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
P32876 UniProt NPD GO	AT5G1_BOVIN	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.09	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein				136
P03929 UniProt NPD GO	ATP8_BOVIN	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.09	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				66
Q9TBJ9 UniProt NPD GO	ATP8_CHAPE	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.09	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q9MGM1 UniProt NPD GO	ATP8_DROSE	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.09	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53
O99820 UniProt NPD GO	ATP8_RHISA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.09	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				52
O21401 UniProt NPD GO	ATP8_STRCA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.09	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
P51242 UniProt NPD GO	ATPA_PORPU	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.09	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				504
Q1XDP5 UniProt NPD GO	ATPA_PORYE	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.09	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				504
P80082 UniProt NPD GO	ATPAM_SPIOL	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14) (Fragment)	0.09	-	nuc	0	Mitochondrion				25
O03077 UniProt NPD GO	ATPB_OSMCI	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.09	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				220
P22068 UniProt NPD GO	ATPB_SCHPO	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.09	-	mit	0	Mitochondrion				525
P83483 UniProt NPD GO	ATPBM_ARATH	ATP synthase subunit beta-1, mitochondrial precursor (EC 3.6.3.14)	0.09	-	mit	0	Mitochondrion				556
Q9NUT2 UniProt NPD GO	ABCB8_HUMAN	ATP-binding cassette sub-family B member 8, mitochondrial precursor (Mitochondrial ATP-binding casse ...	0.09	-	end	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	ATP-binding cassette (ABC) transporter complex [TAS] membrane fraction [TAS] mitochondrial envelope [TAS]	605464		735
P16965 UniProt NPD GO	STF2_YEAST	ATPase-stabilizing factor 15 kDa protein	0.09	-	nuc	0	Mitochondrion	proton-transporting ATP synthase complex (s... [TAS]			83
P81463 UniProt NPD GO	ABAE_BOMPA	Abaecin	0.09	-	nuc	0	Secreted protein				39
P07342 UniProt NPD GO	ILVB_YEAST	Acetolactate synthase catalytic subunit, mitochondrial precursor (EC 2.2.1.6) (Acetohydroxy-acid syn ...	0.09	-	mit	0	Mitochondrion	acetolactate synthase complex [IDA] mitochondrion [IDA]		1T9D	687
P69683 UniProt NPD GO	ILVB_PORPU	Acetolactate synthase large subunit (EC 2.2.1.6) (AHAS) (Acetohydroxy-acid synthase large subunit) ( ...	0.09	-	nuc	0	Plastid; chloroplast				590
P69684 UniProt NPD GO	ILVB_PORUM	Acetolactate synthase large subunit (EC 2.2.1.6) (AHAS) (Acetohydroxy-acid synthase large subunit) ( ...	0.09	-	nuc	0	Plastid; chloroplast				590
Q754Q2 UniProt NPD GO	ACH1_ASHGO	Acetyl-CoA hydrolase (EC 3.1.2.1) (Acetyl-CoA deacylase) (Acetyl-CoA acylase)	0.09	-	nuc	0	Cytoplasm (By similarity)				523
P16929 UniProt NPD GO	ACSA_NEUCR	Acetyl-coenzyme A synthetase (EC 6.2.1.1) (Acetate--CoA ligase) (Acyl-activating enzyme)	0.09	-	cyt	0					667
Q6BQF2 UniProt NPD GO	ACS1_DEBHA	Acetyl-coenzyme A synthetase 1 (EC 6.2.1.1) (Acetate--CoA ligase 1) (Acyl-activating enzyme 1)	0.09	-	nuc	0					671
Q750T7 UniProt NPD GO	ACS2_ASHGO	Acetyl-coenzyme A synthetase 2 (EC 6.2.1.1) (Acetate--CoA ligase 2) (Acyl-activating enzyme 2)	0.09	-	nuc	0					687
Q9NR19 UniProt NPD GO	ACSA_HUMAN	Acetyl-coenzyme A synthetase, cytoplasmic (EC 6.2.1.1) (Acetate--CoA ligase) (Acyl-activating enzyme ...	0.09	-	mit	0	Cytoplasm	cytoplasm [IC]	605832		701
