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
Q9SI64 UniProt NPD GO	SPE1_ARATH	Arginine decarboxylase 1 (EC 4.1.1.19) (ARGDC 1) (ADC 1) (ADC-O)	0.04	-	cyt	0					702
P22675 UniProt NPD GO	ARLY_CHLRE	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL)	0.04	-	nuc	0					473
Q01752 UniProt NPD GO	AAD_PHACH	Aryl-alcohol dehydrogenase [NADP+] (EC 1.1.1.91) (AAD)	0.04	-	cyt	0					385
Q00050 UniProt NPD GO	ASPH_ASPFU	Asp-hemolysin precursor (Asp-HS)	0.04	-	cyt	0					139
P49093 UniProt NPD GO	ASNS2_LOTJA	Asparagine synthetase [glutamine-hydrolyzing] 2 (EC 6.3.5.4) (Glutamine-dependent asparagine synthet ...	0.04	-	mit	0					585
P41908 UniProt NPD GO	SYNC_SACDO	Asparaginyl-tRNA synthetase, cytoplasmic (EC 6.1.1.22) (Asparagine--tRNA ligase) (AsnRS) (Fragment)	0.04	-	cyt	0	Cytoplasm				87
P58519 UniProt NPD GO	API5_SOLTU	Aspartic protease inhibitor 5 precursor (pi13) (PI-13)	0.04	-	exc	1 *	Vacuole (By similarity)				220
Q9R1T5 UniProt NPD GO	ACY2_RAT	Aspartoacylase (EC 3.5.1.15) (Aminoacylase-2) (ACY-2)	0.04	-	cyt	0				2GU2	314
O74971 UniProt NPD GO	ATG5_SCHPO	Autophagy protein 5	0.04	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				261
Q6CUZ1 UniProt NPD GO	ATG22_KLULA	Autophagy-related protein 22	0.04	-	end	12 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				492
Q6PFS7 UniProt NPD GO	ATG3_BRARE	Autophagy-related protein 3 (APG3-like)	0.04	-	nuc	0	Cytoplasm (By similarity)				317
Q6C4Q9 UniProt NPD GO	ATG3_YARLI	Autophagy-related protein 3 (Autophagy-related E2-like conjugation enzyme ATG3)	0.04	-	cyt	0	Cytoplasm (By similarity)				366
Q7SDY2 UniProt NPD GO	ATG3_NEUCR	Autophagy-related protein 3 (Autophagy-related E2-like conjugation enzyme atg-3)	0.04	-	mit	0	Cytoplasm (By similarity)				352
Q9FEL6 UniProt NPD GO	LAX3_MEDTR	Auxin transporter-like protein 3 (AUX1-like protein 3) (MtLAX3)	0.04	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				465
Q38832 UniProt NPD GO	IAA14_ARATH	Auxin-responsive protein IAA14 (Indoleacetic acid-induced protein 14) (SOLITARY-ROOT protein)	0.04	-	nuc	0	Nucleus				228
P93830 UniProt NPD GO	IAA17_ARATH	Auxin-responsive protein IAA17 (Indoleacetic acid-induced protein 17) (Auxin response 3)	0.04	-	nuc	0	Nucleus				229
P11393 UniProt NPD GO	PHEB_PORCR	B-phycoerythrin beta chain	0.04	-	mit	0	Periphery of the rods of the phycobilisome				177
P29948 UniProt NPD GO	PHEB_PORSO	B-phycoerythrin beta chain	0.04	-	mit	0	Periphery of the rods of the phycobilisome				177
Q02037 UniProt NPD GO	PHEB_RHOVL	B-phycoerythrin beta chain	0.04	-	nuc	0	Periphery of the rods of the phycobilisome				177
Q8C1E1 UniProt NPD GO	BPIL1_MOUSE	Bactericidal/permeability-increasing protein-like 1 precursor	0.04	-	vac	1 *	Secreted protein (By similarity)				462
P28027 UniProt NPD GO	BRA2_CHITH	Balbiani ring A 28 kDa protein precursor	0.04	-	end	0	Secreted protein				245
Q6P026 UniProt NPD GO	BAF_BRARE	Barrier-to-autointegration factor	0.04	-	cyt	0	Nucleus (By similarity)				90
P11670 UniProt NPD GO	PRB1_TOBAC	Basic form of pathogenesis-related protein 1 precursor (PRP 1)	0.04	-	vac	0					177
P22584 UniProt NPD GO	LECB1_PSOSC	Basic lectin B1 (Fragment)	0.04	-		0					14
P04971 UniProt NPD GO	VSPA_BOTAT	Batroxobin precursor (EC 3.4.21.74) (BX) (Bothrops atrox serine proteinase) (Venombin A) (Defibrase) ...	0.04	-	exc	0	Secreted protein				255
Q7T381 UniProt NPD GO	BOK_BRARE	Bcl-2-related ovarian killer protein homolog	0.04	-	nuc	0					211
Q8ISB6 UniProt NPD GO	BGBP2_MANSE	Beta-1,3-glucan-binding protein 2 precursor (BGBP-2) (Beta-1,3-glucan recognition protein 2) (BetaGR ...	0.04	-	mit	0	Secreted protein	extracellular region [IDA]			482
