Align 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase; AONS/AKB ligase; 7-keto-8-amino-pelargonic acid synthase; 7-KAP synthase; KAPA synthase; 8-amino-7-ketopelargonate synthase; Alpha-oxoamine synthase; Glycine acetyltransferase; EC 2.3.1.29; EC 2.3.1.47 (characterized)
to candidate HSERO_RS12245 HSERO_RS12245 8-amino-7-oxononanoate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__HerbieS:HSERO_RS12245 Length = 385 Score = 263 bits (672), Expect = 6e-75 Identities = 151/373 (40%), Positives = 221/373 (59%), Gaps = 2/373 (0%) Query: 11 EELERLKREGLYISPKVLEAPQEPVTRVEGREVVNLASNNYLGFANHPYLKEKARQYLEK 70 ++L+ L R+ L + + + + Q P+ VE R ++ SN+YLG ANHP + A L + Sbjct: 6 QQLDELARQSLLRTRRTVSSAQGPLLTVEARPYLSFCSNDYLGLANHPAITAAAVTALGQ 65 Query: 71 WGAGSGAVRTIAGTFTYHVELEEALARFKGTESALVLQSGFTANQGVLGALLKEGDVVFS 130 +G G+ A I+G H LE ALA F G +AL SG+ AN GV+GAL+ GD V Sbjct: 66 YGMGAAASALISGHSAAHETLERALAEFTGLPAALGFGSGYMANMGVIGALVGAGDTVVV 125 Query: 131 DELNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTDGLKLIVTDGVFSMDGDIAPL 190 D L+HAS+IDG RL+ A+ VF H D L+ +L A G KL+VTD VFSMDGD APL Sbjct: 126 DRLSHASLIDGARLSGASLKVFPHNDTQRLDHVL-ARCGSGRKLVVTDAVFSMDGDQAPL 184 Query: 191 DKIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATLSKAWAGIGGY 250 ++ + ++ A + VDDAHG GVLG +G+G++ H G + P V+ + TL KA G + Sbjct: 185 SELAEICARHGAWLLVDDAHGFGVLGPQGRGSLAHAGV-RAPHVLCMGTLGKAAGVAGAF 243 Query: 251 AAGARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEPERVERLWENTRYFKREL 310 AG R+L ++ +AR ++FST+HPPA+ A +L +I + R L ++ L Sbjct: 244 VAGERDLLAWIMQRARTYMFSTAHPPALAAAATASLAVIAADEWRRTHLRALVAQLRKGL 303 Query: 311 ARLGYDTLGSQTPITPVLFGEAPLAFEASRLLLEEGVFAVGIGFPTVPRGKARIRNIVTA 370 A L + L SQTPI P++ G+ A + L E+G++ I PTVPR AR+R ++A Sbjct: 304 AGLSWQLLPSQTPIQPLIIGDNARARALMQQLREQGIWVPAICPPTVPRMTARLRISLSA 363 Query: 371 AHTKEMLDKALEA 383 HT+E + + +EA Sbjct: 364 LHTQEQVAQLIEA 376 Lambda K H 0.319 0.137 0.394 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 334 Number of extensions: 12 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 395 Length of database: 385 Length adjustment: 31 Effective length of query: 364 Effective length of database: 354 Effective search space: 128856 Effective search space used: 128856 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory