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
P84656 UniProt NPD GO	PVK1_CYRPO	Periviscerokinin-1 (Cyrpo-PVK-1)	0.02	-		0	Secreted protein				11
P84659 UniProt NPD GO	PVK1_DERVE	Periviscerokinin-1 (Derve-PVK-1)	0.02	-		0	Secreted protein				12
P83921 UniProt NPD GO	PVK1_LEUMA	Periviscerokinin-1 (Lem-PVK-1)	0.02	-		0	Secreted protein				11
P83923 UniProt NPD GO	PVK1_BLACR	Periviscerokinin-1 (PVK-1)	0.02	-		0	Secreted protein				11
P83924 UniProt NPD GO	PVK1_BLADU	Periviscerokinin-1 (PVK-1)	0.02	-		0	Secreted protein				11
P84591 UniProt NPD GO	PVK1_BLAGI	Periviscerokinin-1 (PVK-1)	0.02	-		0	Secreted protein				11
P83925 UniProt NPD GO	PVK1_GROPO	Periviscerokinin-1 (PVK-1)	0.02	-		0	Secreted protein				11
P83922 UniProt NPD GO	PVK1_NAUCI	Periviscerokinin-1 (PVK-1)	0.02	-		0	Secreted protein				11
P84657 UniProt NPD GO	PVK1_PERVR	Periviscerokinin-1 (Pervi-PVK-1)	0.02	-		0	Secreted protein				11
P84654 UniProt NPD GO	PVK1_PYCSU	Periviscerokinin-1 (Pycsu-PVK-1)	0.02	-		0	Secreted protein				11
P84660 UniProt NPD GO	PVK2_DERVE	Periviscerokinin-2 (Derve-PVK-2)	0.02	-		0	Secreted protein				12
P84353 UniProt NPD GO	PVK2_SARBU	Periviscerokinin-2 (Neobu-PVK-2)	0.02	-		0	Secreted protein				9
P84374 UniProt NPD GO	PVK21_CELBM	Periviscerokinin-2 type 1 (PVK-2 type 1)	0.02	-		0	Secreted protein				12
P84661 UniProt NPD GO	PVK3_APTFU	Periviscerokinin-3 (Aptfu-PVK-3)	0.02	-		0	Secreted protein				11
Q9SLH7 UniProt NPD GO	PER20_ARATH	Peroxidase 20 precursor (EC 1.11.1.7) (Atperox P20) (ATP28a)	0.02	-	cyt	1 *	Secreted protein (By similarity)				336
Q96510 UniProt NPD GO	PER35_ARATH	Peroxidase 35 precursor (EC 1.11.1.7) (Atperox P35) (ATP21a)	0.02	-	end	0	Secreted protein (By similarity)				329
Q96509 UniProt NPD GO	PER55_ARATH	Peroxidase 55 precursor (EC 1.11.1.7) (Atperox P55) (ATP20a)	0.02	-	cyt	0	Secreted protein (By similarity)				330
Q39034 UniProt NPD GO	PER59_ARATH	Peroxidase 59 precursor (EC 1.11.1.7) (Atperox P59) (Peroxidase N) (ATPN)	0.02	-	exc	1 *	Secreted protein (By similarity)			1QGJ	328
Q9FMI7 UniProt NPD GO	PER70_ARATH	Peroxidase 70 precursor (EC 1.11.1.7) (Atperox P70) (ATP45)	0.02	-	end	0	Secreted protein (By similarity)				330
Q43873 UniProt NPD GO	PER73_ARATH	Peroxidase 73 precursor (EC 1.11.1.7) (Atperox P73) (PRXR11) (ATP10a)	0.02	-	end	0	Secreted protein (By similarity)				329
P84753 UniProt NPD GO	PERB_ALOVR	Peroxidase B (EC 1.11.1.7) (Fragments)	0.02	-	cyt	0	Secreted protein (By similarity)				188
Q42517 UniProt NPD GO	PERN_ARMRU	Peroxidase N precursor (EC 1.11.1.7) (Neutral peroxidase)	0.02	-	exc	1 *	Secreted protein (By similarity)				327
Q91191 UniProt NPD GO	TDX_ONCMY	Peroxiredoxin (EC 1.11.1.15) (Thioredoxin peroxidase) (Thioredoxin-dependent peroxide reductase) (Na ...	0.02	-	cyt	0	Cytoplasm (By similarity)				200
P40581 UniProt NPD GO	GPX3_YEAST	Peroxiredoxin HYR1 (EC 1.11.1.15) (Hydrogen peroxide resistance protein 1) (Oxidant receptor peroxid ...	0.02	-	cyt	0	Cytoplasm	intracellular [IPI]			163
P99029 UniProt NPD GO	PRDX5_MOUSE	Peroxiredoxin-5, mitochondrial precursor (EC 1.11.1.15) (Prx-V) (Peroxisomal antioxidant enzyme) (PL ...	0.02	-	mit	0	Mitochondrion. Cytoplasm. Peroxisome	mitochondrion [IDA]			210
Q9BGI1 UniProt NPD GO	PRDX5_BOVIN	Peroxiredoxin-5, mitochondrial precursor (EC 1.11.1.15) (Prx-V) (Thioredoxin reductase)	0.02	-	mit	0	Mitochondrion (By similarity). Cytoplasm (By similarity). Peroxisome (By similarity)				219
O77834 UniProt NPD GO	PRDX6_BOVIN	Peroxiredoxin-6 (EC 1.11.1.15) (Antioxidant protein 2) (1-Cys peroxiredoxin) (1-Cys PRX) (Acidic cal ...	0.02	-	cyt	0	Cytoplasm (By similarity). Lysosome (By similarity). Cytoplasmic vesicle (By similarity). And also f ...				223
Q6NV34 UniProt NPD GO	DECR2_BRARE	Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) (2,4-dienoyl-CoA reductase 2)	0.02	-	pox	0	Peroxisome (By similarity)				300
