HHsearch alignment for GI: 254780675 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=98.25  E-value=3.4e-06  Score=63.75  Aligned_cols=76  Identities=17%  Similarity=0.387  Sum_probs=50.5

Q ss_pred             CCCCCCHHHHHCC---CCCCCCHHHHHHCCC-----CCCCCEEEEECCCCEEE---EECCCEEECCCCEEEEEC-CCCCC
Q ss_conf             1222100122012---332210013442022-----34310124403674021---102322430574220000-23222
Q gi|254780675|r  231 ISQFVQRSLQKRG---IKILTESKISSVKQK-----GDMVSVQVERKDGSVSS---MQAEKLLLSAGVQGNIEN-IGLEK  298 (481)
Q Consensus       231 ~~~~~~~~l~~~G---v~i~~~~~v~~v~~~-----~~~~~v~~~~~dG~~~~---i~~D~vl~a~Gr~Pn~~~-L~Le~  298 (481)
T Consensus       125 ~~~aL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~L~--~G--~~~~~l~a~LlvgADG~~S~vR~~~gI~~  200 (445)
T TIGR01988       125 LQQALWEALQELPNEKVTLLCPARVEELPRHSSKNDSDEVELTLS--DG--RQKLLLRARLLVGADGANSKVRQLAGIPT  200 (445)
T ss_pred             HHHHHHHHHHHCCCCEEEEECCCEEEEEECCCCCCCCCCEEEEEC--CC--CEEEEEEECEEEEECCCCHHHHHHHCCCC
T ss_conf             999999999966896477516721477403677568860799970--89--47678985327873586525799718884


Q ss_pred             CCC-CCCCEEEEE
Q ss_conf             112-357326642
Q gi|254780675|r  299 IGV-KTSNGCIIV  310 (481)
Q Consensus       299 ~gi-~~~~g~i~v  310 (481)
T Consensus       201 ~~~R~Y~Q~a~Va  213 (445)
T TIGR01988       201 TGWRDYGQSAVVA  213 (445)
T ss_pred             CEEECCCCEEEEE
T ss_conf             3011645538999