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_RS00930 RR42_RS00930 8-amino-7-oxononanoate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Cup4G11:RR42_RS00930 Length = 405 Score = 215 bits (548), Expect = 2e-60 Identities = 145/374 (38%), Positives = 203/374 (54%), Gaps = 15/374 (4%) Query: 30 APQEPVTRVEGREVVNL---ASNNYLGFANHPYLKEKARQYLEKWGAGSGAVRTIAGTFT 86 APQ+ V+ G E+ +L SN+YLG ANHP L + ++GAGSGA ++G Sbjct: 30 APQQAVSDACGGEMHSLLTFCSNDYLGLANHPALIAAMAEGARQFGAGSGASHLVSGHSL 89 Query: 87 YHVELEEALARFKGTE----SALVLQSGFTANQGVLGALLKEGDVVFSDELNHASIIDGL 142 H LE LA + +AL +G+ AN VL AL +F + LNHAS+IDG Sbjct: 90 AHHRLEGELAAWFAPNIPHAAALYFSTGYMANMAVLTALGSADATLFCEALNHASLIDGA 149 Query: 143 RLTKATRLVFRHADVAHLEELLKAHDTDGLKLIVTDGVFSMDGDIAPLDKIVPLAKKYKA 202 RL +A + H ++A LE LL A T LKLIVTD VFSMDGD APL +++ LA+++ A Sbjct: 150 RLARAEVRRYAHRNMAELEGLLVA-STSPLKLIVTDSVFSMDGDFAPLAELLALAERHDA 208 Query: 203 VVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATLSKAWAGIGGYAAGARELKDLLI 262 + +DDAHG GVLGE+G G + H P + + TL KA G + A + D L+ Sbjct: 209 WIILDDAHGFGVLGEQGHGVLEHLAL-TSPRFIYIGTLGKAAGVAGAFVAAHETIIDHLV 267 Query: 263 NKARPFLFSTSHPPAVVGALLGALELIEKEPER-----VERLWENTRYFKRELARLGYDT 317 N AR ++++T+ PPAV AL +L LI + R +++L R L R Sbjct: 268 NTARQYIYTTASPPAVAHALSASLALIAGDEGRQRRAQLDKLIHTLRSGLAGLTRAAGWR 327 Query: 318 LG-SQTPITPVLFGEAPLAFEASRLLLEEGVFAVGIGFPTVPRGKARIRNIVTAAHTKEM 376 LG S T I PV+ G+ A S L +G+ I PTVP G AR+R ++A+HT Sbjct: 328 LGESSTAIQPVIVGDNVAALALSAALEADGIRVGAIRPPTVPVGTARLRITLSASHTVAD 387 Query: 377 LDKALEAYEKVGKR 390 +++ L + V R Sbjct: 388 VERLLASLASVVPR 401 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: 325 Number of extensions: 12 Number of successful extensions: 4 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: 405 Length adjustment: 31 Effective length of query: 364 Effective length of database: 374 Effective search space: 136136 Effective search space used: 136136 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