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
P00858 UniProt NPD GO	ATP8_ASPAM	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.04	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				48
P68528 UniProt NPD GO	ATP8_ONCMY	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.04	-	vac	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q02653 UniProt NPD GO	ATP8_PODAN	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.04	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				50
Q9XN27 UniProt NPD GO	ATP8_SALAL	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.04	-	vac	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
P68529 UniProt NPD GO	ATP8_SALSA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.04	-	vac	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q6FSD5 UniProt NPD GO	ATPO_CANGA	ATP synthase subunit 5, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral prot ...	0.04	-	mit	0	Mitochondrion				207
P00828 UniProt NPD GO	ATPB_HORVU	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.04	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P05037 UniProt NPD GO	ATPB_PEA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.04	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				491
O03073 UniProt NPD GO	ATPB_LONHI	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.04	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				208
O03080 UniProt NPD GO	ATPB_PTEES	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.04	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				473
P80083 UniProt NPD GO	ATPBM_SPIOL	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) (Fragment)	0.04	-		0	Mitochondrion				15
P46561 UniProt NPD GO	ATPB_CAEEL	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.04	-	mit	0	Mitochondrion				538
Q8VEJ1 UniProt NPD GO	ATPBB_MOUSE	ATP-binding domain 1 family member B	0.04	-	cyt	0					310
Q09134 UniProt NPD GO	GRPA_MEDFA	Abscisic acid and environmental stress-inducible protein	0.04	-	cyt	0					159
Q8I6R7 UniProt NPD GO	ACN2_ACAGO	Acanthoscurrin-2 precursor (Fragment)	0.04	+	cyt	0	Secreted protein	extracellular region [IDA]			131
O46227 UniProt NPD GO	A33A_DROME	Accessory gland peptide Acp33A precursor	0.04	-	exc	1 *	Secreted protein (Probable)	extracellular region [TAS]			47
O46200 UniProt NPD GO	A63F_DROME	Accessory gland protein Acp63F precursor	0.04	-	exc	0	Secreted protein (Probable)				81
Q9V3J3 UniProt NPD GO	MS57C_DROME	Accessory gland-specific peptide 57Dc precursor (Male accessory gland secretory protein 57Dc) (45 kD ...	0.04	-	cyt	0	Secreted protein	extracellular region [NAS]			103
P05623 UniProt NPD GO	A70A_DROME	Accessory gland-specific peptide 70A precursor (Paragonial peptide B)	0.04	-	vac	0	Secreted protein	extracellular region [TAS]			55
O78518 UniProt NPD GO	ILVB_GUITH	Acetolactate synthase large subunit (EC 2.2.1.6) (AHAS) (Acetohydroxy-acid synthase large subunit) ( ...	0.04	-	nuc	0	Plastid; chloroplast				575
Q9TLY1 UniProt NPD GO	ILVH_CYACA	Acetolactate synthase small subunit (EC 2.2.1.6) (AHAS) (Acetohydroxy-acid synthase small subunit) ( ...	0.04	-	cyt	0	Plastid; chloroplast				172
P51230 UniProt NPD GO	ILVH_PORPU	Acetolactate synthase small subunit (EC 2.2.1.6) (AHAS) (Acetohydroxy-acid synthase small subunit) ( ...	0.04	-	mit	0	Plastid; chloroplast				174
P36620 UniProt NPD GO	ILVB_SCHPO	Acetolactate synthase, mitochondrial precursor (EC 2.2.1.6) (Acetohydroxy-acid synthase) (ALS) (AHAS ...	0.04	-	mit	0	Mitochondrion				669
Q8CAY6 UniProt NPD GO	THIC_MOUSE	Acetyl-CoA acetyltransferase, cytosolic (EC 2.3.1.9) (Cytosolic acetoacetyl-CoA thiolase)	0.04	-	nuc	0	Cytoplasm (By similarity)				397
