HHsearch alignment for GI: 254780676 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=97.87 E-value=0.0014 Score=46.97 Aligned_cols=194 Identities=16% Similarity=0.161 Sum_probs=123.1
Q ss_pred CCCCCCCCCCCCCCCCCCCCC--CHHHHHHHHHHHHHHCCCEEEEEC---CCCCCCCCCHHHHHHHHHHHHHHHCCCCEE
Q ss_conf 652235352234467899888--823579999999970775189850---544534532589999999999853358689
Q gi|254780676|r 93 GAICTRACTFCNVATGKPQPL--DPQEPENISWAVRSMKLSHVVITS---VDRDDLDDGGAQHFAEVISAIRESAPSTTI 167 (329)
Q Consensus 93 G~~CTR~C~FC~V~~G~P~~~--D~~EP~rvA~av~~l~Lk~vViTS---V~RDDL~DgGA~hfa~~I~~Ir~~~P~~~I 167 (329)
T Consensus 35 t~rCNL~C~~C~~i-~~~~~~l~~~Ls~ee~~~~~~e~Gap~V~itGGEPLLr~d--------l~eIv~~a~~~g--~~v 103 (318)
T TIGR03470 35 LFRCNLACAGCGKI-QYPAEILKQRLSVEECLRAVDECGAPVVSIPGGEPLLHPE--------IDEIVRGLVARK--KFV 103 (318)
T ss_pred CCCCCCCCCCCCCC-CCCCHHHHCCCCHHHHHHHHHHCCCCEEEECCCCCCCCCC--------HHHHHHHHHHCC--CEE
T ss_conf 13226778899741-3676465443899999999998499789951887455647--------999999999759--979
Q ss_pred EEECCCCCCCHHHHHHHHHCCCHHHHHCCCCCCCCCCC-CCCCCHHHHHHHHHHHHHHCCCEEEECCCEEEEEEECHHHH
Q ss_conf 98154623446899987410702332013830002756-38970358999999999970891670140488764206889
Q gi|254780676|r 168 EVLTPDFLRKPHALEKVVSAKPDVFNHNLETVASNYLM-VRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEI 246 (329)
Q Consensus 168 EvLiPDf~G~~~al~~v~~A~pdV~nHNiETV~rLy~~-VRp~a~Y~rSL~vL~~aK~~~~~i~TKSGlMvGLGEt~eEi 246 (329)
T Consensus 104 ~l~TNG~Ll-~k~i~~~~~~~~~~~~VsLDG~~e~HD~~r~~~G~Fd~av~aIr~ak~~G~~V~iN~Tv--f~~~n~~~i 180 (318)
T TIGR03470 104 YLCTNALLL-EKKLDKFEPSPYLTFSVHLDGLREHHDASVCREGVFDRAVEAIREAKARGFRVTTNTTL--FNDTDPEEV 180 (318)
T ss_pred EEECCHHHH-HHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCEEEEEEE--ECCCCHHHH
T ss_conf 997755200-99999985188836999801787886688717977999999999999869946799897--068999999
Q ss_pred HHHHHHHHHCCCCEEECCHHCC----CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEE
Q ss_conf 9999999966993997502227----861007800023846999999999974962434
Q gi|254780676|r 247 LQLMDDLRTADVDFLTMGQYLQ----PTRKHHKVESFVTPQDFKSYETIAYSKGFLMVS 301 (329)
Q Consensus 247 ~e~l~DLr~~gvdilTiGQYL~----Ps~~h~pV~ryv~P~eF~~~~~~a~~~Gf~~V~ 301 (329)
T Consensus 181 ~~~~d~~~~lgVdgi~isp~y~Ye~ap~q~~-fl~r~~~~~lfr~il~~~~~k~w~~n~ 238 (318)
T TIGR03470 181 AEFFDYLTDLGVDGMTISPGYAYEKAPDQDH-FLGRRQTKKLFREVLSNGNGKRWRFNH 238 (318)
T ss_pred HHHHHHHHHCCCCEEEECCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 9999999876997389766531023763111-158999999999999864565841126