HHsearch alignment for GI: 254781024 and conserved domain: TIGR01988

>TIGR01988 Ubi-OHases Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; InterPro: IPR010971 This entry represents a family of FAD-dependent hydroxylases (monooxygenases) which are all believed to act in the aerobic ubiquinone biosynthesis pathway . A separate set of hydroxylases, as yet undiscovered, are believed to be active under anaerobic conditions . In Escherichia coli, three enzyme activities have been described: UbiB (which acts first at position 6, see IPR010232 from INTERPRO), UbiH (which acts at position 4, ) and UbiF (which acts at position 5, ). UbiH and UbiF are similar to one another and form the basis of this subfamily. Interestingly, E. coli contains another hydroxylase gene, called visC, that is highly similar to UbiF, adjacent to UbiH and, when mutated, results in a phenotype similar to that of UbiH (which has also been named visB) . Several other species appear to have three homologs in this family, although they assort themselves differently on phylogenetic trees (e.g. Xylella and Mesorhizobium) making it difficult to ascribe a specific activity to each one. Eukaryotes appear to have only a single homologue in this subfamily (COQ6, ) which complements UbiH, but also possess a non-orthologous gene, COQ7 which complements UbiF.; GO: 0016709 oxidoreductase activity acting on paired donors with incorporation or reduction of molecular oxygen NADH or NADPH as one donor and incorporation of one atom of oxygen, 0050660 FAD binding, 0006744 ubiquinone biosynthetic process.
Probab=99.91  E-value=3.8e-22  Score=172.77  Aligned_cols=342  Identities=17%  Similarity=0.109  Sum_probs=211.5

Q ss_pred             CEEEECCCHHHHHHHHHHHHCC---CCCEEEEEECCCCCCC-CCCCCCEECHH-------H---HHHHCCCHHHHCCCCC
Q ss_conf             7799989768999999999808---9973999978677898-64027403336-------7---8886787264148854
Q gi|254781024|r   16 DVVIIGAGPAGLAAAIRCKQIN---PHLSVVILEKSAEVGA-HILSGAIIDPI-------G---IDSLLPRWREDKGHPF   81 (554)
Q Consensus        16 DVvIVGaGPAG~saA~~La~~g---~~l~VlvlEK~~~pG~-~i~sG~vl~p~-------a---L~eL~Pd~~e~~g~pl   81 (554)
T Consensus         1 Di~IvGgG~VG~~lA~aL~~~~~~~~~L~~~l~e~~~~~~~~~~~~~~~~D~R~~Al~~~S~~~L~~-lG~W~~~~-~~~   78 (445)
T TIGR01988         1 DIVIVGGGMVGLALALALASSGSRLKGLKVALIEAQPAEAPSFFAATPGFDNRVSALSAASIRLLEK-LGVWDKIE-PDR   78 (445)
T ss_pred             CEEEECCCHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEHHHHHHHHHHH-CCCCHHHH-HHH
T ss_conf             9688847388999999984186312473179960521144221125876552201010799999986-79644520-121


Q ss_pred             CCEEEEEEEEEECCCC------CEECCCCCCCCCC--CCCCCEEEEHHHHHHHHHHHHHHCC---CEECCCCEEEEEEEC
Q ss_conf             3224366999977997------6773654356544--6788268888898999999998749---533068224347762
Q gi|254781024|r   82 HTVVKRDLYWFLNAQR------SIQIPHFCLPDFM--DNKEHYIVSLGQVCRWLKNKAEALG---VEIYCGFTATEIYYG  150 (554)
Q Consensus        82 ~~~v~~d~~~~l~~~~------~~~~p~~~~p~~~--~~~g~yiv~r~~fd~~L~~~Ae~~G---vei~~g~~v~~i~~~  150 (554)
T Consensus        79 ~~p~~~~~V~D~~~~g~~~~P~~~~F~~~~---~~~~~~~LG~~ven~~~~~aL~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (445)
T TIGR01988        79 AQPIRDIHVSDGGSFGRAPHPAALHFDADE---VGGPAEALGYVVENRVLQQALWEALQELPNEKVTLLCPARVEELPRH  155 (445)
T ss_pred             CCCCCEEEEEECCCCCCCCCCEEEEECHHH---CCCCCCCCCEEECHHHHHHHHHHHHHHCCCCEEEEECCCEEEEEECC
T ss_conf             263204888726788888886368744344---17880112367118899999999999668964775167214774036


