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 RR42_RS10140 RR42_RS10140 8-amino-7-oxononanoate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Cup4G11:RR42_RS10140 Length = 407 Score = 217 bits (553), Expect = 4e-61 Identities = 141/373 (37%), Positives = 198/373 (53%), Gaps = 17/373 (4%) Query: 30 APQEPVTRV--EGREVVNLASNNYLGFANHPYLKEKARQYLEKWGAGSGAVRTIAGTFTY 87 AP + V+ E R +++ SN+YLG ANHP + + ++GAGSGA + G Sbjct: 30 APHQEVSHGCGEPRTLLSFCSNDYLGLANHPTVISAFAEGAYRYGAGSGASHVVNGHSLA 89 Query: 88 HVELEEALARFKGTE----SALVLQSGFTANQGVLGALLKEGDVVFSDELNHASIIDGLR 143 H LE LAR+ + AL SG+ AN VL AL G +F D+LNHAS+IDG Sbjct: 90 HDHLENELARWLDSHIPGAQALYFCSGYMANMAVLSALGTAGATLFCDKLNHASLIDGAL 149 Query: 144 LTKATRLVFRHADVAHLEELLKAHDTDGLKLIVTDGVFSMDGDIAPLDKIVPLAKKYKAV 203 L +A + H + L LL D+ LKLIVTD VFSMDGDIAPL +++ LA+++ A Sbjct: 150 LARAHVKRYPHGNTTALARLLAGSDSP-LKLIVTDSVFSMDGDIAPLVELLALAERHDAW 208 Query: 204 VYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATLSKAWAGIGGYAAGARELKDLLIN 263 + VDDAHG GVLGE G+G + H + + + TL KA G + A + + L+N Sbjct: 209 IVVDDAHGFGVLGESGRGVLEHLALASE-RFIYIGTLGKAAGVAGAFVAAHATIVEHLVN 267 Query: 264 KARPFLFSTSHPPAVVGALLGALELI-----EKEPERVERLWENTRYFKREL----ARLG 314 ARP++++T+ PPA ALL +L LI + V +L R L A G Sbjct: 268 VARPYIYTTAAPPAAAHALLASLALIAGAEGRRRRAHVAQLIGQLRAGLETLLACHAEAG 327 Query: 315 YDTLGSQTPITPVLFGEAPLAFEASRLLLEEGVFAVGIGFPTVPRGKARIRNIVTAAHTK 374 + S TPI P++ G A S L +G+ I PTVP G AR+R ++AAHT Sbjct: 328 WQLADSDTPIQPLIVGGNAAAMALSAALEADGIRVTAIRPPTVPEGTARLRIALSAAHTA 387 Query: 375 EMLDKALEAYEKV 387 + + L+ + Sbjct: 388 GDIARLLDCLSAI 400 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: 359 Number of extensions: 21 Number of successful extensions: 5 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: 407 Length adjustment: 31 Effective length of query: 364 Effective length of database: 376 Effective search space: 136864 Effective search space used: 136864 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