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 Ac3H11_3830 8-amino-7-oxononanoate synthase (EC 2.3.1.47)
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3830 Length = 423 Score = 224 bits (571), Expect = 4e-63 Identities = 139/378 (36%), Positives = 210/378 (55%), Gaps = 8/378 (2%) Query: 13 LERLKREGLYISPKVLEAPQEPVTRVEGREVVNLASNNYLGFANHPYLKEKARQYLEKWG 72 L ++R L +V+E RV+G+ ++ SN+YLG A+HP L E AR+ +G Sbjct: 19 LADIERAHLLRRRRVVEPAGGARLRVDGQPMLAFCSNDYLGLAHHPALAEAAREATHHFG 78 Query: 73 AGSGAVRTIAGTFTYHVELEEALARFKGTESALVLQSGFTANQGVLGALLKEGDVVFSDE 132 GSG ++G + LE LA F AL +G+ N G++ AL+ +GDV+FSD Sbjct: 79 VGSGGSPLVSGHSAANDALEHELAAFVQLPRALYFYAGYATNTGIIPALVGDGDVLFSDA 138 Query: 133 LNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTDGLKLIVTDGVFSMDGDIAPLDK 192 LNHA +IDG RL++AT + HAD+A LE L A KL+++D VFSMDGD+ + Sbjct: 139 LNHACLIDGARLSRATIHRYPHADLAALEAQLAASPA-RRKLVISDAVFSMDGDLIDIPA 197 Query: 193 IVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGF---HQDPDVVQVATLSKAWAGIGG 249 ++ L ++Y A++ +DDAHG GVLG +G+G++ G + V+ +ATL KA G Sbjct: 198 LLALCERYDALLLLDDAHGFGVLGPQGRGSLAKAGLTGANASRRVLYMATLGKAAGVAGA 257 Query: 250 YAAGARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEPERVERLWENTRYFKRE 309 + AG L + L+ K R ++F+T+ PP + AL +L L+E +R L +R Sbjct: 258 FVAGDAALIEWLLQKTRTYIFATAAPPLLASALRQSLRLMEAADDRRAHLDGLIAQLRRG 317 Query: 310 LA----RLGYDTLGSQTPITPVLFGEAPLAFEASRLLLEEGVFAVGIGFPTVPRGKARIR 365 LA LG+ L S T + ++ G A A L + G++ I PTVP G AR+R Sbjct: 318 LATLPPELGWHLLPSHTAVQALVIGSNEAALAAMESLRQRGLWVPAIRPPTVPVGTARLR 377 Query: 366 NIVTAAHTKEMLDKALEA 383 ++AAHT +++ L A Sbjct: 378 IALSAAHTAADVEELLAA 395 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: 331 Number of extensions: 19 Number of successful extensions: 4 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: 423 Length adjustment: 31 Effective length of query: 364 Effective length of database: 392 Effective search space: 142688 Effective search space used: 142688 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