HHsearch alignment for GI: 254780628 and conserved domain: TIGR03470
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH
Probab=98.70 E-value=9.6e-07 Score=64.83 Aligned_cols=215 Identities=14% Similarity=0.181 Sum_probs=136.3
Q ss_pred HHHHHCCCCCCCEEEEEECCC-CCCCCCCCCCEEEE---CCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCC
Q ss_conf 998842889885499994065-11837657730245---78866288999999999999987618950589996288888
Q gi|254780628|r 7 YENNMTGQGSNSLGVYVHWPF-CVKKCPYCDFNSHV---RRYKVGQENFIQSFLTEMQWMRQLTGPRSISSIFFGGGTPS 82 (395)
Q Consensus 7 ~~~~~~~~~~~~l~lYihiPF-C~~~C~yC~f~~~~---~~~~~~~~~y~~~l~~Ei~~~~~~~~~~~~~~iy~GGGTPs 82 (395)
T Consensus 16 ~~~~~~g~kr~Plvl~le~t~rCNL~C~~C~~i~~~~~~l~~~Ls~ee~~~~~-------~e~--Gap~--V~itGGEPL 84 (318)
T TIGR03470 16 IKQKLNGRKRFPLVLMLEPLFRCNLACAGCGKIQYPAEILKQRLSVEECLRAV-------DEC--GAPV--VSIPGGEPL 84 (318)
T ss_pred HHHHHCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHH-------HHC--CCCE--EEECCCCCC
T ss_conf 98773376466758873121322677889974136764654438999999999-------984--9978--995188745
Q ss_pred CCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHCCCCCHHHHHHHH
Q ss_conf 78999999999766404764443321133210410023477663034541143234332013455422443134789999
Q gi|254780628|r 83 LIEPQNIALILDGIAKNWTVSSNVEITIEANPSSVEVNNFQGYRKAGVNRISLGVQSLEEQSLRFLGRNHNASEAIAAIH 162 (395)
Q Consensus 83 ~l~~~~l~~ll~~i~~~~~~~~~~e~t~E~~P~~~~~~~l~~l~~~Gv~RiS~GvQs~~~~~l~~~~R~~~~~~~~~~~~ 162 (395)
T Consensus 85 L-r-~dl~eIv~~a~~~g~-----~v~l~TNG-~Ll~k~i~~~~~~~~~~~~VsLDG~~e~HD~~r~~~G~Fd~av~aIr 156 (318)
T TIGR03470 85 L-H-PEIDEIVRGLVARKK-----FVYLCTNA-LLLEKKLDKFEPSPYLTFSVHLDGLREHHDASVCREGVFDRAVEAIR 156 (318)
T ss_pred C-C-CCHHHHHHHHHHCCC-----EEEEECCH-HHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 5-6-479999999997599-----79997755-20099999985188836999801787886688717977999999999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEEEEEEEECCCEEHHHHHCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 86302444333210002585432211127887531800123464688259600014544980211035678899986557
Q gi|254780628|r 163 LARNIFPRMSFDLIYALPKQTMTQWEMELQRALSYAVDHLSLYQLTIEKGTLFYKMHKDGDLVLPSENVAVDLYNLTQSI 242 (395)
Q Consensus 163 ~~~~~~~~v~iDli~GlPgqt~e~~~~~l~~~~~l~p~~is~Y~l~i~~~t~l~~~~~~~~~~~p~~~~~~~~~~~a~e~ 242 (395)
T Consensus 157 ~ak~~G~~V~iN~Tv-f~~~n~~~i~~~~d~~~~lgVdgi~i-----sp~y~Ye~ap~q-~-~fl~r~~~~~lfr~il~~ 228 (318)
T TIGR03470 157 EAKARGFRVTTNTTL-FNDTDPEEVAEFFDYLTDLGVDGMTI-----SPGYAYEKAPDQ-D-HFLGRRQTKKLFREVLSN 228 (318)
T ss_pred HHHHCCCCEEEEEEE-ECCCCHHHHHHHHHHHHHCCCCEEEE-----CCCCCCCCCCCC-C-CCCCHHHHHHHHHHHHHH
T ss_conf 999869946799897-06899999999999998769973897-----665310237631-1-115899999999999986
Q ss_pred HHHCCC
Q ss_conf 887096
Q gi|254780628|r 243 TSAHGL 248 (395)
Q Consensus 243 L~~~GY 248 (395)
T Consensus 229 ~~~k~w 234 (318)
T TIGR03470 229 GNGKRW 234 (318)
T ss_pred CCCCCC
T ss_conf 456584