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
P80044 UniProt NPD GO	HBB_PAGBE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0				1S5Y	146
Q6Y239 UniProt NPD GO	HBB_PAGMA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					147
P04244 UniProt NPD GO	HBB_PANPO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P07406 UniProt NPD GO	HBB_PASMO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P10782 UniProt NPD GO	HBB_PHACA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	nuc	0					146
P02113 UniProt NPD GO	HBB_PHACO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02121 UniProt NPD GO	HBB_PHORU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	nuc	0					146
P09909 UniProt NPD GO	HBB_PHOVI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02067 UniProt NPD GO	HBB_PIG	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0				2PGH	146
P23020 UniProt NPD GO	HBB_PROCR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02086 UniProt NPD GO	HBB_PROHA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P18989 UniProt NPD GO	HBB_PROLO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P21668 UniProt NPD GO	HBB_PSIKR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	mit	0					146
P02135 UniProt NPD GO	HBB_RANCA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					140
P02134 UniProt NPD GO	HBB_RANES	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					140
P21380 UniProt NPD GO	HBB_RANTA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					145
P02124 UniProt NPD GO	HBB_RHEAM	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	nuc	0					146
Q91473 UniProt NPD GO	HBB_SALSA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					147
Q2KPA4 UniProt NPD GO	HBB_SCAAQ	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
Q2KPA3 UniProt NPD GO	HBB_SCAOR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
O13163 UniProt NPD GO	HBB_SILAS	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					147
P02090 UniProt NPD GO	HBB_SPAEH	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P09421 UniProt NPD GO	HBB_SPECI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P07409 UniProt NPD GO	HBB_SQUAC	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					142
P02123 UniProt NPD GO	HBB_STRCA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
Q7LZB9 UniProt NPD GO	HBB_STROE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	mit	0					146
P02126 UniProt NPD GO	HBB_STUVU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02061 UniProt NPD GO	HBB_TALEU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P11749 UniProt NPD GO	HBB_THUTH	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
O93351 UniProt NPD GO	HBB_TREHA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P07415 UniProt NPD GO	HBB_TRIIN	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P68062 UniProt NPD GO	HBB_TRIOC	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02052 UniProt NPD GO	HBB_TUPGL	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P14524 UniProt NPD GO	HBB_TURME	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P68011 UniProt NPD GO	HBB_URSMA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P68013 UniProt NPD GO	HBB_URSML	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P68012 UniProt NPD GO	HBB_URSTH	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P07411 UniProt NPD GO	HBB_VULGR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	nuc	0					146
P21201 UniProt NPD GO	HBB_VULVU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P83761 UniProt NPD GO	HBB_OREMO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin) (Fragment)	0.01	-		0					14
P02094 UniProt NPD GO	HBB_MESAU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin) (Hemoglobin beta-major chain)	0.01	-	cyt	0					146
P82345 UniProt NPD GO	HBB0_PAGBO	Hemoglobin subunit beta-0 (Hemoglobin beta-0 chain) (Beta-0-globin) (Hb 0)	0.01	-	cyt	0					146
P83272 UniProt NPD GO	HBB1_ANAMI	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.01	-	cyt	0					146
Q1AGS7 UniProt NPD GO	HBB1_BORSA	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.01	-	cyt	0					146
P23017 UniProt NPD GO	HBB1_CYGMA	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.01	-	cyt	0					146
P84610 UniProt NPD GO	HBB1_GADMO	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.01	-	cyt	0					146
P83612 UniProt NPD GO	HBB1_GOBGI	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.01	-	cyt	0		hemoglobin complex [NAS]			146
P18987 UniProt NPD GO	HBB1_IGUIG	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.01	-	cyt	0					146
P68050 UniProt NPD GO	HBB1_PANLE	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.01	-	cyt	0					146
P68049 UniProt NPD GO	HBB1_PANON	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.01	-	cyt	0					146

You are viewing entries 88801 to 88850 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.