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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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