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
O22582 UniProt NPD GO	H2B_GOSHI	Histone H2B	0.23	+	nuc	0	Nucleus				146
Q9SI96 UniProt NPD GO	H2B3_ARATH	Histone H2B.3 (HTB3)	0.23	+	nuc	0	Nucleus (By similarity)				150
Q43216 UniProt NPD GO	H2B5_WHEAT	Histone H2B.5 (wcH2B-6)	0.23	-	nuc	0	Nucleus (By similarity)				135
P90516 UniProt NPD GO	H42_BLEJA	Histone H4 (Fragment)	0.23	-	nuc	0	Nucleus (By similarity)				89
Q5KDT9 UniProt NPD GO	HAT2_CRYNE	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.23	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				435
Q6BK34 UniProt NPD GO	HAT2_DEBHA	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.23	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				415
Q61647 UniProt NPD GO	HAS1_MOUSE	Hyaluronan synthase 1 (EC 2.4.1.212) (Hyaluronate synthase 1) (Hyaluronic acid synthase 1) (HA synth ...	0.23	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				583
O57427 UniProt NPD GO	HAS2_XENLA	Hyaluronan synthase 2 (EC 2.4.1.212) (Hyaluronate synthase 2) (Hyaluronic acid synthase 2) (HA synth ...	0.23	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				551
Q9U8G7 UniProt NPD GO	P29_ECHGR	Hydatid disease diagnostic antigen P-29	0.23	-	nuc	0					238
Q7XAD0 UniProt NPD GO	HSY1_LYCES	Hydroxyproline-rich systemin precursor (Defense-signaling glycopeptide hormone) [Contains: HypSys I ...	0.23	-	exc	1 *	Cytoplasm	intracellular [NAS]			146
P38284 UniProt NPD GO	YB07_YEAST	Hypothetical 12.1 kDa protein in CNS1-CDC28 intergenic region	0.23	-	nuc	0					106
P53205 UniProt NPD GO	YG16_YEAST	Hypothetical 12.4 kDa protein in SEC9-MSB2 intergenic region	0.23	-	cyt	0					108
P47174 UniProt NPD GO	YJ9K_YEAST	Hypothetical 13.2 kDa protein in RPS4A-BAT2 intergenic region	0.23	-	nuc	0					117
P48231 UniProt NPD GO	YNI7_YEAST	Hypothetical 132.5 kDa protein in TOP2-MKT1 intergenic region	0.23	-	end	1	Membrane; multi-pass membrane protein (Potential)	bud [IDA]			1178
Q6L3C9 UniProt NPD GO	YCF68_SACHY	Hypothetical 14 kDa protein ycf68 (ORF 134)	0.23	-	mit	0	Plastid; chloroplast				134
Q6ENQ5 UniProt NPD GO	YCF68_SACOF	Hypothetical 14 kDa protein ycf68 (ORF 134)	0.23	-	mit	0	Plastid; chloroplast				134
P47073 UniProt NPD GO	YJB5_YEAST	Hypothetical 15.2 kDa protein in PET130-CCT3 intergenic region	0.23	-	cyt	0					124
P40519 UniProt NPD GO	YIG0_YEAST	Hypothetical 15.7 kDa protein in SNP1-GPP1 intergenic region	0.23	-	end	0					144
P58146 UniProt NPD GO	YCX8_ASTLO	Hypothetical 15.7 kDa protein in rpl14-rpl12 intergenic region (ORF125b)	0.23	+	nuc	2 *	Plastid				125
P51372 UniProt NPD GO	YCF22_PORPU	Hypothetical 23.7 kDa protein ycf22 (ORF209)	0.23	-	mit	1 *	Plastid; chloroplast				209
P47055 UniProt NPD GO	YJD8_YEAST	Hypothetical 24.8 kDa protein in NSP1-TAD2 intergenic region	0.23	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				219
P14758 UniProt NPD GO	YCY5_ASTLO	Hypothetical 25.9 kDa protein in rpl12-rps7 intergenic region (ORF211)	0.23	-	nuc	1 *	Plastid				211
P38279 UniProt NPD GO	YBZ7_YEAST	Hypothetical 33.5 kDa protein in MRPS9-YSW1 intergenic region	0.23	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				296
