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
P80222 UniProt NPD GO	ADH1_ALLMI	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase, major)	0.01	-	cyt	0	Cytoplasm				374
P25405 UniProt NPD GO	ADH1A_UROHA	Alcohol dehydrogenase 1A (EC 1.1.1.1) (Alcohol dehydrogenase I-A) (ADH IA)	0.01	-	nuc	0	Cytoplasm				375
Q9P4C2 UniProt NPD GO	ADH2_KLUMA	Alcohol dehydrogenase 2 (EC 1.1.1.1) (Alcohol dehydrogenase II)	0.01	-	cyt	0	Cytoplasm				347
O13309 UniProt NPD GO	ADH2_PICST	Alcohol dehydrogenase 2 (EC 1.1.1.1) (Alcohol dehydrogenase II) (ADH 1)	0.01	-	nuc	0	Cytoplasm				348
Q09669 UniProt NPD GO	ADH4_SCHPO	Alcohol dehydrogenase 4 (EC 1.1.1.1) (Alcohol dehydrogenase IV)	0.01	-	mit	0					422
P00327 UniProt NPD GO	ADH1E_HORSE	Alcohol dehydrogenase E chain (EC 1.1.1.1)	0.01	-	mit	0	Cytoplasm			8ADH	374
P00328 UniProt NPD GO	ADH1S_HORSE	Alcohol dehydrogenase S chain (EC 1.1.1.1)	0.01	-	mit	0	Cytoplasm			1EE2	373
O70473 UniProt NPD GO	AK1A1_CRIGR	Alcohol dehydrogenase [NADP+] (EC 1.1.1.2) (Aldehyde reductase) (Aldo-keto reductase family 1 member ...	0.01	-	cyt	0					228
Q17335 UniProt NPD GO	ADHX_CAEEL	Alcohol dehydrogenase class 3 (EC 1.1.1.1) (Alcohol dehydrogenase class III) (S-(hydroxymethyl)gluta ...	0.01	-	mit	0	Cytoplasm (Potential)	cytoplasm [NAS]			384
Q96533 UniProt NPD GO	ADHX_ARATH	Alcohol dehydrogenase class 3 (EC 1.1.1.1) (Alcohol dehydrogenase class III) (S-(hydroxymethyl)gluta ...	0.01	-	cyt	0	Cytoplasm (Potential)				379
P93436 UniProt NPD GO	ADHX_ORYSA	Alcohol dehydrogenase class 3 (EC 1.1.1.1) (Alcohol dehydrogenase class III) (S-(hydroxymethyl)gluta ...	0.01	-	mit	0	Cytoplasm (Potential)				381
P80572 UniProt NPD GO	ADHX_PEA	Alcohol dehydrogenase class 3 (EC 1.1.1.1) (Alcohol dehydrogenase class III) (S-(hydroxymethyl)gluta ...	0.01	-	mit	0	Cytoplasm				378
P41682 UniProt NPD GO	ADH7_RAT	Alcohol dehydrogenase class 4 mu/sigma chain (EC 1.1.1.1) (Alcohol dehydrogenase class IV mu/sigma c ...	0.01	-	mit	0	Cytoplasm				374
P40394 UniProt NPD GO	ADH7_HUMAN	Alcohol dehydrogenase class 4 mu/sigma chain (EC 1.1.1.1) (Alcohol dehydrogenase class IV mu/sigma c ...	0.01	-	mit	0	Cytoplasm		600086	1D1T	374
Q64437 UniProt NPD GO	ADH7_MOUSE	Alcohol dehydrogenase class 4 mu/sigma chain (EC 1.1.1.1) (Alcohol dehydrogenase class IV mu/sigma c ...	0.01	-	mit	0	Cytoplasm				374
P28485 UniProt NPD GO	ADHR_DROER	Alcohol dehydrogenase-related 31 kDa protein (Fragment)	0.01	-	cyt	0					202
P08157 UniProt NPD GO	ALDH_EMENI	Aldehyde dehydrogenase (EC 1.2.1.3) (ALDDH)	0.01	-	cyt	0					497
P42041 UniProt NPD GO	ALDH_ALTAL	Aldehyde dehydrogenase (EC 1.2.1.3) (ALDDH) (Allergen Alt a 10) (Alt a X)	0.01	-	cyt	0	Cytoplasm (Probable)				497
P47771 UniProt NPD GO	ALDH2_YEAST	Aldehyde dehydrogenase [NAD(P)+] 1 (EC 1.2.1.5)	0.01	-	cyt	0	Cytoplasm (Potential)	cytoplasm [IDA]			506
Q28399 UniProt NPD GO	ALDH1_ELEED	Aldehyde dehydrogenase, cytosolic 1 (EC 1.2.1.3) (ALDH class 1) (ETA-crystallin)	0.01	-	cyt	0	Cytoplasm (By similarity)			1PEJ	501
Q29490 UniProt NPD GO	ALDH1_MACPR	Aldehyde dehydrogenase, cytosolic 1 (EC 1.2.1.3) (ALDH class 1) (ETA-crystallin)	0.01	-	cyt	0	Cytoplasm (By similarity)				501
Q5EA79 UniProt NPD GO	GALM_BOVIN	Aldose 1-epimerase (EC 5.1.3.3) (Galactose mutarotase)	0.01	-	cyt	0	Cytoplasm (Probable)				342
P80276 UniProt NPD GO	ALDR_PIG	Aldose reductase (EC 1.1.1.21) (AR) (Aldehyde reductase)	0.01	-	cyt	0	Cytoplasm			1EKO	315
Q60WT2 UniProt NPD GO	ACASE_CAEBR	Alkaline ceramidase (EC 3.5.1.23) (AlkCDase) (Alkaline acylsphingosine deacylase) (Alkaline N-acylsp ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				272
