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
P84461 UniProt NPD GO	HCY1_LIODE	Hemocyanin subunit 1 (Fragment)	0.01	-		0	Secreted protein; extracellular space				12
P82297 UniProt NPD GO	HCY2_HOMAM	Hemocyanin subunit 2 (Fragment)	0.01	-	nuc	0	Secreted protein; extracellular space				30
P82298 UniProt NPD GO	HCY3_HOMAM	Hemocyanin subunit 3 (Fragment)	0.01	-	cyt	0	Secreted protein; extracellular space				26
P82299 UniProt NPD GO	HCY4_HOMAM	Hemocyanin subunit 4 (Fragment)	0.01	-	cyt	0	Secreted protein; extracellular space				22
P82305 UniProt NPD GO	HCY4_MAISQ	Hemocyanin subunit 4 (Fragment)	0.01	-	cyt	0	Secreted protein; extracellular space				21
P82301 UniProt NPD GO	HCY6_HOMAM	Hemocyanin subunit 6 (Fragment)	0.01	-		0	Secreted protein; extracellular space				20
Q95P07 UniProt NPD GO	HCYD_SCUCO	Hemocyanin subunit D precursor	0.01	-	exc	0	Secreted protein; extracellular space	extracellular region [IDA]			668
P82312 UniProt NPD GO	HCY2_PANJA	Hemocyanin subunit II (Fragment)	0.01	-		0	Secreted protein; extracellular space				20
P82313 UniProt NPD GO	HCY3_PANJA	Hemocyanin subunit III (Fragment)	0.01	-		0	Secreted protein; extracellular space				19
Q42665 UniProt NPD GO	HBPA_CASGL	Hemoglobin A	0.01	-	cyt	0					151
P83133 UniProt NPD GO	HBB_ALDEL	Hemoglobin A/D subunit beta (Hemoglobin A/D beta chain)	0.01	-	cyt	0				1WMU	146
P84205 UniProt NPD GO	HBAA_GYMUN	Hemoglobin anodic subunit alpha (Hemoglobin anodic alpha chain)	0.01	-	cyt	0					142
P84206 UniProt NPD GO	HBBA_GYMUN	Hemoglobin anodic subunit beta (Hemoglobin anodic beta chain)	0.01	-	cyt	0					147
P80727 UniProt NPD GO	HBBC_ANGAN	Hemoglobin cathodic subunit beta (Hemoglobin cathodic beta chain)	0.01	-	cyt	0					146
P83478 UniProt NPD GO	HBBC_CONCO	Hemoglobin cathodic subunit beta (Hemoglobin cathodic beta chain)	0.01	-	mit	0					146
P84204 UniProt NPD GO	HBBC_GYMUN	Hemoglobin cathodic subunit beta (Hemoglobin cathodic beta chain)	0.01	-	nuc	0					146
P82316 UniProt NPD GO	HBBC_HOPLI	Hemoglobin cathodic subunit beta (Hemoglobin cathodic beta chain) (Hb(Ca) beta chain)	0.01	-	cyt	0					146
P02081 UniProt NPD GO	HBBF_BOVIN	Hemoglobin fetal subunit beta (Hemoglobin beta chain, fetal) (Beta-globin, fetal) (Hemoglobin gamma ...	0.01	-	cyt	0					145
P02082 UniProt NPD GO	HBBF_CAPHI	Hemoglobin fetal subunit beta (Hemoglobin beta chain, fetal) (Beta-globin, fetal) (Hemoglobin gamma ...	0.01	-	cyt	0					145
P02083 UniProt NPD GO	HBBF_SHEEP	Hemoglobin fetal subunit beta (Hemoglobin beta chain, fetal) (Beta-globin, fetal) (Hemoglobin gamma ...	0.01	-	cyt	0					145
P02137 UniProt NPD GO	HBBL_XENLA	Hemoglobin larval subunit beta-1 (Hemoglobin beta-1 chain, larval) (Beta-1-globin)	0.01	-	nuc	0					146
P18970 UniProt NPD GO	HBA_AILME	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P01999 UniProt NPD GO	HBA_ALLMI	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	mit	0					141
P84216 UniProt NPD GO	HBA_BATEA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P60529 UniProt NPD GO	HBA_CANFA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P60530 UniProt NPD GO	HBA_CANLA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P02017 UniProt NPD GO	HBA_CATCL	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					142
P80270 UniProt NPD GO	HBA_CHEKU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	mit	0					142
P60523 UniProt NPD GO	HBA_CHRBR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0				1FHJ	141
P01998 UniProt NPD GO	HBA_CRONI	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	mit	0					141
P23016 UniProt NPD GO	HBA_CYGMA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					142
P11753 UniProt NPD GO	HBA_CYNSP	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P56691 UniProt NPD GO	HBA_DASAK	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	nuc	0				1CG8	141
P01973 UniProt NPD GO	HBA_LAMGL	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P67815 UniProt NPD GO	HBA_LAMGU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P67816 UniProt NPD GO	HBA_LAMPA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P07425 UniProt NPD GO	HBA_LAMVI	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P56250 UniProt NPD GO	HBA_LEIXA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0				1SPG	143
P15448 UniProt NPD GO	HBA_MELCA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P01942 UniProt NPD GO	HBA_MOUSE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0		mitochondrion [IDA]			141
P10778 UniProt NPD GO	HBA_ODORO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P01979 UniProt NPD GO	HBA_ORNAN	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P82990 UniProt NPD GO	HBA_PAGBO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					142
P18977 UniProt NPD GO	HBA_PROLO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P10885 UniProt NPD GO	HBA_PTEBR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P11251 UniProt NPD GO	HBA_SALSA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					142
P11748 UniProt NPD GO	HBA_THUTH	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					143
P07414 UniProt NPD GO	HBA_TRIIN	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P18978 UniProt NPD GO	HBA_TURTR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141
P21200 UniProt NPD GO	HBA_VULVU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.01	-	cyt	0					141

You are viewing entries 88651 to 88700 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.