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 3607773 Dshi_1182 5-aminolevulinic acid synthase (RefSeq)
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Dino:3607773 Length = 407 Score = 224 bits (570), Expect = 5e-63 Identities = 137/403 (33%), Positives = 204/403 (50%), Gaps = 11/403 (2%) Query: 3 LDLRARVREELERLKREGLY-----ISPKVLEAPQEPVTRVEGR--EVVNLASNNYLGFA 55 +D + L+RL EG Y I+ P+ TR +G+ ++ N+YLG Sbjct: 1 MDYTGHLDTALQRLHDEGRYRTFIDIARTKDAFPRAVWTRPDGQKQDITVWCGNDYLGMG 60 Query: 56 NHPYLKEKARQYLEKWGAGSGAVRTIAGTFTYHVELEEALARFKGTESALVLQSGFTANQ 115 HP + + L+ GAGSG R I+GT YH LEE LA G E+AL+ S + AN Sbjct: 61 QHPVVLAAMHEALDATGAGSGGTRNISGTTVYHNALEEELADLHGKEAALLFTSAYIAND 120 Query: 116 GVLGAL--LKEGDVVFSDELNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTDGLK 173 L L L G + SD LNHAS+I G+R + +FRH D+ HL E+L++ D K Sbjct: 121 ATLSTLPILFPGLHIISDALNHASMIQGIRHGNCPKHIFRHNDLTHLREILESLPADAPK 180 Query: 174 LIVTDGVFSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPD 233 +I + V+SMDGD P++ I LA + A+ Y+D+ H G+ G +G G G D Sbjct: 181 VIAFESVYSMDGDFGPIEAICDLADAFGALTYIDEVHAVGMYGPRGAGVCEKLGLMDRID 240 Query: 234 VVQVATLSKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEP 293 ++ TL KA+ +GGY A + ++ D + + A F+F+TS PPAV ++ ++ + Sbjct: 241 IIN-GTLGKAFGVMGGYIAASAKMVDAVRSYAPGFIFTTSIPPAVAAGAAASVRHLKTDT 299 Query: 294 ERVERLWENTRYFKRELARLGYDTLGSQTPITPVLFGE-APLAFEASRLLLEEGVFAVGI 352 R E + K L LG + + I PV G+ + RLL E G++ I Sbjct: 300 ARREAHQMGAKILKMRLKGLGLPIIDHGSHIVPVHVGDPVKCKMISDRLLSEHGIYVQPI 359 Query: 353 GFPTVPRGKARIRNIVTAAHTKEMLDKALEAYEKVGKRLGIIR 395 FPTVPRG R+R + HT EM+ K + A + + + R Sbjct: 360 NFPTVPRGTERLRFTPSPVHTPEMISKLVHAMDDLWSHCALSR 402 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: 346 Number of extensions: 19 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: 407 Length adjustment: 31 Effective length of query: 364 Effective length of database: 376 Effective search space: 136864 Effective search space used: 136864 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