P40169 UniProt NPD GO	YNT4_YEAST	Hypothetical 34.1 kDa protein in WHI3-CHS1 intergenic region	0.23	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	cell cortex [IDA] cytoplasm [IDA] endoplasmic reticulum [IDA]			301
Q9LEW8 UniProt NPD GO	FN3X_ARATH	Hypothetical 35.5 kDa protein At3g61080	0.23	-	mit	0					318
Q04216 UniProt NPD GO	YM12_YEAST	Hypothetical 39.2 kDa protein in GCR3-SAS2 intergenic region	0.23	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				342
P31561 UniProt NPD GO	YCXA_EUGGR	Hypothetical 40.9 kDa protein in 16S rRNA 3'region (ORF350)	0.23	-	mit	4 *	Plastid; chloroplast				350
P47051 UniProt NPD GO	YJE6_YEAST	Hypothetical 52.1 kDa protein in MTR4-GYP6 intergenic region	0.23	-	cyt	0					451
P47090 UniProt NPD GO	YJY5_YEAST	Hypothetical 58.1 kDa protein in SPC1-ILV3 intergenic region	0.23	-	end	6	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA] endoplasmic reticulum [IDA]			510
P39994 UniProt NPD GO	YEC0_YEAST	Hypothetical 61.3 kDa protein in URA3-MMS21 intergenic region	0.23	-	nuc	0		cytoplasm [IDA]			560
Q9FHD3 UniProt NPD GO	UDU3_ARATH	Hypothetical DUF26 domain-containing protein 3 precursor	0.23	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				287
Q9SUB0 UniProt NPD GO	DOF43_ARATH	Hypothetical Dof zinc finger protein DOF4.3 (AtDOF4.3)	0.23	-	nuc	0	Nucleus (Probable)				232
Q9XWV0 UniProt NPD GO	TMM33_CAEEL	Hypothetical UPF0121 protein Y37D8A.17 in chromosome I	0.23	-	end	3	Membrane; multi-pass membrane protein (Potential)				271
Q9SR32 UniProt NPD GO	U161_ARATH	Hypothetical UPF0161 protein At3g09310	0.23	-	mit	0					90
Q11111 UniProt NPD GO	YX04_CAEEL	Hypothetical protein C03B1.4	0.23	-	nuc	0					253
O74460 UniProt NPD GO	YCGG_SCHPO	Hypothetical protein C16C4.16c in chromosome III	0.23	-	nuc	0					161
Q10484 UniProt NPD GO	YDFC_SCHPO	Hypothetical protein C17C9.12 in chromosome I	0.23	-	nuc	1					319
Q9UTD8 UniProt NPD GO	YID1_SCHPO	Hypothetical protein C227.01c in chromosome I	0.23	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				373
Q9P7S1 UniProt NPD GO	YIFC_SCHPO	Hypothetical protein C23G3.12c in chromosome I	0.23	-	cyt	0					996
Q09244 UniProt NPD GO	YP95_CAEEL	Hypothetical protein C28H8.5 precursor	0.23	-	mit	0					302
Q09257 UniProt NPD GO	YQB4_CAEEL	Hypothetical protein C30G12.4	0.23	-	mit	1					258
Q5FC62 UniProt NPD GO	YE1A_CAEEL	Hypothetical protein C35A5.10	0.23	-	exc	0					286
Q9P3W4 UniProt NPD GO	YLI4_SCHPO	Hypothetical protein C458.04c in chromosome I	0.23	-	nuc	0					340
Q10214 UniProt NPD GO	YAY6_SCHPO	Hypothetical protein C4H3.06 in chromosome I	0.23	-	nuc	0					137
Q09292 UniProt NPD GO	YQL3_CAEEL	Hypothetical protein C56G7.3 in chromosome III	0.23	-	nuc	0					322
P41949 UniProt NPD GO	YLK1_CAEEL	Hypothetical protein D1044.1	0.23	-	cyt	0					382
Q8SQI8 UniProt NPD GO	Y121_ENCCU	Hypothetical protein ECU01_0210/ECU01_1400	0.23	-	cyt	0					179
Q19910 UniProt NPD GO	YKYL_CAEEL	Hypothetical protein F30B5.4 in chromosome IV	0.23	-	cyt	0					455
P52882 UniProt NPD GO	YAF4_CAEEL	Hypothetical protein F46C5.4	0.23	-	mit	0					179
P83502 UniProt NPD GO	YFEI_CAEEL	Hypothetical protein T04A11.12	0.23	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				327

You are viewing entries 47451 to 47500 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.