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
P82759 UniProt NPD GO	LCR44_ARATH	Putative low-molecular-weight cysteine-rich protein LCR44 precursor	0.01	-	exc	0					63
P82764 UniProt NPD GO	LCR49_ARATH	Putative low-molecular-weight cysteine-rich protein LCR49 precursor	0.01	-	exc	0					80
P82765 UniProt NPD GO	LCR50_ARATH	Putative low-molecular-weight cysteine-rich protein LCR50 precursor	0.01	-	exc	1 *					83
P82770 UniProt NPD GO	LCR56_ARATH	Putative low-molecular-weight cysteine-rich protein LCR56 precursor	0.01	-	cyt	0					77
P82774 UniProt NPD GO	LCR60_ARATH	Putative low-molecular-weight cysteine-rich protein LCR60 precursor	0.01	-	nuc	1 *					84
P82776 UniProt NPD GO	LCR62_ARATH	Putative low-molecular-weight cysteine-rich protein LCR62 precursor	0.01	-	mit	1 *					78
P82781 UniProt NPD GO	LCR71_ARATH	Putative low-molecular-weight cysteine-rich protein LCR71	0.01	-	nuc	0	Secreted protein (Potential)				73
P82792 UniProt NPD GO	LCR83_ARATH	Putative low-molecular-weight cysteine-rich protein LCR83 precursor	0.01	-	exc	0					82
Q74ZB5 UniProt NPD GO	NNT1_ASHGO	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.01	-	cyt	0	Cytoplasm (By similarity)				265
Q6FJ22 UniProt NPD GO	NNT1_CANGA	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.01	-	mit	0	Cytoplasm (By similarity)				256
Q7S634 UniProt NPD GO	NNT1_NEUCR	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.01	-	nuc	0	Cytoplasm (By similarity)				282
Q6CHE9 UniProt NPD GO	NNT1_YARLI	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.01	-	cyt	0	Cytoplasm (By similarity)				273
Q05874 UniProt NPD GO	NNT1_YEAST	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.01	-	cyt	0	Cytoplasm	cytoplasm [IDA]			261
Q09297 UniProt NPD GO	NDX6_CAEEL	Putative nudix hydrolase 6 (EC 3.-.-.-)	0.01	-	cyt	0					260
Q9VT92 UniProt NPD GO	OR67D_DROME	Putative odorant receptor 67d	0.01	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			391
Q9FWX6 UniProt NPD GO	KCO4_ARATH	Putative outward-rectifying potassium channel 4 (AtKCO4)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				246
Q10216 UniProt NPD GO	YAY8_SCHPO	Putative oxidoreductase C4H3.08 (EC 1.-.-.-)	0.01	-	cyt	0					286
P40579 UniProt NPD GO	YIV5_YEAST	Putative oxidoreductase YIR035C (EC 1.-.-.-)	0.01	-	cyt	0		cytoplasm [IDA]			254
P40580 UniProt NPD GO	YIV6_YEAST	Putative oxidoreductase YIR036C (EC 1.-.-.-)	0.01	-	nuc	0		cytoplasm [IDA]			263
P84727 UniProt NPD GO	PSBP_PINST	Putative oxygen-evolving enhancer protein 2 (OEE2) (23 kDa subunit of oxygen evolving system of phot ...	0.01	-		0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex (By ...				11
P15974 UniProt NPD GO	PHXR4_MOUSE	Putative per-hexamer repeat protein 4	0.01	-	end	2 *					95
P19476 UniProt NPD GO	CR29_ENTHI	Putative peroxiredoxin (EC 1.11.1.15) (Thioredoxin peroxidase) (29 kDa cysteine-rich surface antigen ...	0.01	-	nuc	0	Membrane; peripheral membrane protein				233
P56577 UniProt NPD GO	MALF2_MALFU	Putative peroxiredoxin (EC 1.11.1.15) (Thioredoxin reductase) (Allergen Mal f 2) (MF1)	0.01	-	cyt	0	Peroxisome (Potential)				177
P54189 UniProt NPD GO	PEBP_PLAFA	Putative phosphatidylethanolamine-binding protein	0.01	-	cyt	0					190
