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 H281DRAFT_02095 H281DRAFT_02095 8-amino-7-oxononanoate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Burk376:H281DRAFT_02095 Length = 394 Score = 229 bits (585), Expect = 8e-65 Identities = 139/395 (35%), Positives = 215/395 (54%), Gaps = 14/395 (3%) Query: 3 LDLRARVREELERLKREGLYISPKVLEAPQEPVTRVEGREVVNLASNNYLGFANHPYLKE 62 + L R+ E L+ + GL + + P V+GRE++ ASN+YLG A HP L Sbjct: 1 MHLLDRLSEGLKEIDERGLRRRRRTADTPCAAHMTVDGREIIGFASNDYLGLAAHPQLIA 60 Query: 63 KARQYLEKWGAGSGAVRTIAGTFTYHVELEEALARFKG----TESALVLQSGFTANQGVL 118 + +++GAGSG + G H +LE+ LA F G T AL +G+ AN L Sbjct: 61 AIAEGAQRYGAGSGGSHLLGGHSRAHAQLEDDLAEFVGGFVDTPRALYFSTGYMANLATL 120 Query: 119 GALLKEGDVVFSDELNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTDGLKLIVTD 178 AL G +FSD LNHAS+IDG RL++A ++ H D+ L +L A D D +K IV+D Sbjct: 121 TALAGRGTTLFSDALNHASLIDGARLSRADVQIYPHCDMEALSAMLDASDAD-VKAIVSD 179 Query: 179 GVFSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVA 238 VFSMDGDIAPL +++ LA+++ A + VDDAHG GVLG +G+G V + P+++ + Sbjct: 180 TVFSMDGDIAPLPRLLELAEQHGAWLIVDDAHGFGVLGPQGRGAVADAAL-RSPNLISIG 238 Query: 239 TLSKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPPAVVGALLGALELI-----EKEP 293 TL KA G + A + + L+ +ARP++F+T+ PA A+ +L +I ++ Sbjct: 239 TLGKAAGVSGAFVAAHETVIEWLVQRARPYIFTTASVPAAAHAVSASLRIIGGNEGDERR 298 Query: 294 ERVERLWENTRYFKRELARLGYDTLGSQTPITPVLFGEAPLAFEASRLLLEEGVFAVGIG 353 + +L E TR + + D S T + P++ G + + L G++ I Sbjct: 299 AHLRQLIERTRAMLKSTPWIPVD---SHTAVQPLVIGANEATLDIAASLDRAGLWVPAIR 355 Query: 354 FPTVPRGKARIRNIVTAAHTKEMLDKALEAYEKVG 388 PTVP G +R+R ++AAH+ LD+ ++ G Sbjct: 356 PPTVPTGTSRLRISLSAAHSHADLDRLEAGLQQAG 390 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: 360 Number of extensions: 17 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: 394 Length adjustment: 31 Effective length of query: 364 Effective length of database: 363 Effective search space: 132132 Effective search space used: 132132 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