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
P22752 UniProt NPD GO	H2A1_MOUSE	Histone H2A type 1	0.22	-	nuc	0	Nucleus				129
P04908 UniProt NPD GO	H2A1B_HUMAN	Histone H2A type 1-B	0.22	-	nuc	0	Nucleus	nucleosome [NAS]	602795		129
P28001 UniProt NPD GO	H2A1E_HUMAN	Histone H2A type 1-E (H2A.2) (H2A/m)	0.22	-	nuc	0	Nucleus	nucleosome [NAS]	602786	2CV5	129
Q8CGP6 UniProt NPD GO	H2A1H_MOUSE	Histone H2A type 1-H	0.22	-	nuc	0	Nucleus (By similarity)			2F8N	127
P27892 UniProt NPD GO	H2A2_LEIIN	Histone H2A.2	0.22	-	nuc	1 *	Nucleus				132
P04912 UniProt NPD GO	H2A2_YEAST	Histone H2A.2	0.22	-	nuc	0	Nucleus	nuclear nucleosome [TAS]			131
Q873G4 UniProt NPD GO	H2AZ_NEUCR	Histone H2A.Z	0.22	-	nuc	0	Nucleus (By similarity)				143
O65821 UniProt NPD GO	H2B1_LYCES	Histone H2B.1 (LeH2B-1)	0.22	-	nuc	0	Nucleus (By similarity)				141
Q4WEI5 UniProt NPD GO	HAT2_ASPFU	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.22	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				436
P56519 UniProt NPD GO	HDAC2_CHICK	Histone deacetylase 2 (HD2)	0.22	-	nuc	0	Nucleus (Potential)	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]			488
Q9Z2V5 UniProt NPD GO	HDAC6_MOUSE	Histone deacetylase 6 (HD6) (Histone deacetylase mHDA2)	0.22	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). It is mainly cytoplasmic, where it is associated ...	cytoplasm [IDA] nucleus [TAS]			1149
P07354 UniProt NPD GO	HPLN1_CHICK	Hyaluronan and proteoglycan link protein 1 precursor (Proteoglycan link protein) (Cartilage link pro ...	0.22	-	vac	0					355
Q9ESM3 UniProt NPD GO	HPLN2_MOUSE	Hyaluronan and proteoglycan link protein 2 precursor (Brain link protein 1)	0.22	-	mit	0	Secreted protein; extracellular space; extracellular matrix				341
P53211 UniProt NPD GO	YG1C_YEAST	Hypothetical 11.9 kDa protein in MSB2-UGA1 intergenic region	0.22	-	nuc	0					109
P53282 UniProt NPD GO	YG3E_YEAST	Hypothetical 14.5 kDa protein in PAS5-CBF2 intergenic region	0.22	-	mit	1					124
Q32616 UniProt NPD GO	YCF66_MARPO	Hypothetical 16.0 kDa protein ycf66 (ORF135)	0.22	+	end	3 *	Plastid; chloroplast				135
P53321 UniProt NPD GO	YG5G_YEAST	Hypothetical 16.1 kDa protein in RAD2-TNA1 intergenic region	0.22	-	mit	0					146
P25350 UniProt NPD GO	YCP6_YEAST	Hypothetical 18.3 kDa protein in CIT2-SAT4 intergenic region	0.22	-	mit	0					157
P40452 UniProt NPD GO	YIP7_YEAST	Hypothetical 22.0 kDa protein in FOX3-UBP7 intergenic region	0.22	-	mit	0		mitochondrion [IDA]			197
P36129 UniProt NPD GO	YK15_YEAST	Hypothetical 23.2 kDa protein in DAL80-GAP1 intergenic region	0.22	-	end	0					213
P53846 UniProt NPD GO	YN00_YEAST	Hypothetical 23.3 kDa protein in ORC5-ATX1 intergenic region	0.22	-	mit	0		cytoplasm [IDA] nucleus [IDA]			198
P51373 UniProt NPD GO	YCF23_PORPU	Hypothetical 29.1 kDa protein ycf23 (ORF265)	0.22	-	nuc	0	Plastid; chloroplast				265
P34776 UniProt NPD GO	YCY2_ASTLO	Hypothetical 34.5 kDa protein in rps12-trnP intergenic region (ORF288)	0.22	-	cyt	0	Plastid				287
Q04223 UniProt NPD GO	YM14_YEAST	Hypothetical 35.3 kDa protein in POM152-REC114 intergenic region	0.22	-	cyt	0					302
