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
P28250 UniProt NPD GO	ATPB_ANGLY	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				492
Q31794 UniProt NPD GO	ATPB_ANTFO	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				492
Q9TMV0 UniProt NPD GO	ATPB_BEARE	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				495
Q9MRR9 UniProt NPD GO	ATPB_BRASC	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
Q8SLY2 UniProt NPD GO	ATPB_CHAGL	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				493
Q9MU80 UniProt NPD GO	ATPB_CHASI	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P06541 UniProt NPD GO	ATPB_CHLRE	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				480
P32978 UniProt NPD GO	ATPB_CHLVU	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				481
P30158 UniProt NPD GO	ATPB_DICDH	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				481
Q9BA84 UniProt NPD GO	ATPB_HYOLA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P07137 UniProt NPD GO	ATPB_IPOBA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				490
Q9BBU0 UniProt NPD GO	ATPB_LOTJA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P06284 UniProt NPD GO	ATPB_MARPO	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				492
Q9TKI7 UniProt NPD GO	ATPB_MEDSA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				490
Q8MBF7 UniProt NPD GO	ATPB_MONCA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
Q9TL34 UniProt NPD GO	ATPB_NEPOL	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				491
P69369 UniProt NPD GO	ATPB_NICBI	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P69370 UniProt NPD GO	ATPB_NICPL	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P26530 UniProt NPD GO	ATPB_NICRU	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P12085 UniProt NPD GO	ATPB_ORYSA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P80658 UniProt NPD GO	ATPB_PHYPA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				494
O47037 UniProt NPD GO	ATPB_PICAB	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				488
P41622 UniProt NPD GO	ATPB_PINTH	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				492
O03081 UniProt NPD GO	ATPB_PSINU	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				492
P00825 UniProt NPD GO	ATPB_SPIOL	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)			1KMH	498
P00826 UniProt NPD GO	ATPB_TOBAC	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
O03066 UniProt NPD GO	ATPB_BLEOC	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				395
O03067 UniProt NPD GO	ATPB_DICAN	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				476
O03069 UniProt NPD GO	ATPB_EQUAR	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				473
O03085 UniProt NPD GO	ATPB_VANDA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				479
P43395 UniProt NPD GO	ATPBM_ACTCH	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) (PKIWI505) (Fragment)	0.01	-	cyt	0	Mitochondrion				173
P38482 UniProt NPD GO	ATPBM_CHLRE	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.01	-	mit	0	Mitochondrion				574
Q9PTY0 UniProt NPD GO	ATPB_CYPCA	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.01	-	gol	0	Mitochondrion				518
Q05825 UniProt NPD GO	ATPB_DROME	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.01	-	mit	0	Mitochondrion				505
P06576 UniProt NPD GO	ATPB_HUMAN	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.01	-	mit	0	Mitochondrion	proton-transporting ATP synthase complex (s... [TAS] proton-transporting ATP synthase, catalytic... [TAS]	102910		529
P56480 UniProt NPD GO	ATPB_MOUSE	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.01	-	mit	0	Mitochondrion	mitochondrial inner membrane [IDA] mitochondrion [IDA]			529
Q5QA83 UniProt NPD GO	CLPP_ACOGR	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.01	-	cyt	0	Plastid; chloroplast				202
Q85FJ8 UniProt NPD GO	CLPP_ADICA	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.01	-	cyt	0	Plastid; chloroplast				200
P56772 UniProt NPD GO	CLPP_ARATH	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.01	-	nuc	2	Plastid; chloroplast			1R8Z	196
P36387 UniProt NPD GO	CLPP_PINCO	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.01	-	nuc	0	Plastid; chloroplast				205
P41609 UniProt NPD GO	CLPP_PINTH	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.01	-	nuc	0	Plastid; chloroplast				196
P15450 UniProt NPD GO	ABAE_APIME	Abaecin precursor	0.01	-	vac	1 *	Secreted protein				53
Q8VCR7 UniProt NPD GO	AB14B_MOUSE	Abhydrolase domain-containing protein 14B (CCG1-interacting factor B)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				210
O46199 UniProt NPD GO	A53E_DROME	Accessory gland protein Acp53Ea precursor	0.01	-	exc	0	Secreted protein (Probable)				120
O46202 UniProt NPD GO	A62F_DROME	Accessory gland protein Acp62F precursor	0.01	-	nuc	0	Secreted protein (Probable)				115
Q9VBL7 UniProt NPD GO	MS57B_DROME	Accessory gland-specific peptide 57Db precursor (Male accessory gland secretory protein 57Db)	0.01	-	exc	0	Secreted protein	extracellular region [NAS]			40
Q6L8K7 UniProt NPD GO	THIL_YARLI	Acetyl-CoA acetyltransferase (EC 2.3.1.9) (Peroxisomal acetoacetyl-CoA thiolase) (Thiolase)	0.01	-	mit	0	Peroxisome				397
Q9BWD1 UniProt NPD GO	THIC_HUMAN	Acetyl-CoA acetyltransferase, cytosolic (EC 2.3.1.9) (Cytosolic acetoacetyl-CoA thiolase) (Acetyl Co ...	0.01	-	nuc	0	Cytoplasm	cytoplasm [TAS]	100678	1WL5	397
P32316 UniProt NPD GO	ACH1_YEAST	Acetyl-CoA hydrolase (EC 3.1.2.1) (Acetyl-CoA deacylase) (Acetyl-CoA acylase)	0.01	-	nuc	0	Cytoplasm	cytosol [IDA] mitochondrion [IDA]			526
Q6BS00 UniProt NPD GO	ACS2_DEBHA	Acetyl-coenzyme A synthetase 2 (EC 6.2.1.1) (Acetate--CoA ligase 2) (Acyl-activating enzyme 2)	0.01	-	nuc	0					679

You are viewing entries 86501 to 86550 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.