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
Q10316 UniProt NPD GO	ARPC5_SCHPO	ARP2/3 complex 16 kDa subunit (p16-ARC)	0.11	-	cyt	0		actin cortical patch [IDA] contractile ring (sensu Fungi) [IDA] medial ring [IDA]			152
P46586 UniProt NPD GO	HIS1_CANAL	ATP phosphoribosyltransferase (EC 2.4.2.17) (ATP-PRTase) (ATP-PRT)	0.11	-	cyt	0	Cytoplasm (By similarity)				298
Q40608 UniProt NPD GO	ATPX_OCHNE	ATP synthase B' chain (EC 3.6.3.14) (Subunit II)	0.11	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				163
O79551 UniProt NPD GO	ATP6_DINSE	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.11	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P07138 UniProt NPD GO	ATPE_IPOBA	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.11	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				133
Q6EW73 UniProt NPD GO	ATPE_NYMAL	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.11	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				134
Q9MTP6 UniProt NPD GO	ATPE_OENHO	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.11	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				133
O79550 UniProt NPD GO	ATP8_DINSE	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.11	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				52
Q8W9N2 UniProt NPD GO	ATP8_DUGDU	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.11	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q34571 UniProt NPD GO	ATP8_GORGO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.11	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				68
Q9MLQ5 UniProt NPD GO	ATP8_LIMPO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.11	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				51
O79674 UniProt NPD GO	ATP8_PELSU	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.11	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
P92896 UniProt NPD GO	ATP8_PONPP	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.11	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				68
Q7SE71 UniProt NPD GO	ATPF_NEUCR	ATP synthase subunit 4, mitochondrial precursor (EC 3.6.3.14)	0.11	-	nuc	0	Mitochondrion (By similarity)				241
Q20EV9 UniProt NPD GO	ATPA_OLTVI	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.11	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
Q3ZJ00 UniProt NPD GO	ATPA_PSEAK	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.11	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				502
P17614 UniProt NPD GO	ATPBM_NICPL	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.11	-	mit	0	Mitochondrion			1PYV	560
Q9C5A9 UniProt NPD GO	ATPBO_ARATH	ATP synthase subunit beta-3, mitochondrial precursor (EC 3.6.3.14)	0.11	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			559
Q2LGZ2 UniProt NPD GO	ATPG_VIGUN	ATP synthase subunit gamma, chloroplast (EC 3.6.3.14) [Contains: Inceptin] (Fragment)	0.11	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane (By similarity)				118
Q9JI39 UniProt NPD GO	ABCBA_MOUSE	ATP-binding cassette sub-family B member 10, mitochondrial precursor (ATP-binding cassette transport ...	0.11	-	mit	5	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			715
Q91VR5 UniProt NPD GO	DDX1_MOUSE	ATP-dependent RNA helicase DDX1 (EC 3.6.1.-) (DEAD box protein 1)	0.11	-	cyt	0					740
Q2U6P7 UniProt NPD GO	SUB2_ASPOR	ATP-dependent RNA helicase sub2 (EC 3.6.1.-)	0.11	-	cyt	0	Nucleus (By similarity)				441
P33740 UniProt NPD GO	MS2B_DROSI	Accessory gland-specific peptide 26Ab precursor (Male accessory gland secretory protein 355B)	0.11	-	vac	0	Secreted protein; extracellular space				90
Q9UUJ9 UniProt NPD GO	ACH1_SCHPO	Acetyl-CoA hydrolase (EC 3.1.2.1) (Acetyl-CoA deacylase) (Acetyl-CoA acylase)	0.11	-	cyt	0	Cytoplasm (By similarity)				521
