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Table 5 List of surface layer homology domain containing proteins of Pjdr2 proposed to be involved in extracellular polysaccharide processing

From: Genomic and transcriptomic analysis of carbohydrate utilization by Paenibacillus sp. JDR-2: systems for bioprocessing plant polysaccharides

LTa

Domain architectureb,c,d

Secretionf

MW (kDa)g

pIg

Putative functionh

0221/ Xyn10A 1

3CBM4,9/GH10/CBM9/3SLH

Yes

157

4.90

β-xylanase

 0680

GH5/FN3/3CBM11/3SLH

Yes

204

4.72

β-mannanase

 0824

3SLH/GH16/3CBM4,9/DUF1533/GH16/3CBM4,9/DUF1533/CBM4,9/DUF1533/CF/DUF1533/CF

Yes

313

4.65

β-glucanase

0951/ Bgl16A 1

3SLH/GH16/2CBM4,9/CBM6/2CBM4,9

Yes

154

4.83

β-glucanase

 0964

RBT/2CBM6/RHB/3SLH

Yes

228

4.81

mycodextranase

 1124

GH43/CBM6/2BIG2/2SLH

Yes

159

4.71

α-L-arabinofuranosidase

 1125

GH20/CBM6/BIG2/2SLHe

Yes

213

4.75

α-glucuronidase

 1167

DUF481/RHB/FN3/CBM9/FN3/3SLH

Yes

185

4.79

polysaccharide lyase

 1173

2PL3/CBM9/3SLH

Yes

210

4.81

pectate lyase

 1611

CCT/PHP/BIG3/3SLH

Yes

230

4.90

chitobiase (CCT/ESD) association

 1796

2FN3/GH18/FN3/3SLH

Yes

128

4.79

chitinase

 1997

CBM4,9/AL3/HP/3SLH

Yes

229

4.90

alginate lyase/heparinase

 2544

2NVS/2FN3/3SLH

Yes

170

4.99

sialidase

 3195

GAG/3SLH

Yes

153

4.85

hyaluronate lyase

 3554

GH30/CBM6/CBM4,9/2FN3/BIG2/3SLH

Yes

173

4.89

endo-1,6-beta-glucosidase

 3565

3KCH/2CCT/5BIG3/CLD/3SLH

Yes

227

4.65

CCT/ESD association

 4054

2CBM6/PL3/RHB/3SLH

Yes

237

4.75

polysaccharide lyase

 4093

3FN3/GH43/CBM6/3SLH

Yes

200

4.70

β-xylosidase

 4104

GH27/3CBMX2/3SLH

Yes

164

4.73

α-galactosidase

 4665

GH59/CBM6/BIG4/BIG3/3SLH

Yes

217

4.52

β-galactosidase

 4730

GH53/BIG4/2CBM4,9/3SLH

Yes

122

4.73

arabinogalactan endo-β-1,4-galactanase

 5040

GH66/5CBM6/AMY/3SLH

Yes

182

4.83

dextranase

 5076

RHB/2CF/FN3/GH65/2CF/3SLH

Yes

273

4.77

alpha-L-fucosidase

5200/ Amy13A 1

4ESD /AMY/2FN3/3SLH

Yes

235

4.75

amylopullulanase

 5272

2CBM11/BIG2/3SLH

Yes

231

4.65

carbohydrate binding

 5379

3SLH/GH18

Yes

59

5.80

peptidoglycan hydrolase

 5534

RHB/2CRD/2CLD/BIG2/3SLH

Yes

176

4.58

polysaccharide lyase

 5572

GH42/3SLH

Yes

162

4.72

β-galactosidase

 6195

3PBX/3SLH

Yes

77

4.53

xylanase

  1. aLT, locus tag annotated as Pjdr2_#### abbreviated to consist only of the numeric portion, ####. Surface anchored proteins directly involved in the utilization of xylan, barley β-glucan and starch are denoted in bold
  2. bDomain predictions result from analysis of the proteins in the CCD (Conserved Domain Database) with an Expect Value threshold set to the default of 0.010 and increased to 0.10 to detect more divergent domains in unaccounted for regions or, as in some cases directly through the pfam database. Domain abbreviations are defined in order of appearance. CBM, Carbohydrate binding module; GH, Glycoside hydrolase; SLH, Surface layer homology domain; FN3, Fibronectin type 3 domain; DUF, Domain of unknown function; CF, Coagulation factor 5/8 C-terminal domain; RBT, Ricin-type beta-trefoil; RHB, Right handed beta helix; BIG, Bacterial Ig-like domain; PL, Pectate lyase; CCT, Chitobiase/beta-hexosaminidase C-terminal domain in the early set domain superfamily; PHP, Polymerase and histidinol phosphatase domain; AL, Alginate lyase; HP, Heparinase; NVS, Non-viral sialidases; GAG, Glycosaminoglycan polysaccharide lyase family; KCH, Galactose oxidase central domain; CLD, Cadherin-like beta sandwich domain; AMY, Alpha amylase catalytic domain family; ESD, Early set domain; CPRD, Carboxypeptidase regulatory-like domain; PBX Putative bacterial xylanases
  3. cFor any given domain an abbreviation is provided as defined under superscript (b), with numbers preceding the abbreviation indicating the number of consecutive occurrences greater than one (> 1) of the domain and numbers following the abbreviation indicating the specific family of the detected domain, if any
  4. dIn each modular protein the domain used to establish the “putative function” (sixth column) is underlined
  5. eAnnotated in the CAZy database as a GH115
  6. fSecretion was deduced by detection of a signal peptide using the Signal-P server
  7. gMolecular weight (MW) and isoelectric point (pI) predictions were obtained through the ProtParam tool available through the ExPASy web server
  8. hPutative function is based either on the predicted function from domain assignment or a justification for assignment as a protein that is involved with sugar manipulations
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BMC Genomics

ISSN: 1471-2164

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