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
Q12354 UniProt NPD GO	APTH1_YEAST	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.01	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			227
P00820 UniProt NPD GO	ACYP2_RABIT	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2) (Acylphosphatase, muscle type isoz ...	0.01	-	cyt	0					98
Q756E2 UniProt NPD GO	APT_ASHGO	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				187
Q5ALX8 UniProt NPD GO	APT_CANAL	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				188
P31166 UniProt NPD GO	APT1_ARATH	Adenine phosphoribosyltransferase 1 (EC 2.4.2.7) (APRT 1)	0.01	-	mit	0	Cytoplasm				243
P49435 UniProt NPD GO	APT1_YEAST	Adenine phosphoribosyltransferase 1 (EC 2.4.2.7) (APRT 1)	0.01	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]		1G2Q	187
P36973 UniProt NPD GO	APT2_YEAST	Adenine phosphoribosyltransferase 2 (EC 2.4.2.7) (APRT 2)	0.01	-	nuc	0	Cytoplasm	cytoplasm [IDA]			181
P30542 UniProt NPD GO	AA1R_HUMAN	Adenosine A1 receptor	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	102775		326
P34970 UniProt NPD GO	AA1R_RABIT	Adenosine A1 receptor	0.01	-	end	7 *	Membrane; multi-pass membrane protein				328
P29275 UniProt NPD GO	AA2BR_HUMAN	Adenosine A2b receptor	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600446		332
Q60614 UniProt NPD GO	AA2BR_MOUSE	Adenosine A2b receptor	0.01	-	end	7 *	Membrane; multi-pass membrane protein				332
P33765 UniProt NPD GO	AA3R_HUMAN	Adenosine A3 receptor	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600445	1R7N	318
O02667 UniProt NPD GO	AA3R_RABIT	Adenosine A3 receptor	0.01	-	end	7 *	Membrane; multi-pass membrane protein				319
O49923 UniProt NPD GO	ADK_PHYPA	Adenosine kinase (EC 2.7.1.20) (AK) (Adenosine 5'-phosphotransferase)	0.01	-	cyt	0					343
O76757 UniProt NPD GO	SAHH_ANOGA	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.01	-	cyt	0					432
P10819 UniProt NPD GO	SAHH_DICDI	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.01	-	cyt	0					430
Q9SWF5 UniProt NPD GO	SAHH_LYCES	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.01	-	cyt	0					485
Q7RKK8 UniProt NPD GO	SAHH_PLAYO	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.01	-	nuc	0					479
O13639 UniProt NPD GO	SAHH_SCHPO	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.01	-	cyt	0					433
P68172 UniProt NPD GO	SAHH_NICSY	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) (Cytokinin-bin ...	0.01	-	nuc	0					485
P68173 UniProt NPD GO	SAHH_TOBAC	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) (Cytokinin-bin ...	0.01	-	nuc	0					485
P27604 UniProt NPD GO	SAHH_CAEEL	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) (Protein dumpy ...	0.01	-	cyt	0					437
P51893 UniProt NPD GO	SAHHA_XENLA	Adenosylhomocysteinase A (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase A) (AdoHcyase A)	0.01	-	cyt	0					433
O93477 UniProt NPD GO	SAHHB_XENLA	Adenosylhomocysteinase B (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase B) (AdoHcyase B)	0.01	-	cyt	0					433
P12115 UniProt NPD GO	KAD_CYPCA	Adenylate kinase (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.01	-	cyt	0	Cytoplasm				193
P43188 UniProt NPD GO	KADC_MAIZE	Adenylate kinase, chloroplast (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.01	-	cyt	0	Plastid; chloroplast			1ZAK	222
