HHsearch alignment for GI: 255764472 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=97.89 E-value=0.00027 Score=51.74 Aligned_cols=172 Identities=10% Similarity=0.088 Sum_probs=105.7
Q ss_pred CCEEEEEECCCCCCCCCCCCHHHHHHH-H-HHHHHHHHHHHHHHHHHCCCCEEEEECCCCCEEEECCCCCCCCCCCHHHH
Q ss_conf 725787412332446811100122137-6-41005889998876310133105873145411341134443100021678
Q gi|255764472|r 175 GVTAFLTIQEGCDKFCTFCVVPYTRGI-E-ISRSLSQVVDEARKLIDNGVCEITLLGQNVNAWRGKGLDGEKCTFSDLLY 252 (469)
Q Consensus 175 ~~~a~ikI~~GC~~~CsfC~ip~~RG~-~-rSr~~~~Iv~ei~~l~~~G~kEi~L~g~d~~~Y~g~~~~~~~~~l~~Ll~ 252 (469)
T Consensus 27 Plvl~le~t~rCNL~C~~C~~i~~~~~~l~~~Ls~ee~~~~~~---e~Gap~V~itG-------GEPL--Lr~dl~eIv~ 94 (318)
T TIGR03470 27 PLVLMLEPLFRCNLACAGCGKIQYPAEILKQRLSVEECLRAVD---ECGAPVVSIPG-------GEPL--LHPEIDEIVR 94 (318)
T ss_pred CEEEEEEECCCCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHH---HCCCCEEEECC-------CCCC--CCCCHHHHHH
T ss_conf 7588731213226778899741367646544389999999999---84997899518-------8745--5647999999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCHHHHHH-HCCCCCCCHHHHHHHHHHHHCCCCCC
Q ss_conf 86204443001354421000100036652022111220133211145789987-30333441146789998740134432
Q gi|255764472|r 253 SLSEIKGLVRLRYTTSHPRDMSDCLIKAHGDLDVLMPYLHLPVQSGSDRILKS-MNRRHTAYEYRQIIDRIRSVRPDIAI 331 (469)
Q Consensus 253 ~l~~i~~~~riR~~s~~P~~~~~~li~~~~~~~~i~~~lhlpiQSgs~~vLk~-M~R~~~~e~~~~~i~~~r~~~p~~~i 331 (469)
T Consensus 95 ~a~~~g--~~v~l-~TNG~Ll-~k~i~~~~~~~~~--~~~VsLDG-~~e~HD~~r~~~G~Fd~av~aIr~ak~~G~~V~i 167 (318)
T TIGR03470 95 GLVARK--KFVYL-CTNALLL-EKKLDKFEPSPYL--TFSVHLDG-LREHHDASVCREGVFDRAVEAIREAKARGFRVTT 167 (318)
T ss_pred HHHHCC--CEEEE-ECCHHHH-HHHHHHHHHCCCC--EEEEECCC-CHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCEEE
T ss_conf 999759--97999-7755200-9999998518883--69998017-8788668871797799999999999986994679
Q ss_pred CEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCHHEE
Q ss_conf 0000013522012478988633221011100200001
Q gi|255764472|r 332 SSDFIVGFPGETDDDFRATMDLVDKIGYAQAFSFKYS 368 (469)
Q Consensus 332 ~tdiIvGfPgETeedf~~Tl~~i~~~~~~~~~vf~yS 368 (469)
T Consensus 168 N~Tv---f~~~n~~~i~~~~d~~~~lgVdgi~isp~y 201 (318)
T TIGR03470 168 NTTL---FNDTDPEEVAEFFDYLTDLGVDGMTISPGY 201 (318)
T ss_pred EEEE---ECCCCHHHHHHHHHHHHHCCCCEEEECCCC
T ss_conf 9897---068999999999999987699738976653