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