HHsearch alignment for GI: 254780485 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=99.40 E-value=1.2e-10 Score=91.03 Aligned_cols=194 Identities=12% Similarity=0.175 Sum_probs=135.0
Q ss_pred CHHHHHHHHHHHHHHHCCCCEEE-EEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEE
Q ss_conf 91899999999988862898569-99864530786834232124335477756410006857999999999964983899
Q gi|254780485|r 31 PFNDLLFWSHTVHRKNFEPNHIQ-LSKLLNIKTGGCPENCGYCNQSVHNKSKLKASKLINVDQVLKEAKNAKENGATRYC 109 (328)
Q Consensus 31 ~~~el~~~Aa~~~r~~~~g~~V~-~~~~in~~TN~C~~~C~fCaf~~~~~~~~~~~~~~~~Eei~~~a~~~~~~G~~~~~ 109 (328)
T Consensus 4 ~~~~~~~~~~y~~~~~~~g~kr~Plvl~le~-t~rCNL~C~~C~~i~~~~~-~l~-~~Ls~ee~~~~~~---e~Gap~V~ 77 (318)
T TIGR03470 4 PLRQNLRVGAYIIKQKLNGRKRFPLVLMLEP-LFRCNLACAGCGKIQYPAE-ILK-QRLSVEECLRAVD---ECGAPVVS 77 (318)
T ss_pred CHHHHHHHHHHHHHHHHCCCCCCCEEEEEEE-CCCCCCCCCCCCCCCCCCH-HHH-CCCCHHHHHHHHH---HCCCCEEE
T ss_conf 4899999999999877337646675887312-1322677889974136764-654-4389999999999---84997899
Q ss_pred EECCCCCCCCCCHHHHHHHHHHHCCCCCCEEE-ECCCCCHHHHHHHHCCCCCEEEEECCCCHHHHHCC-CCCCCHHHHHH
Q ss_conf 73036888744289999988762136883241-02569999999874157606975134377773205-88889899999
Q gi|254780485|r 110 MGAAWREPKERDLSIIVDMIKGVKSLGLETCM-TLGMLSFEQAQILSKAGLDYYNHNIDTSERFYPHV-TTTHTFEDRLQ 187 (328)
Q Consensus 110 l~~~~~~~~~~~~~~~~e~i~~i~~~~~~i~~-~~g~~~~~~~~~Lk~aG~~~~~~~let~~~~~~~~-~~~~~~~~~l~ 187 (328)
T Consensus 78 i-tGGEPLLr~dl~eI---v~~a~~~g~~v~l~TNG~Ll~k~i~~~~~~~~~~~~VsLDG~~e~HD~~r~~~G~Fd~av~ 153 (318)
T TIGR03470 78 I-PGGEPLLHPEIDEI---VRGLVARKKFVYLCTNALLLEKKLDKFEPSPYLTFSVHLDGLREHHDASVCREGVFDRAVE 153 (318)
T ss_pred E-CCCCCCCCCCHHHH---HHHHHHCCCEEEEECCHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCHHHHHHH
T ss_conf 5-18874556479999---9999975997999775520099999985188836999801787886688717977999999
Q ss_pred HHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCCCCEEECCCE
Q ss_conf 9999998798557707866898999999999999740888860205411
Q gi|254780485|r 188 TLENVRKSGIKVCCGGILGLGEMIDDRIDMLLTLANLSTPPESIPINLL 236 (328)
Q Consensus 188 ~~~~a~~~G~~~~sg~l~G~gEt~eeri~~l~~lr~l~~~~~~v~~~~~ 236 (328)
T Consensus 154 aIr~ak~~G~~V~iN~Tvf~~~n~~~i~~~~d~~~~lgV--dgi~isp~ 200 (318)
T TIGR03470 154 AIREAKARGFRVTTNTTLFNDTDPEEVAEFFDYLTDLGV--DGMTISPG 200 (318)
T ss_pred HHHHHHHCCCCEEEEEEEECCCCHHHHHHHHHHHHHCCC--CEEEECCC
T ss_conf 999999869946799897068999999999999987699--73897665