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
P12715 UniProt NPD GO	ACT1_OXYNO	Actin, cytoplasmic (Actin, macronuclear)	0.04	-	cyt	0	Cytoplasm				375
P55805 UniProt NPD GO	ACT2_OXYNO	Actin, cytoplasmic (Actin, micronuclear)	0.04	-	cyt	0	Cytoplasm				375
P10992 UniProt NPD GO	ACT1_TETTH	Actin, macronuclear	0.04	-	cyt	0	Cytoplasm			1DEJ	375
P35432 UniProt NPD GO	ACT1_ECHGR	Actin-1	0.04	-	cyt	0	Cytoplasm				375
Q9NJV4 UniProt NPD GO	ACT1_NAEGR	Actin-1	0.04	-	cyt	0	Cytoplasm				374
Q96292 UniProt NPD GO	ACT2_ARATH	Actin-2	0.04	-	cyt	0	Cytoplasm				377
P23344 UniProt NPD GO	ACT2_DAUCA	Actin-2	0.04	-	cyt	0	Cytoplasm				381
P17298 UniProt NPD GO	ACT2_ORYSA	Actin-2	0.04	-	cyt	0	Cytoplasm	actin cytoskeleton [IEP] cytoplasm [IEP]			377
P53471 UniProt NPD GO	ACT2_SCHMA	Actin-2	0.04	-	cyt	0	Cytoplasm				376
P17299 UniProt NPD GO	ACT3_ORYSA	Actin-3	0.04	-	cyt	0	Cytoplasm	actin cytoskeleton [IEP] cytoplasm [IEP]			377
Q96482 UniProt NPD GO	ACT1_LYCES	Actin-41 (Fragment)	0.04	-	cyt	0	Cytoplasm				336
P30167 UniProt NPD GO	ACT3_SOLTU	Actin-58	0.04	-	cyt	0	Cytoplasm				377
P53492 UniProt NPD GO	ACT7_ARATH	Actin-7 (Actin-2)	0.04	-	cyt	0	Cytoplasm				377
Q96293 UniProt NPD GO	ACT8_ARATH	Actin-8	0.04	-	cyt	0	Cytoplasm				377
P30171 UniProt NPD GO	ACT11_SOLTU	Actin-97	0.04	-	cyt	0	Cytoplasm				377
P53490 UniProt NPD GO	ARP3_ACACA	Actin-like protein 3 (Actin-related protein 3)	0.04	-	cyt	0					427
P32392 UniProt NPD GO	ARP3_DROME	Actin-like protein 3 (Actin-related protein 3) (Actin-like protein 66B) (Actin-2)	0.04	-	cyt	0					418
Q9QZB7 UniProt NPD GO	ARP10_MOUSE	Actin-related protein 10	0.04	-	cyt	0		dynactin complex [IDA]			417
O96623 UniProt NPD GO	ARPC2_DICDI	Actin-related protein 2/3 complex subunit 2 (ARP2/3 complex 34 kDa subunit) (p34-ARC)	0.04	-	cyt	0					293
Q8TDY3 UniProt NPD GO	ARPM2_HUMAN	Actin-related protein T2 (ARP-T2) (Actin-related protein M2)	0.04	-	cyt	0			608535		377
Q5I2B1 UniProt NPD GO	ACTPG_OULOR	Actinoporin Or-G (Fragment)	0.04	-	cyt	0	Secreted protein. Found in nematocyst				173
P36896 UniProt NPD GO	ACV1B_HUMAN	Activin receptor type 1B precursor (EC 2.7.11.30) (ACTR-IB) (Serine/threonine-protein kinase recepto ...	0.04	-	nuc	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	601300		505
P93092 UniProt NPD GO	ACP1_CASGL	Acyl carrier protein 1, chloroplast precursor (ACP 1)	0.04	-	mit	0	Plastid; chloroplast				136
P23235 UniProt NPD GO	ACP2_SPIOL	Acyl carrier protein 2, chloroplast precursor (Acyl carrier protein II) (ACP II)	0.04	-	mit	0	Plastid; chloroplast				130
P11943 UniProt NPD GO	ACPM_NEUCR	Acyl carrier protein, mitochondrial precursor (ACP) (NADH-ubiquinone oxidoreductase 9.6 kDa subunit) ...	0.04	-	mit	0	Mitochondrion				134
P31786 UniProt NPD GO	ACBP_MOUSE	Acyl-CoA-binding protein (ACBP) (Diazepam-binding inhibitor) (DBI) (Endozepine) (EP)	0.04	-	cyt	0		mitochondrion [IDA]			86
P11030 UniProt NPD GO	ACBP_RAT	Acyl-CoA-binding protein (ACBP) (Diazepam-binding inhibitor) (DBI) (Endozepine) (EP) [Contains: Tria ...	0.04	-	cyt	0					86
P46253 UniProt NPD GO	STAD_SOLTU	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.04	-	mit	0	Plastid; chloroplast (By similarity). In green tissue, found in chloroplasts. Plastid (By similarity ...				393
