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