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
Q00670 UniProt NPD GO	ADH_DROCR	Alcohol dehydrogenase (EC 1.1.1.1)	0.04	-	cyt	0					254
P25988 UniProt NPD GO	ADH_SCAAL	Alcohol dehydrogenase (EC 1.1.1.1)	0.04	-	cyt	0					254
P48586 UniProt NPD GO	ADH1_DROMN	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.04	-	cyt	0					253
P23991 UniProt NPD GO	ADH1_CHICK	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase I) (ADH-1)	0.04	-	nuc	0	Cytoplasm				375
P19631 UniProt NPD GO	ADH1_COTJA	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase alpha subunit) (ADH3)	0.04	-	nuc	0	Cytoplasm				375
P50578 UniProt NPD GO	AK1A1_PIG	Alcohol dehydrogenase [NADP+] (EC 1.1.1.2) (Aldehyde reductase) (Aldo-keto reductase family 1 member ...	0.04	-	cyt	0				2AO0	324
Q09007 UniProt NPD GO	ADHR_DROGU	Alcohol dehydrogenase-related 31 kDa protein	0.04	-	cyt	0					279
Q9UUN9 UniProt NPD GO	ALD2_SPOSA	Aldehyde reductase 2 (EC 1.1.1.2) (Aldehyde reductase II) (ARII)	0.04	-	nuc	0				1ZZE	342
O60218 UniProt NPD GO	AK1BA_HUMAN	Aldo-keto reductase family 1 member B10 (EC 1.1.1.-) (Aldose reductase-like) (ARL-1) (Small intestin ...	0.04	-	cyt	0	Cytoplasm (Probable)		604707		316
P82809 UniProt NPD GO	AK1CD_MESAU	Aldo-keto reductase family 1 member C13 (EC 1.1.1.-) (Morphine 6-dehydrogenase) (EC 1.1.1.218)	0.04	-	cyt	0					322
P21300 UniProt NPD GO	ALD1_MOUSE	Aldose reductase-related protein 1 (EC 1.1.1.21) (AR) (Aldehyde reductase) (VAS deferens androgen-de ...	0.04	-	cyt	0	Cytoplasm (By similarity)				315
Q92058 UniProt NPD GO	PPBT_CHICK	Alkaline phosphatase, tissue-nonspecific isozyme precursor (EC 3.1.3.1) (AP-TNAP) (Liver/bone/kidney ...	0.04	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				519
P83610 UniProt NPD GO	ALP_FUSCU	Alkaline proteinase (EC 3.4.21.-) (ALP) (Fragments)	0.04	-	cyt	0	Secreted protein (By similarity)				62
P18407 UniProt NPD GO	ALLC_NEUCR	Allantoicase (EC 3.5.3.4)	0.04	-	cyt	0					354
P00314 UniProt NPD GO	PHAA_GALSU	Allophycocyanin alpha chain	0.04	-	cyt	0	Plastid; chloroplast				161
P51261 UniProt NPD GO	PHAB_PORPU	Allophycocyanin beta chain	0.04	-	cyt	0	Plastid; chloroplast				161
Q6PD74 UniProt NPD GO	P34_HUMAN	Alpha- and gamma-adaptin-binding protein p34	0.04	-	vac	0					315
Q9R0Z7 UniProt NPD GO	P34_RAT	Alpha- and gamma-adaptin-binding protein p34	0.04	-	cyt	0					315
Q6CN27 UniProt NPD GO	ALG10_KLULA	Alpha-1,2 glucosyltransferase ALG10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10) (Dolichyl-phosp ...	0.04	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				533
P38028 UniProt NPD GO	A1AT1_HORSE	Alpha-1-antiproteinase 1 (Alpha-1-antitrypsin 1) (Alpha-1-proteinase inhibitor 1) (SPI1) (Fragments) ...	0.04	-	nuc	0	Secreted protein				53
P23035 UniProt NPD GO	A1AF_RABIT	Alpha-1-antiproteinase F precursor (Alpha-1-antitrypsin) (Alpha-1-proteinase inhibitor) (APF)	0.04	-	end	0	Secreted protein				413
Q64118 UniProt NPD GO	A1AT_MERUN	Alpha-1-antitrypsin precursor (Alpha-1 protease inhibitor) (Alpha-1-antiproteinase)	0.04	-	end	0	Secreted protein (By similarity)				406
P50447 UniProt NPD GO	A1AT_PIG	Alpha-1-antitrypsin precursor (Alpha-1 protease inhibitor) (Alpha-1-antiproteinase)	0.04	-	end	1 *	Secreted protein				421
O54757 UniProt NPD GO	ALMM_TAMSI	Alpha-1-antitrypsin-like protein CM55-MM precursor	0.04	-	end	0	Secreted protein (By similarity)				413
P39092 UniProt NPD GO	A1BG_PIG	Alpha-1B-glycoprotein (Alpha-1-B glycoprotein) (Plasma protein PO2-F) (Fragment)	0.04	-	cyt	0	Secreted protein				40
