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
P55059 UniProt NPD GO	PDI_HUMIN	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI)	0.00	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)			2DJK	505
P80284 UniProt NPD GO	PDI_HORVU	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI) (Endosperm protein E-1)	0.00	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				513
Q00216 UniProt NPD GO	TIGA_ASPNG	Protein disulfide-isomerase tigA precursor (EC 5.3.4.1)	0.00	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				359
P34102 UniProt NPD GO	PK3_DICDI	Protein kinase 3 (EC 2.7.11.1) (Fragment)	0.00	-	cyt	0					41
P34104 UniProt NPD GO	PK5_DICDI	Protein kinase 5 (EC 2.7.11.1) (Fragment)	0.00	-	cyt	0					33
P50594 UniProt NPD GO	MGN_CHICK	Protein mago nashi homolog (Fragment)	0.00	-	cyt	0	Nucleus (By similarity)				26
Q24437 UniProt NPD GO	MST40_DROME	Protein male-specific 40	0.00	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			23
Q9UR06 UniProt NPD GO	MMF2_SCHPO	Protein mmf2, mitochondrial precursor (Maintenance of mitochondrial function 2)	0.00	-	cyt	0	Mitochondrion (By similarity). Cytoplasm (By similarity)				126
Q9BRQ5 UniProt NPD GO	ORAI3_HUMAN	Protein orai-3	0.00	-	end	3	Membrane; multi-pass membrane protein (By similarity)				295
P36993 UniProt NPD GO	PP2CB_MOUSE	Protein phosphatase 2C isoform beta (EC 3.1.3.16) (PP2C-beta) (IA) (Protein phosphatase 1B)	0.00	-	cyt	0					390
P35815 UniProt NPD GO	PP2CB_RAT	Protein phosphatase 2C isoform beta (EC 3.1.3.16) (PP2C-beta) (IA) (Protein phosphatase 1B)	0.00	-	cyt	0					390
Q2TXA2 UniProt NPD GO	SYM1_ASPOR	Protein sym1	0.00	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				173
P04399 UniProt NPD GO	RIP2_HORVU	Protein synthesis inhibitor II (EC 3.2.2.22) (Ribosome-inactivating protein II) (rRNA N-glycosidase) ...	0.00	-	cyt	0	Starchy endosperm of mature seeds				280
Q9VBV3 UniProt NPD GO	TAKT_DROME	Protein takeout precursor	0.00	-	mit	0	Secreted protein	extracellular region [IDA]			249
Q8AY33 UniProt NPD GO	SC61A_BORSA	Protein transport protein Sec61 subunit alpha	0.00	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q8AY31 UniProt NPD GO	SC61A_BOVVA	Protein transport protein Sec61 subunit alpha	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q7T277 UniProt NPD GO	SC61A_DISMA	Protein transport protein Sec61 subunit alpha	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q8AY32 UniProt NPD GO	SC61A_GADOC	Protein transport protein Sec61 subunit alpha	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q25147 UniProt NPD GO	SC61A_HALRO	Protein transport protein Sec61 subunit alpha	0.00	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q7T278 UniProt NPD GO	SC61A_HARAN	Protein transport protein Sec61 subunit alpha	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q8AY34 UniProt NPD GO	SC61A_HEMAM	Protein transport protein Sec61 subunit alpha	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q8AY35 UniProt NPD GO	SC61A_NOTAN	Protein transport protein Sec61 subunit alpha	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q8AY36 UniProt NPD GO	SC61A_PAGBO	Protein transport protein Sec61 subunit alpha	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q5EA68 UniProt NPD GO	S61A1_BOVIN	Protein transport protein Sec61 subunit alpha isoform 1 (Sec61 alpha-1)	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
P38377 UniProt NPD GO	S61A1_CANFA	Protein transport protein Sec61 subunit alpha isoform 1 (Sec61 alpha-1)	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				475
P61619 UniProt NPD GO	S61A1_HUMAN	Protein transport protein Sec61 subunit alpha isoform 1 (Sec61 alpha-1)	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein		609213		475
P61620 UniProt NPD GO	S61A1_MOUSE	Protein transport protein Sec61 subunit alpha isoform 1 (Sec61 alpha-1)	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				475
Q5R5L5 UniProt NPD GO	S61A1_PONPY	Protein transport protein Sec61 subunit alpha isoform 1 (Sec61 alpha-1)	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
P61621 UniProt NPD GO	S61A1_RAT	Protein transport protein Sec61 subunit alpha isoform 1 (Sec61 alpha-1)	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				475
Q2KHX4 UniProt NPD GO	S61A2_BOVIN	Protein transport protein Sec61 subunit alpha isoform 2 (Sec61 alpha-2)	0.00	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q9H9S3 UniProt NPD GO	S61A2_HUMAN	Protein transport protein Sec61 subunit alpha isoform 2 (Sec61 alpha-2)	0.00	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q9JLR1 UniProt NPD GO	S61A2_MOUSE	Protein transport protein Sec61 subunit alpha isoform 2 (Sec61 alpha-2)	0.00	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q90ZM2 UniProt NPD GO	S61A1_BRARE	Protein transport protein Sec61 subunit alpha isoform A	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q98SN9 UniProt NPD GO	S61A1_ONCMY	Protein transport protein Sec61 subunit alpha isoform A	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q90YL4 UniProt NPD GO	S61A2_BRARE	Protein transport protein Sec61 subunit alpha isoform B	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q98SN8 UniProt NPD GO	S61A2_ONCMY	Protein transport protein Sec61 subunit alpha isoform B	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q85AJ6 UniProt NPD GO	YCF12_ANTFO	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
P50370 UniProt NPD GO	YCF12_CHLRE	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
P56328 UniProt NPD GO	YCF12_CHLVU	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q85G86 UniProt NPD GO	YCF12_CYAME	Protein ycf12	0.00	-	exc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				34
P48256 UniProt NPD GO	YCF12_CYAPA	Protein ycf12	0.00	-	nuc	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (Potential)				36
Q9MS75 UniProt NPD GO	YCF12_EUGAN	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q9MS69 UniProt NPD GO	YCF12_EUGDE	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q9MS66 UniProt NPD GO	YCF12_EUGMU	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q9MS63 UniProt NPD GO	YCF12_EUGMY	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q9MS60 UniProt NPD GO	YCF12_EUGSA	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q9MS57 UniProt NPD GO	YCF12_EUGST	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q9MS54 UniProt NPD GO	YCF12_EUGVI	Protein ycf12	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				32
Q5SCX7 UniProt NPD GO	YCF12_HUPLU	Protein ycf12	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q9MS72 UniProt NPD GO	YCF12_LEPBU	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33

You are viewing entries 97351 to 97400 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.