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 CCNA_01647 CCNA_01647 8-amino-7-oxononanoate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Caulo:CCNA_01647 Length = 384 Score = 214 bits (546), Expect = 3e-60 Identities = 140/354 (39%), Positives = 192/354 (54%), Gaps = 9/354 (2%) Query: 35 VTRVEGREVVNLASNNYLGFANHPYLKEKARQYLEKWGAGSGAVRTIAGTFTYHVELEEA 94 V +G+ +++ + N+YL + H ++ A + +GAG+ A R + G +LE+ Sbjct: 34 VVERDGKRMISFSCNDYLNLSQHHLVRAAAAEAALNYGAGAAASRLVTGDHPLLSDLEKR 93 Query: 95 LARFKGTESALVLQSGFTANQGVLGALLKEGDVVFSDELNHASIIDGLRLTKATRLVFRH 154 LA KGTE+A V SG+ AN GV+ L+ GDV+ D L HA I G +L+ A + F H Sbjct: 94 LAHLKGTEAACVFGSGYLANTGVIPTLVGPGDVILIDALAHACIWAGAQLSGAKVVKFAH 153 Query: 155 ADVAHLEELLKA-HDTDGLKLIVTDGVFSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSG 213 D A LE LL A L+ TDGVFSMDGDIAPLD + L +++ A + DDAHG G Sbjct: 154 NDPADLERLLLAERGAARHALVATDGVFSMDGDIAPLDALSELCQRHDAWLLSDDAHGVG 213 Query: 214 VLGEKGKGTVHHFGFHQDPDVVQVATLSKAWAGIGGYAAGARELKDLLINKARPFLFSTS 273 VL E G+G+ F + P +Q+ TLSKA GGY G++ + DLL +AR +++T Sbjct: 214 VLAE-GRGSGALFPTAKIP--LQMGTLSKALGSYGGYLCGSQAVVDLLKTRARTLVYATG 270 Query: 274 HPPAVVGALLGALELIEKEPERVERLWENTRYFKRELARLGYDTLGSQTPITPVLFGEAP 333 PPA A L +L+LI P E R F R RLG S PI PV+ G A Sbjct: 271 LPPASAAAALASLDLIAANPTMTEVPLAKARLFTR---RLGLPEACS--PIVPVVLGSAE 325 Query: 334 LAFEASRLLLEEGVFAVGIGFPTVPRGKARIRNIVTAAHTKEMLDKALEAYEKV 387 A AS L +G V I PTVP G AR+R +AAH + + +A K+ Sbjct: 326 SALAASTELQNQGFLVVAIRPPTVPDGTARLRIAFSAAHEDADIIRLADAIAKL 379 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: 336 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: 384 Length adjustment: 30 Effective length of query: 365 Effective length of database: 354 Effective search space: 129210 Effective search space used: 129210 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