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
P30755 UniProt NPD GO	H2B1_MAIZE	Histone H2B.1	0.08	+	nuc	0	Nucleus				150
Q6C7Q4 UniProt NPD GO	HAT2_YARLI	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				452
Q9WVG6 UniProt NPD GO	CARM1_MOUSE	Histone-arginine methyltransferase CARM1 (EC 2.1.1.125) (EC 2.1.1.-) (Protein arginine N-methyltrans ...	0.08	-	cyt	0	Nucleus. Cytoplasm				608
Q5RF92 UniProt NPD GO	RBBP4_PONPY	Histone-binding protein RBBP4 (Retinoblastoma-binding protein 4) (RBBP-4)	0.08	-	cyt	0	Nucleus (By similarity)				424
Q9W7I5 UniProt NPD GO	RBBP4_CHICK	Histone-binding protein RBBP4 (Retinoblastoma-binding protein 4) (RBBP-4) (Retinoblastoma-binding pr ...	0.08	-	cyt	0	Nucleus (By similarity)				424
Q6INH0 UniProt NPD GO	RBP4B_XENLA	Histone-binding protein RBBP4-B (Retinoblastoma-binding protein 4-B) (RBBP-4-B) (Retinoblastoma-bind ...	0.08	-	cyt	0	Nucleus				424
Q64202 UniProt NPD GO	DLX1_RAT	Homeobox protein DLX-1 (Fragment)	0.08	-	nuc	0	Nucleus (Potential)				44
Q2U9G3 UniProt NPD GO	LYS4_ASPOR	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.08	-	mit	0	Mitochondrion (By similarity)				775
Q5A644 UniProt NPD GO	LYS4_CANAL	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.08	-	mit	0	Mitochondrion (By similarity)				684
Q93099 UniProt NPD GO	HGD_HUMAN	Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (Homogentisicase) (Homogentisate oxygenase) (Homogentis ...	0.08	-	cyt	0			203500	1EYB	445
O00219 UniProt NPD GO	HAS3_HUMAN	Hyaluronan synthase 3 (EC 2.4.1.212) (Hyaluronate synthase 3) (Hyaluronic acid synthase 3) (HA synth ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS]	602428		553
O08650 UniProt NPD GO	HAS3_MOUSE	Hyaluronan synthase 3 (EC 2.4.1.212) (Hyaluronate synthase 3) (Hyaluronic acid synthase 3) (HA synth ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				554
Q9NYQ2 UniProt NPD GO	HAOX2_MOUSE	Hydroxyacid oxidase 2 (EC 1.1.3.15) (HAOX2) ((S)-2-hydroxy-acid oxidase, peroxisomal) (Medium chain ...	0.08	-	mit	0	Peroxisome	peroxisome [TAS]			353
Q05584 UniProt NPD GO	GLO2_YEAST	Hydroxyacylglutathione hydrolase, cytoplasmic isozyme (EC 3.1.2.6) (Glyoxalase II) (Glx II)	0.08	-	cyt	0	Cytoplasm	cytoplasm [IDA]			274
P10950 UniProt NPD GO	HIOM_BOVIN	Hydroxyindole O-methyltransferase (EC 2.1.1.4) (HIOMT) (Acetylserotonin O-methyltransferase) (ASMT)	0.08	-	cyt	0					345
P38466 UniProt NPD GO	YMF23_MARPO	Hypothetical 11.1 kDa protein in NAD3-NAD7 intergenic region (ORF 99)	0.08	-	mit	0					99
P53308 UniProt NPD GO	YG4U_YEAST	Hypothetical 11.9 kDa protein in DIE2-SMI1 intergenic region	0.08	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				114
P53181 UniProt NPD GO	YGE2_YEAST	Hypothetical 12.1 kDa protein in DST1-HEM2 intergenic region	0.08	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				101
P15811 UniProt NPD GO	YCF49_CYAPA	Hypothetical 12.3 kDa protein ycf49 (ORF102)	0.08	-	end	3 *	Plastid; cyanelle; cyanelle membrane; multi-pass membrane protein (Potential)				102
P53245 UniProt NPD GO	YG2C_YEAST	Hypothetical 13.6 kDa protein in VHT1-ROM1 intergenic region	0.08	-	nuc	1 *					111
P58148 UniProt NPD GO	YCX9_ASTLO	Hypothetical 15.0 kDa protein in rpl12-rps7 intergenic region (ORF122)	0.08	-	nuc	0	Plastid				122
P36082 UniProt NPD GO	YKH6_YEAST	Hypothetical 15.2 kDa protein in SMY1-MUD2 intergenic region	0.08	-	mit	0					127