Q ss_pred             -----CCCCEEEEEECCCCCCCCCCCCCCCCCEEE---EEEEEEEEECCCCCHHHHHHHHHCCCC-CCCCHHHHHHHHHH
Q ss_conf             -----776201454124324434665787563026---774257860664432554211224899-88889899889888
Q gi|254781024|r  151 -----KKGEALGILTGEKGKNYDGTQGKHYIAPML---LLSKYMLVGEGACGSLTRQLIERYSLM-DGRQPQKFGLGIKE  221 (554)
Q Consensus       151 -----e~g~vvgv~t~~~G~~k~~~~~~~~~~g~~---i~Ak~vI~AdG~~s~lak~l~~~~~l~-~~~~p~~~~~gvke  221 (554)
T Consensus       156 ~~~~~~~~v~~--~L~~---------------G~~~~~l~a~LlvgADG~~S~vR~~~gI~~~~~R~Y~--Q-~--a~--  211 (445)
T TIGR01988       156 SSKNDSDEVEL--TLSD---------------GRQKLLLRARLLVGADGANSKVRQLAGIPTTGWRDYG--Q-S--AV--  211 (445)
T ss_pred             CCCCCCCCEEE--EECC---------------CCEEEEEEECEEEEECCCCHHHHHHHCCCCCEEECCC--C-E--EE--
T ss_conf             77568860799--9708---------------9476789853278735865257997188843011645--5-3--89--


Q ss_pred             HHHHCCCCCCCCEEEEEECCCCCCCCCCCEEEEECC---CCEEEEEEEECCCCCCC--CCCHHHHHHHHHHCCCHHHHHC
Q ss_conf             875165667888089950434768766412576647---98059999832666566--8898899999860800456503
Q gi|254781024|r  222 LWKIKPQYHRRGLALHSIGWPLDMNTSGGGFVYHFD---DNLVSIGFVLHLDYRNP--WISAYEELQRFKTHPDIRIIFT  296 (554)
Q Consensus       222 ~~ei~~~~~~~G~~~h~~g~~~~~~~~gggwiy~~~---d~~~~iG~v~~ld~~~~--~~~~~~~lq~fk~hp~i~~~l~  296 (554)
T Consensus       212 Va~v~~~~~h~~~A~erF~---~-~~GP~AlL-PL~~~dd~~~slVW~~~~~~A~~L~~l~~~~F~~~L~~--~F~~~l-  283 (445)
T TIGR01988       212 VANVKHERPHQGTAWERFL---P-DTGPLALL-PLPDNDDNRSSLVWTLPPEEAERLLALDDEEFLAELNR--AFGSRL-  283 (445)
T ss_pred             EEEEEECCCCCCEEEEEEE---C-CCCCEEEC-CCCCCCCCEEEEEEECCHHHHHHHHCCCHHHHHHHHHH--HHHHHC-
T ss_conf             9999714788964799982---7-99857873-58888896038997389799999867899899999999--853315-


Q ss_pred             C----------------------------CCEECCCCEECCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHH
Q ss_conf             8----------------------------826303513400542124874230887996123233136643522689999
Q gi|254781024|r  297 E----------------------------GERLEYGARVISEGGWQSVPKLSFPGGSLIGCAAGFVNLLRIKGSHNAIIS  348 (554)
Q Consensus       297 g----------------------------g~~~~yga~~ip~gg~~s~pk~~~~g~lLvGDAAG~vnP~~g~GI~~Am~S  348 (554)
T Consensus       284 G~~~~~~~~~~~l~~~~~~~~~~~~pp~~~~~~~~~R~~fPL~~~~-A~~yv~~R~aLiGDAAHt~HPlAGQG~NLG~rD  362 (445)
T TIGR01988       284 GDLPYLDQTDFALNELFFRSSEEQYPPLGAITLVGERAAFPLSLRH-AKRYVAPRLALIGDAAHTVHPLAGQGLNLGLRD  362 (445)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCEECCCEEEEECCCCCCCCCHHHH-HHHHHCCCEEEEECCCCCCCCCCCCCCCCCHHH
T ss_conf             7965567899999998732024400682378876876304403343-587625985898054135787100100200789


Q ss_pred             HHHHHHHHHHHHHCC-CCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999987458-865--303678998642046678887422566887
Q gi|254781024|r  349 GMLAAEKIVERLSNG-KKH--DDPIEIEDSWRQTQIGKDLWIIRNIKPLLS  396 (554)
Q Consensus       349 G~lAAEai~eal~~g-~~~--~~l~~Ye~~~~~s~~~~el~~~rn~~~~~~  396 (554)
T Consensus       363 v~~La~~l~~a~~~g~DiG~~~~L~~Y~r~R~~d-n~~~~~~~D~L~~lF~  412 (445)
T TIGR01988       363 VAALAEVLVEARRRGEDIGSLAVLQRYERRRRFD-NAAMLGATDGLNRLFS  412 (445)
T ss_pred             HHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_conf             9999999999884566857777899999974998-9999999999998740