Q6FW75 UniProt NPD GO	APTH1_CANGA	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.04	-	cyt	0	Cytoplasm (By similarity)				230
P24540 UniProt NPD GO	ACYP1_PIG	Acylphosphatase-1 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 1) (Acylphosphatase, organ-common typ ...	0.04	-	cyt	0					100
Q9VF36 UniProt NPD GO	ACYP2_DROME	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2) (AcPDro2)	0.04	-	cyt	0		cytoplasm [TAS]		1URR	102
P56375 UniProt NPD GO	ACYP2_MOUSE	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2) (Acylphosphatase, muscle type isoz ...	0.04	-	cyt	0					97
P35745 UniProt NPD GO	ACYP2_RAT	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2) (Acylphosphatase, muscle type isoz ...	0.04	-	cyt	0					96
P12426 UniProt NPD GO	APT_DROME	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.04	-	cyt	0	Cytoplasm				182
P54363 UniProt NPD GO	APT_DROPS	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.04	-	nuc	0	Cytoplasm				181
P08030 UniProt NPD GO	APT_MOUSE	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.04	-	mit	0	Cytoplasm				180
P31107 UniProt NPD GO	DMS2_PHYBI	Adenoregulin precursor (Dermaseptin BII) (Dermaseptin B2)	0.04	-	exc	0	Secreted protein				81
P28647 UniProt NPD GO	AA3R_RAT	Adenosine A3 receptor (TGPCR1)	0.04	-	end	7 *	Membrane; multi-pass membrane protein	presynaptic membrane [IDA]			320
Q9LK36 UniProt NPD GO	SAHH2_ARATH	Adenosylhomocysteinase 2 (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase 1) (SAH hydrolase 2) (Ado ...	0.04	-	nuc	0					485
Q08479 UniProt NPD GO	KAD1_ORYSA	Adenylate kinase A (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.04	-	cyt	0					241
Q9Y3D8 UniProt NPD GO	KAD6_HUMAN	Adenylate kinase isoenzyme 6 (EC 2.7.4.3) (ATP-AMP transphosphorylase 6)	0.04	-	cyt	0	Nucleus			1RKB	172
Q8VCP8 UniProt NPD GO	KAD6_MOUSE	Adenylate kinase isoenzyme 6 (EC 2.7.4.3) (ATP-AMP transphosphorylase 6)	0.04	-	cyt	0	Nucleus (By similarity)				172
Q15848 UniProt NPD GO	ADIPO_HUMAN	Adiponectin precursor (Adipocyte, C1q and collagen domain-containing protein) (30 kDa adipocyte comp ...	0.04	-	end	0	Secreted protein	extracellular region [NAS]	605441		244
Q9TU77 UniProt NPD GO	ACTHR_SHEEP	Adrenocorticotropic hormone receptor (ACTH receptor) (ACTH-R) (Melanocortin receptor 2) (MC2-R) (Adr ...	0.04	-	end	7 *	Membrane; multi-pass membrane protein				295
P80517 UniProt NPD GO	CU26_ARADI	Adult-specific rigid cuticular protein 12.6 (ACP 12.6)	0.04	-	cyt	0					127
O42717 UniProt NPD GO	AAPR1_AGRAE	Aegerolysin Aa-Pri1 precursor	0.04	-	nuc	0					145
Q9S8T1 UniProt NPD GO	LECB1_ARTTO	Agglutinin beta-1 chain (Agglutinin beta-I chain) (Jacalin beta-I chain) (Fragment)	0.04	-		0					20
P52894 UniProt NPD GO	ALA2_HORVU	Alanine aminotransferase 2 (EC 2.6.1.2) (GPT) (Glutamic--pyruvic transaminase 2) (Glutamic--alanine ...	0.04	-	cyt	0					482
P40825 UniProt NPD GO	SYAC_YEAST	Alanyl-tRNA synthetase, cytoplasmic (EC 6.1.1.7) (Alanine--tRNA ligase) (AlaRS)	0.04	-	cyt	0	Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]			958
P62930 UniProt NPD GO	ALB1E_PEA	Albumin-1 E precursor (PA1 E) (PsaA1b014) (Psa) [Contains: Albumin-1 E chain b (PA1b E) (Leginsulin ...	0.04	-	nuc	0					130

You are viewing entries 76201 to 76250 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.