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
Q93341 UniProt NPD GO	DYR_CAEEL	Putative dihydrofolate reductase (EC 1.5.1.3)	0.04	-	cyt	0					189
Q9BN19 UniProt NPD GO	HSP6_HETGL	Putative esophageal gland cell secretory protein 6 precursor	0.04	-	end	0					244
O60124 UniProt NPD GO	RRP42_SCHPO	Putative exosome complex exonuclease RRP42 (EC 3.1.13.-) (Ribosomal RNA-processing protein 42)	0.04	-	mit	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				299
Q9M069 UniProt NPD GO	E137_ARATH	Putative glucan endo-1,3-beta-glucosidase 7 precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolas ...	0.04	-	end	0	Secreted protein. Cell wall				356
P36132 UniProt NPD GO	KAE1_YEAST	Putative glycoprotein endopeptidase KAE1 (EC 3.4.24.-) (Kinase-associated endopeptidase 1)	0.04	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			386
Q9FXG2 UniProt NPD GO	SYGC_ARATH	Putative glycyl-tRNA synthetase, cytoplasmic (EC 6.1.1.14) (Glycine--tRNA ligase) (GlyRS)	0.04	-	cyt	0	Cytoplasm (Potential)				464
Q9V4K2 UniProt NPD GO	GR43A_DROME	Putative gustatory receptor 43a	0.04	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			427
Q8IN58 UniProt NPD GO	GR92A_DROME	Putative gustatory receptor 92a	0.04	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			386
P35897 UniProt NPD GO	GU38_RAT	Putative gustatory receptor clone PTE38 (Fragment)	0.04	-	end	3 *	Membrane; multi-pass membrane protein				234
P84717 UniProt NPD GO	HSP01_PINST	Putative heat-shock protein PS1 (Fragments)	0.04	-	cyt	0					104
Q4WLG9 UniProt NPD GO	CCPR2_ASPFU	Putative heme-binding peroxidase (EC 1.11.1.-)	0.04	-	pox	0					322
O16277 UniProt NPD GO	H16_CAEEL	Putative histone H1.6 (Histone H1-like protein 6)	0.04	-	nuc	0	Nucleus (By similarity)				189
O15225 UniProt NPD GO	INE1_HUMAN	Putative inactivation escape 1 protein (DXS6974E)	0.04	-	nuc	0			300164		51
Q8GT41 UniProt NPD GO	PLA1_PLAAC	Putative invertase inhibitor precursor (Pollen allergen Pla a 1)	0.04	-	exc	1 *	Secreted protein				179
P82726 UniProt NPD GO	LCR11_ARATH	Putative low-molecular-weight cysteine-rich protein LCR11 precursor	0.04	-	nuc	1 *					102
P82747 UniProt NPD GO	LCR32_ARATH	Putative low-molecular-weight cysteine-rich protein LCR32 precursor	0.04	-	exc	1 *					82
P82749 UniProt NPD GO	LCR34_ARATH	Putative low-molecular-weight cysteine-rich protein LCR34 precursor	0.04	-	mit	1 *					85
P82753 UniProt NPD GO	LCR38_ARATH	Putative low-molecular-weight cysteine-rich protein LCR38 precursor	0.04	-	nuc	1 *					76
P82766 UniProt NPD GO	LCR52_ARATH	Putative low-molecular-weight cysteine-rich protein LCR52 precursor	0.04	-	nuc	0					77
Q4WYS7 UniProt NPD GO	NNT1_ASPFU	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.04	-	cyt	0	Cytoplasm (By similarity)				259
P40446 UniProt NPD GO	YIQ5_YEAST	Putative nitrilase-like protein YIL165C	0.04	-	cyt	0					119
Q9VLE5 UniProt NPD GO	OR30A_DROME	Putative odorant receptor 30a	0.04	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			377
Q9VAZ3 UniProt NPD GO	OR98A_DROME	Putative odorant receptor 98a	0.04	-	mit	6 *	Membrane; multi-pass membrane protein (Potential)				397
Q93761 UniProt NPD GO	YXEK_CAEEL	Putative oxidoreductase F53C11.3 (EC 1.-.-.-)	0.04	-	pox	0					313
O43099 UniProt NPD GO	PMP20_ASPFU	Putative peroxiredoxin pmp20 (EC 1.11.1.15) (Thioredoxin reductase) (Peroxisomal membrane protein pm ...	0.04	-	cyt	0	Peroxisome (Potential)				168
