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 GFF898 PGA1_c09130 8-amino-7-oxononanoate synthase BioF
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Phaeo:GFF898 Length = 379 Score = 189 bits (479), Expect = 1e-52 Identities = 125/347 (36%), Positives = 178/347 (51%), Gaps = 9/347 (2%) Query: 41 REVVNLASNNYLGFANHPYLKEKARQYLEKW-GAGSGAVRTIAGTFTYHVELEEALARFK 99 R+ + ASN+YLG A L A L + G+G R + G H LE A F Sbjct: 27 RDGHDFASNDYLGLAGSDVLHAAAADALARGVPVGAGGSRLLRGNDAEHQLLEAEAAAFF 86 Query: 100 GTESALVLQSGFTANQGVLGALLKEGDVVFSDELNHASIIDGLRLTKATRLVFRHADVAH 159 GTE+AL + GFTANQ + L ++GD+V D L HAS DG+RL +A F H DV Sbjct: 87 GTEAALFMGGGFTANQAIFSTLPQQGDLVLYDALIHASTHDGMRLGRAETRSFAHGDVED 146 Query: 160 LEELLKAHDTD---GLKLIVTDGVFSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLG 216 +LKA + G I + V+SMDGD+APLD ++ LA AV+ VD+AH +GV G Sbjct: 147 ASRVLKAWRAEGGTGQVWIAVEAVYSMDGDLAPLDALMALADADGAVLVVDEAHSTGVFG 206 Query: 217 EKGKGTVHHFGFHQDPDVVQVATLSKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPP 276 + G+G Q +V+ + T KA G G + L + LINKAR F+F+T+ P Sbjct: 207 DLGRGLAQGIAHRQ--NVLSLHTCGKALGASGALICGQKVLIETLINKARGFIFATAPSP 264 Query: 277 AVVGALLGALELIEKEPERVERLWENTRYFKRELARL-GYDTLGSQTPITPVLFGEAPLA 335 + AL +++ R E+ W+ + + E RL G D G Q+ I PV+ G+ Sbjct: 265 LNAALVRAALAELQQNTGRREQAWQGITHAQAEAKRLCGLD--GFQSQILPVVIGDDKRT 322 Query: 336 FEASRLLLEEGVFAVGIGFPTVPRGKARIRNIVTAAHTKEMLDKALE 382 + + G GI PTVPRG AR+R +T ++++ E Sbjct: 323 MALASAMQGHGYDIRGIRPPTVPRGTARLRLSITLNTPEQVITDMFE 369 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: 348 Number of extensions: 27 Number of successful extensions: 6 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: 379 Length adjustment: 30 Effective length of query: 365 Effective length of database: 349 Effective search space: 127385 Effective search space used: 127385 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