HHsearch alignment for GI: 254781120 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=98.75  E-value=9.7e-07  Score=70.96  Aligned_cols=184  Identities=16%  Similarity=0.279  Sum_probs=118.0

Q ss_pred             CCCHHCCCCCC---CCCCHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHH
Q ss_conf             65100486132---244111027898999999999999722203444434344454586110144101454454289999
Q gi|254781120|r  122 VGCSLTCSFCY---TGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKISNIVMMGMGEPLCNFDNVK  198 (384)
Q Consensus       122 vGC~m~C~FCa---Tg~~G~~RNLt~~EIv~Qv~~~~~~l~~~~~~~~~~~~~~~~~~~~i~NiVfMGmGEPl~N~d~v~  198 (384)
T Consensus        36 ~rCNL~C~~C~~i~~~~~~l~~~Ls~ee~~~~~~----e-----------------~Gap~--V~itG-GEPLLr~-dl~   90 (318)
T TIGR03470        36 FRCNLACAGCGKIQYPAEILKQRLSVEECLRAVD----E-----------------CGAPV--VSIPG-GEPLLHP-EID   90 (318)
T ss_pred             CCCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHH----H-----------------CCCCE--EEECC-CCCCCCC-CHH
T ss_conf             3226778899741367646544389999999999----8-----------------49978--99518-8745564-799


Q ss_pred             HHHHCCCCCCCCCCCCCEEEEEECCCC--HHHHHHHCCCCCCEEEEEECCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             996037684577877536888513874--147886012565179984045511344412331257899999999999862
Q gi|254781120|r  199 KSLSIASDSMGLSFSKRRITLSTSGFV--PNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGL  276 (384)
Q Consensus       199 ~ai~~l~~~~g~~~~~r~ITvST~Gi~--p~I~~la~~~~~~LAiSLha~~~~~R~~lmPi~~~~~l~~l~~a~~~y~~~  276 (384)
T Consensus        91 eIv~~a~~-~g-----~~v~l~TNG~Ll~k~i~~~~~~~~~~~~VsLDG~~-e~HD~~r~~~G--~Fd~av~aIr~a--k  159 (318)
T TIGR03470        91 EIVRGLVA-RK-----KFVYLCTNALLLEKKLDKFEPSPYLTFSVHLDGLR-EHHDASVCREG--VFDRAVEAIREA--K  159 (318)
T ss_pred             HHHHHHHH-CC-----CEEEEECCHHHHHHHHHHHHHCCCCEEEEECCCCH-HHHHHHHCCCC--HHHHHHHHHHHH--H
T ss_conf             99999997-59-----97999775520099999985188836999801787-88668871797--799999999999--9


Q ss_pred             CCCCEEEEEEEEECCCCCCHHHHHHHHHHHCCCCC-EEEEEECCCCCCC---CCCCCCHHHHHHHHHHHHH
Q ss_conf             58945999998726999888999999998325453-1667512778879---8868898999999999998
Q gi|254781120|r  277 SNARRITFEYVMLKGINDSPRDALNLIKILKGIPA-KINLIPFNPWPGC---EYLCSDQKDIVTFSECIKR  343 (384)
Q Consensus       277 ~~~rrit~EYvli~gvNDs~e~a~~L~~ll~~~~~-~vNLIp~N~~~~~---~~~~~~~~~i~~F~~~L~~  343 (384)
T Consensus       160 ~~G~~V~iN~Tvf~~--~n~~~i~~~~d~~~~lgVdgi~isp~y~Ye~ap~q~~fl~r~~~~~lfr~il~~  228 (318)
T TIGR03470       160 ARGFRVTTNTTLFND--TDPEEVAEFFDYLTDLGVDGMTISPGYAYEKAPDQDHFLGRRQTKKLFREVLSN  228 (318)
T ss_pred             HCCCCEEEEEEEECC--CCHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             869946799897068--999999999999987699738976653102376311115899999999999986