P47177 UniProt NPD GO	YJ9N_YEAST	Hypothetical 45.1 kDa protein in BAT2-DAL5 intergenic region	0.22	-	cyt	0		cytoplasm [IDA]			404
P38318 UniProt NPD GO	YB70_YEAST	Hypothetical 63.0 kDa protein in PYC2-PDB1 intergenic region	0.22	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				560
P53925 UniProt NPD GO	YNL5_YEAST	Hypothetical 74.0 kDa protein in MLS1-RPC19 intergenic region	0.22	-	end	5	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			644
O49550 UniProt NPD GO	DOF45_ARATH	Hypothetical Dof zinc finger protein DOF4.5 (AtDOF4.5)	0.22	-	nuc	0	Nucleus (Probable)				249
Q11096 UniProt NPD GO	YWZ6_CAEEL	Hypothetical RING finger protein C02B8.6 in chromosome X	0.22	-	cyt	0					347
Q09786 UniProt NPD GO	YA98_SCHPO	Hypothetical WD repeat protein C13G6.08 in chromosome I	0.22	-	nuc	0					535
P93300 UniProt NPD GO	M440_ARATH	Hypothetical mitochondrial protein AtMg00440/AtMg01140 (ORF152a/ORF152b)	0.22	-	nuc	0	Mitochondrion (Potential)				152
P93317 UniProt NPD GO	M630_ARATH	Hypothetical mitochondrial protein AtMg00630 (ORF110b)	0.22	-	nuc	0	Mitochondrion (Potential)				110
P14589 UniProt NPD GO	YDH3_PLAFS	Hypothetical protein 3' to Asp-rich and His-rich proteins (Fragment)	0.22	-	mit	0					53
O80873 UniProt NPD GO	PHF5_ARATH	Hypothetical protein At1g07170/At2g30000	0.22	-	nuc	0					110
Q11092 UniProt NPD GO	YWZ2_CAEEL	Hypothetical protein C02B8.2	0.22	-	mit	0					181
Q8TFI0 UniProt NPD GO	YIB4_SCHPO	Hypothetical protein C1751.04 in chromosome I	0.22	-	nuc	0					123
Q10149 UniProt NPD GO	YAT2_SCHPO	Hypothetical protein C1D4.02c in chromosome I	0.22	-	nuc	0					345
Q10346 UniProt NPD GO	YDA4_SCHPO	Hypothetical protein C1F12.04c in chromosome I	0.22	-	cyt	0					191
O13913 UniProt NPD GO	YDW7_SCHPO	Hypothetical protein C23C11.07 in chromosome I	0.22	-	nuc	0					110
P87151 UniProt NPD GO	YB0A_SCHPO	Hypothetical protein C25H2.10c in chromosome II	0.22	-	mit	0					287
Q8WQG1 UniProt NPD GO	YLC1_CAEEL	Hypothetical protein C35D10.1	0.22	-	end	1					222
Q9Y7V0 UniProt NPD GO	YCHB_SCHPO	Hypothetical protein C645.11c in chromosome III	0.22	-	nuc	1 *					186
Q9VNA4 UniProt NPD GO	Y1161_DROME	Hypothetical protein CG1161	0.22	-	exc	2 *	Membrane; multi-pass membrane protein (Potential)				227
Q8STG1 UniProt NPD GO	Y103_ENCCU	Hypothetical protein ECU01_0030/ECU01_1580/ECU04_0040/ECU05_0010/ ECU08_2140/ECU10_1890	0.22	-	cyt	0					123
Q8SUI0 UniProt NPD GO	Y8K6_ENCCU	Hypothetical protein ECU08_2060	0.22	-	end	7 *					263
P34385 UniProt NPD GO	YLPC_CAEEL	Hypothetical protein F02A9.4a in chromosome III	0.22	-	nuc	0					608
Q09951 UniProt NPD GO	YSR3_CAEEL	Hypothetical protein F59B10.3	0.22	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				233
Q9HDT9 UniProt NPD GO	YHEI_SCHPO	Hypothetical protein PB2B2.18 in chromosome II	0.22	-	mit	0					175
Q09422 UniProt NPD GO	YRO5_CAEEL	Hypothetical protein R07G3.5	0.22	-	cyt	0					284
P41845 UniProt NPD GO	YO95_CAEEL	Hypothetical protein T20B12.5	0.22	-	nuc	0					131

You are viewing entries 48501 to 48550 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.