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
P35242 UniProt NPD GO	SFTPA_MOUSE	Pulmonary surfactant-associated protein A precursor (SP-A) (PSP-A) (PSAP)	0.07	-	end	0	Secreted protein; extracellular space				248
P15783 UniProt NPD GO	PSPC_BOVIN	Pulmonary surfactant-associated protein C precursor (SP-C) (Pulmonary surfactant-associated proteoli ...	0.07	-	gol	1 *	Secreted protein; extracellular space				190
O94574 UniProt NPD GO	YGDH_SCHPO	Putative 2-hydroxyacid dehydrogenase C1773.17c (EC 1.-.-.-)	0.07	-	cyt	0					340
Q9SRX7 UniProt NPD GO	RL221_ARATH	Putative 60S ribosomal protein L22-1	0.07	-	mit	0					127
Q9GZL8 UniProt NPD GO	BPEC1_HUMAN	Putative BPES syndrome breakpoint region protein (BPES candidate 1)	0.07	-	mit	0					116
Q13014 UniProt NPD GO	BAK2_HUMAN	Putative Bcl-2 homologous antagonist/killer 2 (Apoptosis regulator BAK-2)	0.07	-	cyt	1	Membrane; single-pass membrane protein (Potential)	membrane [NAS]			211
Q09473 UniProt NPD GO	ERD22_CAEEL	Putative ER lumen protein retaining receptor C28H8.4	0.07	-	end	5 *	Membrane; multi-pass membrane protein				213
Q8BG09 UniProt NPD GO	CV005_MOUSE	Putative MAP kinase-activating protein C22orf5 homolog	0.07	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				407
Q9LJL6 UniProt NPD GO	ATL3H_ARATH	Putative RING-H2 finger protein ATL3H	0.07	-	mit	0					141
Q18081 UniProt NPD GO	UGT48_CAEEL	Putative UDP-glucuronosyltransferase ugt-48 precursor (EC 2.4.1.17) (UDPGT)	0.07	-	end	1					526
Q10088 UniProt NPD GO	SPEB1_SCHPO	Putative agmatinase 1 precursor (EC 3.5.3.11) (Agmatine ureohydrolase) (AUH)	0.07	-	exc	0					394
P49713 UniProt NPD GO	FUCO_CAEEL	Putative alpha-L-fucosidase precursor (EC 3.2.1.51) (Alpha-L-fucoside fucohydrolase)	0.07	-	exc	0					482
P53066 UniProt NPD GO	YGZ2_YEAST	Putative ankyrin repeat-containing protein YGL242C	0.07	-	nuc	0					181
Q53JG7 UniProt NPD GO	LAX4_ORYSA	Putative auxin transporter-like protein 4	0.07	-	end	9	Cell membrane; multi-pass membrane protein (By similarity)				480
Q00662 UniProt NPD GO	BGAL_DIACA	Putative beta-galactosidase precursor (EC 3.2.1.23) (Lactase) (SR12 protein)	0.07	-	mit	1 *					731
Q9M1P7 UniProt NPD GO	BOR2_ARATH	Putative boron transporter 2	0.07	-	end	10 *	Membrane; multi-pass membrane protein (By similarity)				703
Q27513 UniProt NPD GO	C13A4_CAEEL	Putative cytochrome P450 CYP13A4 (EC 1.14.-.-)	0.07	-	nuc	2 *					520
Q27516 UniProt NPD GO	C13A8_CAEEL	Putative cytochrome P450 CYP13A8 (EC 1.14.-.-)	0.07	-	cyt	0					509
O60774 UniProt NPD GO	FMO6_HUMAN	Putative dimethylaniline monooxygenase [N-oxide-forming] 6 (EC 1.14.13.8) (Flavin-containing monooxy ...	0.07	-	end	0	Microsome (By similarity)				539
P38068 UniProt NPD GO	YBM4_YEAST	Putative glutaredoxin-like protein YBR014C precursor	0.07	-	exc	1 *		membrane fraction [IDA] vacuole (sensu Fungi) [IDA]			203
P54002 UniProt NPD GO	YTH3_CAEEL	Putative glycosyl transferase C14A4.3 in chromosome II (EC 2.-.-.-)	0.07	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				603
P82751 UniProt NPD GO	LCR36_ARATH	Putative low-molecular-weight cysteine-rich protein LCR36 precursor	0.07	-	nuc	0					73
P82782 UniProt NPD GO	LCR73_ARATH	Putative low-molecular-weight cysteine-rich protein LCR73 precursor	0.07	-	exc	1 *	Secreted protein (Potential)				80
Q9BQN2 UniProt NPD GO	CT127_HUMAN	Putative metallothionein C20orf127	0.07	-	nuc	0					58
