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 PP_0363 PP_0363 8-amino-7-oxononanoate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Putida:PP_0363 Length = 390 Score = 270 bits (691), Expect = 4e-77 Identities = 157/383 (40%), Positives = 216/383 (56%), Gaps = 6/383 (1%) Query: 1 MSLDLRARVREELERLKREGLYISPKVLEAPQEPVTRVEGREVVNLASNNYLGFANHPYL 60 M+ DL AR+ E + LY +LE+PQ P V+G+ ++ SN+YLG ANHP + Sbjct: 1 MAFDLAARLAER----RAADLYRQRPLLESPQGPEVVVDGQRLLAFCSNDYLGLANHPEV 56 Query: 61 KEKARQYLEKWGAGSGAVRTIAGTFTYHVELEEALARFKGTESALVLQSGFTANQGVLGA 120 + E+WG G GA + G T H ++EEALA G AL+ +G+ AN G + A Sbjct: 57 IAAWQAGAERWGVGGGASHLVVGHSTPHHQVEEALAELTGRPRALLFSTGYMANLGAITA 116 Query: 121 LLKEGDVVFSDELNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTDGLKLIVTDGV 180 L+ +GD V D LNHAS++DG L+ A + H D A L L G L+VTDGV Sbjct: 117 LVGQGDTVLQDRLNHASLLDGGLLSGARFNRYLHNDPASLASRLDK--AVGNTLVVTDGV 174 Query: 181 FSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATL 240 FSMDGD+A L + +A+ A + VDDAHG G LG KG G V HFG D V + TL Sbjct: 175 FSMDGDLADLPALANVARARGAWLMVDDAHGLGTLGAKGGGIVEHFGLGVDDVPVLIGTL 234 Query: 241 SKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEPERVERLW 300 KA G + AG+ L + L+ ARP++++TS PPA+ A L +LEL+ +E R E L Sbjct: 235 GKACGTAGAFVAGSEALIEALVQFARPYIYTTSQPPALACATLKSLELLRRETWRREHLA 294 Query: 301 ENTRYFKRELARLGYDTLGSQTPITPVLFGEAPLAFEASRLLLEEGVFAVGIGFPTVPRG 360 R F+ +LG + S TPI P++ G++ A SRLL E G+ I PTVP G Sbjct: 295 ALIRQFREGAQQLGLQLMDSPTPIQPIVIGDSAQALRLSRLLRERGLLVTAIRPPTVPAG 354 Query: 361 KARIRNIVTAAHTKEMLDKALEA 383 AR+R ++AAH++ + L A Sbjct: 355 SARLRVTLSAAHSEAQVQLLLNA 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: 345 Number of extensions: 16 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: 390 Length adjustment: 31 Effective length of query: 364 Effective length of database: 359 Effective search space: 130676 Effective search space used: 130676 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