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
P53489 UniProt NPD GO	ARP2_CAEEL	Actin-like protein 2 (Actin-related protein 2) (Actin-like protein C)	0.05	-	cyt	0					395
P27041 UniProt NPD GO	AVR2B_XENLA	Activin receptor type 2B precursor (EC 2.7.11.30) (Activin receptor type IIB) (ACTR-IIB)	0.05	-	end	1	Membrane; single-pass type I membrane protein				511
P52505 UniProt NPD GO	ACPM_BOVIN	Acyl carrier protein, mitochondrial precursor (ACP) (NADH-ubiquinone oxidoreductase 9.6 kDa subunit) ...	0.05	-	mit	0	Mitochondrion	mitochondrial matrix [IDA] mitochondrial membrane [IDA]			156
Q5RJK8 UniProt NPD GO	ACBD6_RAT	Acyl-CoA-binding domain-containing protein 6	0.05	-	cyt	0					282
P07311 UniProt NPD GO	ACYP1_HUMAN	Acylphosphatase-1 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 1) (Acylphosphatase, organ-common typ ...	0.05	-	cyt	0			600875		98
P11617 UniProt NPD GO	AA2AR_CANFA	Adenosine A2a receptor	0.05	-	end	7 *	Membrane; multi-pass membrane protein				412
P30543 UniProt NPD GO	AA2AR_RAT	Adenosine A2a receptor	0.05	-	end	7 *	Membrane; multi-pass membrane protein	membrane fraction [IDA]			410
P03958 UniProt NPD GO	ADA_MOUSE	Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase)	0.05	-	cyt	0		cytoplasm [IDA]		2ADA	351
O23255 UniProt NPD GO	SAHH1_ARATH	Adenosylhomocysteinase 1 (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase 1) (SAH hydrolase 1) (Ado ...	0.05	-	nuc	0					485
Q9FK35 UniProt NPD GO	KAD2_ARATH	Adenylate kinase 2 (EC 2.7.4.3) (ATP-AMP transphosphorylase 2)	0.05	-	cyt	0					248
Q9TTU2 UniProt NPD GO	KAD6_RABIT	Adenylate kinase isoenzyme 6 (EC 2.7.4.3) (ATP-AMP transphosphorylase 6)	0.05	-	cyt	0	Nucleus (By similarity)				172
Q08163 UniProt NPD GO	CAP1_RAT	Adenylyl cyclase-associated protein 1 (CAP 1)	0.05	-	nuc	0	Cell membrane (By similarity)				473
O49204 UniProt NPD GO	KAPS_CATRO	Adenylyl-sulfate kinase, chloroplast precursor (EC 2.7.1.25) (APS kinase) (Adenosine-5'phosphosulfat ...	0.05	-	nuc	0	Plastid; chloroplast (By similarity)				312
Q64326 UniProt NPD GO	ACTHR_MOUSE	Adrenocorticotropic hormone receptor (ACTH receptor) (ACTH-R) (Melanocortin receptor 2) (MC2-R) (Adr ...	0.05	-	end	7 *	Membrane; multi-pass membrane protein				296
Q8HYN8 UniProt NPD GO	ACTHR_PIG	Adrenocorticotropic hormone receptor (ACTH receptor) (ACTH-R) (Melanocortin receptor 2) (MC2-R) (Adr ...	0.05	-	end	7 *	Membrane; multi-pass membrane protein				297
Q28670 UniProt NPD GO	PGCA_RABIT	Aggrecan core protein (Cartilage-specific proteoglycan core protein) (CSPCP) (Fragment)	0.05	-	nuc	0					394
Q5RFA3 UniProt NPD GO	AGT2_PONPY	Alanine--glyoxylate aminotransferase 2, mitochondrial precursor (EC 2.6.1.44) ((R)-3-amino-2-methylp ...	0.05	-	mit	0	Mitochondrion (Potential)				514
P81115 UniProt NPD GO	ABBA_TRIAB	Alboaggregin-B subunit alpha	0.05	-	cyt	0	Secreted protein				132
Q9FRT8 UniProt NPD GO	ALB1_PHAAU	Albumin-1 precursor (A1) [Contains: Albumin-1 chain b (A1b) (Leginsulin); Albumin-1 chain a (A1a)] ( ...	0.05	-	nuc	0					89
Q00669 UniProt NPD GO	ADH_DROAD	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					253
P21518 UniProt NPD GO	ADH_DROAF	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					253
P48584 UniProt NPD GO	ADH_DROBO	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					253
P22245 UniProt NPD GO	ADH_DRODI	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					253
