HHsearch alignment for GI: 254780610 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=95.67  E-value=0.023  Score=33.84  Aligned_cols=52  Identities=19%  Similarity=0.203  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf             87578999987176889899999998599049989932867580489889997
Q gi|254780610|r   22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT   74 (340)
Q Consensus        22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~   74 (340)
T Consensus         8 yITLgQlLK~~-~~i~sGG~AK~fL~e~~V~vNGe~e~RRGkKL~~gD~i~i~   59 (60)
T TIGR02988         8 YITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP   59 (60)
T ss_pred             EECHHHHHHHH-HHHCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEC
T ss_conf             16276786688-56228257889870695554784404588700489668826