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
P84726 UniProt NPD GO	PS10_PINST	Putative disease resistance protein PS10 (TIR-NBS-LRR) (Fragments)	0.05	-		0					17
P46236 UniProt NPD GO	GUNB_FUSOX	Putative endoglucanase type B precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase)	0.05	-	exc	0					462
Q8INZ2 UniProt NPD GO	GR36C_DROME	Putative gustatory receptor 36c	0.05	-	nuc	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			390
P58959 UniProt NPD GO	G39AD_DROME	Putative gustatory receptor 39a, isoform A	0.05	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			371
P58956 UniProt NPD GO	G39AA_DROME	Putative gustatory receptor 39a, isoform B	0.05	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			372
Q9VZJ6 UniProt NPD GO	GR64D_DROME	Putative gustatory receptor 64d	0.05	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			429
P35896 UniProt NPD GO	GU33_RAT	Putative gustatory receptor clone PTE33 (Fragment)	0.05	-	end	5 *	Membrane; multi-pass membrane protein				234
Q6ZLA7 UniProt NPD GO	GH310_ORYSA	Putative indole-3-acetic acid-amido synthetase GH3.10 (EC 6.3.2.-) (Auxin-responsive GH3-like protei ...	0.05	-	mit	0					478
O13934 UniProt NPD GO	ATG15_SCHPO	Putative lipase atg15 (EC 3.1.1.3) (Autophagy-related protein 15)	0.05	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				424
P82744 UniProt NPD GO	LCR29_ARATH	Putative low-molecular-weight cysteine-rich protein LCR29 precursor	0.05	-	mit	1 *					81
P82777 UniProt NPD GO	LCR63_ARATH	Putative low-molecular-weight cysteine-rich protein LCR63 precursor	0.05	-	mit	1 *					78
P82785 UniProt NPD GO	LCR76_ARATH	Putative low-molecular-weight cysteine-rich protein LCR76 precursor	0.05	-	mit	1 *	Secreted protein (By similarity)				86
P82791 UniProt NPD GO	LCR82_ARATH	Putative low-molecular-weight cysteine-rich protein LCR82 precursor	0.05	-	nuc	1 *					101
P82795 UniProt NPD GO	LCR86_ARATH	Putative low-molecular-weight cysteine-rich protein LCR86 precursor	0.05	-	exc	1 *					85
Q9P6I4 UniProt NPD GO	YHG6_SCHPO	Putative mannan endo-1,6-alpha-mannosidase C1198.06c precursor (EC 3.2.1.101) (Endo-alpha-1->6-D-man ...	0.05	-	end	3 *					466
P87147 UniProt NPD GO	NACA_SCHPO	Putative nascent polypeptide-associated complex subunit alpha-like protein (NAC-alpha-like protein) ...	0.05	-	cyt	0					173
O61902 UniProt NPD GO	NDX2_CAEEL	Putative nudix hydrolase 2 (EC 3.6.1.-)	0.05	-	cyt	0					223
Q9VT90 UniProt NPD GO	OR67C_DROME	Putative odorant receptor 67c	0.05	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			404
Q9VU27 UniProt NPD GO	OR69A_DROME	Putative odorant receptor 69a, isoform A	0.05	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			393
Q9W2U9 UniProt NPD GO	OR9A_DROME	Putative odorant receptor 9a	0.05	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			392
P53134 UniProt NPD GO	YGL4_YEAST	Putative oligopeptide transporter YGL114W	0.05	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				725
O14351 UniProt NPD GO	YB45_SCHPO	Putative oxidoreductase C30D10.05c (EC 1.-.-.-)	0.05	-	cyt	0					247
O95650 UniProt NPD GO	KI16_HUMAN	Putative protein KiSS-16	0.05	-	nuc	0					54
Q6H5X0 UniProt NPD GO	RIP2_ORYSA	Putative ripening-related protein 2 precursor	0.05	-	exc	1 *	Secreted protein (Potential)				192
Q08942 UniProt NPD GO	NRKA_TRYBB	Putative serine/threonine-protein kinase A (EC 2.7.11.1)	0.05	-	cyt	0					431
