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
P07246 UniProt NPD GO	ADH3_YEAST	Alcohol dehydrogenase III, mitochondrial precursor (EC 1.1.1.1) (YADH-3)	0.00	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA] soluble fraction [IDA]			375
P12711 UniProt NPD GO	ADHX_RAT	Alcohol dehydrogenase class 3 (EC 1.1.1.1) (Alcohol dehydrogenase class III) (Alcohol dehydrogenase ...	0.00	-	nuc	0	Cytoplasm				373
P28474 UniProt NPD GO	ADHX_MOUSE	Alcohol dehydrogenase class 3 (EC 1.1.1.1) (Alcohol dehydrogenase class III) (Alcohol dehydrogenase ...	0.00	-	nuc	0	Cytoplasm			1OTQ	373
P81431 UniProt NPD GO	ADHX_OCTVU	Alcohol dehydrogenase class 3 (EC 1.1.1.1) (Alcohol dehydrogenase class III) (S-(hydroxymethyl)gluta ...	0.00	-	mit	0	Cytoplasm				378
P80467 UniProt NPD GO	ADHX_UROHA	Alcohol dehydrogenase class 3 (EC 1.1.1.1) (Alcohol dehydrogenase class III) (S-(hydroxymethyl)gluta ...	0.00	-	nuc	0	Cytoplasm				373
P80360 UniProt NPD GO	ADHX_MYXGL	Alcohol dehydrogenase class 3 (EC 1.1.1.1) (Alcohol dehydrogenase class III) (S-(hydroxymethyl)gluta ...	0.00	-	nuc	0	Cytoplasm				376
P79896 UniProt NPD GO	ADHX_SPAAU	Alcohol dehydrogenase class 3 (EC 1.1.1.1) (Alcohol dehydrogenase class III) (S-(hydroxymethyl)gluta ...	0.00	-	nuc	0	Cytoplasm (Potential)				376
P93629 UniProt NPD GO	ADHX_MAIZE	Alcohol dehydrogenase class 3 (EC 1.1.1.1) (Alcohol dehydrogenase class III) (S-(hydroxymethyl)gluta ...	0.00	-	mit	0	Cytoplasm (Potential)				381
P46415 UniProt NPD GO	ADHX_DROME	Alcohol dehydrogenase class 3 (EC 1.1.1.1) (Alcohol dehydrogenase class III) (S-(hydroxymethyl)gluta ...	0.00	-	nuc	0					378
P81600 UniProt NPD GO	ADHH_GADMO	Alcohol dehydrogenase class 3 H chain (EC 1.1.1.1) (Alcohol dehydrogenase class III H chain) (S-(hyd ...	0.00	-	nuc	0	Cytoplasm				375
P81601 UniProt NPD GO	ADHL_GADMO	Alcohol dehydrogenase class 3 L chain (EC 1.1.1.1) (Alcohol dehydrogenase class III L chain) (S-(hyd ...	0.00	-	nuc	0	Cytoplasm				375
P19854 UniProt NPD GO	ADHX_HORSE	Alcohol dehydrogenase class 3 chain (EC 1.1.1.1) (Alcohol dehydrogenase class III chain) (S-(hydroxy ...	0.00	-	nuc	0	Cytoplasm				373
O19053 UniProt NPD GO	ADHX_RABIT	Alcohol dehydrogenase class 3 chain (EC 1.1.1.1) (Alcohol dehydrogenase class III chain) (S-(hydroxy ...	0.00	-	nuc	0	Cytoplasm				373
P11766 UniProt NPD GO	ADHX_HUMAN	Alcohol dehydrogenase class 3 chi chain (EC 1.1.1.1) (Alcohol dehydrogenase class III chi chain) (S- ...	0.00	-	nuc	0	Cytoplasm		103710	1TEH	373
O46649 UniProt NPD GO	ADHP_RABIT	Alcohol dehydrogenase class II isozyme 1 (EC 1.1.1.1)	0.00	-	mit	0	Cytoplasm				378
Q07587 UniProt NPD GO	ADHR_DROLE	Alcohol dehydrogenase-related 31 kDa protein	0.00	-	cyt	0					269
P28487 UniProt NPD GO	ADHR_DROYA	Alcohol dehydrogenase-related 31 kDa protein (Fragment)	0.00	-	cyt	0					32
P04842 UniProt NPD GO	ALOX_PICPA	Alcohol oxidase (EC 1.1.3.13) (AOX) (Methanol oxidase) (MOX) (Fragment)	0.00	-	mit	0	Peroxisome				33
O74187 UniProt NPD GO	ALDH_AGABI	Aldehyde dehydrogenase (EC 1.2.1.3) (ALDDH)	0.00	-	cyt	0					500
P41751 UniProt NPD GO	ALDH_ASPNG	Aldehyde dehydrogenase (EC 1.2.1.3) (ALDDH)	0.00	-	cyt	0					497
P83402 UniProt NPD GO	AL7A1_ACASC	Aldehyde dehydrogenase family 7 member A1 (EC 1.2.1.3) (Antiquitin-1) (Fragment)	0.00	-		0					18
P84463 UniProt NPD GO	AL7A1_CTEID	Aldehyde dehydrogenase family 7 member A1 (EC 1.2.1.3) (Antiquitin-1) (Fragment)	0.00	-	nuc	0					21
Q8K157 UniProt NPD GO	GALM_MOUSE	Aldose 1-epimerase (EC 5.1.3.3) (Galactose mutarotase)	0.00	-	cyt	0	Cytoplasm (Probable)				342
