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
P48815 UniProt NPD GO	ADH2_CERCA	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.02	-	cyt	0					258
P07754 UniProt NPD GO	ADH3_EMENI	Alcohol dehydrogenase 3 (EC 1.1.1.1) (Alcohol dehydrogenase III) (ADH III)	0.02	-	cyt	0	Cytoplasm				352
P49385 UniProt NPD GO	ADH4_KLULA	Alcohol dehydrogenase IV, mitochondrial precursor (EC 1.1.1.1)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix				375
P14550 UniProt NPD GO	AK1A1_HUMAN	Alcohol dehydrogenase [NADP+] (EC 1.1.1.2) (Aldehyde reductase) (Aldo-keto reductase family 1 member ...	0.02	-	cyt	0			103830	2ALR	324
Q9JII6 UniProt NPD GO	AK1A1_MOUSE	Alcohol dehydrogenase [NADP+] (EC 1.1.1.2) (Aldehyde reductase) (Aldo-keto reductase family 1 member ...	0.02	-	cyt	0		apical plasma membrane [IDA] cytosol [IDA]			324
P51635 UniProt NPD GO	AK1A1_RAT	Alcohol dehydrogenase [NADP+] (EC 1.1.1.2) (Aldehyde reductase) (Aldo-keto reductase family 1 member ...	0.02	-	cyt	0					324
O46650 UniProt NPD GO	ADHQ_RABIT	Alcohol dehydrogenase class II isozyme 2 (EC 1.1.1.1)	0.02	-	nuc	0	Cytoplasm				378
P25143 UniProt NPD GO	ADHR_DROAM	Alcohol dehydrogenase-related 31 kDa protein	0.02	-	cyt	0					281
Q07586 UniProt NPD GO	ADHR_DROIM	Alcohol dehydrogenase-related 31 kDa protein	0.02	-	cyt	0					273
P91615 UniProt NPD GO	ADHR_DROME	Alcohol dehydrogenase-related 31 kDa protein	0.02	-	cyt	0					272
O16091 UniProt NPD GO	ADHR_DROPE	Alcohol dehydrogenase-related 31 kDa protein	0.02	-	cyt	0					278
P81764 UniProt NPD GO	ADHR_DROPS	Alcohol dehydrogenase-related 31 kDa protein	0.02	-	cyt	0					278
P26620 UniProt NPD GO	ADHR_DROMA	Alcohol dehydrogenase-related 31 kDa protein (Fragment)	0.02	-	cyt	0					272
P28486 UniProt NPD GO	ADHR_DROTE	Alcohol dehydrogenase-related 31 kDa protein (Fragment)	0.02	-	cyt	0					272
P50235 UniProt NPD GO	SUH3_RAT	Alcohol sulfotransferase (EC 2.8.2.2) (Hydroxysteroid sulfotransferase) (ST) (ST-60)	0.02	-	cyt	0	Cytoplasm				285
P22789 UniProt NPD GO	ST2A2_RAT	Alcohol sulfotransferase A (EC 2.8.2.2) (Hydroxysteroid sulfotransferase A) (STA) (Androsterone-sulf ...	0.02	-	cyt	0	Cytoplasm				283
P40108 UniProt NPD GO	ALDH_CLAHE	Aldehyde dehydrogenase (EC 1.2.1.3) (ALDDH) (Allergen Cla h 10) (Cla h 3) (Cla h III)	0.02	-	cyt	0	Cytoplasm (Probable)				496
Q2KJC9 UniProt NPD GO	AL7A1_BOVIN	Aldehyde dehydrogenase family 7 member A1 (EC 1.2.1.3)	0.02	-	nuc	0					510
P49419 UniProt NPD GO	AL7A1_HUMAN	Aldehyde dehydrogenase family 7 member A1 (EC 1.2.1.3) (Antiquitin-1)	0.02	-	nuc	0			107323		510
Q9DBF1 UniProt NPD GO	AL7A1_MOUSE	Aldehyde dehydrogenase family 7 member A1 (EC 1.2.1.3) (Antiquitin-1)	0.02	-	end	0		mitochondrion [IDA]			510
P13601 UniProt NPD GO	AL1A4_RAT	Aldehyde dehydrogenase, cytosolic 1 (EC 1.2.1.3) (ALDH class 1) (ALHDII) (ALDH-E1) (Aldehyde dehydro ...	0.02	-	cyt	0	Cytoplasm	cytosol [NAS]			500
Q29491 UniProt NPD GO	ALDH2_MACPR	Aldehyde dehydrogenase, cytosolic 2 (EC 1.2.1.3) (ALDH class 1) (Non-lens ALDH1) (ALDH1-NL) (Fragmen ...	0.02	-	mit	0	Cytoplasm (By similarity)				240
P23901 UniProt NPD GO	ALDR_HORVU	Aldose reductase (EC 1.1.1.21) (AR) (Aldehyde reductase)	0.02	-	cyt	0				2BGS	320
P15121 UniProt NPD GO	ALDR_HUMAN	Aldose reductase (EC 1.1.1.21) (AR) (Aldehyde reductase)	0.02	-	cyt	0	Cytoplasm	extracellular space [TAS]	103880	2F2K	315
P38298 UniProt NPD GO	YPC1_YEAST	Alkaline ceramidase YPC1 (EC 3.5.1.-)	0.02	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [IDA]			316
P09487 UniProt NPD GO	PPBT_BOVIN	Alkaline phosphatase, tissue-nonspecific isozyme precursor (EC 3.1.3.1) (AP-TNAP) (Liver/bone/kidney ...	0.02	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				524
