Table 1

Newly predicted domains in the Mycoplasma gallisepticum genome.

S.No.

Domain Name

Description

Full

Partial


1.

AAA

ATPase family associated with various cellular activities

NP_853502.1 = 9-182

-


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

-


3.

ATP-synt_ab_C

ATP synthase alpha/beta chain, C terminal domain.

NP_853478.1 = 140-221

-


4.

ATP-synt_ab_N

ATP synthase alpha/beta family, beta-barrel domain

NP_853438.1 = 4-126

NP_853439.1 = 2-125

-


5.

BPD_transp_1

Binding-protein-dependent transport system inner membrane component.

NP_853029.1 = 53-260

NP_853249.1 = 59-232

-


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

-


7.

DUF-30

Domain of Unknown Function 30

NP_853479.1 = 370-770

-


8.

DUF-31

Domain of Unknown Function 31

NP_853440.1 = 220-317

NP_853441.1 = 233-337

NP_853488.1 = 220-340

-


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

-


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

-


11.

GMP_synt_C $

GMP synthase C terminal domain.

NP_852801.1 = 220-275

-


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

-


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

-


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

-


15.

HTH_11 #

Helix-turn-helix domain present in a wide variety of proteins.

NP_853136.1 = 28-73

-


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

-


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

-


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

-


19.

Lactamase_B

Metallo-beta-lactamase superfamily.

NP_852865.1 = 40-248

-


20.

RMMBL

RNA-metabolising metallo-beta-lactamase.

NP_852865.1 = 320-360

-


21.

Lipoprotein_17

Lipoprotein associated domain.

NP_852799.1 = 49-160

-


22.

MatE

Multi Antimicrobial Extrusion (MATE) family function as drug/sodium antiporters.

NP_853011.1 = 364-530

-


23.

Methyltransf_3 $

O-methyltransferase

NP_852906.1 = 7-185

-


24.

MFS_1 $

Major Facilitator Superfamily

NP_852970.1 = 480-922

-


25.

NusB $

The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination.

NP_853291.1 = 13-130

-


26.

Peptidase_M23 $

Peptidase family M23

NP_853190.1 = 484-657

-


27.

PGM_PMM_IV $

Phosphoglucomutase/phosphomannomutae, C-terminal domain

NP_853364.1 = 481-550

-


28.

PTS_EIIB

phosphotransferase system, EIIB

NP_853326.1 = 47-85

-


29.

SBP_bac_1 $

Bacterial extracellular solute-binding protein

NP_852821.1 = 1-385

NP_852814.1 = 6-181


30.

Sigma70_r1_1 #

Sigma-70 factor, region 1.1.

NP_853171.1 = 288-342

-


31.

Sigma70_r1_2 $

Sigma-70 factor, region 1.2

NP_853171.1 = 357-398

-


32.

Sigma70_r4_2 $

Sigma-70, region 4

NP_852863.1 = 120-170

-


33.

TGS $

ThrRS, GTPase, and SpoT domain.

NP_852968.1 = 417-487

-


34.

THUMP $

thiouridine synthases, methylases and PSUSs domain.

NP_853282.1 = 78-170

-


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

-


36.

tRNA_anti

OB-fold nucleic acid binding domain

NP_852876.1 = 230-310

-


37.

VapD_N #

Virulence-associated protein D

NP_853458.1 = 7-49

-


38.

Lipoprotein_X

Mycoplasma MG185/MG260 protein.

-

NP_852988.1 = 247-404

NP_852899.1 = 257-414


39.

Lipoprotein_10

Putative mycoplasma lipoprotein, C-terminal region

NP_852988.1 = 444-563

-


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


41.

ABC_membrane

ABC transporter transmembrane region.

-

NP_852786.1 = 2-126


42.

ABC_tran

ABC transporter

-

NP_853051.1 = 317-467


43.

DUF258

Domain of Unknown Function 258

-

NP_853404.1 = 7-104


44.

GTP_EFTU

-

NP_853200.1 = 68-151


45.

RecO #

Recombination protein O

-

NP_853174.1 = 1-74


46.

SBP_bac_5 $

-

NP_853298.1 = 461-889


47.

Transposase_mut

Transposase, Mutator family

-

NP_852891.1 = 6-108

NP_853257.1 = 16-83

NP_852883.1 = 2-121


48.

HNH $

HNH endonuclease

NP_853456.1 = 650-708

-


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

Reddy et al. BMC Research Notes 2010 3:98   doi:10.1186/1756-0500-3-98

Open Data