Table 1 |
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Newly predicted domains in the Mycoplasma gallisepticum genome. |
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S.No. |
Domain Name |
Description |
Full |
Partial |
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1. |
AAA |
ATPase family associated with various cellular activities |
NP_853502.1 = 9-182 |
- |
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2. |
Anticodon_1 |
Anticodon-binding domain. This domain is found valyl and leucyl tRNA synthetases. It binds to the anticodon of the tRNA. |
NP_852939.1 = 397-590 NP_852935.1 = 55-218 NP_853215.1 = 620-850 |
- |
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3. |
ATP-synt_ab_C |
ATP synthase alpha/beta chain, C terminal domain. |
NP_853478.1 = 140-221 |
- |
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4. |
ATP-synt_ab_N |
ATP synthase alpha/beta family, beta-barrel domain |
NP_853438.1 = 4-126 NP_853439.1 = 2-125 |
- |
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5. |
BPD_transp_1 |
Binding-protein-dependent transport system inner membrane component. |
NP_853029.1 = 53-260 NP_853249.1 = 59-232 |
- |
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6. |
CHASE-3 # |
Cyclases/Histidine kinases Associated Sensory Extracellular) present in diverse receptor-like proteins with histidine kinase and nucleotide cyclase domains |
NP_853387.1 = 55-582 |
- |
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7. |
DUF-30 |
Domain of Unknown Function 30 |
NP_853479.1 = 370-770 |
- |
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8. |
DUF-31 |
Domain of Unknown Function 31 |
NP_853440.1 = 220-317 NP_853441.1 = 233-337 NP_853488.1 = 220-340 |
- |
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9. |
LMP $ |
LMP repeated region. Found in the LMP group of surface-located membrane proteins of Mycoplasma hominis. |
NP_853333.1 = 1260-1320, 1420-1580, 1600-1760 |
- |
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10. |
Ferritin $ |
Ferritin-like domain is one of the major non-haem iron storage proteins in animals, plants, and microorganisms |
NP_852976.1 = 5-143 |
- |
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11. |
GMP_synt_C $ |
GMP synthase C terminal domain. |
NP_852801.1 = 220-275 |
- |
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12. |
Helicase_C |
Helicase conserved C-terminal domain. Found in a wide variety of helicases and helicase related proteins. |
NP_852813.1 = 440-530 NP_853467.1 = 660-730 |
- |
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13. |
HGTP_anticodon |
Anticodon binding domain. tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases. |
NP_852966.1 = 342-423 |
- |
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14. |
HHH # |
The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. |
NP_853482.1 = 589-619 NP_853386.1 = 63-92, 98-127 |
- |
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15. |
HTH_11 # |
Helix-turn-helix domain present in a wide variety of proteins. |
NP_853136.1 = 28-73 |
- |
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16. |
HTH_12 # |
Ribonuclease R winged-helix domain. Found found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea. |
NP_853240.1 = 38-89 |
- |
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17. |
S1 |
The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. |
NP_852895.1 = 140-210 |
- |
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18. |
KH_1 |
The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins. |
NP_852895.1 = 333-393 |
- |
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19. |
Lactamase_B |
Metallo-beta-lactamase superfamily. |
NP_852865.1 = 40-248 |
- |
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20. |
RMMBL |
RNA-metabolising metallo-beta-lactamase. |
NP_852865.1 = 320-360 |
- |
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21. |
Lipoprotein_17 |
Lipoprotein associated domain. |
NP_852799.1 = 49-160 |
- |
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22. |
MatE |
Multi Antimicrobial Extrusion (MATE) family function as drug/sodium antiporters. |
NP_853011.1 = 364-530 |
- |
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23. |
Methyltransf_3 $ |
O-methyltransferase |
NP_852906.1 = 7-185 |
- |
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24. |
MFS_1 $ |
Major Facilitator Superfamily |
NP_852970.1 = 480-922 |
- |
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25. |
NusB $ |
