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 BWI76_RS08765 BWI76_RS08765 8-amino-7-oxononanoate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Koxy:BWI76_RS08765 Length = 385 Score = 218 bits (555), Expect = 2e-61 Identities = 135/353 (38%), Positives = 197/353 (55%), Gaps = 6/353 (1%) Query: 39 EGREVVNLASNNYLGFANHPYLKEKARQYLEKWGAGSGAVRTIAGTFTYHVELEEALARF 98 EGR +N +SN+YLG + HP + + +Q E++G GSG ++G H LEE LA + Sbjct: 37 EGRRWLNFSSNDYLGLSQHPAIVKAWQQGAERYGVGSGGSGHVSGYSEAHRALEEQLADW 96 Query: 99 KGTESALVLQSGFTANQGVLGALLKEGDVVFSDELNHASIIDGLRLTKATRLVFRHADVA 158 G AL+ SGF ANQ V+ AL + D + +D L+HAS+++ L+ A F+H D Sbjct: 97 LGYPRALLFISGFAANQAVIAALAGKEDRIVADRLSHASLLEAASLSPAQLRRFQHNDCR 156 Query: 159 HLEELLKAHDTDGLKLIVTDGVFSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLGEK 218 HL+ELL A G +L+VT+G+FSMDGD APL ++ A+ A++ VDDAHG G LGE+ Sbjct: 157 HLDELL-AKPLTGQQLVVTEGIFSMDGDSAPLAEVCQAARAAGALLLVDDAHGIGALGEE 215 Query: 219 GKGTVHHFGFHQDPDVVQVATLSKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPPAV 278 G+G+ H D + + T KA+ G + L D L+ AR ++ST+ PPA Sbjct: 216 GRGSCHTQQVRPD---LLIVTFGKAFGVSGAAVLCSEALADYLLQFARHLIYSTAMPPAQ 272 Query: 279 VGALLGALELI--EKEPERVERLWENTRYFKRELARLGYDTLGSQTPITPVLFGEAPLAF 336 AL ALE+I ++ R E L + F+R + R + S + I P++ G+ A Sbjct: 273 AVALSAALEVIRGDEGQARRETLAGHIADFRRGMTRYPGELTDSGSAIQPLIVGDNARAL 332 Query: 337 EASRLLLEEGVFAVGIGFPTVPRGKARIRNIVTAAHTKEMLDKALEAYEKVGK 389 + L EEG +A I PTVP G AR+R +TAAH + + LE G+ Sbjct: 333 RLAARLREEGCWATAIRPPTVPVGSARLRLTLTAAHKSADIARLLEVLHDGGE 385 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: 321 Number of extensions: 14 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