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
P14754 UniProt NPD GO	SERA_MANSE	Alaserpin precursor (Serpin-1)	0.00	-	end	0	Secreted protein; extracellular space			1SEK	392
Q9ZQX0 UniProt NPD GO	ALB1_GLYSO	Albumin-1 precursor (A1) [Contains: Albumin-1 chain b (A1b) (Leginsulin); Albumin-1 chain a (A1a)]	0.00	-	nuc	0					119
Q39837 UniProt NPD GO	ALB1_SOYBN	Albumin-1 precursor (A1) [Contains: Albumin-1 chain b (A1b) (Leginsulin); Albumin-1 chain a (A1a)]	0.00	-	nuc	0				1JU8	119
Q96474 UniProt NPD GO	ALB1_LUPAN	Albumin-1 precursor (A1) [Contains: Albumin-1 chain b (A1b) (Leginsulin); Albumin-1 chain a (A1a)] ( ...	0.00	-	mit	0					81
P06525 UniProt NPD GO	ADH1_ARATH	Alcohol dehydrogenase (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm				379
Q00671 UniProt NPD GO	ADH_DROMM	Alcohol dehydrogenase (EC 1.1.1.1)	0.00	-	cyt	0					253
P23278 UniProt NPD GO	ADH_DROSL	Alcohol dehydrogenase (EC 1.1.1.1)	0.00	-	cyt	0					253
P17648 UniProt NPD GO	ADH_FRAAN	Alcohol dehydrogenase (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm				380
P48977 UniProt NPD GO	ADH_MALDO	Alcohol dehydrogenase (EC 1.1.1.1)	0.00	-	mit	0	Cytoplasm				380
P00332 UniProt NPD GO	ADH_SCHPO	Alcohol dehydrogenase (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm				350
P26325 UniProt NPD GO	ADH1_GADCA	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.00	-	nuc	0	Cytoplasm			1CDO	375
P05336 UniProt NPD GO	ADH1_HORVU	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm				379
Q07288 UniProt NPD GO	ADH1_KLUMA	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm				348
P00333 UniProt NPD GO	ADH1_MAIZE	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm				379
P20306 UniProt NPD GO	ADH1_ORYSA	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA]			379
P12886 UniProt NPD GO	ADH1_PEA	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm				380
P14673 UniProt NPD GO	ADH1_SOLTU	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.00	-	mit	0	Cytoplasm				380
P13603 UniProt NPD GO	ADH1_TRIRP	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.00	-	mit	0	Cytoplasm				380
P43067 UniProt NPD GO	ADH1_CANAL	Alcohol dehydrogenase 1 (EC 1.1.1.1) (40 kDa allergen) (Allergen Cand a 1) (Can a 1) (Can a I)	0.00	-	cyt	0	Cytoplasm (Probable)				350
P14219 UniProt NPD GO	ADH1_PENAM	Alcohol dehydrogenase 1 (EC 1.1.1.1) (ADH slow-allele)	0.00	-	cyt	0	Cytoplasm				379
P41747 UniProt NPD GO	ADH1_ASPFL	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase I)	0.00	-	cyt	0	Cytoplasm				349
P20369 UniProt NPD GO	ADH1_KLULA	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase I)	0.00	-	cyt	0	Cytoplasm				350
Q9P6C8 UniProt NPD GO	ADH1_NEUCR	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase I)	0.00	-	cyt	0	Cytoplasm				353
P00330 UniProt NPD GO	ADH1_YEAST	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase I) (YADH-1)	0.00	-	cyt	0	Cytoplasm				347
Q07264 UniProt NPD GO	ADH1_ZEALU	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Fragment)	0.00	-	cyt	0	Cytoplasm				293
P28469 UniProt NPD GO	ADH1A_MACMU	Alcohol dehydrogenase 1A (EC 1.1.1.1) (Alcohol dehydrogenase alpha subunit)	0.00	-	mit	0	Cytoplasm				374