Q9P7G9 UniProt NPD GO	KAPS_SCHPO	Adenylyl-sulfate kinase (EC 2.7.1.25) (APS kinase) (Adenosine-5'phosphosulfate kinase) (ATP adenosin ...	0.01	-	nuc	0					202
Q60994 UniProt NPD GO	ADIPO_MOUSE	Adiponectin precursor (Adipocyte, C1q and collagen domain-containing protein) (30 kDa adipocyte comp ...	0.01	-	exc	0	Secreted protein	endoplasmic reticulum [IDA] extracellular space [IDA]		1C3H	247
Q9Z1S9 UniProt NPD GO	ACTHR_CAVPO	Adrenocorticotropic hormone receptor (ACTH receptor) (ACTH-R) (Melanocortin receptor 2) (MC2-R) (Adr ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein				297
Q01718 UniProt NPD GO	ACTHR_HUMAN	Adrenocorticotropic hormone receptor (ACTH receptor) (ACTH-R) (Melanocortin receptor 2) (MC2-R) (Adr ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	607397		297
P80518 UniProt NPD GO	CU55_ARADI	Adult-specific rigid cuticular protein 15.5 (ACP 15.5)	0.01	-	nuc	0					156
P80519 UniProt NPD GO	CU57_ARADI	Adult-specific rigid cuticular protein 15.7 (ACP 15.7)	0.01	-	nuc	0					159
P83672 UniProt NPD GO	AGG1_POMFL	Agglutinin 1 (PFA-1) (Fragments)	0.01	-	cyt	0					49
P18673 UniProt NPD GO	LECB3_ARTIN	Agglutinin beta-3 chain (Jacalin beta-3 chain)	0.01	-		0				1M26	20
P84797 UniProt NPD GO	AFAGR_AGRCY	Agrocybin (Fragment)	0.01	-		0					15
O59828 UniProt NPD GO	ALR1_SCHPO	Alanine racemase, catabolic (EC 5.1.1.1)	0.01	-	cyt	0					375
Q64565 UniProt NPD GO	AGT2_RAT	Alanine--glyoxylate aminotransferase 2, mitochondrial precursor (EC 2.6.1.44) ((R)-3-amino-2-methylp ...	0.01	-	mit	0	Mitochondrion (Potential)				512
P50475 UniProt NPD GO	SYA_RAT	Alanyl-tRNA synthetase (EC 6.1.1.7) (Alanine--tRNA ligase) (AlaRS) (Fragment)	0.01	-	cyt	0	Cytoplasm (Potential)				21
P80512 UniProt NPD GO	ADH1_NAJNA	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.01	-	nuc	0	Cytoplasm				375
P25141 UniProt NPD GO	ADH1_PETHY	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.01	-	mit	0	Cytoplasm				382
Q64413 UniProt NPD GO	ADH1_GEOBU	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase A subunit)	0.01	-	mit	0	Cytoplasm				374
Q64415 UniProt NPD GO	ADH1_GEOKN	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase A subunit)	0.01	-	mit	0	Cytoplasm				374
P41680 UniProt NPD GO	ADH1_PERMA	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase A subunit)	0.01	-	mit	0	Cytoplasm				374
P06757 UniProt NPD GO	ADH1_RAT	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase A subunit)	0.01	-	end	0	Cytoplasm				375
P00329 UniProt NPD GO	ADH1_MOUSE	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase A subunit) (ADH-A2)	0.01	-	mit	0	Cytoplasm				374
P49645 UniProt NPD GO	ADH1_APTAU	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase I)	0.01	-	nuc	0	Cytoplasm				374
P80338 UniProt NPD GO	ADH1_STRCA	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase I)	0.01	-	nuc	0	Cytoplasm				374
O00097 UniProt NPD GO	ADH1_PICST	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase I) (ADH 2)	0.01	-	mit	0	Cytoplasm				348
P08843 UniProt NPD GO	ADH1_EMENI	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase I) (ADH I)	0.01	-	cyt	0	Cytoplasm				349
Q03505 UniProt NPD GO	ADH1_RABIT	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase alpha subunit)	0.01	-	mit	0	Cytoplasm				374

You are viewing entries 86601 to 86650 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.