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
P48498 UniProt NPD GO	METK_PETHY	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.01	-	cyt	0					390
Q96551 UniProt NPD GO	METK_CATRO	S-adenosylmethionine synthetase 1 (EC 2.5.1.6) (Methionine adenosyltransferase 1) (AdoMet synthetase ...	0.01	-	cyt	0					393
P43280 UniProt NPD GO	METK_LYCES	S-adenosylmethionine synthetase 1 (EC 2.5.1.6) (Methionine adenosyltransferase 1) (AdoMet synthetase ...	0.01	-	cyt	0					393
P10659 UniProt NPD GO	METK_YEAST	S-adenosylmethionine synthetase 1 (EC 2.5.1.6) (Methionine adenosyltransferase 1) (AdoMet synthetase ...	0.01	-	cyt	0		cytoplasm [IDA]			382
Q96552 UniProt NPD GO	METL_CATRO	S-adenosylmethionine synthetase 2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoMet synthetase ...	0.01	-	cyt	0					393
P24260 UniProt NPD GO	METL_DIACA	S-adenosylmethionine synthetase 2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoMet synthetase ...	0.01	-	cyt	0					396
P43282 UniProt NPD GO	METM_LYCES	S-adenosylmethionine synthetase 3 (EC 2.5.1.6) (Methionine adenosyltransferase 3) (AdoMet synthetase ...	0.01	-	cyt	0					390
P50303 UniProt NPD GO	METM_ACTCH	S-adenosylmethionine synthetase 3 (EC 2.5.1.6) (Methionine adenosyltransferase 3) (AdoMet synthetase ...	0.01	-	cyt	0					360
Q91X83 UniProt NPD GO	METK1_MOUSE	S-adenosylmethionine synthetase isoform type-1 (EC 2.5.1.6) (Methionine adenosyltransferase 1) (AdoM ...	0.01	-	cyt	0					396
Q13126 UniProt NPD GO	MTAP_HUMAN	S-methyl-5-thioadenosine phosphorylase (EC 2.4.2.28) (5'-methylthioadenosine phosphorylase) (MTA pho ...	0.01	-	cyt	0	Cytoplasm		156540	1SD2	283
Q9CQ65 UniProt NPD GO	MTAP_MOUSE	S-methyl-5-thioadenosine phosphorylase (EC 2.4.2.28) (5'-methylthioadenosine phosphorylase) (MTA pho ...	0.01	-	cyt	0	Cytoplasm				283
O49623 UniProt NPD GO	DPNP2_ARATH	SAL2 phosphatase (3'(2'),5'-bisphosphate nucleotidase 2) (EC 3.1.3.7) (3'(2'),5'-bisphosphonucleosid ...	0.01	-	nuc	0					347
P80968 UniProt NPD GO	SMBP_RAT	SM-11044-binding protein (Fragments)	0.01	-	cyt	0					25
P20112 UniProt NPD GO	SPRC_PIG	SPARC (Secreted protein acidic and rich in cysteine) (Osteonectin) (ON) (Basement-membrane protein 4 ...	0.01	-	cyt	0					35
P13213 UniProt NPD GO	SPRC_BOVIN	SPARC precursor (Secreted protein acidic and rich in cysteine) (Osteonectin) (ON) (Basement-membrane ...	0.01	-	exc	0					304
P36233 UniProt NPD GO	SPRC_RABIT	SPARC precursor (Secreted protein acidic and rich in cysteine) (Osteonectin) (ON) (Basement-membrane ...	0.01	-	exc	0					273
P43065 UniProt NPD GO	LYS1_CANAL	Saccharopine dehydrogenase [NAD+, L-lysine-forming] (EC 1.5.1.7) (Lysine--2-oxoglutarate reductase) ...	0.01	-	cyt	0					382
Q6FU27 UniProt NPD GO	LYS1_CANGA	Saccharopine dehydrogenase [NAD+, L-lysine-forming] (EC 1.5.1.7) (Lysine--2-oxoglutarate reductase) ...	0.01	-	pox	0					372
Q9P4R4 UniProt NPD GO	LYS9_MAGGR	Saccharopine dehydrogenase [NADP+, L-glutamate-forming] (EC 1.5.1.10) (Saccharopine reductase)	0.01	-	cyt	0				1FF9	450
P82238 UniProt NPD GO	SAL2A_ONCMY	Salmocidin-2A (Fragment)	0.01	-		0	Secreted protein				13
P24120 UniProt NPD GO	SALT_ORYSA	Salt stress-induced protein (Salt protein) (Protein lectin-like) (Protein mannose-binding lectin)	0.01	-	cyt	0					144
P18313 UniProt NPD GO	SAPE_SARPE	Sapecin precursor	0.01	-	vac	1 *	Secreted protein			1L4V	94
P81405 UniProt NPD GO	SAP_PIG	Saposin B-Val [Contains: Saposin B (Cerebroside sulfate activator) (CS-ACT) (Non-specific activator) ...	0.01	-	cyt	0					80
P31727 UniProt NPD GO	CYTA_SARPE	Sarcocystatin A precursor	0.01	-	exc	0					122
O00631 UniProt NPD GO	SARCO_HUMAN	Sarcolipin	0.01	-	nuc	1 *	Sarcoplasmic reticulum; sarcoplasmic reticulum membrane; single-pass membrane protein	integral to membrane [TAS]	602203	1JDM	31
