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 Ga0059261_2444 Ga0059261_2444 5-aminolevulinic acid synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Korea:Ga0059261_2444 Length = 413 Score = 214 bits (546), Expect = 3e-60 Identities = 129/392 (32%), Positives = 203/392 (51%), Gaps = 10/392 (2%) Query: 3 LDLRARVREELERLKREGLYISPKVLEAPQEPVTRVEGREVVNLASNNYLGFANHPYLKE 62 L R R ++ L+ +G++ + + P + + SN+YL HP + Sbjct: 23 LHAEGRYRVFIDILRNKGMFPNARCFHGHNGP------KPITVWCSNDYLAMGQHPKVIA 76 Query: 63 KARQYLEKWGAGSGAVRTIAGTFTYHVELEEALARFKGTESALVLQSGFTANQGVLGALL 122 + L GAGSG R I G YHV+LE LA G + AL+ SG+ +N+ L L Sbjct: 77 AMEEALHDVGAGSGGTRNIGGNTHYHVDLEGELADLHGKQGALLFTSGYVSNEATLSTLA 136 Query: 123 K--EGDVVFSDELNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTDGLKLIVTDGV 180 K G +++SDELNHAS+I G+R + + V+RH D+ HLEELL A D KLI + + Sbjct: 137 KVLPGCIIYSDELNHASMIAGIRNSGCEKRVWRHNDITHLEELLAADDPTAPKLIAFESI 196 Query: 181 FSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATL 240 +SMDGD+AP+ I LA KY A+ Y+D+ H G+ G +G G +++ TL Sbjct: 197 YSMDGDVAPIHAICDLADKYNALTYLDEVHAVGMYGARGGGISERDEAASRLTIIE-GTL 255 Query: 241 SKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEPERVERLW 300 KA+ +GGY A + + D++ + A F+F+TS P +V +L ++ +++ + Sbjct: 256 GKAFGVMGGYIAADQTIIDVIRSYAPGFIFTTSLSPVLVAGVLASVRHLKQSSTERDGQQ 315 Query: 301 ENTRYFKRELARLGYDTLGSQTPITPVLFGEAPLAFEASRLLLEE-GVFAVGIGFPTVPR 359 K +A G + + T I P++ G+ A S +LL E G++ I +PTVPR Sbjct: 316 AAAARLKAMMADAGLPVMNTTTHIVPLMVGDPVKAKRISDILLAEYGMYVQPINYPTVPR 375 Query: 360 GKARIRNIVTAAHTKEMLDKALEAYEKVGKRL 391 G R+R AH + M+ A ++ +RL Sbjct: 376 GTERLRFTPGPAHDEAMMRDLTAALVEIWERL 407 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: 357 Number of extensions: 15 Number of successful extensions: 3 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: 413 Length adjustment: 31 Effective length of query: 364 Effective length of database: 382 Effective search space: 139048 Effective search space used: 139048 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