Q03428 UniProt NPD GO	NRKB_TRYBB	Putative serine/threonine-protein kinase B (EC 2.7.11.1)	0.05	-	cyt	0					431
Q39593 UniProt NPD GO	SAC1_CHLRE	Putative sulfur deprivation response regulator	0.05	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				585
Q10097 UniProt NPD GO	YAOI_SCHPO	Putative transporter C11D3.18C	0.05	-	end	11	Membrane; multi-pass membrane protein (Potential)				498
Q8NEQ6 UniProt NPD GO	CA064_HUMAN	Putative uncharacterized protein C1orf64	0.05	-	nuc	0					169
P37264 UniProt NPD GO	YCG5_YEAST	Putative uncharacterized protein YCL065W	0.05	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				122
P40092 UniProt NPD GO	YEY0_YEAST	Putative uncharacterized protein YER150W precursor	0.05	-	exc	0		cell wall (sensu Fungi) [IDA]			148
P53054 UniProt NPD GO	YGZG_YEAST	Putative uncharacterized protein YGL262W	0.05	-	nuc	0					175
P38832 UniProt NPD GO	YHS6_YEAST	Putative uncharacterized protein YHR126C	0.05	-	exc	0					159
Q8TGK0 UniProt NPD GO	YH1E_YEAST	Putative uncharacterized protein YHR214C-E	0.05	-	cyt	1 *					99
P38897 UniProt NPD GO	YH14_YEAST	Putative uncharacterized protein YHR214W	0.05	-	exc	0					203
Q12138 UniProt NPD GO	YL125_YEAST	Putative uncharacterized protein YLR125W	0.05	-	nuc	0					136
P53826 UniProt NPD GO	YN59_YEAST	Putative uncharacterized protein YNL319W precursor	0.05	-	end	1 *					146
Q8W1X2 UniProt NPD GO	PDXK_ARATH	Pyridoxal kinase (EC 2.7.1.35) (Pyridoxine kinase) (Pyridoxal kinase-like protein SOS4) (Salt overly ...	0.05	-	nuc	0					309
Q9UW83 UniProt NPD GO	PDX1_EMENI	Pyridoxin biosynthesis protein pyroA (Pdx1 homolog)	0.05	+	cyt	0					304
P82618 UniProt NPD GO	PPK3_PERAM	Pyrokinin-3 (Pea-PK-3) (FXPRL-amide)	0.05	-		0	Secreted protein				8
Q41140 UniProt NPD GO	PFPA_RICCO	Pyrophosphate--fructose 6-phosphate 1-phosphotransferase alpha subunit (EC 2.7.1.90) (PFP) (6-phosph ...	0.05	-	cyt	0					617
Q56ZN6 UniProt NPD GO	AVP2_ARATH	Pyrophosphate-energized membrane proton pump 2 (EC 3.6.1.1) (Pyrophosphate-energized inorganic pyrop ...	0.05	-	end	16 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein				802
Q04708 UniProt NPD GO	P5CR_PEA	Pyrroline-5-carboxylate reductase (EC 1.5.1.2) (P5CR) (P5C reductase)	0.05	-	cyt	0	Cytoplasm				273
P06169 UniProt NPD GO	PDC1_YEAST	Pyruvate decarboxylase isozyme 1 (EC 4.1.1.1) (EC 4.1.1.-)	0.05	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]		1QPB	562
P16467 UniProt NPD GO	PDC5_YEAST	Pyruvate decarboxylase isozyme 2 (EC 4.1.1.1) (EC 4.1.1.-)	0.05	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			562
Q38799 UniProt NPD GO	ODPB_ARATH	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial precursor (EC 1.2.4.1) (PDHE1-B)	0.05	-	mit	0	Mitochondrion; mitochondrial matrix				363
Q09171 UniProt NPD GO	ODPB_SCHPO	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial precursor (EC 1.2.4.1) (PDHE1-B)	0.05	-	cyt	0	Mitochondrion; mitochondrial matrix				366
Q04668 UniProt NPD GO	KPYK_LEIBR	Pyruvate kinase (EC 2.7.1.40) (PK) (Fragment)	0.05	-	mit	0					91
P30615 UniProt NPD GO	KPYK1_TRYBB	Pyruvate kinase 1 (EC 2.7.1.40) (PK 1)	0.05	-	cyt	0					499
P53657 UniProt NPD GO	KPYR_MOUSE	Pyruvate kinase isozymes R/L (EC 2.7.1.40) (L-PK)	0.05	-	cyt	0					574

You are viewing entries 75501 to 75550 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.