O60513 UniProt NPD GO	B4GT4_HUMAN	Beta-1,4-galactosyltransferase 4 (EC 2.4.1.-) (Beta-1,4-GalTase 4) (Beta4Gal-T4) (b4Gal-T4) (UDP-gal ...	0.04	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Trans cist ...	integral to membrane [TAS]	604015		344
Q9JJ04 UniProt NPD GO	B4GT4_MOUSE	Beta-1,4-galactosyltransferase 4 (EC 2.4.1.-) (Beta-1,4-GalTase 4) (Beta4Gal-T4) (b4Gal-T4) (UDP-gal ...	0.04	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				344
Q95M68 UniProt NPD GO	BD01_GORGO	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.04	-	exc	1 *	Secreted protein				68
Q8R2I3 UniProt NPD GO	BD35_MOUSE	Beta-defensin 35 precursor (Defensin, beta 35) (BD-35) (mBD-35)	0.04	-	mit	1 *	Secreted protein (By similarity)				63
Q8C1G4 UniProt NPD GO	BD41_MOUSE	Beta-defensin 41 precursor (Defensin, beta 41) (BD-41) (mBD-41)	0.04	-	mit	0	Secreted protein (By similarity)				62
P01205 UniProt NPD GO	END2_ONCKE	Beta-endorphin-2 (Beta-endorphin II) [Contains: Met-enkephalin]	0.04	-	cyt	0					30
Q9SKU2 UniProt NPD GO	EXPB1_ARATH	Beta-expansin 1 precursor (AtEXPB1) (At-EXPB1) (Ath-ExpBeta-1.5)	0.04	-	exc	0	Cell wall; peripheral membrane protein				271
P26792 UniProt NPD GO	INV1_DAUCA	Beta-fructofuranosidase, insoluble isoenzyme 1 precursor (EC 3.2.1.26) (Sucrose hydrolase 1) (Invert ...	0.04	-	end	0	Cell wall. Ionically bound to the cell wall				592
Q56UD1 UniProt NPD GO	INV5_ORYSA	Beta-fructofuranosidase, insoluble isoenzyme 5 (EC 3.2.1.26) (Sucrose hydrolase 5) (Invertase 5) (Ce ...	0.04	-	cyt	0	Secreted protein; extracellular space; apoplast (Probable). Cell wall (Probable). Associated to the ...				526
P43077 UniProt NPD GO	HEX1_CANAL	Beta-hexosaminidase precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-GlcNAcase) (Beta-N ...	0.04	-	cyt	0					562
Q92012 UniProt NPD GO	KRFJ_COTJA	Beta-keratin-related protein	0.04	-	nuc	0					108
P11944 UniProt NPD GO	LACB_MACGI	Beta-lactoglobulin (Beta-LG)	0.04	-	cyt	0					155
P83242 UniProt NPD GO	MSMB_STRCA	Beta-microseminoprotein	0.04	-	nuc	0	Secreted protein	extracellular region [TAS]			90
O24174 UniProt NPD GO	BADH_ORYSA	Betaine-aldehyde dehydrogenase (EC 1.2.1.8) (BADH)	0.04	-	pox	0	Peroxisome				505
P42757 UniProt NPD GO	BADH_ATRHO	Betaine-aldehyde dehydrogenase, chloroplast precursor (EC 1.2.1.8) (BADH)	0.04	-	cyt	0	Plastid; chloroplast				502
Q9IB75 UniProt NPD GO	PGS1_XENLA	Biglycan precursor	0.04	-	vac	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				368
Q9Y2P5 UniProt NPD GO	S27A5_HUMAN	Bile acyl-CoA synthetase (EC 6.2.1.7) (BACS) (Bile acid CoA ligase) (BA-CoA ligase) (BAL) (Cholate-- ...	0.04	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS]	603314		690
Q12737 UniProt NPD GO	BLRO_MYRVE	Bilirubin oxidase precursor (EC 1.3.3.5)	0.04	-	vac	0					572
Q8AV84 UniProt NPD GO	BTD_FUGRU	Biotinidase precursor (EC 3.5.1.12)	0.04	-	vac	0	Secreted protein; extracellular space (By similarity)				504
Q8R016 UniProt NPD GO	BLMH_MOUSE	Bleomycin hydrolase (EC 3.4.22.40) (BLM hydrolase) (BMH) (BH)	0.04	-	cyt	0	Cytoplasm (By similarity)	soluble fraction [IDA]			455
Q41001 UniProt NPD GO	BCP_PEA	Blue copper protein precursor	0.04	-	mit	2 *					189
P03999 UniProt NPD GO	OPSB_HUMAN	Blue-sensitive opsin (BOP) (Blue cone photoreceptor pigment)	0.04	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	190900	1KPN	348
P60573 UniProt NPD GO	OPSB_PANPA	Blue-sensitive opsin (BOP) (Blue cone photoreceptor pigment)	0.04	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				348

You are viewing entries 76351 to 76400 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.