HHsearch alignment for GI: 254780787 and conserved domain: cd04163

>cd04163 Era Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.
Probab=99.84  E-value=2.9e-20  Score=156.55  Aligned_cols=156  Identities=24%  Similarity=0.275  Sum_probs=117.2

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHH-CCCCCCEECCCEEEEECCCCEEEEEECCCH----HHHHH----HHHHHH
Q ss_conf             553038986236850446777886422210-012310001214999517843888851661----57899----986664
Q gi|254780787|r  381 IRPPVVTIMGHVDHGKTSLLDAIRKADVAK-GEIGGITQHIGAYQVAYQGKNITFLDTPGH----AAFYE----MRARGA  451 (884)
Q Consensus       381 ~R~pvv~v~ghvd~GKt~lld~~r~~~~~~-~e~ggitq~iga~~~~~~~~~~~~iDtPGh----~~f~~----~r~rg~  451 (884)
T Consensus         1 ~~~~~V~ivG~pN~GKSsL~N~L~~~~~a~vs~~~gtTr~~~~~~~~~~~~~~~l~DtpG~~~~~~~~~~~~~~~~~~~l   80 (168)
T cd04163           1 FKSGFVAIVGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIYTDDDAQIIFVDTPGIHKPKKKLGERMVKAAWSAL   80 (168)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCEEEECCCCCEEECCCEEEEEECCEEEEEEECCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             99868999999999999999999589703323889826344236898499789999589866514567789999999865


Q ss_pred             HCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEEEEECCCC
Q ss_conf             20680599998366740235777898997099415612331244332000221000013200012347403631100247
Q gi|254780787|r  452 RVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNL  531 (884)
Q Consensus       452 ~~~d~~ilvv~~~~g~~~qt~e~~~~~~~~~~p~iva~nk~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  531 (884)
T Consensus        81 ~~~D~il~vvD~~~~~~~~d~~i~~~l~~~~~~~iivlNK~Dl~~~~~-----~~~~~~~~~~~~~~~~~vi~iSA~~g~  155 (168)
T cd04163          81 KDVDLVLFVVDASEPIGEGDEFILELLKKSKTPVILVLNKIDLVKDKE-----DLLPLLEKLKELGPFAEIFPISALKGE  155 (168)
T ss_pred             HCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECEEECCCHH-----HHHHHHHHHHHHCCCCCEEEEECCCCC
T ss_conf             136558999978989866779999999980998599997887047877-----899999999961899968999777896


Q ss_pred             CCCCCCCCHH
Q ss_conf             7411221000
Q gi|254780787|r  532 NLDKLLDAIL  541 (884)
Q Consensus       532 ~~~~~~~~~~  541 (884)
T Consensus       156 Gid~L~~~i~  165 (168)
T cd04163         156 NVDELLEEIV  165 (168)
T ss_pred             CHHHHHHHHH
T ss_conf             9999999999