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
Q9BYD9 UniProt NPD GO	ARPM1_HUMAN	Actin-related protein M1	0.02	-	mit	0			608534		372
Q9D9L5 UniProt NPD GO	ARPM2_MOUSE	Actin-related protein T2 (ARP-T2) (Actin-related protein M2)	0.02	-	nuc	0					377
P18281 UniProt NPD GO	ACTO_ACACA	Actobindin	0.02	-	cyt	0					88
Q6B8U3 UniProt NPD GO	ACP_GRATL	Acyl carrier protein (ACP)	0.02	-	mit	0	Plastid; chloroplast				82
P29189 UniProt NPD GO	ACP_GUITH	Acyl carrier protein (ACP)	0.02	-	cyt	0	Plastid; chloroplast				81
P53665 UniProt NPD GO	ACPM_ARATH	Acyl carrier protein, mitochondrial precursor (ACP) (NADH-ubiquinone oxidoreductase 9.6 kDa subunit) ...	0.02	-	mit	0	Mitochondrion				122
Q3SZF0 UniProt NPD GO	ACBD7_BOVIN	Acyl-CoA-binding domain-containing protein 7	0.02	-	cyt	0					88
Q8N6N7 UniProt NPD GO	ACBD7_HUMAN	Acyl-CoA-binding domain-containing protein 7	0.02	-	cyt	0					88
Q86TX2 UniProt NPD GO	ACOT1_HUMAN	Acyl-coenzyme A thioesterase 1 (EC 3.1.2.2) (Acyl-CoA thioesterase 1) (Inducible cytosolic acyl-coen ...	0.02	-	mit	0	Cytoplasm (By similarity)				421
Q9QYR9 UniProt NPD GO	ACOT2_MOUSE	Acyl-coenzyme A thioesterase 2, mitochondrial precursor (EC 3.1.2.2) (Acyl-CoA thioesterase 2) (Acyl ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			453
O55171 UniProt NPD GO	ACOT2_RAT	Acyl-coenzyme A thioesterase 2, mitochondrial precursor (EC 3.1.2.2) (Acyl-CoA thioesterase 2) (Acyl ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix				453
Q3MHR0 UniProt NPD GO	LYPA1_BOVIN	Acyl-protein thioesterase 1 (EC 3.1.2.-) (Lysophospholipase 1) (Lysophospholipase I)	0.02	-	cyt	0	Cytoplasm (By similarity)				230
O75608 UniProt NPD GO	LYPA1_HUMAN	Acyl-protein thioesterase 1 (EC 3.1.2.-) (Lysophospholipase 1) (Lysophospholipase I)	0.02	-	cyt	0	Cytoplasm (By similarity)		605599	1FJ2	230
P70470 UniProt NPD GO	LYPA1_RAT	Acyl-protein thioesterase 1 (EC 3.1.2.-) (Lysophospholipase 1) (Lysophospholipase I)	0.02	-	cyt	0	Cytoplasm				230
O77821 UniProt NPD GO	LYPA1_RABIT	Acyl-protein thioesterase 1 (EC 3.1.2.-) (Lysophospholipase 1) (Lysophospholipase I) (Calcium-indepe ...	0.02	-	cyt	0	Cytoplasm (By similarity)				230
P97823 UniProt NPD GO	LYPA1_MOUSE	Acyl-protein thioesterase 1 (EC 3.1.2.-) (Lysophospholipase 1) (Lysophospholipase I) (LysoPLA I)	0.02	-	cyt	0	Cytoplasm (By similarity)	mitochondrion [IDA]			230
P80227 UniProt NPD GO	ACPH_BOVIN	Acylamino-acid-releasing enzyme (EC 3.4.19.1) (AARE) (Acyl-peptide hydrolase) (APH) (Acylaminoacyl-p ...	0.02	-		0	Cytoplasm				20
Q5EBE1 UniProt NPD GO	ACYP2_XENTR	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2)	0.02	-	cyt	0					103
P00818 UniProt NPD GO	ACYP2_HORSE	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2) (Acylphosphatase, muscle type isoz ...	0.02	-	cyt	0				1APS	98
Q6CWV0 UniProt NPD GO	APT_KLULA	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				187
Q6CA53 UniProt NPD GO	APT_YARLI	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.02	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				182
P28190 UniProt NPD GO	AA1R_BOVIN	Adenosine A1 receptor	0.02	-	end	7 *	Membrane; multi-pass membrane protein				326
Q6TLI7 UniProt NPD GO	AA2AR_HORSE	Adenosine A2a receptor	0.02	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				412
P29274 UniProt NPD GO	AA2AR_HUMAN	Adenosine A2a receptor	0.02	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS] plasma membrane [TAS]	102776	1MMH	412
O13076 UniProt NPD GO	AA2BR_CHICK	Adenosine A2b receptor (Adenosine receptor 2b)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				340