P38139 UniProt NPD GO	YB54_YEAST	Putative peroxisomal lipase in CDC47-KTR3 intergenic region (EC 3.1.1.-)	0.04	-	pox	0	Peroxisome (Potential)				375
Q9U3D4 UniProt NPD GO	SMS1_CAEEL	Putative phosphatidylcholine:ceramide cholinephosphotransferase 1 (EC 2.7.-.-) (Sphingomyelin syntha ...	0.04	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to Golgi membrane [ISS]			490
Q9LPS9 UniProt NPD GO	PIRL1_ARATH	Putative pirin-like protein At1g50590	0.04	-	cyt	0	Nucleus (By similarity)				310
O74248 UniProt NPD GO	GPT1_CANAL	Putative polyamine transporter	0.04	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				553
P50272 UniProt NPD GO	PSBP_PORPU	Putative polysaccharide-binding protein precursor	0.04	-	exc	0					210
O43716 UniProt NPD GO	15E2_HUMAN	Putative protein 15E1.2	0.04	-	mit	0					136
Q9FWR2 UniProt NPD GO	AVPX_ARATH	Putative pyrophosphate-energized membrane proton pump 3 (EC 3.6.1.1) (Pyrophosphate-energized inorga ...	0.04	-	end	16 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				802
Q7XVA8 UniProt NPD GO	RIP1_ORYSA	Putative ripening-related protein 1 precursor	0.04	-	exc	0	Secreted protein (Potential)				183
Q9FWU1 UniProt NPD GO	RIP4_ORYSA	Putative ripening-related protein 4 precursor	0.04	-	end	0	Secreted protein (Potential)				377
Q21353 UniProt NPD GO	EAA3_CAEEL	Putative sodium-dependent excitatory amino acid transporter glt-3	0.04	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				532
P36624 UniProt NPD GO	DHSO_SCHPO	Putative sorbitol dehydrogenase (EC 1.1.1.14) (L-iditol 2-dehydrogenase) (Protein tms1)	0.04	-	mit	0					360
Q00717 UniProt NPD GO	STCT_EMENI	Putative sterigmatocystin biosynthesis protein stcT	0.04	-	nuc	0					215
Q17704 UniProt NPD GO	DHBW_CAEEL	Putative steroid dehydrogenase C06B3.5 (EC 1.1.1.-)	0.04	-	end	2 *					349
O57314 UniProt NPD GO	DHBX_ANAPL	Putative steroid dehydrogenase SPM2 (EC 1.1.1.-)	0.04	-	mit	4 *					312
O17730 UniProt NPD GO	THT2_CAEEL	Putative thiosulfate sulfurtransferase D2023.5 (EC 2.8.1.1)	0.04	-	cyt	0					328
P34519 UniProt NPD GO	TXTP_CAEEL	Putative tricarboxylate transport protein, mitochondrial precursor (Citrate transport protein) (CTP) ...	0.04	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				312
O81916 UniProt NPD GO	YC22_ARATH	Putative uncharacterized calcium-binding protein At1g02270	0.04	-	cyt	0					232
Q12486 UniProt NPD GO	YOR31_YEAST	Putative uncharacterized hydrolase YOR131C (EC 3.-.-.-)	0.04	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			218
P53111 UniProt NPD GO	YGP7_YEAST	Putative uncharacterized oxidoreductase YGL157W (EC 1.1.1.-)	0.04	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			347
P40049 UniProt NPD GO	YEQ6_YEAST	Putative uncharacterized protein YER076C precursor	0.04	-	vac	0		membrane fraction [IDA] mitochondrion [IDA]			302
P47121 UniProt NPD GO	YJ41_YEAST	Putative uncharacterized protein YJR071W precursor	0.04	-	mit	0					122
P82684 UniProt NPD GO	PPK1_CARMO	Pyrokinin-1 (Cam-PK-1) (FXPRL-Amide)	0.04	-		0	Secreted protein				11
P82692 UniProt NPD GO	PPK2_PERAM	Pyrokinin-2 (Pea-PK-2) (FXPRL-amide)	0.04	-		0	Secreted protein				8
O04016 UniProt NPD GO	P5CR_ACTCH	Pyrroline-5-carboxylate reductase (EC 1.5.1.2) (P5CR) (P5C reductase)	0.04	-	cyt	0	Cytoplasm				278
Q96C36 UniProt NPD GO	P5CR2_HUMAN	Pyrroline-5-carboxylate reductase 2 (EC 1.5.1.2) (P5CR 2) (P5C reductase 2)	0.04	-	cyt	0					320

You are viewing entries 78251 to 78300 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.