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 Dsui_2881 Dsui_2881 8-amino-7-oxononanoate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__PS:Dsui_2881 Length = 391 Score = 263 bits (672), Expect = 6e-75 Identities = 152/381 (39%), Positives = 225/381 (59%), Gaps = 6/381 (1%) Query: 12 ELERLKREGLYISPKVLEAPQEPVTRVEGREVVNLASNNYLGFANHPYLKEKARQYLEKW 71 EL+ ++ EGL +++++P P +G+ V+ SN+YLG ANHP + E + +W Sbjct: 9 ELKAIEAEGLTRRRRIVDSPCGPEMVADGKPVLAFCSNDYLGLANHPEIAEAMAEGARQW 68 Query: 72 GAGSGAVRTIAGTFTYHVELEEALARFKGTESALVLQSGFTANQGVLGALLKEGDVVFSD 131 GAGSGA ++G H +LEEALA F + AL +G+ AN ++ AL+ GD VF+D Sbjct: 69 GAGSGASHLVSGHLRPHHQLEEALAAFVMRQRALYFSTGYMANLAMIPALVGRGDAVFAD 128 Query: 132 ELNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTDGLKLIVTDGVFSMDGDIAPLD 191 +LNHAS+ID ++L++A +RH D+AHLE L A K+IVTD +FSMDGDIAPL+ Sbjct: 129 KLNHASLIDAVQLSRADSHRYRHLDLAHLESQLAASQAP-RKMIVTDAIFSMDGDIAPLE 187 Query: 192 KIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATLSKAWAGIGGYA 251 ++ LA+KY + +DDAHG GV+G+ G+G+ P V+ + TL KA G + Sbjct: 188 ELYELAEKYDTWLVIDDAHGFGVVGQ-GRGSAAAVKLIPSPRVLYMGTLGKAAGVSGAFV 246 Query: 252 AGARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEPERVERLWENTRYFKREL- 310 AG+ ++ + L+ KAR ++F+T+ PAV AL +LELI ER L + L Sbjct: 247 AGSAKVLEWLLQKARTYIFTTAASPAVACALQKSLELIAAGSERRAHLVTLIARLRLGLE 306 Query: 311 ---ARLGYDTLGSQTPITPVLFGEAPLAFEASRLLLEEGVFAVGIGFPTVPRGKARIRNI 367 A G+ L S TPI P++ G+ SR LLE G++ I PTV +G+AR+R Sbjct: 307 PLCAERGWQLLDSPTPIQPLVIGDNEPTLALSRALLERGIWVPAIRPPTVAKGQARLRIT 366 Query: 368 VTAAHTKEMLDKALEAYEKVG 388 ++AAHT +D + A + G Sbjct: 367 LSAAHTVGQVDALVAALAECG 387 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: 342 Number of extensions: 21 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: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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