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 Echvi_3961 Echvi_3961 7-keto-8-aminopelargonate synthetase and related enzymes
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Cola:Echvi_3961 Length = 416 Score = 206 bits (525), Expect = 8e-58 Identities = 135/381 (35%), Positives = 202/381 (53%), Gaps = 10/381 (2%) Query: 19 EGLYISPKVLEAPQEPVTRVEGREVVNLASNNYLGFANHPYLKEKARQYLEKWGAGSG-A 77 EG ++ PK LE P + +G EV+ + NNYLG ANHP +++ + ++WGA Sbjct: 22 EGYFMFPK-LEGEIAPRMKFKGEEVLTWSLNNYLGLANHPEIRKADAEAAKRWGAAYPMG 80 Query: 78 VRTIAGTFTYHVELEEALARFKGTESALVLQSGFTANQGVLGALLKEGDVVFSDELNHAS 137 R ++G H +LE LA F G E A +L G+ V+ +L+ DV+ D HAS Sbjct: 81 ARMMSGNTDMHEQLENELAAFVGKEKAYLLNYGYQGIMSVIDSLVDRKDVIVYDSECHAS 140 Query: 138 IIDGLRLTKATRLVFRHADVAHLE-ELLKA----HDTDGLKLIVTDGVFSMDGDIAPLDK 192 IIDGLR+ R V+ H D+ E +L++A ++T G L++T+GVF M G++ L Sbjct: 141 IIDGLRMHMGKRFVYPHNDMESFEKQLIRAEKLTNETGGGILVITEGVFGMTGNMGDLKG 200 Query: 193 IVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATLSKAWAGIGGYAA 252 IV +KY+ + VDDAHG G +G G G G QD + +T +K+ AGIG + A Sbjct: 201 IVKYKEKYQFRLVVDDAHGFGTMGPTGAGAGEAQGV-QDQVDLYFSTFAKSMAGIGAFVA 259 Query: 253 GARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEPERVERLWENTRYFKRELAR 312 G ++ L R +F+ + P V L LE+I + P+ ERLWE + L Sbjct: 260 GDTKVVHYLKYNMRSQIFAKALPMIFVEGALKRLEMIRENPKHKERLWEVVNALQNGLKE 319 Query: 313 LGYDTLGSQTPITP-VLFGEAPLAFEASRLLLEE-GVFAVGIGFPTVPRGKARIRNIVTA 370 G+ + TP+TP VL G A S+ L E +F + +P VP+G +R I TA Sbjct: 320 KGFSIGTTTTPVTPVVLNGTVGEAATLSKDLRENYNIFCSVVIYPVVPKGMIILRLIPTA 379 Query: 371 AHTKEMLDKALEAYEKVGKRL 391 AHT E + + + A+E + +L Sbjct: 380 AHTLEDVSETIIAFEAIKDKL 400 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: 367 Number of extensions: 18 Number of successful extensions: 5 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: 416 Length adjustment: 31 Effective length of query: 364 Effective length of database: 385 Effective search space: 140140 Effective search space used: 140140 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