Q04399 UniProt NPD GO	YD506_YEAST	Putative multicopper oxidase YDR506C (EC 1.-.-.-)	0.07	-	end	1					608
Q5KDV2 UniProt NPD GO	NNT1_CRYNE	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.07	-	mit	0	Cytoplasm (By similarity)				299
Q5BAD0 UniProt NPD GO	NNT1_EMENI	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.07	-	cyt	0	Cytoplasm (By similarity)				262
P40447 UniProt NPD GO	NIT1_YEAST	Putative nitrilase-like protein NIT1	0.07	-	cyt	0					199
Q8IRZ5 UniProt NPD GO	OR19B_DROME	Putative odorant receptor 19b	0.07	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			387
Q9VCS8 UniProt NPD GO	OR94B_DROME	Putative odorant receptor 94b	0.07	-	mit	7 *	Membrane; multi-pass membrane protein (Potential)				383
O65388 UniProt NPD GO	PEL2_ARATH	Putative pectate lyase 2 precursor (EC 4.2.2.2)	0.07	-	exc	0					390
P38744 UniProt NPD GO	PHS_YEAST	Putative pterin-4-alpha-carbinolamine dehydratase (EC 4.2.1.96) (PHS) (4-alpha-hydroxy-tetrahydropte ...	0.07	-	cyt	0		mitochondrion [IDA]			120
Q7XD65 UniProt NPD GO	RIP7_ORYSA	Putative ripening-related protein 7 precursor	0.07	-	cyt	1 *	Secreted protein (Potential)				162
P83740 UniProt NPD GO	SC5A6_DROME	Putative sodium-dependent multivitamin transporter (Na(+)-dependent multivitamin transporter)	0.07	-	end	13 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			604
Q00727 UniProt NPD GO	STCV_EMENI	Putative sterigmatocystin biosynthesis dehydrogenase stcV (EC 1.1.1.-)	0.07	-	cyt	0					387
Q9URV9 UniProt NPD GO	SRX1_SCHPO	Putative sulfiredoxin (EC 1.8.98.2)	0.07	-	nuc	0					124
P53228 UniProt NPD GO	TAL2_YEAST	Putative transaldolase YGR043C (EC 2.2.1.2)	0.07	-	cyt	0		nucleus [IDA]			333
P53183 UniProt NPD GO	YGD9_YEAST	Putative uncharacterized oxidoreductase YGL039W (EC 1.1.1.-)	0.07	-	mit	0		cytoplasm [IDA]			348
Q9BZ19 UniProt NPD GO	CT086_HUMAN	Putative uncharacterized protein C20orf86	0.07	-	cyt	0					240
P39703 UniProt NPD GO	YAA4_YEAST	Putative uncharacterized protein YAL004W	0.07	-	nuc	0					215
P39566 UniProt NPD GO	YAO0_YEAST	Putative uncharacterized protein YAR070C	0.07	-	cyt	0					99
P53339 UniProt NPD GO	YG61_YEAST	Putative uncharacterized protein YGR290W precursor	0.07	-	end	2 *					147
Q04898 UniProt NPD GO	YM99_YEAST	Putative uncharacterized protein YMR321C	0.07	-	nuc	0					105
O46560 UniProt NPD GO	PDXK_PIG	Pyridoxal kinase (EC 2.7.1.35) (Pyridoxine kinase)	0.07	-	cyt	0	Cytoplasm				322
P82197 UniProt NPD GO	PDXK_SHEEP	Pyridoxal kinase (EC 2.7.1.35) (Pyridoxine kinase)	0.07	-	cyt	0	Cytoplasm			1YHJ	312
Q8VD52 UniProt NPD GO	PLPP_RAT	Pyridoxal phosphate phosphatase (EC 3.1.3.74) (PLP phosphatase) (Reg I-binding protein 1)	0.07	-	cyt	0					309
Q8TCD6 UniProt NPD GO	PHOP2_HUMAN	Pyridoxal phosphate phosphatase PHOSPHO2 (EC 3.1.3.74)	0.07	-	cyt	0					241
P21342 UniProt NPD GO	PFPA_SOLTU	Pyrophosphate--fructose 6-phosphate 1-phosphotransferase alpha subunit (EC 2.7.1.90) (PFP) (6-phosph ...	0.07	-	cyt	0					616
P51844 UniProt NPD GO	PDC_ASPPA	Pyruvate decarboxylase (EC 4.1.1.1)	0.07	-	cyt	0					577
Q10489 UniProt NPD GO	ODPA_SCHPO	Pyruvate dehydrogenase E1 component alpha subunit, mitochondrial precursor (EC 1.2.4.1) (PDHE1-A)	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				409

You are viewing entries 70901 to 70950 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.