Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate Ga0059261_3672 Ga0059261_3672 7-keto-8-aminopelargonate synthetase and related enzymes
Query= reanno::ANA3:7026975 (397 letters) >FitnessBrowser__Korea:Ga0059261_3672 Length = 369 Score = 148 bits (373), Expect = 3e-40 Identities = 106/345 (30%), Positives = 172/345 (49%), Gaps = 8/345 (2%) Query: 45 VNFCANNYLGLANHPELIKAAQQGLDSH-GFGMASVRFICGTQDIHKQLEASLSEFLGME 103 ++F +N+YLGLAN L A LD G R + G LEA + E Sbjct: 28 IDFASNDYLGLANDQRLRDAVAAALDRGLAVGSGGSRLLRGNDPEIATLEAEAAAMFRAE 87 Query: 104 DTILYSSCFDANAGLFETLLDAEDAIISDALNHASIIDGVRLCKAKRFRYANNDMADLET 163 + +S+ F AN L TL D I+ DAL HAS+ DG++L +A A+ND ++ Sbjct: 88 AALFFSTGFAANVALLATLPQPGDLIVHDALIHASVHDGLKLSRAPSVAAAHNDAQAVDD 147 Query: 164 QLIAAKA-AGARNILIATDGVFSMDGVIANLQGVCDLADKYGALVMVDDSHAVGFVGLNG 222 + + + GA IA + ++SMDG A + + ++A ++ A++++D++HA G G G Sbjct: 148 AIASWRGQGGAGTPWIAVESLYSMDGDRAPIAALAEVAARHDAMLIIDEAHATGIWGNGG 207 Query: 223 RGSHEHCGVMGRVDIIT-GTLGKALGGASGGFTSGKKEVIDWLRQRSRPYLFSNSLAPSI 281 RG + G+ +IIT T GKAL G G G + ID+L R+RP++FS + +P + Sbjct: 208 RGL--AATLEGQPNIITLHTCGKAL-GCEGALVCGARVFIDFLVNRARPFIFSTAPSPLM 264 Query: 282 VTASIHVLEMLKSGQALREAVWENSRYFREKMSAAGFTLGGADHAIIPVMIGDAKLASDF 341 A L ++ A RE + + ++ G T G+ ++P+++G Sbjct: 265 AAAVREALRIVADEPARRETLHWLIAHAERVLAPLGVTPTGSQ--VLPLIVGGDAETMAR 322 Query: 342 ANRLLAEHIYVIGFSFPVVPKGQARIRTQMSAAHTREQLDKAIEA 386 A L A+ V G P VP G AR+R ++ T+ +D+ +A Sbjct: 323 AAALQAKGFDVRGIRPPTVPAGTARLRISLTLNVTQGDIDRLADA 367 Lambda K H 0.321 0.134 0.385 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: 314 Number of extensions: 11 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: 397 Length of database: 369 Length adjustment: 30 Effective length of query: 367 Effective length of database: 339 Effective search space: 124413 Effective search space used: 124413 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 (21.9 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