P48585 UniProt NPD GO	ADH_DROFL	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					253
P51551 UniProt NPD GO	ADH_DROGR	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					253
P21898 UniProt NPD GO	ADH_DROHE	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					253
Q07588 UniProt NPD GO	ADH_DROIM	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					253
Q27404 UniProt NPD GO	ADH_DROLA	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					254
P10807 UniProt NPD GO	ADH_DROLE	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0				1SBY	254
Q00672 UniProt NPD GO	ADH_DRONI	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					253
P23361 UniProt NPD GO	ADH_DROPI	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					253
P23277 UniProt NPD GO	ADH_DROPL	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					253
P51552 UniProt NPD GO	ADH_ZAPTU	Alcohol dehydrogenase (EC 1.1.1.1)	0.05	-	cyt	0					256
P23236 UniProt NPD GO	ADH1_DROHY	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.05	-	cyt	0					253
P09370 UniProt NPD GO	ADH1_DROMO	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.05	-	cyt	0					253
P22246 UniProt NPD GO	ADH1_DROMT	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.05	-	cyt	0					253
P07161 UniProt NPD GO	ADH1_DROMU	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.05	-	cyt	0					253
P23237 UniProt NPD GO	ADH2_DROHY	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.05	-	cyt	0					253
P48587 UniProt NPD GO	ADH2_DROMN	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.05	-	cyt	0					253
Q00922 UniProt NPD GO	ALOX_CANBO	Alcohol oxidase (EC 1.1.3.13) (AOX) (Methanol oxidase) (MOX)	0.05	-	cyt	0	Peroxisome				663
P04841 UniProt NPD GO	ALOX_PICAN	Alcohol oxidase (EC 1.1.3.13) (AOX) (Methanol oxidase) (MOX)	0.05	-	cyt	0	Peroxisome				664
P32872 UniProt NPD GO	ALDHY_YEAST	Aldehyde dehydrogenase 2, mitochondrial precursor (EC 1.2.1.3)	0.05	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				511
P54114 UniProt NPD GO	ALDH3_YEAST	Aldehyde dehydrogenase [NAD(P)+] 2 (EC 1.2.1.5)	0.05	-	cyt	0					506
P25795 UniProt NPD GO	AL7A1_PEA	Aldehyde dehydrogenase family 7 member A1 (EC 1.2.1.3) (Turgor-responsive protein 26G) (Antiquitin-1 ...	0.05	-	nuc	0					507
P47739 UniProt NPD GO	AL3A1_MOUSE	Aldehyde dehydrogenase, dimeric NADP-preferring (EC 1.2.1.5) (ALDH class 3) (Dioxin-inducible aldehy ...	0.05	-	mit	0	Cytoplasm	cytoplasm [IEP] cytosol [ISS]			453
P40047 UniProt NPD GO	ALDH5_YEAST	Aldehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.3)	0.05	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)	mitochondrion [IDA]			519
P45376 UniProt NPD GO	ALDR_MOUSE	Aldose reductase (EC 1.1.1.21) (AR) (Aldehyde reductase)	0.05	-	cyt	0	Cytoplasm				315
P15122 UniProt NPD GO	ALDR_RABIT	Aldose reductase (EC 1.1.1.21) (AR) (Aldehyde reductase)	0.05	-	cyt	0	Cytoplasm				315
Q568I2 UniProt NPD GO	ASAH3_BRARE	Alkaline ceramidase 1 (EC 3.5.1.23) (Alkaline CDase-1) (AlkCDase 1) (Acylsphingosine deacylase 3) (N ...	0.05	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				266
Q5QJU3 UniProt NPD GO	ASA3L_HUMAN	Alkaline ceramidase 2 (EC 3.5.1.23) (AlkCDase 2) (Acylsphingosine deacylase 3-like) (N-acylsphingosi ...	0.05	-	end	5 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein				275

You are viewing entries 73751 to 73800 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.