P35342 UniProt NPD GO	AA3R_SHEEP	Adenosine A3 receptor	0.02	-	end	7 *	Membrane; multi-pass membrane protein				317
P84520 UniProt NPD GO	ADA2_CHICK	Adenosine deaminase 2 (EC 3.5.4.4) (Fragment)	0.02	-		0					12
O93919 UniProt NPD GO	ADK_SCHCO	Adenosine kinase (EC 2.7.1.20)	0.02	-	cyt	0					344
P55262 UniProt NPD GO	ADK_CRIGR	Adenosine kinase (EC 2.7.1.20) (AK) (Adenosine 5'-phosphotransferase)	0.02	-	cyt	0					361
Q01781 UniProt NPD GO	SAHH_PETCR	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.02	-	cyt	0					485
P32112 UniProt NPD GO	SAHH_WHEAT	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.02	-	nuc	0					485
P50250 UniProt NPD GO	SAHH_PLAF7	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) (PfSAHH)	0.02	-	cyt	0				1V8B	479
P50277 UniProt NPD GO	BIOA_YEAST	Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) (7,8-diamino-pelargonic aci ...	0.02	-	cyt	0					480
Q5EB68 UniProt NPD GO	KAD6_RAT	Adenylate kinase isoenzyme 6 (EC 2.7.4.3) (ATP-AMP transphosphorylase 6)	0.02	-	cyt	0	Nucleus (By similarity)				172
P35807 UniProt NPD GO	AKH2_SCHNI	Adipokinetic prohormone type 2 precursor [Contains: Adipokinetic hormone 2 (Adipokinetic hormone II) ...	0.02	-	exc	1 *	Secreted protein				61
Q91VH1 UniProt NPD GO	ADR1_MOUSE	Adiponectin receptor protein 1	0.02	-	end	7	Membrane; multi-pass membrane protein (By similarity). Localized to the cell membrane and intracellu ...	integral to membrane [ISS]			375
Q96A54 UniProt NPD GO	ADR1_HUMAN	Adiponectin receptor protein 1 (Progestin and adipoQ receptor family member I)	0.02	-	end	7	Membrane; multi-pass membrane protein. Localized to the cell membrane and intracellular organelles	integral to membrane [NAS]	607945		375
P70115 UniProt NPD GO	ACTHR_MESAU	Adrenocorticotropic hormone receptor (ACTH receptor) (ACTH-R) (Melanocortin receptor 2) (MC2-R) (Adr ...	0.02	-	end	7 *	Membrane; multi-pass membrane protein				297
P00258 UniProt NPD GO	ADX_PIG	Adrenodoxin, mitochondrial precursor (Adrenal ferredoxin) (Ferredoxin-1)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix				186
P13216 UniProt NPD GO	ADX_CHICK	Adrenodoxin, mitochondrial precursor (Adrenal ferredoxin) (Fragment)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix				143
Q26416 UniProt NPD GO	CUA1_DROME	Adult cuticle protein 1 precursor (dACP-1)	0.02	-	mit	0					135
P26967 UniProt NPD GO	CU20_TENMO	Adult-specific cuticular protein ACP-20 precursor	0.02	-	mit	3 *					208
P80516 UniProt NPD GO	CU24_ARADI	Adult-specific rigid cuticular protein 12.4 (ACP 12.4)	0.02	-	cyt	0					126
Q00022 UniProt NPD GO	ABL_AGABI	Agaricus bisporus lectin (ABL) (Gal-beta-1,3-GalNAc-binding lectin) (Agaricus bisporus agglutinin) ( ...	0.02	-	mit	0				1Y2X	142
P18677 UniProt NPD GO	LECB3_MACPO	Agglutinin beta-3 chain (MPA)	0.02	-		0					20
Q90XD2 UniProt NPD GO	SPEB_CHICK	Agmatinase, mitochondrial precursor (EC 3.5.3.11) (Agmatine ureohydrolase) (AUH)	0.02	-	cyt	0	Mitochondrion (By similarity)				340
P08688 UniProt NPD GO	ALB2_PEA	Albumin-2 (PA2)	0.02	-	cyt	0	Cytoplasm; cytosol. In the cytosol of the cotyledon cells rather than in vacuoles or protein bodies				231
Q9NAR7 UniProt NPD GO	ADH_BACOL	Alcohol dehydrogenase (EC 1.1.1.1)	0.02	-	cyt	0					258
P48814 UniProt NPD GO	ADH1_CERCA	Alcohol dehydrogenase 1 (EC 1.1.1.1)	0.02	-	cyt	0					257
P22797 UniProt NPD GO	ADH1_RANPE	Alcohol dehydrogenase 1 (EC 1.1.1.1) (Alcohol dehydrogenase, major)	0.02	-	mit	0	Cytoplasm				375

You are viewing entries 82351 to 82400 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.