Как переформатировать вывод Kegg Mapper в Linux?

Как далеко это заведет вас:

awk '
!NF             {next                                                   # don"t process empty lines
                }
/^[0-9]+ /      {sub (/\([0-9]*\)/, "(" CNT ")", PRT)                   # for the "glycan" lines (leading numerical)
                                                                        # correct the count in parentheses
                 if (PRT) print PRT                                     # print the PRT buffer (NOT first line when empty)
                 PRT = ""                                               # empty it after print
                 CNT = gsub (/K[0-9]*/, "&") - 1                        # get this line"s "K..." count, corr.for later incr.
                }
                {PRT = sprintf ("%s%s%s", PRT, PRT?" ":"", $0)          # append this line to buffer
                 CNT++                                                  # increment "K..." count
                }
END             {sub (/\([0-9]*\)/, "(" CNT ")", PRT)                   # see above
                 print PRT
                }
' file
00550 Peptidoglycan biosynthesis (2) K01000 K02563
00511 Other glycan degradation (6) K01190   K01191 K01192 K01201 K01227 K12309