HHsearch alignment for GI: 254780725 and conserved domain: TIGR00416
>TIGR00416 sms DNA repair protein RadA; InterPro: IPR004504 RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=94.85 E-value=0.1 Score=29.69 Aligned_cols=158 Identities=20% Similarity=0.257 Sum_probs=83.0
Q ss_pred CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCH---HHCCCCCCCCHHHHHCCCCCHHHHHHHHHH
Q ss_conf 53799974698877568999999999962699499997879898603---343899878988863184561243376532
Q gi|254780725|r 161 GCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTAN---INFDKDPINSISDAIYPVGRIDKAFVSRLP 237 (427)
Q Consensus 161 grvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~---~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l 237 (427)
T Consensus 103 Gsl-iLiGG~PG~GKSTLLLqV~~~LA~~-~~~~LYVsGEES~~Q~klRA~RLG------it~~~~~s------------ 162 (481)
T TIGR00416 103 GSL-ILIGGDPGIGKSTLLLQVACQLAKN-SMKVLYVSGEESLQQIKLRATRLG------ITDLVEPS------------ 162 (481)
T ss_pred CCE-EEECCCCCCCHHHHHHHHHHHHHHC-CCCEEEEEECCHHHHHHHHHHHCC------CCCCCCHH------------
T ss_conf 416-9846889963567899999998404-881689972301677888875455------32478702------------
Q ss_pred HCCCCCEEEEECCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEECC------------CCCCCH---HHHHHHHHC--CCC
Q ss_conf 024898068724876120320799999998999851288899738------------888898---999998620--125
Q gi|254780725|r 238 VFYAENLSILTAPAMLSRTYDFDEKMIVPVLDILEQIFPLVILDV------------PHVWNS---WTQEVLTLS--DKV 300 (427)
Q Consensus 238 ~~~~~gL~lL~a~~~~~~~~~~~~~~l~~ll~~l~~~yd~VIiD~------------p~~~~~---~~~~~L~~A--D~v 300 (427)
T Consensus 163 -qaqdGinnlahdG~L~~L~Et~~e~I~~~~e~~--~P~~~ViDSIQ~ly~~di~SaPGSVsQVRE~t~~Lmr~AKt~~i 239 (481)
T TIGR00416 163 -QAQDGINNLAHDGNLYVLSETNLEQICAEIEEL--NPQVVVIDSIQTLYLPDISSAPGSVSQVRECTAELMRLAKTRGI 239 (481)
T ss_pred -HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHH--CCCEEEEECCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf -344324543026753215757989999999852--99489991421000000025888423888999999876521686
Q ss_pred --CCCC----CCCHHHHHHHHHHHHHHHHC-CCCC---CCCEEEEECCCCC
Q ss_conf --4357----87768899999999999981-9876---7538999565898
Q gi|254780725|r 301 --VITT----SLDLAGLRNSKNLIDVLKKL-RPAD---KPPYLVLNQVKTP 341 (427)
Q Consensus 301 --viV~----~p~~~slr~a~~ll~~l~~~-~~~~---~~~~iVlNr~~~~ 341 (427)
T Consensus 240 aifiVGHVTKeGsiAGPkvLEH~vD~vLyfeGd~~~~~R~LRS~KNRFGat 290 (481)
T TIGR00416 240 AIFIVGHVTKEGSIAGPKVLEHMVDTVLYFEGDRDSRFRILRSVKNRFGAT 290 (481)
T ss_pred CEEEEEEECCCCCCCCCHHHHHHHHHHEECCCCCCCCCCHHHCCCCCCCCC
T ss_conf 579970043567543404666343311011588753444010001567873