The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. |
NP_853291.1 = 13-130 |
- |
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26. |
Peptidase_M23 $ |
Peptidase family M23 |
NP_853190.1 = 484-657 |
- |
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27. |
PGM_PMM_IV $ |
Phosphoglucomutase/phosphomannomutae, C-terminal domain |
NP_853364.1 = 481-550 |
- |
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28. |
PTS_EIIB |
phosphotransferase system, EIIB |
NP_853326.1 = 47-85 |
- |
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29. |
SBP_bac_1 $ |
Bacterial extracellular solute-binding protein |
NP_852821.1 = 1-385 |
NP_852814.1 = 6-181 |
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30. |
Sigma70_r1_1 # |
Sigma-70 factor, region 1.1. |
NP_853171.1 = 288-342 |
- |
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31. |
Sigma70_r1_2 $ |
Sigma-70 factor, region 1.2 |
NP_853171.1 = 357-398 |
- |
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32. |
Sigma70_r4_2 $ |
Sigma-70, region 4 |
NP_852863.1 = 120-170 |
- |
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33. |
TGS $ |
ThrRS, GTPase, and SpoT domain. |
NP_852968.1 = 417-487 |
- |
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34. |
THUMP $ |
thiouridine synthases, methylases and PSUSs domain. |
NP_853282.1 = 78-170 |
- |
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35. |
Transketolase_C |
The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site |
NP_852812.1 = 530-641 NP_853134.1 = 138-262 |
- |
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36. |
tRNA_anti |
OB-fold nucleic acid binding domain |
NP_852876.1 = 230-310 |
- |
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37. |
VapD_N # |
Virulence-associated protein D |
NP_853458.1 = 7-49 |
- |
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38. |
Lipoprotein_X |
Mycoplasma MG185/MG260 protein. |
- |
NP_852988.1 = 247-404 NP_852899.1 = 257-414 |
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39. |
Lipoprotein_10 |
Putative mycoplasma lipoprotein, C-terminal region |
NP_852988.1 = 444-563 |
- |
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40. |
DEAD |
Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. |
- |
NP_852877.1 = 596-722 |
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41. |
ABC_membrane |
ABC transporter transmembrane region. |
- |
NP_852786.1 = 2-126 |
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42. |
ABC_tran |
ABC transporter |
- |
NP_853051.1 = 317-467 |
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43. |
DUF258 |
Domain of Unknown Function 258 |
- |
NP_853404.1 = 7-104 |
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44. |
GTP_EFTU |
- |
NP_853200.1 = 68-151 |
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45. |
RecO # |
Recombination protein O |
- |
NP_853174.1 = 1-74 |
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46. |
SBP_bac_5 $ |
- |
NP_853298.1 = 461-889 |
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47. |
Transposase_mut |
Transposase, Mutator family |
- |
NP_852891.1 = 6-108 NP_853257.1 = 16-83 NP_852883.1 = 2-121 |
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48. |
HNH $ |
HNH endonuclease |
NP_853456.1 = 650-708 |
- |
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Among probable new domains, some of the them are first time identified in Mycoplasma gallisepticum genome (indicated by $ or #). Among those unique domains, some are not even present in other Mycoplasmas (indicated by #), while some of them are present in other Mycoplasmas (indicated by $). Second column indicates the name of the domain, third column a brief description about the domain and fourth and fifth columns indicate the kind of association which may be full association (we refer 'fully associated' when at least 75% of unassigned region is indirectly aligned with domain region) or partial association (we call partial associated when at most 75% of unassigned region is indirectly aligned with domain region). Under full and partial columns, we indicate the protein id and start and end residue number of probable new domain. # Unique domain, this domain was not presently identified in entire Mycoplasmataceae family $ Unique domain but present in other Mycoplasmataceae family members |
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Reddy et al. BMC Research Notes 2010 3:98 doi:10.1186/1756-0500-3-98 |
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