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
P20822 UniProt NPD GO	UBX_DROPS	Homeotic protein ultrabithorax (Fragment)	0.25	+	nuc	0	Nucleus				306
P08465 UniProt NPD GO	MET2_YEAST	Homoserine O-acetyltransferase (EC 2.3.1.31) (Homoserine O-trans-acetylase)	0.25	-	nuc	0		cytoplasm [IDA]			486
Q92839 UniProt NPD GO	HAS1_HUMAN	Hyaluronan synthase 1 (EC 2.4.1.212) (Hyaluronate synthase 1) (Hyaluronic acid synthase 1) (HA synth ...	0.25	-	end	7 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS]	601463		578
O57424 UniProt NPD GO	HAS2_CHICK	Hyaluronan synthase 2 (EC 2.4.1.212) (Hyaluronate synthase 2) (Hyaluronic acid synthase 2) (HA synth ...	0.25	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				552
Q5E985 UniProt NPD GO	HYAL1_BOVIN	Hyaluronidase-1 precursor (EC 3.2.1.35) (Hyal-1) (Hyaluronoglucosaminidase-1)	0.25	-	end	0	Secreted protein (By similarity). Lysosome (By similarity)				450
P49370 UniProt NPD GO	HUGA_VESVU	Hyalurononglucosaminidase (EC 3.2.1.35) (Hyaluronidase) (Allergen Ves v 2) (Ves v II)	0.25	-	cyt	0				2ATM	331
P47106 UniProt NPD GO	YJ08_YEAST	Hypothetical 13.0 kDa protein in HUL4-GEF1 intergenic region	0.25	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				120
P39972 UniProt NPD GO	YEI5_YEAST	Hypothetical 14.0 kDa protein in DLD3 5'region	0.25	-	cyt	0					122
P40104 UniProt NPD GO	YE19_YEAST	Hypothetical 14.0 kDa protein in ISC10 3'region	0.25	-	cyt	0					122
P47094 UniProt NPD GO	YJZ3_YEAST	Hypothetical 15.3 kDa protein in MER2-BNA1 intergenic region	0.25	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				133
P53074 UniProt NPD GO	YGY0_YEAST	Hypothetical 17.3 kDa protein in SEC15-SAP4 intergenic region	0.25	-	nuc	1					147
P47087 UniProt NPD GO	YJY2_YEAST	Hypothetical 23.2 kDa protein in SPC1-ILV3 intergenic region	0.25	-	nuc	1 *					207
P51202 UniProt NPD GO	YCF53_PORPU	Hypothetical 28.1 kDa protein ycf53 (ORF238)	0.25	-	nuc	0	Plastid; chloroplast				238
P38855 UniProt NPD GO	YHW0_YEAST	Hypothetical 32.0 kDa protein in REC104-SOL3 intergenic region	0.25	-	nuc	0		cytosol [IDA] peroxisome [IDA]			283
P34251 UniProt NPD GO	YKK7_YEAST	Hypothetical 34.5 kDa protein in HAP4-AAT1 intergenic region	0.25	-	nuc	0					309
P25606 UniProt NPD GO	YCZ0_YEAST	Hypothetical 35.2 kDa protein in GIT1-PAU3 intergenic region	0.25	-	cyt	0					316
P48330 UniProt NPD GO	YCX9_CYAPA	Hypothetical 5.7 kDa protein in psbM-psbX intergenic region (ORF48)	0.25	-	nuc	1 *	Plastid; cyanelle				48
P53270 UniProt NPD GO	YG32_YEAST	Hypothetical 53.4 kDa protein in SPT6-RPS23A intergenic region	0.25	-	nuc	0		cytoplasm [IDA]			476
P25203 UniProt NPD GO	YRP3_GIALA	Hypothetical 59.1 kDa protein in rpoA3 5'region	0.25	-	end	0					528
P40514 UniProt NPD GO	YIG7_YEAST	Hypothetical 75.5 kDa protein in SEC6-RNR3 intergenic region	0.25	-	end	8	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			678
P53121 UniProt NPD GO	YGN9_YEAST	Hypothetical 90.8 kDa protein in HUL5-SEC27 intergenic region	0.25	-	end	10	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			802
