HHsearch alignment for GI: 254781043 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=98.72  E-value=4.9e-07  Score=64.59  Aligned_cols=151  Identities=25%  Similarity=0.339  Sum_probs=88.7

Q ss_pred             CEEEECCCHHHHHHHHHHHHCC-----CCEEEEECCCCCCCCCHHCCCCEEEECCCCCCCCHHHHHHHHHHHCCCCCCHH
Q ss_conf             5889899689999999999889-----82999986898852104116534251378999999999998998458877999
Q gi|254781043|r   19 DVVVVGAGGAGLRATLGMAEKG-----FKTACITKVFPTRSHTVAAQGGIAASLANMTPDSWQWHLYDTIKGSDWLGDVD   93 (611)
Q Consensus        19 DVlVIG~G~AGl~AAi~A~e~G-----~~V~lieK~~~~~g~s~~A~GGi~a~~~~~~~Ds~~~~~~Dt~~~g~~l~d~~   93 (611)
T Consensus         1 Di~IvGgG~VG~~lA~aL~~~~~~~~~L~~~l~e~~~~~~~~~~~~~~~~---------D~------------------R   53 (445)
T TIGR01988         1 DIVIVGGGMVGLALALALASSGSRLKGLKVALIEAQPAEAPSFFAATPGF---------DN------------------R   53 (445)
T ss_pred             CEEEECCCHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCC---------CC------------------C
T ss_conf             96888473889999999841863124731799605211442211258765---------52------------------2


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCC-----------------CCCCC------CEEEECCCCCCCCCCCCCCCCEEEEECC
Q ss_conf             999999988999999998699813-----------------27998------5510014641145678765640798666
Q gi|254781043|r   94 AIQYLAMEAPQSVYELEHYGVPFS-----------------RNEAG------KIYQRPFGGHMQNYGEGPPVQRTCAAAD  150 (611)
Q Consensus        94 lv~~~~~~a~~~i~~Le~~Gv~f~-----------------r~~~G------~~~~~~~gg~~~~~~~g~~~~R~~~~~d  150 (611)
T Consensus        54 -~~A---l~~~S~~~L~~lG~-W~~~~~~~~~p~~~~~V~D~~~~g~~~~P~~~~F~~---~~~--~-~-~~~~LG~~ve  121 (445)
T TIGR01988        54 -VSA---LSAASIRLLEKLGV-WDKIEPDRAQPIRDIHVSDGGSFGRAPHPAALHFDA---DEV--G-G-PAEALGYVVE  121 (445)
T ss_pred             -EEE---HHHHHHHHHHHCCC-CHHHHHHHCCCCCEEEEEECCCCCCCCCCEEEEECH---HHC--C-C-CCCCCCEEEC
T ss_conf             -010---10799999986796-445201212632048887267888888863687443---441--7-8-8011236711


Q ss_pred             CCCHHHHHHHHHHHHHCC---CEEECCCEEEEEEEC-----CCCCCEEEEEEEECCCEEEE---ECCCCEEEECCCCC
Q ss_conf             542667899999987312---303113156520001-----34430124689805870899---50672474157656
Q gi|254781043|r  151 RTGHAILHTLYGQALKNN---AEFFIEYFALDLIIN-----SEGCCVGVVAWQLETGEIHR---FSAKLVVLATGGYG  217 (611)
Q Consensus       151 ~tG~~i~~~L~~~~~~~g---v~i~~~~~~~~Li~d-----~dG~V~Gav~~~~~~G~~~~---i~AkaVILATGG~~  217 (611)
T Consensus       122 --n~~~~~aL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~----v~~~L~~G~--~~~~l~a~LlvgADG~~S  190 (445)
T TIGR01988       122 --NRVLQQALWEALQELPNEKVTLLCPARVEELPRHSSKNDSD-E----VELTLSDGR--QKLLLRARLLVGADGANS  190 (445)
T ss_pred             --HHHHHHHHHHHHHHCCCCEEEEECCCEEEEEECCCCCCCCC-C----EEEEECCCC--EEEEEEECEEEEECCCCH
T ss_conf             --88999999999996689647751672147740367756886-0----799970894--767898532787358652