Q758X0 UniProt NPD GO	ACS1_ASHGO	Acetyl-coenzyme A synthetase 1 (EC 6.2.1.1) (Acetate--CoA ligase 1) (Acyl-activating enzyme 1)	0.11	-	nuc	0	Microsome (Potential)				694
Q99J27 UniProt NPD GO	ACATN_MOUSE	Acetyl-coenzyme A transporter 1 (AT-1) (Acetyl-CoA transporter) (Solute carrier family 33 member 1)	0.11	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				550
P25109 UniProt NPD GO	ACHB_RAT	Acetylcholine receptor protein subunit beta precursor	0.11	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [IMP]			501
P23795 UniProt NPD GO	ACES_BOVIN	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.11	-	exc	0					613
P07692 UniProt NPD GO	ACES_TORMA	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.11	-	end	0	Isoform H: Cell membrane; lipid-anchor; GPI-anchor. Isoform T: Cell membrane; peripheral membrane pr ...				590
Q29499 UniProt NPD GO	ACES_RABIT	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE) (Fragment)	0.11	-	cyt	0					584
Q9WV54 UniProt NPD GO	ASAH1_MOUSE	Acid ceramidase precursor (EC 3.5.1.23) (Acylsphingosine deacylase) (N-acylsphingosine amidohydrolas ...	0.11	-	exc	0	Lysosome				394
Q05539 UniProt NPD GO	CHIA_LYCES	Acidic 26 kDa endochitinase precursor (EC 3.2.1.14)	0.11	-	vac	1 *	Secreted protein; extracellular space				253
Q40114 UniProt NPD GO	CHIA_LYCCI	Acidic endochitinase pcht28 precursor (EC 3.2.1.14)	0.11	-	vac	1 *	Secreted protein; extracellular space				253
P22327 UniProt NPD GO	AJSP1_TRINI	Acidic juvenile hormone-suppressible protein 1 precursor (AJHSP1)	0.11	-	exc	0	Secreted protein; extracellular space				624
P16276 UniProt NPD GO	ACON_PIG	Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase)	0.11	-	mit	0	Mitochondrion			7ACN	781
P02583 UniProt NPD GO	ACT2_OXYFA	Actin, cytoplasmic (Actin, micronuclear)	0.11	-	cyt	0	Cytoplasm				357
P53460 UniProt NPD GO	ACT1_HALRO	Actin, muscle 1A	0.11	-	cyt	0	Cytoplasm				378
Q9FVI1 UniProt NPD GO	ADF2_PETHY	Actin-depolymerizing factor 2 (ADF 2)	0.11	-	cyt	0					143
Q9ZSK3 UniProt NPD GO	ADF4_ARATH	Actin-depolymerizing factor 4 (ADF-4) (AtADF4)	0.11	-	cyt	0					139
P61160 UniProt NPD GO	ARP2_HUMAN	Actin-like protein 2 (Actin-related protein 2)	0.11	-	cyt	0			604221		394
P61161 UniProt NPD GO	ARP2_MOUSE	Actin-like protein 2 (Actin-related protein 2)	0.11	-	cyt	0					394
Q5R4K0 UniProt NPD GO	ARP2_PONPY	Actin-like protein 2 (Actin-related protein 2)	0.11	-	cyt	0					394
Q5M7U6 UniProt NPD GO	ARP2_RAT	Actin-like protein 2 (Actin-related protein 2)	0.11	-	cyt	0					394
Q9UUJ1 UniProt NPD GO	ARP2_SCHPO	Actin-like protein 2 (Actin-related protein 2)	0.11	-	cyt	0		Arp2/3 protein complex [TAS]			390
P32381 UniProt NPD GO	ARP2_YEAST	Actin-like protein 2 (Actin-related protein 2) (Actin-like protein ARP2)	0.11	-	cyt	0		Arp2/3 protein complex [IDA] mitochondrion [TAS]			391
Q9PW35 UniProt NPD GO	ACLA_AGKAC	Acutolysin-A precursor (EC 3.4.24.-) (HI)	0.11	-	nuc	0	Secreted protein			1BUD	413
P25702 UniProt NPD GO	ACP3_ARATH	Acyl carrier protein 3, chloroplast precursor (ACP)	0.11	-	mit	0	Plastid; chloroplast				136
P10352 UniProt NPD GO	ACP1_BRANA	Acyl carrier protein, chloroplast precursor (ACP) (ACP05) (Clone 29C08)	0.11	-	mit	0	Plastid; chloroplast				134
Q9CR21 UniProt NPD GO	ACPM_MOUSE	Acyl carrier protein, mitochondrial precursor (ACP) (NADH-ubiquinone oxidoreductase 9.6 kDa subunit) ...	0.11	-	mit	0	Mitochondrion	mitochondrion [IDA]			156
Q5ASI2 UniProt NPD GO	APTH1_EMENI	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.11	-	cyt	0	Cytoplasm (By similarity)				239

You are viewing entries 62251 to 62300 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.