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
P26667 UniProt NPD GO	RBS2_WHEAT	Ribulose bisphosphate carboxylase small chain PW9, chloroplast precursor (EC 4.1.1.39) (RuBisCO smal ...	0.00	-	mit	0	Plastid; chloroplast				175
P05346 UniProt NPD GO	RBS1_BRANA	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.00	-	mit	0	Plastid; chloroplast				181
P16031 UniProt NPD GO	RBS_LARLA	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.00	-	mit	0	Plastid; chloroplast				189
P81084 UniProt NPD GO	RCA_PINPS	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast (RuBisCO activase) (RA) (Water str ...	0.00	-		0	Plastid; chloroplast; chloroplast stroma (By similarity)				10
Q755M2 UniProt NPD GO	RPE_ASHGO	Ribulose-phosphate 3-epimerase (EC 5.1.3.1) (Pentose-5-phosphate 3-epimerase) (PPE) (RPE)	0.00	-	cyt	0					239
Q6FL81 UniProt NPD GO	RPE_CANGA	Ribulose-phosphate 3-epimerase (EC 5.1.3.1) (Pentose-5-phosphate 3-epimerase) (PPE) (RPE)	0.00	-	cyt	0					246
P83937 UniProt NPD GO	VHR1_VIOHE	Root cyclotide 1 (Vhr1)	0.00	-	nuc	0					30
P84581 UniProt NPD GO	RUBB_POPEU	RuBisCO large subunit-binding protein subunit beta, chloroplast (60 kDa chaperonin subunit beta) (CP ...	0.00	-	cyt	0	Plastid; chloroplast				24
P82070 UniProt NPD GO	RBE11_LITRU	Rubellidin-1.1	0.00	-		0	Secreted protein				5
P82071 UniProt NPD GO	RBE21_LITRU	Rubellidin-2.1	0.00	-		0	Secreted protein				5
P82072 UniProt NPD GO	RBE31_LITRU	Rubellidin-3.1	0.00	-		0	Secreted protein				5
P82075 UniProt NPD GO	RBE42_LITRU	Rubellidin-4.2/4.3	0.00	-		0	Secreted protein				9
P80954 UniProt NPD GO	RUGA_RANRU	Rugosin-A	0.00	-	cyt	0	Secreted protein				33
P80956 UniProt NPD GO	RUGC_RANRU	Rugosin-C	0.00	-	cyt	0	Secreted protein				37
P08635 UniProt NPD GO	SAST_RAT	S-acyl fatty acid synthase thioesterase, medium chain (EC 3.1.2.14) (Oleoyl-ACP hydrolase) (Thioeste ...	0.00	-	mit	0					263
O76240 UniProt NPD GO	DCAM_TRYCR	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.00	-	cyt	0					370
P93254 UniProt NPD GO	METK_MESCR	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.00	-	cyt	0					392
P47916 UniProt NPD GO	METK_POPDE	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.00	-	cyt	0					395
P50301 UniProt NPD GO	METK_ACTCH	S-adenosylmethionine synthetase 1 (EC 2.5.1.6) (Methionine adenosyltransferase 1) (AdoMet synthetase ...	0.00	-	cyt	0					390
P23686 UniProt NPD GO	METK_ARATH	S-adenosylmethionine synthetase 1 (EC 2.5.1.6) (Methionine adenosyltransferase 1) (AdoMet synthetase ...	0.00	-	cyt	0					393
P50299 UniProt NPD GO	METK_HORVU	S-adenosylmethionine synthetase 1 (EC 2.5.1.6) (Methionine adenosyltransferase 1) (AdoMet synthetase ...	0.00	-	cyt	0					394
P46611 UniProt NPD GO	METK_ORYSA	S-adenosylmethionine synthetase 1 (EC 2.5.1.6) (Methionine adenosyltransferase 1) (AdoMet synthetase ...	0.00	-	cyt	0					396
P49612 UniProt NPD GO	METK_PEA	S-adenosylmethionine synthetase 1 (EC 2.5.1.6) (Methionine adenosyltransferase 1) (AdoMet synthetase ...	0.00	-	cyt	0					366
P31155 UniProt NPD GO	METK_PETCR	S-adenosylmethionine synthetase 1 (EC 2.5.1.6) (Methionine adenosyltransferase 1) (AdoMet synthetase ...	0.00	-	cyt	0					234
P50302 UniProt NPD GO	METL_ACTCH	S-adenosylmethionine synthetase 2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoMet synthetase ...	0.00	-	cyt	0					390
P43281 UniProt NPD GO	METL_LYCES	S-adenosylmethionine synthetase 2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoMet synthetase ...	0.00	-	cyt	0					393