Q5RBP7 UniProt NPD GO	ADH1A_PONPY	Alcohol dehydrogenase 1A (EC 1.1.1.1) (Alcohol dehydrogenase alpha subunit)	0.00	-	nuc	0	Cytoplasm				374
P00325 UniProt NPD GO	ADH1B_HUMAN	Alcohol dehydrogenase 1B (EC 1.1.1.1) (Alcohol dehydrogenase beta subunit)	0.00	-	nuc	0	Cytoplasm		103720	3HUD	374
Q5R1W2 UniProt NPD GO	ADH1B_PANTR	Alcohol dehydrogenase 1B (EC 1.1.1.1) (Alcohol dehydrogenase beta subunit)	0.00	-	nuc	0	Cytoplasm (By similarity)				374
P14139 UniProt NPD GO	ADH1B_PAPHA	Alcohol dehydrogenase 1B (EC 1.1.1.1) (Alcohol dehydrogenase subunit beta)	0.00	-	nuc	0	Cytoplasm				374
P00326 UniProt NPD GO	ADH1G_HUMAN	Alcohol dehydrogenase 1C (EC 1.1.1.1) (Alcohol dehydrogenase gamma subunit)	0.00	-	mit	0	Cytoplasm	cytoplasm [NAS]	103730	1U3W	374
O97959 UniProt NPD GO	ADH1G_PAPHA	Alcohol dehydrogenase 1C (EC 1.1.1.1) (Alcohol dehydrogenase gamma subunit)	0.00	-	mit	0	Cytoplasm (By similarity)				374
O94038 UniProt NPD GO	ADH2_CANAL	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm (Probable)				348
P10847 UniProt NPD GO	ADH2_HORVU	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm				373
P28032 UniProt NPD GO	ADH2_LYCES	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.00	-	mit	0	Cytoplasm				380
P04707 UniProt NPD GO	ADH2_MAIZE	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm				379
P18332 UniProt NPD GO	ADH2_ORYSA	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA]			379
P14674 UniProt NPD GO	ADH2_SOLTU	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.00	-	mit	0	Cytoplasm				380
P49383 UniProt NPD GO	ADH2_KLULA	Alcohol dehydrogenase 2 (EC 1.1.1.1) (Alcohol dehydrogenase II)	0.00	-	cyt	0	Cytoplasm (By similarity)				348
P00331 UniProt NPD GO	ADH2_YEAST	Alcohol dehydrogenase 2 (EC 1.1.1.1) (Alcohol dehydrogenase II) (YADH-2)	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA]			347
P10848 UniProt NPD GO	ADH3_HORVU	Alcohol dehydrogenase 3 (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm				379
P14675 UniProt NPD GO	ADH3_SOLTU	Alcohol dehydrogenase 3 (EC 1.1.1.1)	0.00	-	mit	0	Cytoplasm				380
Q24857 UniProt NPD GO	ADH3_ENTHI	Alcohol dehydrogenase 3 (EC 1.1.1.2) (ADH)	0.00	-	cyt	0					395
P08319 UniProt NPD GO	ADH4_HUMAN	Alcohol dehydrogenase 4 (EC 1.1.1.1) (Alcohol dehydrogenase class II pi chain)	0.00	-	mit	0	Cytoplasm		103740		379
P80468 UniProt NPD GO	ADH4_STRCA	Alcohol dehydrogenase 4 (EC 1.1.1.1) (Alcohol dehydrogenase class II)	0.00	-	nuc	0	Cytoplasm				379
P28332 UniProt NPD GO	ADH6_HUMAN	Alcohol dehydrogenase 6 (EC 1.1.1.1)	0.00	-	end	0	Cytoplasm		103735		368
Q5R7Z8 UniProt NPD GO	ADH6_PONPY	Alcohol dehydrogenase 6 (EC 1.1.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				375
Q5XI95 UniProt NPD GO	ADH6_RAT	Alcohol dehydrogenase 6 (EC 1.1.1.1)	0.00	-	nuc	0	Cytoplasm				376
P41681 UniProt NPD GO	ADH6_PERMA	Alcohol dehydrogenase 6 (EC 1.1.1.1) (Alcohol dehydrogenase 2) (ADH-2)	0.00	-	nuc	0	Cytoplasm				375
P49384 UniProt NPD GO	ADH3_KLULA	Alcohol dehydrogenase III, mitochondrial precursor (EC 1.1.1.1)	0.00	-	mit	0	Mitochondrion; mitochondrial matrix				374

You are viewing entries 92551 to 92600 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.