P83456 UniProt NPD GO	PPB_GADMO	Alkaline phosphatase (EC 3.1.3.1) (AP)	0.01	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor				477
P05186 UniProt NPD GO	PPBT_HUMAN	Alkaline phosphatase, tissue-nonspecific isozyme precursor (EC 3.1.3.1) (AP-TNAP) (Liver/bone/kidney ...	0.01	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor		241510		524
P08289 UniProt NPD GO	PPBT_RAT	Alkaline phosphatase, tissue-nonspecific isozyme precursor (EC 3.1.3.1) (AP-TNAP) (Liver/bone/kidney ...	0.01	-	end	0	Cell membrane; lipid-anchor; GPI-anchor				524
P09242 UniProt NPD GO	PPBT_MOUSE	Alkaline phosphatase, tissue-nonspecific isozyme precursor (EC 3.1.3.1) (AP-TNAP) (TNSALP)	0.01	-	end	0	Cell membrane; lipid-anchor; GPI-anchor				524
Q9NUN7 UniProt NPD GO	APHC_HUMAN	Alkaline phytoceramidase (EC 3.5.1.-) (aPHC) (Alkaline ceramidase) (Alkaline dihydroceramidase SB89) ...	0.01	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				267
P83454 UniProt NPD GO	NCP3_COPCM	Alkaline protease Cc3 (EC 3.4.21.-) (Fragment)	0.01	-		0					12
P82678 UniProt NPD GO	ALLC_CHLRE	Allantoicase (EC 3.5.3.4) (Allantoate amidinohydrolase) (Fragment)	0.01	-		0					9
Q7M1G9 UniProt NPD GO	ALL2_ARTVU	Allergen Art v 2 (Art v II) (Allergen Ag7) (Fragments)	0.01	-	cyt	0					71
Q5VFH6 UniProt NPD GO	ALL4_FELCA	Allergen Fel d 4 precursor	0.01	-	exc	0	Secreted protein				186
P81010 UniProt NPD GO	FUSS_FUSSO	Allergen Fus s I3596* (Fragment)	0.01	-		0					8
P83412 UniProt NPD GO	AFN_CALVI	Alloferon-1 [Contains: Alloferon-2]	0.01	-		0	Secreted protein				13
P97277 UniProt NPD GO	A1AT_MESAU	Alpha-1-antitrypsin precursor (Alpha-1 protease inhibitor) (Alpha-1-antiproteinase)	0.01	-	end	0	Secreted protein (By similarity)				413
P39090 UniProt NPD GO	A1BG_EQUAS	Alpha-1B-glycoprotein (Alpha-1-B glycoprotein) (Postalbumin) (Fragment)	0.01	-		0	Secreted protein				20
P20738 UniProt NPD GO	A2M_PACLE	Alpha-2-macroglobulin homolog (Alpha-2-M) (Fragments)	0.01	-	cyt	0	Secreted protein				32
P49274 UniProt NPD GO	AMY_DERPT	Alpha-amylase (EC 3.2.1.1) (Allergen Der p 4) (Der p IV) (Fragment)	0.01	-		0	Secreted protein				19
Q02905 UniProt NPD GO	AMYA_ASPAW	Alpha-amylase A precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase A)	0.01	-	mit	0					498
P0C1B3 UniProt NPD GO	AMYA1_ASPOR	Alpha-amylase A type-1/2 precursor (EC 3.2.1.1) (Taka-amylase A) (TAA) (1,4-alpha-D-glucan glucanohy ...	0.01	-	end	0				7TAA	499
P0C1B4 UniProt NPD GO	AMYA3_ASPOR	Alpha-amylase A type-3 precursor (EC 3.2.1.1) (Taka-amylase A) (TAA) (1,4-alpha-D-glucan glucanohydr ...	0.01	-	end	0					499
Q02906 UniProt NPD GO	AMYB_ASPAW	Alpha-amylase B precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase B)	0.01	-	end	0					499
P83048 UniProt NPD GO	IAA_SECCE	Alpha-amylase inhibitor (Fragment)	0.01	-	cyt	0	Secreted protein				25
P01083 UniProt NPD GO	IAA2_WHEAT	Alpha-amylase inhibitor 0.28 precursor (CIII) (WMAI-1)	0.01	-	vac	1 *	Secreted protein				153
P01084 UniProt NPD GO	IAA5_WHEAT	Alpha-amylase inhibitor 0.53	0.01	-	cyt	0	Secreted protein				124
P13691 UniProt NPD GO	IAA2_HORVU	Alpha-amylase inhibitor BDAI-I precursor	0.01	-	exc	0	Secreted protein				152
P27935 UniProt NPD GO	AMY2A_ORYSA	Alpha-amylase isozyme 2A precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (Alpha-amylase ...	0.01	-	exc	0					445
P27933 UniProt NPD GO	AMY3D_ORYSA	Alpha-amylase isozyme 3D precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.01	-	vac	1 *					436
P27934 UniProt NPD GO	AMY3E_ORYSA	Alpha-amylase isozyme 3E precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.01	-	exc	1 *					437

You are viewing entries 86651 to 86700 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.