Q29486 UniProt NPD GO	PPBT_FELCA	Alkaline phosphatase, tissue-nonspecific isozyme precursor (EC 3.1.3.1) (AP-TNAP) (Liver/bone/kidney ...	0.02	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				524
P48087 UniProt NPD GO	PHAF_CYAPA	Allophycocyanin B18 subunit	0.02	-	cyt	0	Plastid; cyanelle				169
P00320 UniProt NPD GO	PHAB_CYAPA	Allophycocyanin beta chain	0.02	-	cyt	0	Plastid; cyanelle				161
Q07158 UniProt NPD GO	TPS1_KLULA	Alpha,alpha-trehalose-phosphate synthase [UDP-forming] 56 kDa subunit (EC 2.4.1.15) (Trehalose-6-pho ...	0.02	-	cyt	0					488
Q00764 UniProt NPD GO	TPS1_YEAST	Alpha,alpha-trehalose-phosphate synthase [UDP-forming] 56 kDa subunit (EC 2.4.1.15) (Trehalose-6-pho ...	0.02	-	cyt	0	Cytoplasm	alpha,alpha-trehalose-phosphate synthase co... [IDA] cytoplasm [IDA]			495
P83973 UniProt NPD GO	LECF_RHIST	Alpha-(1-6)-linked fucose-specific lectin (RSL) (Fragment)	0.02	-	cyt	0	Secreted protein				28
Q755C1 UniProt NPD GO	ALG2_ASHGO	Alpha-1,3-mannosyltransferase ALG2 (EC 2.4.1.-) (GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransfe ...	0.02	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				514
P38029 UniProt NPD GO	A1AT2_HORSE	Alpha-1-antiproteinase 2 precursor (Alpha-1-antitrypsin 2) (Alpha-1-proteinase inhibitor 2) (SPI2)	0.02	-	end	0	Secreted protein				421
P38030 UniProt NPD GO	A1AT3_HORSE	Alpha-1-antiproteinase 3 (Alpha-1-antitrypsin 3) (Alpha-1-proteinase inhibitor 3) (SPI3) (Fragments) ...	0.02	-	cyt	0	Secreted protein				52
P22324 UniProt NPD GO	A1AF_CAVPO	Alpha-1-antiproteinase F precursor (Alpha-1-antitrypsin) (Alpha-1-proteinase inhibitor) (APF) (Fragm ...	0.02	-	end	0	Secreted protein				403
P22325 UniProt NPD GO	A1AS_CAVPO	Alpha-1-antiproteinase S precursor (Alpha-1-antitrypsin) (Alpha-1-proteinase inhibitor) (APS)	0.02	-	end	0	Secreted protein				405
P34955 UniProt NPD GO	A1AT_BOVIN	Alpha-1-antiproteinase precursor (Alpha-1-antitrypsin) (Alpha-1-proteinase inhibitor)	0.02	-	end	0	Secreted protein				416
O54763 UniProt NPD GO	A1AT_CALCN	Alpha-1-antiproteinase precursor (Alpha-1-antitrypsin) (Alpha-1-proteinase inhibitor)	0.02	-	end	0	Secreted protein				412
P01009 UniProt NPD GO	A1AT_HUMAN	Alpha-1-antitrypsin precursor (Alpha-1 protease inhibitor) (Alpha-1-antiproteinase)	0.02	-	end	0	Secreted protein	extracellular region [NAS] extracellular space [IMP]	107400	9API	418
O54761 UniProt NPD GO	ALMS_SPETR	Alpha-1-antitrypsin-like protein GS55-MS precursor	0.02	-	end	0	Secreted protein (By similarity)				413
P29699 UniProt NPD GO	FETUA_MOUSE	Alpha-2-HS-glycoprotein precursor (Fetuin-A) (Countertrypin)	0.02	-	exc	0	Secreted protein	extracellular space [ISS]			345
Q7SIH1 UniProt NPD GO	A2MG_BOVIN	Alpha-2-macroglobulin (Alpha-2-M) (Fragment)	0.02	-	cyt	0	Secreted protein			1AYO	130
P69746 UniProt NPD GO	CXA4A_CONOB	Alpha-A(1-3) conotoxin OIVA (Alpha-A-OIVA) (Conotoxin o4a)	0.02	-		0	Secreted protein				18
P10901 UniProt NPD GO	FUCO_DICDI	Alpha-L-fucosidase precursor (EC 3.2.1.51) (Alpha-L-fucoside fucohydrolase)	0.02	-	end	0					461
Q66H12 UniProt NPD GO	NAGAB_RAT	Alpha-N-acetylgalactosaminidase precursor (EC 3.2.1.49) (Alpha-galactosidase B)	0.02	-	cyt	0	Lysosome (By similarity)				415
P19961 UniProt NPD GO	AMYC_HUMAN	Alpha-amylase 2B precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (Alpha-amylase carcino ...	0.02	-	pox	0	Secreted protein (By similarity)		104660		511
P81368 UniProt NPD GO	IAA5_SORBI	Alpha-amylase inhibitor 5 (SI alpha-5)	0.02	-	cyt	0	Secreted protein				116
P27937 UniProt NPD GO	AMY3B_ORYSA	Alpha-amylase isozyme 3B precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.02	-	exc	0					438
P27939 UniProt NPD GO	AMY3C_ORYSA	Alpha-amylase isozyme 3C precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.02	-	vac	1 *					437

You are viewing entries 82401 to 82450 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.