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 GFF411 Psest_0412 8-amino-7-oxononanoate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__psRCH2:GFF411 Length = 392 Score = 266 bits (679), Expect = 1e-75 Identities = 161/383 (42%), Positives = 210/383 (54%), Gaps = 6/383 (1%) Query: 1 MSLDLRARVREELERLKREGLYISPKVLEAPQEPVTRVEGREVVNLASNNYLGFANHPYL 60 M+ DL +R+ E + LY +LE PQ+P V+G ++ SN+YLG A+HP + Sbjct: 1 MTFDLASRLAER----RAAHLYRQRPLLETPQQPEVMVDGERLLAFCSNDYLGLASHPEV 56 Query: 61 KEKARQYLEKWGAGSGAVRTIAGTFTYHVELEEALARFKGTESALVLQSGFTANQGVLGA 120 +Q KWG G GA + G T H +LEEALA F G AL+ +G+ AN + A Sbjct: 57 IAAMQQGAAKWGVGGGASHLVIGHSTPHHQLEEALADFTGRPRALLFSTGYMANLAAVTA 116 Query: 121 LLKEGDVVFSDELNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTDGLKLIVTDGV 180 L+ +GD V D LNHAS++D L+ A + H D L + L G L+VTDGV Sbjct: 117 LVGQGDTVLEDRLNHASLLDAGLLSGARFSRYLHNDAEILAKRLDK--AGGNTLVVTDGV 174 Query: 181 FSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATL 240 FSMDGD+A L I AK A V VDDAHG G LG G G V FG D V V TL Sbjct: 175 FSMDGDLADLPAICATAKPRGAWVMVDDAHGFGPLGATGGGIVEQFGLGIDDVPVLVGTL 234 Query: 241 SKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEPERVERLW 300 KA+ G + AG+ EL + LI ARP++++TS PPAV A L +LEL+ E R E L Sbjct: 235 GKAFGTAGAFVAGSEELIETLIQFARPYIYTTSQPPAVACATLKSLELLSSEGWRREHLN 294 Query: 301 ENTRYFKRELARLGYDTLGSQTPITPVLFGEAPLAFEASRLLLEEGVFAVGIGFPTVPRG 360 F+ ++G + S TPI PVL G + A S LL E G+ I PTVP G Sbjct: 295 RLVARFREGAQQIGLTLMDSPTPIQPVLVGSSERALRLSALLRERGILVGAIRPPTVPAG 354 Query: 361 KARIRNIVTAAHTKEMLDKALEA 383 AR+R TA+H+ L++ LEA Sbjct: 355 SARLRITFTASHSDAQLERLLEA 377 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: 350 Number of extensions: 18 Number of successful extensions: 2 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: 392 Length adjustment: 31 Effective length of query: 364 Effective length of database: 361 Effective search space: 131404 Effective search space used: 131404 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