P47036 UniProt NPD GO	YJH5_YEAST	Hypothetical 15.7 kDa protein in SCP160-SMC3 intergenic region	0.08	-	cyt	0					138
P25640 UniProt NPD GO	YCV4_YEAST	Hypothetical 15.8 kDa protein in SUP61-RAD18 intergenic region	0.08	-	cyt	0					136
P25338 UniProt NPD GO	YGB0_YEAST	Hypothetical 20.2 kDa protein in PRS2-LEU1 intergenic region	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			174
P46998 UniProt NPD GO	YJQ1_YEAST	Hypothetical 20.2 kDa protein in TPK1-CCW7 intergenic region	0.08	-	mit	0	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			180
P50946 UniProt NPD GO	YNJ9_YEAST	Hypothetical 27.2 kDa protein in POL1-RAS2 intergenic region	0.08	-	cyt	0		cytoplasm [IDA]			238
P49836 UniProt NPD GO	YCXA_ODOSI	Hypothetical 3.3 kDa protein in rpl11-trnW intergenic region (ORF27)	0.08	-	cyt	0	Plastid; chloroplast				27
P28321 UniProt NPD GO	YKJ4_YEAST	Hypothetical 35.5 kDa protein in CWP1-MBR1 intergenic region	0.08	-	cyt	0		cytoplasm [IDA] lipid particle [IDA] mitochondrial outer membrane [IDA]			313
P47120 UniProt NPD GO	YJ40_YEAST	Hypothetical 36.2 kDa protein in HAM1-PEM2 intergenic region	0.08	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			325
P49827 UniProt NPD GO	YCF89_ODOSI	Hypothetical 41.6 kDa protein ycf89 (ORF355)	0.08	-	mit	0	Plastid; chloroplast				355
P38468 UniProt NPD GO	YMF26_MARPO	Hypothetical 7.1 kDa protein in NAD2 3'region (ORF 63)	0.08	-	cyt	0					63
Q9MUM6 UniProt NPD GO	YCX6_MESVI	Hypothetical 7.4 kDa protein in ndhF-psbD intergenic region	0.08	-	nuc	0	Plastid; chloroplast				65
O78421 UniProt NPD GO	YCX2_GUITH	Hypothetical 8.1 kDa protein (ORF65)	0.08	-	cyt	0	Plastid; chloroplast				65
P38465 UniProt NPD GO	YMF22_MARPO	Hypothetical 9.3 kDa protein in NAD3-NAD7 intergenic region (ORF 79)	0.08	-	nuc	0					79
Q96VH5 UniProt NPD GO	YCF7_YEAST	Hypothetical UPF0327 protein YCL057C-A	0.08	-	cyt	1 *					97
P30644 UniProt NPD GO	YNE5_CAEEL	Hypothetical calcium-binding protein R08D7.5 in chromosome III	0.08	-	cyt	0					148
P92517 UniProt NPD GO	M760_ARATH	Hypothetical mitochondrial protein AtMg00760 (ORF109b)	0.08	-	mit	0	Mitochondrion (Potential)				109
P92543 UniProt NPD GO	M1110_ARATH	Hypothetical mitochondrial protein AtMg01110 (ORF251)	0.08	-	cyt	0	Mitochondrion (Potential)				251
Q11070 UniProt NPD GO	YT42_CAEEL	Hypothetical protein B0416.2 precursor	0.08	-	vac	0					167
Q11115 UniProt NPD GO	YX09_CAEEL	Hypothetical protein C03B1.9	0.08	-	mit	0					230
P34290 UniProt NPD GO	YKO2_CAEEL	Hypothetical protein C05B5.2	0.08	-	end	5					385
Q10093 UniProt NPD GO	YAOE_SCHPO	Hypothetical protein C11D3.14c in chromosome I	0.08	-	cyt	0					1260
P34327 UniProt NPD GO	YKX2_CAEEL	Hypothetical protein C13G5.2	0.08	-	mit	0					351
P50437 UniProt NPD GO	YY23_CAEEL	Hypothetical protein C28C12.3	0.08	-	mit	1 *					195
Q09271 UniProt NPD GO	YQF7_CAEEL	Hypothetical protein C34C12.7	0.08	-	nuc	0					204
Q5FC79 UniProt NPD GO	YQGA_CAEEL	Hypothetical protein C41C4.10	0.08	-	cyt	4	Membrane; multi-pass membrane protein (Potential)				331
O14165 UniProt NPD GO	YDX1_SCHPO	Hypothetical protein C4C5.01 in chromosome I	0.08	-	cyt	0					246
Q19191 UniProt NPD GO	YZ10_CAEEL	Hypothetical protein F08B12.4	0.08	-	nuc	0					102
P34456 UniProt NPD GO	YMD2_CAEEL	Hypothetical protein F54H12.2	0.08	-	cyt	0					419

You are viewing entries 68201 to 68250 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.