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 Synpcc7942_0027 Synpcc7942_0027 8-amino-7-oxononanoate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__SynE:Synpcc7942_0027 Length = 388 Score = 205 bits (522), Expect = 2e-57 Identities = 129/346 (37%), Positives = 191/346 (55%), Gaps = 8/346 (2%) Query: 34 PVTRVEGREVVNLASNNYLGFANHPYLKEKARQYLEKWGAGSGAVRTIAGTFTYHVELEE 93 P R R +++ +SN+YLG A P L A + ++G G+ A R + G+F H +LEE Sbjct: 37 PYLRQGDRPLLDFSSNDYLGLAQDPRLIAAATAAMRRYGTGAMASRLVCGSFPLHQQLEE 96 Query: 94 ALARFKGTESALVLQSGFTANQGVLGALLKEGDVVFSDELNHASIIDGLRLTKATRLVFR 153 ALA F E+AL+ SG+ AN +L L +V D L H S++ G++ +KA +R Sbjct: 97 ALAAFSQREAALLFSSGYQANATLLPTLFDRQSLVLVDRLAHNSLLFGVQASKAQWRRYR 156 Query: 154 HADVAHLEELLKAHDTDGLKL-IVTDGVFSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGS 212 H D HLE+LL+ G++L IV++ VFSMDGD +D++ LA +Y A++Y+DDAH Sbjct: 157 HNDFDHLEQLLQQAPA-GVRLGIVSETVFSMDGDRTDVDRLADLADRYGAILYLDDAHAL 215 Query: 213 GVLGEKGKGTVHHFGFHQDPDVVQVATLSKAWAGIGGYAAGARELKDLLINKARPFLFST 272 GVLG +G G H DV V T KA G + +R L D IN +++T Sbjct: 216 GVLGTEGSGLALR---HPRVDVA-VGTFGKACGSAGAFVVASRSLCDYWINTCPGLIYTT 271 Query: 273 SHPPAVVGALLGALELI-EKEPERVERLWENTRYFKRELARLGYDTLGSQTPITPVLFGE 331 + P VV A L A++L+ E EPER + L ++ G+D S+T I P+L GE Sbjct: 272 AIAPPVVAAALAAVQLLPELEPER-QHLQAIAAELRQSCRDRGWDCGPSETQIVPLLVGE 330 Query: 332 APLAFEASRLLLEEGVFAVGIGFPTVPRGKARIRNIVTAAHTKEML 377 + A ++ L G+ A+ I PTVP G AR+R ++ + H + L Sbjct: 331 SEQALALAQRLEAAGILAIAIRPPTVPEGTARLRLVLRSDHQPQHL 376 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: 292 Number of extensions: 8 Number of successful extensions: 3 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: 388 Length adjustment: 31 Effective length of query: 364 Effective length of database: 357 Effective search space: 129948 Effective search space used: 129948 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