P15937 UniProt NPD GO	ACH1_NEUCR	Acetyl-CoA hydrolase (EC 3.1.2.1) (Acetyl-CoA deacylase) (Acetyl-CoA acylase) (Acetate utilization p ...	0.04	-	mit	0	Cytoplasm (By similarity)				525
P83773 UniProt NPD GO	ACH1_CANAL	Acetyl-CoA hydrolase (EC 3.1.2.1) (Acetyl-CoA deacylase) (Acetyl-CoA acylase) (Fragments)	0.04	-		0	Cytoplasm				20
Q27549 UniProt NPD GO	ACSA_CRYPV	Acetyl-coenzyme A synthetase (EC 6.2.1.1) (Acetate--CoA ligase) (Acyl-activating enzyme)	0.04	-	cyt	0					694
P36333 UniProt NPD GO	ACSA_PENCH	Acetyl-coenzyme A synthetase (EC 6.2.1.1) (Acetate--CoA ligase) (Acyl-activating enzyme)	0.04	-	end	0					669
Q8NJN3 UniProt NPD GO	ACS2_CANAL	Acetyl-coenzyme A synthetase 2 (EC 6.2.1.1) (Acetate--CoA ligase 2) (Acyl-activating enzyme 2) (Frag ...	0.04	-	nuc	0					581
P02709 UniProt NPD GO	ACHA_BOVIN	Acetylcholine receptor protein subunit alpha precursor	0.04	-	end	4	Membrane; multi-pass membrane protein				457
Q98880 UniProt NPD GO	ACHA_BRARE	Acetylcholine receptor protein subunit alpha precursor	0.04	-	end	4	Membrane; multi-pass membrane protein				456
P02708 UniProt NPD GO	ACHA_HUMAN	Acetylcholine receptor protein subunit alpha precursor	0.04	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]	608930		482
P04756 UniProt NPD GO	ACHA_MOUSE	Acetylcholine receptor protein subunit alpha precursor	0.04	-	end	4	Membrane; multi-pass membrane protein	Golgi apparatus [IDA] plasma membrane [IDA]			457
P25108 UniProt NPD GO	ACHA_RAT	Acetylcholine receptor protein subunit alpha precursor	0.04	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]			457
P02711 UniProt NPD GO	ACHA_TORMA	Acetylcholine receptor protein subunit alpha precursor	0.04	-	end	6 *	Membrane; multi-pass membrane protein			2BG9	461
P20782 UniProt NPD GO	ACHE_MOUSE	Acetylcholine receptor protein subunit epsilon precursor	0.04	-	end	4	Membrane; multi-pass membrane protein	postsynaptic membrane [IDA]			493
Q6FXA4 UniProt NPD GO	ARGD_CANGA	Acetylornithine aminotransferase, mitochondrial precursor (EC 2.6.1.11) (ACOAT)	0.04	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				427
Q9P3I3 UniProt NPD GO	ARGD_NEUCR	Acetylornithine aminotransferase, mitochondrial precursor (EC 2.6.1.11) (ACOAT)	0.04	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				461
P35903 UniProt NPD GO	ACHC_ACHFU	Achacin precursor	0.04	-	end	0					531
Q12546 UniProt NPD GO	PPA_ASPFI	Acid phosphatase precursor (EC 3.1.3.2) (pH 6-optimum acid phosphatase) (APase6)	0.04	-	exc	0	Secreted protein				614
P17541 UniProt NPD GO	CHIA_CUCSA	Acidic endochitinase precursor (EC 3.2.1.14)	0.04	-	exc	0	Secreted protein; extracellular space				292
Q6RY07 UniProt NPD GO	CHIA_RAT	Acidic mammalian chitinase precursor (EC 3.2.1.14) (AMCase)	0.04	-	exc	0	Secreted protein (By similarity)				473
Q9BZP6 UniProt NPD GO	CHIA_HUMAN	Acidic mammalian chitinase precursor (EC 3.2.1.14) (AMCase) (TSA1902)	0.04	-	cyt	0	Secreted protein (Probable). Isoform 2, isoform 3: Cytoplasm	cytoplasm [NAS] extracellular space [IC]	606080		476
P01000 UniProt NPD GO	IAC1_BOVIN	Acrosin inhibitor I (BUSI-I)	0.04	-	nuc	0	Secreted protein				63
P53500 UniProt NPD GO	ACT_CYAME	Actin	0.04	-	cyt	0	Cytoplasm				377
P11426 UniProt NPD GO	ACT_ENTHI	Actin	0.04	-	nuc	0	Cytoplasm				376
O81221 UniProt NPD GO	ACT_GOSHI	Actin	0.04	-	cyt	0	Cytoplasm				377
P13363 UniProt NPD GO	ACT_PHYME	Actin	0.04	-	cyt	0	Cytoplasm				375
Q9UVF3 UniProt NPD GO	ACT_YARLI	Actin	0.04	-	cyt	0	Cytoplasm				375
Q00215 UniProt NPD GO	ACTC_STYPL	Actin, cytoplasmic	0.04	-	cyt	0	Cytoplasm				375

You are viewing entries 76151 to 76200 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.