Q5RBV3 UniProt NPD GO	DECR2_PONPY	Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) (2,4-dienoyl-CoA reductase 2)	0.02	-	pox	0	Peroxisome (By similarity)				292
Q9NUI1 UniProt NPD GO	DECR2_HUMAN	Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) (2,4-dienoyl-CoA reductase 2) (pDCR)	0.02	-	pox	0	Peroxisome (By similarity)				292
Q865R1 UniProt NPD GO	PAOX_BOVIN	Peroxisomal N1-acetyl-spermine/spermidine oxidase precursor (EC 1.5.3.11) (Polyamine oxidase)	0.02	-	mit	0	Peroxisome (By similarity). Cytoplasm (By similarity)				512
Q12462 UniProt NPD GO	PEX11_YEAST	Peroxisomal membrane protein PMP27 (Peroxin-11)	0.02	-	cyt	0	Peroxisome; peroxisomal membrane; peripheral membrane protein				235
Q8R537 UniProt NPD GO	PEX7_CRIGR	Peroxisomal targeting signal 2 receptor (PTS2 receptor) (Peroxin-7)	0.02	-	mit	0	Peroxisome. Cytoplasm				318
O00628 UniProt NPD GO	PEX7_HUMAN	Peroxisomal targeting signal 2 receptor (PTS2 receptor) (Peroxin-7)	0.02	-	cyt	0	Peroxisome. Cytoplasm	peroxisome [TAS]	601757		323
P97865 UniProt NPD GO	PEX7_MOUSE	Peroxisomal targeting signal 2 receptor (PTS2 receptor) (Peroxin-7)	0.02	-	mit	0	Peroxisome. Cytoplasm				318
Q5RCH8 UniProt NPD GO	PECR_PONPY	Peroxisomal trans-2-enoyl-CoA reductase (EC 1.3.1.38)	0.02	-	mit	0	Peroxisome (By similarity)				303
P24392 UniProt NPD GO	PEX2_RAT	Peroxisome assembly factor 1 (PAF-1) (Peroxin-2) (Peroxisomal membrane protein 3)	0.02	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein	peroxisomal membrane [IDA]			305
P28328 UniProt NPD GO	PEX2_HUMAN	Peroxisome assembly factor 1 (PAF-1) (Peroxin-2) (Peroxisomal membrane protein 3) (35 kDa peroxisoma ...	0.02	-	mit	1	Peroxisome; peroxisomal membrane; multi-pass membrane protein		266510		305
P81132 UniProt NPD GO	PER2_VOLCA	Perphorin-2 (Perphorin II) (Fragment)	0.02	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				484
P34175 UniProt NPD GO	PBP_HYACE	Pheromone-binding protein (PBP) (Fragment)	0.02	-	nuc	0					35
Q95VF0 UniProt NPD GO	PBP2_EPIPO	Pheromone-binding protein 2 precursor (PBP 2)	0.02	-	end	0					164
P84789 UniProt NPD GO	PHIG1_SARGI	Philibertain g 1 (EC 3.4.22.-) (Philibertain g I) (Fragment)	0.02	-	cyt	0					23
Q00325 UniProt NPD GO	MPCP_HUMAN	Phosphate carrier protein, mitochondrial precursor (PTP) (Solute carrier family 25 member 3)	0.02	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to plasma membrane [TAS] mitochondrial inner membrane [TAS] mitochondrion [TAS]	600370		362
P37274 UniProt NPD GO	PHOA_PENCH	Phosphate-repressible acid phosphatase precursor (EC 3.1.3.2)	0.02	-	exc	0	Secreted protein				412
O95674 UniProt NPD GO	CDS2_HUMAN	Phosphatidate cytidylyltransferase 2 (EC 2.7.7.41) (CDP-diglyceride synthetase 2) (CDP-diglyceride p ...	0.02	-	end	8	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (Potential)	integral to membrane [NAS] mitochondrial inner membrane [NAS]	603549		445
O35724 UniProt NPD GO	LCAT_MICMN	Phosphatidylcholine-sterol acyltransferase (EC 2.3.1.43) (Lecithin-cholesterol acyltransferase) (Pho ...	0.02	-	cyt	0					299
O35840 UniProt NPD GO	LCAT_TATKG	Phosphatidylcholine-sterol acyltransferase (EC 2.3.1.43) (Lecithin-cholesterol acyltransferase) (Pho ...	0.02	-	nuc	0					293
P30930 UniProt NPD GO	LCAT_PIG	Phosphatidylcholine-sterol acyltransferase (EC 2.3.1.43) (Lecithin-cholesterol acyltransferase) (Pho ...	0.02	-	cyt	0					188
Q9UBM1 UniProt NPD GO	PEMT_HUMAN	Phosphatidylethanolamine N-methyltransferase (EC 2.1.1.17) (PEAMT) (PEMT) (PEMT2)	0.02	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential). Mito ...		602391		198
Q61907 UniProt NPD GO	PEMT_MOUSE	Phosphatidylethanolamine N-methyltransferase (EC 2.1.1.17) (PEAMT) (PEMT) (PEMT2)	0.02	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential). Mito ...	endoplasmic reticulum membrane [IDA] mitochondrial envelope [TAS]			198

You are viewing entries 84901 to 84950 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.