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 8500251 DvMF_1008 aminotransferase class I and II (RefSeq)
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Miya:8500251 Length = 446 Score = 127 bits (320), Expect = 5e-34 Identities = 107/384 (27%), Positives = 162/384 (42%), Gaps = 29/384 (7%) Query: 29 EAPQEPVTRVEGREVVNLASNNYLGFANHPYLKEKARQYLEKWGAGSGAVRTIAGTFTYH 88 ++P + R+EGR +++ A N+YLG A + + A R AG Sbjct: 55 QSPSPALVRMEGRPLLHFAGNDYLGLAADEDWRATVAACFARHAPSGTASRLAAGHTALT 114 Query: 89 VELEEALARFKGTESALVLQSGFTANQGVLGALLKEGDVVFSDELNHASIIDGLRLTKAT 148 E E A A + G L L SG+ AN +L LL GD VF D HAS+ L T A Sbjct: 115 AEAETAWADYFGYAECLFLPSGYQANLALLWGLLGHGDAVFLDRRVHASMAHALPPTGAR 174 Query: 149 RLVFRHADVAHLEELLKA--HDTDG-----------------LKLIVTDGVFSMDGDIAP 189 RHAD+ L L A H++D +++ + ++SMDG + Sbjct: 175 LHTHRHADMDDLSRRLAAWRHNSDNDSGGHDGPPACGTACAPQPVVLAESLYSMDGTLPD 234 Query: 190 LDKIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATLSKAWAGIGG 249 + ++ + +++ A V VD+AH G LG G+G H V V TL KA G Sbjct: 235 MARLGAVTREHGAFVIVDEAHAFGTLGAGGRGRAHGVA------DVAVGTLGKALGLFGA 288 Query: 250 YAAGARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEPERVERLWENTRYFKRE 309 + R ++ L N A P + ST+ P A L L+L+ + +R L + Sbjct: 289 FLLLPRGTRNALENLASPLIHSTALPEAHAACCLALLDLLPRLDDRRHHLAALGAALRTG 348 Query: 310 LARLGYDTLGSQTPITPVLFGEAPLAFEASRLLLE----EGVFAVGIGFPTVPRGKARIR 365 L G + + E A+RL GV A+ PTVPRG A +R Sbjct: 349 LRAEGVPAREGAHVVCVDVGDEDRCTRLAARLRTPADGGPGVLALAARHPTVPRGAATLR 408 Query: 366 NIVTAAHTKEMLDKALEAYEKVGK 389 +TA H + + + ++ + K Sbjct: 409 LGLTALHRVDDVARCVDLLARAWK 432 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: 403 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: 446 Length adjustment: 32 Effective length of query: 363 Effective length of database: 414 Effective search space: 150282 Effective search space used: 150282 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