt NPD GO	RBL_CHRHI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	nuc	0	Plastid; chloroplast				459
P43228 UniProt NPD GO	RBL_CIBBA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				415
O20346 UniProt NPD GO	RBL_CLITE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
Q31948 UniProt NPD GO	RBL_CORAT	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				468
P28393 UniProt NPD GO	RBL_CORCA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
Q31983 UniProt NPD GO	RBL_CORFO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
Q33369 UniProt NPD GO	RBL_CORKO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P28394 UniProt NPD GO	RBL_CORMY	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
Q32040 UniProt NPD GO	RBL_COROB	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
Q32042 UniProt NPD GO	RBL_COROF	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P43229 UniProt NPD GO	RBL_CREBI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				406
P48696 UniProt NPD GO	RBL_CRYJA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				460
Q32026 UniProt NPD GO	RBL_CUNLA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				460
P28396 UniProt NPD GO	RBL_CYRRA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P48698 UniProt NPD GO	RBL_DATST	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				468
Q33406 UniProt NPD GO	RBL_DEPGR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				471
P28400 UniProt NPD GO	RBL_DILIN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
P28402 UniProt NPD GO	RBL_DRIWI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
P28404 UniProt NPD GO	RBL_DROBR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				435
P28405 UniProt NPD GO	RBL_DROCA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466

You are viewing entries 97701 to 97750 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.