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_0093 Echvi_0093 7-keto-8-aminopelargonate synthetase and related enzymes
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Cola:Echvi_0093 Length = 373 Score = 162 bits (411), Expect = 1e-44 Identities = 105/342 (30%), Positives = 178/342 (52%), Gaps = 9/342 (2%) Query: 44 VNLASNNYLGFANHPYLKEKARQYLEKWGAGSGAVRTIAGTFTYHVELEEALARFKGTES 103 ++ SN+YLG+A +LK+ + G+ R I+G +LE +A+F + Sbjct: 32 IDFFSNDYLGYATKGFLKQATNPAYDAAWTGATGSRLISGNHPEMEQLERDVAKFMDCPA 91 Query: 104 ALVLQSGFTANQGVLGALLKEGDVVFSDELNHASIIDGLRLTKATRLVFRHADVAHLEEL 163 AL+ SG+ AN G+L AL + + DE HASI +G+RL + F+H D+ LE Sbjct: 92 ALLYNSGYMANTGLLSALGDKDSIFLFDEHVHASIKEGMRLGFGQKAAFKHHDLEDLERK 151 Query: 164 LKAHDTDGLKL-IVTDGVFSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLGEKGKGT 222 L HD G +L ++T+G+FSM GDI + K++ + +K+ A + +D+AH G LG++ KG Sbjct: 152 LTHHDQKGKRLFVLTEGLFSMHGDIPDVGKLLGICEKHGAALIIDEAHALGTLGKEKKGV 211 Query: 223 VHHFGFHQDPDVVQVATLSKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPPAVVGAL 282 H F H + + ++ T KA G G G +L+ L+N +R F+++T+ V ++ Sbjct: 212 SHEFSRHPNL-LARIITFGKAAGGHGAMVLGNEDLRSFLVNFSRAFIYTTAPSRDQVRSI 270 Query: 283 LGALELIEKEPERVERLWENTRYFKRELARLGYDTLGSQTPITPVLF---GEAPLAFEAS 339 A++L+ + E + F L + + G I+P+ + + PL E Sbjct: 271 DAAMKLMAAK-VNFEAMDRAVATF---LETVPSSSTGFSKNISPIQYWRCADVPLLKEKV 326 Query: 340 RLLLEEGVFAVGIGFPTVPRGKARIRNIVTAAHTKEMLDKAL 381 L + G+ I PTV +G+ RIR ++ A +T E + K + Sbjct: 327 NQLQQSGINCYPILSPTVKKGEERIRIVLHAFNTPEEIKKLI 368 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: 317 Number of extensions: 21 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: 373 Length adjustment: 30 Effective length of query: 365 Effective length of database: 343 Effective search space: 125195 Effective search space used: 125195 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