P18889 UniProt NPD GO	PORF1_RAT	Putative preoptic regulatory factor 1 precursor (PORF-1)	0.01	-	cyt	0	Secreted protein (Potential)				37
Q9FH13 UniProt NPD GO	RRAA3_ARATH	Putative regulator of ribonuclease-like protein 3	0.01	-	cyt	0					166
O60116 UniProt NPD GO	RBSK_SCHPO	Putative ribokinase (EC 2.7.1.15)	0.01	-	cyt	0					318
Q18006 UniProt NPD GO	SOX_CAEEL	Putative sarcosine oxidase (EC 1.5.3.1)	0.01	-	cyt	0					384
Q09991 UniProt NPD GO	YSS2_CAEEL	Putative serine carboxypeptidase K10B2.2 precursor (EC 3.4.16.-)	0.01	-	vac	0					470
P22614 UniProt NPD GO	SAA3_HUMAN	Putative serum amyloid A-3 protein	0.01	-	vac	0		extracellular region [NAS]			122
Q9BZL3 UniProt NPD GO	NID67_HUMAN	Putative small membrane protein NID67 (NGF-induced differentiation clone 67 protein)	0.01	-	nuc	1 *			608324		60
Q9VCI5 UniProt NPD GO	DHSD_DROME	Putative succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (C ...	0.01	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [ISS]			182
Q10487 UniProt NPD GO	YDFG_SCHPO	Putative transporter C17C9.16c	0.01	-	end	13	Membrane; multi-pass membrane protein (Potential)				531
Q9BYT1 UniProt NPD GO	CT059_HUMAN	Putative transporter C20orf59	0.01	-	end	9	Membrane; multi-pass membrane protein (Potential)				436
O22869 UniProt NPD GO	ITI6_ARATH	Putative trypsin inhibitor At2g43550 precursor	0.01	-	mit	1 *	Secreted protein (Potential)				89
P55905 UniProt NPD GO	A41_LEIDO	Putative ubiquinone biosynthesis methyltransferase A41 (EC 2.1.1.-) (Amastigote-specific protein A41 ...	0.01	-	cyt	0					288
Q9HAF5 UniProt NPD GO	CO028_HUMAN	Putative uncharacterized protein C15orf28	0.01	-	vac	0					125
P40587 UniProt NPD GO	YIW3_YEAST	Putative uncharacterized protein YIR043C	0.01	-	nuc	1					230
Q86ZR7 UniProt NPD GO	YKD3A_YEAST	Putative uncharacterized protein YKL033W-A	0.01	-	cyt	0					236
Q9SEH5 UniProt NPD GO	PMT3_TOBAC	Putrescine N-methyltransferase 3 (EC 2.1.1.53) (PMT 3)	0.01	-	cyt	0					381
P47183 UniProt NPD GO	THI11_YEAST	Pyrimidine precursor biosynthesis enzyme THI11	0.01	-	mit	0					340
P42883 UniProt NPD GO	THI12_YEAST	Pyrimidine precursor biosynthesis enzyme THI12	0.01	-	mit	0					340
Q07748 UniProt NPD GO	THI13_YEAST	Pyrimidine precursor biosynthesis enzyme THI13	0.01	-	mit	0					340
P84670 UniProt NPD GO	PPK5_PANVI	Pyrokinin-5 (Panvi-PK-5) (FXPRL-amide)	0.01	-		0	Secreted protein				17
P84370 UniProt NPD GO	PPK6_EURFL	Pyrokinin-6 (Eurfl-PK-6) (FXPRL-amide)	0.01	-		0	Secreted protein				14
P84420 UniProt NPD GO	PPK6_BLAOR	Pyrokinin-6 (FXPRL-amide)	0.01	-		0	Secreted protein				14
P84421 UniProt NPD GO	PPK6_SHELA	Pyrokinin-6 (FXPRL-amide)	0.01	-		0	Secreted protein				14
P82693 UniProt NPD GO	PPK6_PERAM	Pyrokinin-6 (Pea-PK-6) (FXPRL-amide)	0.01	-		0	Secreted protein				14
P84371 UniProt NPD GO	PPK6_PSEFO	Pyrokinin-6 (Psefo-PK-6) (FXPRL-amide)	0.01	-		0	Secreted protein				14
Q06572 UniProt NPD GO	AVP_HORVU	Pyrophosphate-energized vacuolar membrane proton pump (EC 3.6.1.1) (Pyrophosphate-energized inorgani ...	0.01	-	end	14 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				762

You are viewing entries 91051 to 91100 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.