Q10912 UniProt NPD GO	YSP4_CAEEL	Hypothetical protein B0034.4	0.25	-	nuc	0					216
Q09439 UniProt NPD GO	YP79_CAEEL	Hypothetical protein B0228.9	0.25	-	cyt	0					338
P34289 UniProt NPD GO	YKO1_CAEEL	Hypothetical protein C05B5.1	0.25	-	nuc	0					154
Q9US57 UniProt NPD GO	YIZ1_SCHPO	Hypothetical protein C1002.01 in chromosome I	0.25	-	mit	1					179
Q10449 UniProt NPD GO	YDEG_SCHPO	Hypothetical protein C12B10.16c in chromosome I	0.25	-	mit	0	Membrane; multi-pass membrane protein (Potential)				509
P49958 UniProt NPD GO	YKY5_CAEEL	Hypothetical protein C14B1.5	0.25	+	cyt	0					396
Q09849 UniProt NPD GO	YAE9_SCHPO	Hypothetical protein C23D3.09 in chromosome I	0.25	-	cyt	0					430
Q9UR21 UniProt NPD GO	YAIE_SCHPO	Hypothetical protein C24B11.14 in chromosome I	0.25	-	mit	0					166
Q10032 UniProt NPD GO	YQ93_CAEEL	Hypothetical protein C27D6.3	0.25	+	nuc	1					118
Q09695 UniProt NPD GO	YA22_SCHPO	Hypothetical protein C2F7.02c in chromosome I	0.25	-	nuc	0					325
O14109 UniProt NPD GO	YEJC_SCHPO	Hypothetical protein C31G5.12c in chromosome I	0.25	-	nuc	0					215
O14183 UniProt NPD GO	YDS8_SCHPO	Hypothetical protein C4F8.08 in chromosome I	0.25	-	cyt	0					151
Q09676 UniProt NPD GO	YA03_SCHPO	Hypothetical protein C5H10.03 in chromosome I	0.25	-	cyt	0					219
Q10312 UniProt NPD GO	YD59_SCHPO	Hypothetical protein C6C3.09 in chromosome I	0.25	-	nuc	0					335
O94696 UniProt NPD GO	YG1C_SCHPO	Hypothetical protein C83.12 in chromosome II	0.25	-	nuc	0					161
Q8ST53 UniProt NPD GO	Y113_ENCCU	Hypothetical protein ECU01_0130/ECU01_1480/ECU08_0060	0.25	-	end	0					366
Q8ST89 UniProt NPD GO	Y7I6_ENCCU	Hypothetical protein ECU07_1860/ECU10_0040/ECU11_2100	0.25	-	cyt	0					135
P34405 UniProt NPD GO	YLW2_CAEEL	Hypothetical protein F22B7.2	0.25	-	mit	0					129
P34468 UniProt NPD GO	YMH1_CAEEL	Hypothetical protein F58A4.1	0.25	-	exc	1 *					254
Q10045 UniProt NPD GO	YRT2_CAEEL	Hypothetical protein T07A5.2	0.25	-	end	5	Membrane; multi-pass membrane protein (Potential)				301
P41844 UniProt NPD GO	YO94_CAEEL	Hypothetical protein T20B12.4	0.25	-	cyt	0					335
Q09337 UniProt NPD GO	YOFA_CAEEL	Hypothetical protein ZK1290.10 precursor	0.25	-	nuc	0					412
Q8TFG9 UniProt NPD GO	YL61_SCHPO	Hypothetical serine/threonine-rich protein PB15E9.01c precursor	0.25	-	exc	0	Secreted protein (Potential)				943
O01735 UniProt NPD GO	YC91_CAEEL	Hypothetical transporter C09D4.1	0.25	-	end	12	Membrane; multi-pass membrane protein (By similarity)				586
P01598 UniProt NPD GO	KV1F_HUMAN	Ig kappa chain V-I region EU	0.25	-	nuc	0		extracellular region [NAS]			108
P80362 UniProt NPD GO	KV1Y_HUMAN	Ig kappa chain V-I region WAT	0.25	-	nuc	0		extracellular region [NAS]		1WTL	108
P04433 UniProt NPD GO	KV3I_HUMAN	Ig kappa chain V-III region VG precursor (Fragment)	0.25	-	nuc	0		extracellular region [NAS]			115
P01651 UniProt NPD GO	KV5R_MOUSE	Ig kappa chain V-V region EPC 109	0.25	-	nuc	0					108
P01636 UniProt NPD GO	KV5D_MOUSE	Ig kappa chain V-V region MOPC 149	0.25	-	nuc	0				1AR1	108

You are viewing entries 45301 to 45350 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.