Q5R8U1 UniProt NPD GO	GALM_PONPY	Aldose 1-epimerase (EC 5.1.3.3) (Galactose mutarotase)	0.00	-	cyt	0	Cytoplasm (Probable)				342
Q66HG4 UniProt NPD GO	GALM_RAT	Aldose 1-epimerase (EC 5.1.3.3) (Galactose mutarotase)	0.00	-	cyt	0	Cytoplasm (Probable)				342
Q96C23 UniProt NPD GO	GALM_HUMAN	Aldose 1-epimerase (EC 5.1.3.3) (Galactose mutarotase) (BLOCK25 protein)	0.00	-	cyt	0	Cytoplasm (Probable)		608883	1SO0	342
O45145 UniProt NPD GO	ACASE_CAEEL	Alkaline ceramidase (EC 3.5.1.23) (AlkCDase) (Alkaline acylsphingosine deacylase) (Alkaline N-acylsp ...	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				272
P32375 UniProt NPD GO	ALN_YEAST	Allantoinase (EC 3.5.2.5)	0.00	-	cyt	0		intracellular [IC]			460
P83885 UniProt NPD GO	ANIS4_ANISI	Allergen Ani s 4 (Fragment)	0.00	-		0	Secreted protein				14
P81943 UniProt NPD GO	ALL5_APIGR	Allergen Api g 5 (Fragments)	0.00	-	cyt	0					86
O60022 UniProt NPD GO	AL15_ASPFU	Allergen Asp f 15 precursor (Asp f 13)	0.00	-	exc	0	Secreted protein (Potential)				152
Q5ULZ4 UniProt NPD GO	FRAA_FRAAN	Allergen Fra a 1 (Fragments)	0.00	-	cyt	0					100
P83886 UniProt NPD GO	ALLI_ALLSA	Allimin (Fragment)	0.00	-	cyt	0					35
P84796 UniProt NPD GO	ALLIU_ALLSA	Alliumin (Fragment)	0.00	-		0					10
P00316 UniProt NPD GO	PHAA_CYAPA	Allophycocyanin alpha chain	0.00	-	cyt	0	Plastid; cyanelle				160
P51262 UniProt NPD GO	PHAA_PORPU	Allophycocyanin alpha chain	0.00	-	cyt	0	Plastid; chloroplast				160
P59856 UniProt NPD GO	PHAA_PORYE	Allophycocyanin alpha chain	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen. Phycobilisome core			1KN1	160
P38026 UniProt NPD GO	A1AT_CHIVI	Alpha-1-antiproteinase (Alpha-1-antitrypsin) (Alpha-1-proteinase inhibitor) (Fragment)	0.00	-	cyt	0	Secreted protein				30
P83168 UniProt NPD GO	A2AP_STRCA	Alpha-2-antiplasmin (Alpha-2-plasmin inhibitor) (Alpha-2-PI) (Alpha-2-AP) (Fragment)	0.00	-		0	Secreted protein				11
P30800 UniProt NPD GO	A2M_OCTVU	Alpha-2-macroglobulin homolog (Alpha-2-M) (Fragment)	0.00	-		0	Secreted protein				18
P00687 UniProt NPD GO	AMYS_MOUSE	Alpha-amylase 1 precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (Salivary and hepatic a ...	0.00	-	exc	0	Secreted protein				511
P09107 UniProt NPD GO	AMY_TRICA	Alpha-amylase precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (Fragment)	0.00	-	pox	1 *					489
P04748 UniProt NPD GO	AMY4_HORVU	Alpha-amylase type B isozyme (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (Clone 103) (Fragmen ...	0.00	-	cyt	0					153
P04063 UniProt NPD GO	AMY2_HORVU	Alpha-amylase type B isozyme precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (AMY2-2) ( ...	0.00	-	exc	1 *				1BG9	427
P04747 UniProt NPD GO	AMY3_HORVU	Alpha-amylase type B isozyme precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (Clone PHV ...	0.00	-	vac	1 *					368
P13867 UniProt NPD GO	IAAT_MAIZE	Alpha-amylase/trypsin inhibitor (Antifungal protein)	0.00	-	mit	0					206
P34951 UniProt NPD GO	IAAC_HORVU	Alpha-amylase/trypsin inhibitor CMc (Chloroform/methanol-soluble protein CMc) (Fragment)	0.00	-	cyt	0	Secreted protein				35
P56639 UniProt NPD GO	CXA1_CONAL	Alpha-conotoxin AuIA	0.00	-		0	Secreted protein				16
P56640 UniProt NPD GO	CXA2_CONAL	Alpha-conotoxin AuIB	0.00	-		0	Secreted protein			1MXP	15
P50984 UniProt NPD GO	CXAA_CONPE	Alpha-conotoxin PnIA (Alpha-PnIA)	0.00	-		0	Secreted protein			2BR8	16

You are viewing entries 92601 to 92650 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.