P04217 UniProt NPD GO	A1BG_HUMAN	Alpha-1B-glycoprotein precursor (Alpha-1-B glycoprotein)	0.04	-	exc	0	Secreted protein	extracellular region [IDA]	138670		495
P29701 UniProt NPD GO	FETUA_SHEEP	Alpha-2-HS-glycoprotein precursor (Fetuin-A)	0.04	-	exc	0	Secreted protein	extracellular space [ISS]			364
P12763 UniProt NPD GO	FETUA_BOVIN	Alpha-2-HS-glycoprotein precursor (Fetuin-A) (Asialofetuin)	0.04	-	end	0	Secreted protein	extracellular space [ISS]			359
P97515 UniProt NPD GO	FETUA_MERUN	Alpha-2-HS-glycoprotein precursor (Fetuin-A) (Countertrypin)	0.04	-	exc	0	Secreted protein				348
P79021 UniProt NPD GO	AXHA_ASPTU	Alpha-L-arabinofuranosidase precursor (EC 3.2.1.55) (Arabinoxylan arabinofuranohydrolase)	0.04	-	exc	0	Secreted protein				332
P54215 UniProt NPD GO	AMYA_DROMA	Alpha-amylase A precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.04	-	pox	0					494
P08144 UniProt NPD GO	AMYA_DROME	Alpha-amylase A precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.04	-	pox	0					494
P83833 UniProt NPD GO	AMYA_DROYA	Alpha-amylase A precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.04	-	pox	0					494
P81641 UniProt NPD GO	AMYB_DROME	Alpha-amylase B precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.04	-	pox	0					494
Q9BN01 UniProt NPD GO	AMYB_DROYA	Alpha-amylase B precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.04	-	pox	0					494
P80403 UniProt NPD GO	IAAI_AMAHP	Alpha-amylase inhibitor AAI	0.04	-	nuc	0				1QFD	32
O77011 UniProt NPD GO	AMYR_DROAP	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.04	-	cyt	0	Secreted protein (Probable)				494
Q9NJN8 UniProt NPD GO	AMYR_DROBP	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.04	-	cyt	0	Secreted protein (Probable)				494
O77012 UniProt NPD GO	AMYR_DROEC	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.04	-	cyt	0	Secreted protein (Probable)				494
Q9NJN7 UniProt NPD GO	AMYR_DROVA	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.04	-	cyt	0	Secreted protein (Probable)				494
O76263 UniProt NPD GO	AMYR_DROWI	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.04	-	pox	0	Secreted protein (Probable)				492
P16852 UniProt NPD GO	IAC17_WHEAT	Alpha-amylase/trypsin inhibitor CM17 (Chloroform/methanol-soluble protein CM17) (Fragment)	0.04	-	nuc	0	Secreted protein				27
P28041 UniProt NPD GO	IAAA_HORVU	Alpha-amylase/trypsin inhibitor CMa precursor (Chloroform/methanol-soluble protein CMa)	0.04	-	exc	1 *	Secreted protein				145
P08734 UniProt NPD GO	ENOA_XENLA	Alpha-enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate hydro-lyase)	0.04	-	cyt	0	Cytoplasm				433
Q38866 UniProt NPD GO	EXPA2_ARATH	Alpha-expansin 2 precursor (AtEXPA2) (At-EXP2) (AtEx2) (Ath-ExpAlpha-1.12)	0.04	-	mit	0	Cell wall; peripheral membrane protein				255
O80932 UniProt NPD GO	EXPA3_ARATH	Alpha-expansin 3 precursor (AtEXPA3) (At-EXP3) (AtEx3) (Ath-ExpAlpha-1.9)	0.04	-	vac	0	Cell wall; peripheral membrane protein				262
P19122 UniProt NPD GO	LALBA_MACGI	Alpha-lactalbumin I (Lactose synthase B protein) (Fragment)	0.04	-	cyt	0	Secreted protein				42
Q9N2G9 UniProt NPD GO	LALBA_CANFA	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.04	-	exc	0	Secreted protein				142
P00713 UniProt NPD GO	LALBA_CAVPO	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.04	-	exc	0	Secreted protein			1HFX	142
P00709 UniProt NPD GO	LALBA_HUMAN	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.04	-	end	0	Secreted protein	extracellular space [TAS]	149750	1HML	142

You are viewing entries 76251 to 76300 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.