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
Q71V17 UniProt NPD GO	HSP1_ANTGO	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71V13 UniProt NPD GO	HSP1_ANTHA	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
O18745 UniProt NPD GO	HSP1_ANTLA	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
Q71V16 UniProt NPD GO	HSP1_ANTLE	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71V14 UniProt NPD GO	HSP1_ANTME	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71V19 UniProt NPD GO	HSP1_ANTMI	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71V12 UniProt NPD GO	HSP1_ANTNA	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
P42129 UniProt NPD GO	HSP1_ANTST	Sperm protamine P1	0.81	+	nuc	0	Nucleus				62
Q71V22 UniProt NPD GO	HSP1_ANTSW	Sperm protamine P1	0.81	+	nuc	0	Nucleus				62
Q9GLQ0 UniProt NPD GO	HSP1_BETPE	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
P42131 UniProt NPD GO	HSP1_CAEFU	Sperm protamine P1	0.81	+	nuc	0	Nucleus				60
P67851 UniProt NPD GO	HSP1_DASAL	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
Q71VG7 UniProt NPD GO	HSP1_DASBY	Sperm protamine P1	0.81	+	mit	0	Nucleus (By similarity)				62
Q71VG8 UniProt NPD GO	HSP1_DASCR	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
P67850 UniProt NPD GO	HSP1_DASGE	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
P67834 UniProt NPD GO	HSP1_DASHA	Sperm protamine P1	0.81	+	nuc	0	Nucleus				60
P62485 UniProt NPD GO	HSP1_DASMA	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
P67830 UniProt NPD GO	HSP1_DASRO	Sperm protamine P1	0.81	+	mit	0	Nucleus				62
P67849 UniProt NPD GO	HSP1_DASSP	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
P67835 UniProt NPD GO	HSP1_DASVI	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
Q9GLQ6 UniProt NPD GO	HSP1_DENDO	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
P67838 UniProt NPD GO	HSP1_DENGO	Sperm protamine P1	0.81	+	nuc	0	Nucleus				60
Q9GLQ4 UniProt NPD GO	HSP1_DORVA	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
P67841 UniProt NPD GO	HSP1_DORVE	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
Q9GLQ1 UniProt NPD GO	HSP1_HYPMS	Sperm protamine P1	0.81	+	nuc	0	Nucleus				63
Q9GLQ2 UniProt NPD GO	HSP1_LAGHI	Sperm protamine P1	0.81	+	mit	0	Nucleus				64
P42137 UniProt NPD GO	HSP1_MACAG	Sperm protamine P1	0.81	+	nuc	0	Nucleus				60
P42138 UniProt NPD GO	HSP1_MACEU	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
P42139 UniProt NPD GO	HSP1_MACGI	Sperm protamine P1	0.81	+	nuc	0	Nucleus				60
Q9GLQ9 UniProt NPD GO	HSP1_MACPA	Sperm protamine P1	0.81	+	nuc	0	Nucleus				60
P67842 UniProt NPD GO	HSP1_MACRG	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
P67848 UniProt NPD GO	HSP1_MURLO	Sperm protamine P1	0.81	+	nuc	0	Nucleus				62
Q71V11 UniProt NPD GO	HSP1_MURRO	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71VH0 UniProt NPD GO	HSP1_MYOME	Sperm protamine P1	0.81	+	mit	0	Nucleus (By similarity)				62
Q71VG9 UniProt NPD GO	HSP1_MYOWA	Sperm protamine P1	0.81	+	mit	0	Nucleus (By similarity)				62
P67845 UniProt NPD GO	HSP1_MYRFA	Sperm protamine P1	0.81	+	nuc	0	Nucleus				62
P67852 UniProt NPD GO	HSP1_NEOLO	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
Q71VP7 UniProt NPD GO	HSP1_NINRI	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71VP5 UniProt NPD GO	HSP1_NINTI	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71VP6 UniProt NPD GO	HSP1_NINYV	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q9GLQ3 UniProt NPD GO	HSP1_ONCFR	Sperm protamine P1	0.81	+	nuc	0	Nucleus				60
P67839 UniProt NPD GO	HSP1_ONYUN	Sperm protamine P1	0.81	+	nuc	0	Nucleus				60
P67831 UniProt NPD GO	HSP1_PARAP	Sperm protamine P1	0.81	+	mit	0	Nucleus				62
O18768 UniProt NPD GO	HSP1_PARBI	Sperm protamine P1	0.81	+	mit	0	Nucleus				61
Q9GLQ5 UniProt NPD GO	HSP1_PERCO	Sperm protamine P1	0.81	+	nuc	0	Nucleus				59
Q9GLQ7 UniProt NPD GO	HSP1_PETXA	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
Q71V10 UniProt NPD GO	HSP1_PHACL	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
P67853 UniProt NPD GO	HSP1_PHADO	Sperm protamine P1	0.81	+	nuc	0	Nucleus				61
P67847 UniProt NPD GO	HSP1_PHATA	Sperm protamine P1	0.81	+	nuc	0	Nucleus				62
Q71VP4 UniProt NPD GO	HSP1_PLAMM	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62

You are viewing entries 8601 to 8650 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.