O00400 UniProt NPD GO	ACATN_HUMAN	Acetyl-coenzyme A transporter 1 (AT-1) (Acetyl-CoA transporter) (Solute carrier family 33 member 1)	0.09	-	end	11	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum membrane [TAS] integral to plasma membrane [TAS] membrane fraction [TAS]	603690		549
P02712 UniProt NPD GO	ACHB_TORCA	Acetylcholine receptor protein subunit beta precursor	0.09	-	end	5 *	Membrane; multi-pass membrane protein			1LK1	493
P02718 UniProt NPD GO	ACHD_TORCA	Acetylcholine receptor protein subunit delta precursor	0.09	-	end	4	Membrane; multi-pass membrane protein			1LK1	522
P22303 UniProt NPD GO	ACES_HUMAN	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.09	-	exc	0		basal lamina [NAS] extracellular region [TAS]	100740	2CLJ	614
Q8NJP6 UniProt NPD GO	AXE1_PENPU	Acetylxylan esterase 1 precursor (EC 3.1.1.72) (AXE I)	0.09	-	mit	0	Secreted protein				382
O59893 UniProt NPD GO	AXE2_PENPU	Acetylxylan esterase 2 precursor (EC 3.1.1.72) (AXE II)	0.09	-	exc	0	Secreted protein			2AXE	234
Q99034 UniProt NPD GO	AXE1_TRIRE	Acetylxylan esterase precursor (EC 3.1.1.72)	0.09	-	exc	0	Secreted protein			1QOZ	302
P93761 UniProt NPD GO	INV1_CAPAN	Acid beta-fructofuranosidase AIV-18 (EC 3.2.1.26) (Acid sucrose hydrolase) (Acid invertase)	0.09	-	cyt	1 *					640
Q92389 UniProt NPD GO	AXP1_YARLI	Acid extracellular protease precursor (EC 3.4.23.-)	0.09	-	exc	0	Secreted protein				397
P08091 UniProt NPD GO	PPA1_SCHPO	Acid phosphatase precursor (EC 3.1.3.2)	0.09	-	vac	0	Cell wall				453
O95626 UniProt NPD GO	AN32D_HUMAN	Acidic leucine-rich nuclear phosphoprotein 32 family member D (Phosphoprotein 32-related protein 2) ...	0.09	-	nuc	0			606878		131
O62220 UniProt NPD GO	AN321_CAEEL	Acidic leucine-rich nuclear phosphoprotein 32-related protein 1 (ANP32/acidic nuclear phosphoprotein ...	0.09	-	cyt	0					229
Q95M17 UniProt NPD GO	CHIA_BOVIN	Acidic mammalian chitinase precursor (EC 3.2.1.14) (AMCase) (Chitin-binding protein b04) (CBPb04)	0.09	-	vac	0	Secreted protein				472
P20004 UniProt NPD GO	ACON_BOVIN	Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase)	0.09	-	mit	0	Mitochondrion	mitochondrion [ISS]		8ACN	780
Q99798 UniProt NPD GO	ACON_HUMAN	Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase)	0.09	-	mit	0	Mitochondrion (By similarity)	mitochondrion [TAS]	100850		780
Q99KI0 UniProt NPD GO	ACON_MOUSE	Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase)	0.09	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			780
O13966 UniProt NPD GO	ACON_SCHPO	Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase)	0.09	-	mit	0	Mitochondrion (Potential)				778
P50138 UniProt NPD GO	ACT_PUCGR	Actin	0.09	-	cyt	0	Cytoplasm				375
P18601 UniProt NPD GO	ACT2_ARTSX	Actin, clone 211	0.09	-	cyt	0	Cytoplasm				376
P15475 UniProt NPD GO	ACTB_XENBO	Actin, cytoplasmic 1 (Beta actin)	0.09	-	cyt	0	Cytoplasm				376
P60712 UniProt NPD GO	ACTB_BOVIN	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm			2BTF	375
O18840 UniProt NPD GO	ACTB_CANFA	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm (By similarity)				375
Q71FK5 UniProt NPD GO	ACTB_CAVPO	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
Q76N69 UniProt NPD GO	ACTB_CERAE	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
P84856 UniProt NPD GO	ACTB_CERPY	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				361
P60706 UniProt NPD GO	ACTB_CHICK	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
P83751 UniProt NPD GO	ACTB_CTEID	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375

You are viewing entries 65601 to 65650 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.