P49613 UniProt NPD GO	METL_PEA	S-adenosylmethionine synthetase 2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoMet synthetase ...	0.00	-	cyt	0					374
P31156 UniProt NPD GO	METL_PETCR	S-adenosylmethionine synthetase 2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoMet synthetase ...	0.00	-	cyt	0					145
Q9D3G2 UniProt NPD GO	SLAF8_MOUSE	SLAM family member 8 precursor (B-lymphocyte activator macrophage expressed)	0.00	-	end	1	Membrane; single-pass type I membrane protein				278
P36379 UniProt NPD GO	SPRC_MUSVI	SPARC (Secreted protein acidic and rich in cysteine) (Osteonectin) (ON) (Basement-membrane protein 4 ...	0.00	-	cyt	0					26
Q5B464 UniProt NPD GO	HSV2_EMENI	SVP1-like protein 2	0.00	-	cyt	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Cytoplasmic vesicle; cytopl ...				317
Q7SFX6 UniProt NPD GO	LYS1_NEUCR	Saccharopine dehydrogenase [NAD+, L-lysine-forming] (EC 1.5.1.7) (Lysine--2-oxoglutarate reductase) ...	0.00	-	nuc	0					372
P38999 UniProt NPD GO	LYS9_YEAST	Saccharopine dehydrogenase [NADP+, L-glutamate-forming] (EC 1.5.1.10) (Saccharopine reductase)	0.00	-	end	0		cytoplasm [IDA]			446
P02842 UniProt NPD GO	SGS8_DROME	Salivary glue protein Sgs-8 precursor	0.00	-	exc	0					75
P81608 UniProt NPD GO	SAL_PIG	Salivary lipocalin precursor (SAL)	0.00	-	exc	0	Secreted protein			1GM6	191
P82239 UniProt NPD GO	SAL2B_ONCMY	Salmocidin-2B (Fragment)	0.00	-		0	Secreted protein				13
P68178 UniProt NPD GO	ESI3_LOPEL	Salt stress-induced hydrophobic peptide ESI3	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				54
P20097 UniProt NPD GO	SAP_CAVPO	Saposin C (CO-beta-glucosidase) (Glucosylceramidase activator) (Sphingolipid activator protein 2) (S ...	0.00	-	mit	0					81
P02636 UniProt NPD GO	SCPA_PENSP	Sarcoplasmic calcium-binding protein, alpha-B and -A chains (SCP alpha chain)	0.00	-	cyt	0					192
P02635 UniProt NPD GO	SCPB_PENSP	Sarcoplasmic calcium-binding protein, beta chain (SCP beta chain)	0.00	-	cyt	0					192
O77696 UniProt NPD GO	AT2A3_PIG	Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 (EC 3.6.3.8) (Calcium pump 3) (SERCA3) (SR Ca(2+ ...	0.00	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				135
O75711 UniProt NPD GO	SCRG1_HUMAN	Scrapie-responsive protein 1 precursor (ScRG-1)	0.00	-	exc	1 *	Secreted protein (Probable)	extracellular space [TAS]	603163		98
O88745 UniProt NPD GO	SCRG1_MOUSE	Scrapie-responsive protein 1 precursor (ScRG-1)	0.00	-	exc	0	Secreted protein (Probable)				98
P08608 UniProt NPD GO	TKN1_SCYCA	Scyliorhinin-1 (Scyliorhinin I)	0.00	-		0	Secreted protein				10
P08609 UniProt NPD GO	TKN2_SCYCA	Scyliorhinin-2 (Scyliorhinin II) (Rectin)	0.00	-		0	Secreted protein				18
Q00455 UniProt NPD GO	SCYD_GLOLA	Scytalone dehydratase (EC 4.2.1.94)	0.00	-	cyt	0					188
P38353 UniProt NPD GO	SSH1_YEAST	Sec sixty-one protein homolog (Ssh1 complex subunit SSH1) (Ssh1 complex subunit alpha)	0.00	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA] translocon complex [TAS]			490
Q9Z0K7 UniProt NPD GO	SLUR1_MOUSE	Secreted Ly-6/uPAR-related protein 1 precursor (SLURP-1) (ARS component B)	0.00	-	exc	0	Secreted protein (By similarity)				110
P46285 UniProt NPD GO	S17P_WHEAT	Sedoheptulose-1,7-bisphosphatase, chloroplast precursor (EC 3.1.3.37) (Sedoheptulose-bisphosphatase) ...	0.00	-	cyt	0	Plastid; chloroplast				393
Q9ASY9 UniProt NPD GO	PM36_ARATH	Seed maturation protein PM36 homolog	0.00	-	cyt	0				2F2G	221

You are viewing entries 97951 to 98000 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.