HHsearch alignment for GI: 254781065 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=99.17 E-value=1.4e-09 Score=88.69 Aligned_cols=190 Identities=19% Similarity=0.318 Sum_probs=136.2
Q ss_pred EEECCCEEEEEECCCCCCHHHCCCCCCEECCCCCCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCHHHHHHHHHHH
Q ss_conf 45207537999727430000011223301255556789899999999997299747999726981324989999999998
Q gi|254781065|r 90 VHRYPDRILLKLLHVCPVYCRFCFRREMVGSQKGTVLSSKDTEAALAYIQEKSQIWEVIFTGGDPLILSHKRLQKVLKTL 169 (352)
Q Consensus 90 ~hkY~~rvLl~~t~~C~~~CryCfR~~~~~~~~~~~~~~~~~~~~~~Yi~~~~eI~eVilSGGDPl~l~~~~L~~ll~~L 169 (352)
T Consensus 23 ~kr~Plvl~le~t~rCNL~C~~C~~i~~~~~~l~~~Ls~ee~~~~~~e~----Gap~V~itGGEPLLr~d--l~eIv~~a 96 (318)
T TIGR03470 23 RKRFPLVLMLEPLFRCNLACAGCGKIQYPAEILKQRLSVEECLRAVDEC----GAPVVSIPGGEPLLHPE--IDEIVRGL 96 (318)
T ss_pred CCCCCEEEEEEECCCCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHC----CCCEEEECCCCCCCCCC--HHHHHHHH
T ss_conf 6466758873121322677889974136764654438999999999984----99789951887455647--99999999
Q ss_pred HCCCCCEEEEEECCEEEEEHHHCCHHHHHHHHHCCCCEEEEECCCCHHHCC----------HHHHHHHHHHHHCCCEEEE
Q ss_conf 619981289874343563434339999999862599389993369958869----------9999999999987989823
Q gi|254781065|r 170 RYIKHVQILRFHSRVPIVDPQRINPELIQCLKEAGKPVYIAIHANHPYEFS----------EEAIAAISRLANAGIILLS 239 (352)
Q Consensus 170 ~~i~hv~~IRi~TR~pv~~P~Rit~~L~~~l~~~~~~~~iv~H~NHp~Elt----------~~~~~A~~~L~~~Gv~v~n 239 (352)
T Consensus 97 ~~~g--~~v~l~TNG~-Ll~-----k~i~~~~~~~-~~~~~VsLDG~~e~HD~~r~~~G~Fd~av~aIr~ak~~G~~V~i 167 (318)
T TIGR03470 97 VARK--KFVYLCTNAL-LLE-----KKLDKFEPSP-YLTFSVHLDGLREHHDASVCREGVFDRAVEAIREAKARGFRVTT 167 (318)
T ss_pred HHCC--CEEEEECCHH-HHH-----HHHHHHHHCC-CCEEEEECCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCEEE
T ss_conf 9759--9799977552-009-----9999985188-83699980178788668871797799999999999986994679
Q ss_pred CHHHHHCCCCCHHHHHHHHHHHHHCCCE-----EEEEECCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 2798623457889999999999986982-----42301134576521011869999999999998
Q gi|254781065|r 240 QSVLLKGINDDPEILANLMRTFVELRIK-----PYYLHHPDLAAGTSHFRLTIEEGQKIVASLKE 299 (352)
Q Consensus 240 QsVLLkgVND~~~~l~~L~~~L~~~gV~-----PYYl~~~d~v~G~~hf~v~~~~~~~i~~~l~~ 299 (352)
T Consensus 168 N~Tvf~--~~n~~~i~~~~d~~~~lgVdgi~isp~y~Ye~--ap~q~~f-l~r~~~~~lfr~il~ 227 (318)
T TIGR03470 168 NTTLFN--DTDPEEVAEFFDYLTDLGVDGMTISPGYAYEK--APDQDHF-LGRRQTKKLFREVLS 227 (318)
T ss_pred EEEEEC--CCCHHHHHHHHHHHHHCCCCEEEECCCCCCCC--CCCCCCC-CCHHHHHHHHHHHHH
T ss_conf 989706--89999999999999876997389766531023--7631111-589999999999998