HHsearch alignment for GI: 254780187 and conserved domain: TIGR02988

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014330 This small protein has a single S4 domain (IPR002942 from INTERPRO); it is also found in bacterial S4 ribosomal proteins, some pseudouridine synthases and tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members that are not near recF are found instead near dnaA and/or dnaN, the usual neighbours of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage..
Probab=96.44  E-value=0.0057  Score=39.98  Aligned_cols=50  Identities=28%  Similarity=0.357  Sum_probs=46.1

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECC
Q ss_conf             88899862121247887887624978788889413534833884788611
Q gi|254780187|r   96 LDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQ  145 (206)
Q Consensus        96 LD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~  145 (206)
T Consensus        11 LgQlLK~~~~i~sGG~AK~fL~e~~V~vNGe~e~RRGkKL~~gD~i~i~~   60 (60)
T TIGR02988        11 LGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIPD   60 (60)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEECC
T ss_conf             76786688562282578898706955547844045887004896688269