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 WP_011384092.1 AMB_RS08510 5-aminolevulinate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >NCBI__GCF_000009985.1:WP_011384092.1 Length = 412 Score = 250 bits (638), Expect = 6e-71 Identities = 147/358 (41%), Positives = 203/358 (56%), Gaps = 4/358 (1%) Query: 39 EGREVVNLASNNYLGFANHPYLKEKARQYLEKWGAGSGAVRTIAGTFTYHVELEEALARF 98 E REVV SN+YLG HP + A + LE+ GAG+G R I+GT YHV LEE LA F Sbjct: 43 EVREVVVWCSNDYLGMGQHPEVIAAAHEALERCGAGAGGTRNISGTNHYHVLLEEELASF 102 Query: 99 KGTESALVLQSGFTANQGVLGAL--LKEGDVVFSDELNHASIIDGLRLTKATRLVFRHAD 156 ES+L+ SG+ ANQ L L G VVFSDELNH S+I+G+R ++ + VFRH D Sbjct: 103 NAKESSLLFTSGYVANQTTLSTLGATIPGCVVFSDELNHNSMIEGIRHGRSAKQVFRHND 162 Query: 157 VAHLEELLKAHDTDGLKLIVTDGVFSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLG 216 HLE+LL A+ + KL+ + V+SMDGDIAP+ +I +A+ + A+ Y+D+ H G+ G Sbjct: 163 PEHLEQLLSAYPKETPKLVAFESVYSMDGDIAPIAEICDVAEAHNAMTYLDEVHAVGMYG 222 Query: 217 EKGKGTVHHFGFHQDPDVVQVATLSKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPP 276 +G G G ++Q TL+KA +GGY A + D + + F+FS+S PP Sbjct: 223 AEGSGVAERDGVRDRITIIQ-GTLAKALGVVGGYIAASASCVDYVRSFGPGFIFSSSMPP 281 Query: 277 AVVGALLGALELIEKEPERVERLWENTRYFKRELARLGYDTLGSQTPITPVLFGEAPLAF 336 A A L ++ + PE +R E KR L+ G L S + I PV+ G A L Sbjct: 282 ATAAAALASIRYLRAHPEIRDRHQERAATAKRLLSARGIPVLPSVSHIVPVMVGNAALCK 341 Query: 337 EASRLLLEE-GVFAVGIGFPTVPRGKARIRNIVTAAHTKEMLDKALEAYEKVGKRLGI 393 EAS LLL E G++ I +PTVP G R+R T H M+ ++A+ V RL + Sbjct: 342 EASDLLLNEYGIYVQPINYPTVPVGTERLRITPTPLHDDAMMAHLVDAFSAVWDRLDL 399 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: 412 Number of extensions: 24 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: 412 Length adjustment: 31 Effective length of query: 364 Effective length of database: 381 Effective search space: 138684 Effective search space used: 138684 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