Q9CQD6 UniProt NPD GO	SARCO_MOUSE	Sarcolipin	0.01	-	nuc	1 *	Sarcoplasmic reticulum; sarcoplasmic reticulum membrane; single-pass membrane protein				31
Q6SLE7 UniProt NPD GO	SARCO_RAT	Sarcolipin	0.01	-	nuc	1 *	Sarcoplasmic reticulum; sarcoplasmic reticulum membrane; single-pass membrane protein (By similarity ...				31
P04571 UniProt NPD GO	SCP_NERDI	Sarcoplasmic calcium-binding protein (SCP)	0.01	-	cyt	0				2SCP	174
P05946 UniProt NPD GO	SCP1_PONLE	Sarcoplasmic calcium-binding protein 1 (Sarcoplasmic calcium-binding protein I) (SCP I)	0.01	-	cyt	0					192
P04570 UniProt NPD GO	SCP2_BRALA	Sarcoplasmic calcium-binding proteins II, V, VI, and VII (SCP II) (SCP V) (SCP VI) (SCP VII)	0.01	-	cyt	0				2SAS	185
Q62147 UniProt NPD GO	SSPN_MOUSE	Sarcospan (K-ras oncogene-associated protein) (Kirsten-Ras-associated protein)	0.01	-	end	4 *	Sarcolemma; sarcolemmal membrane; multi-pass membrane protein (By similarity). Also found in myotend ...				216
P08376 UniProt NPD GO	SRX1B_SARPE	Sarcotoxin-1B precursor (Sarcotoxin IB)	0.01	-	end	1 *	Secreted protein				63
P84306 UniProt NPD GO	FARP_LOCMI	SchistoFLRFamide (PDVDHFLRF-amide) (Cardioexcitatory neuropeptide)	0.01	-		0	Secreted protein				10
P84307 UniProt NPD GO	FARP_SCHGR	SchistoFLRFamide (PDVDHFLRF-amide) (Cardioexcitatory neuropeptide)	0.01	-		0	Secreted protein				10
Q5G8A6 UniProt NPD GO	KBXL_TITCO	Scorpine-like peptide Tco 41.46-2 precursor [Contains: Scorpine-like peptide Tco 42.14]	0.01	-	mit	0	Secreted protein				87
Q9Z0K6 UniProt NPD GO	SCRG1_RAT	Scrapie-responsive protein 1 precursor (ScRG-1)	0.01	-	exc	1 *	Secreted protein (Probable)				98
Q7M742 UniProt NPD GO	SG1C1_MOUSE	Secretoglobin family 1C member 1 precursor (Secretoglobin RYD5)	0.01	-	exc	0	Secreted protein (By similarity)				95
Q05702 UniProt NPD GO	SG1C1_RAT	Secretoglobin family 1C member 1 precursor (Secretoglobin RYD5)	0.01	-	exc	0	Secreted protein (By similarity)				94
Q969E2 UniProt NPD GO	SCAM4_HUMAN	Secretory carrier-associated membrane protein 4 (Secretory carrier membrane protein 4)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				229
Q9JKV5 UniProt NPD GO	SCAM4_MOUSE	Secretory carrier-associated membrane protein 4 (Secretory carrier membrane protein 4) (SC4)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				230
Q9ET20 UniProt NPD GO	SCAM4_RAT	Secretory carrier-associated membrane protein 4 (Secretory carrier membrane protein 4) (SCAMP-4)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				230
Q8TAC9 UniProt NPD GO	SCAM5_HUMAN	Secretory carrier-associated membrane protein 5 (Secretory carrier membrane protein 5)	0.01	-	end	4 *	Cell membrane; multi-pass membrane protein. Highly enriched in synaptic vesicles (By similarity)				235
Q9JKD3 UniProt NPD GO	SCAM5_MOUSE	Secretory carrier-associated membrane protein 5 (Secretory carrier membrane protein 5)	0.01	-	end	4 *	Cell membrane; multi-pass membrane protein. Highly enriched in synaptic vesicles				235
O20252 UniProt NPD GO	S17P_SPIOL	Sedoheptulose-1,7-bisphosphatase, chloroplast precursor (EC 3.1.3.37) (Sedoheptulose-bisphosphatase) ...	0.01	-	mit	0	Plastid; chloroplast				387
P81098 UniProt NPD GO	SFAH_HELAN	Seed fatty acyl-ester hydrolase (EC 3.1.1.1) (Fragment)	0.01	-		0					18
P93535 UniProt NPD GO	LECS_SOPJA	Seed lectin precursor (LECSJASG)	0.01	-	cyt	1 *					292
P29420 UniProt NPD GO	NLTP_RAPSA	Seed nonspecific lipid transfer protein-like (LTP) (Fragment)	0.01	-	nuc	0					43
P04557 UniProt NPD GO	SFP3_BOVIN	Seminal plasma protein A3 precursor (BSP-A3)	0.01	-	mit	0	Secreted protein			2CEC	140
Q8S895 UniProt NPD GO	SAT2_ARATH	Serine acetyltransferase 2 (EC 2.3.1.30) (AtSAT-2) (AtSERAT3;1)	0.01	-	nuc	0	Cytoplasm				323
P32826 UniProt NPD GO	CBPX_ARATH	Serine carboxypeptidase precursor (EC 3.4.16.-)	0.01	-	cyt	1 *					516

You are viewing entries 91401 to 91450 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.