Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate N515DRAFT_0547 N515DRAFT_0547 8-amino-7-oxononanoate synthase
Query= reanno::Koxy:BWI76_RS27255 (397 letters) >FitnessBrowser__Dyella79:N515DRAFT_0547 Length = 397 Score = 255 bits (651), Expect = 2e-72 Identities = 146/368 (39%), Positives = 216/368 (58%), Gaps = 5/368 (1%) Query: 21 LFKEERIITSAQQADITVGGSQVINFCANNYLGLANHPELIAAAKSGMDSHGFGMASVRF 80 L + R I A+ + GG +++ FC N+YLGLA HP +IAA K D G G + Sbjct: 22 LLRRLRTIEHAEGPWLESGGRRLLGFCGNDYLGLAQHPLVIAAFKRTADDEGVGSTAAHL 81 Query: 81 ICGTQDSHKALEKKLADFLGMEDAILYSSCFDANGGLFETLLGAEDAIISDALNHASIID 140 ICG + H ALE+ LAD+ G E A L+S+ + AN G+ + LL A D + D LNHA ++D Sbjct: 82 ICGHRAEHAALEEALADWTGRERAALFSTGYLANLGVMQALLRAGDMCVQDKLNHACLLD 141 Query: 141 GVRLCKAKRFRYANNDMVELEARLKEARDAGARHVLIATDGVFSMDGVIANLKGVCDLAD 200 G L A+ RY +ND+ +L +AGA L+ATDG+FSMDG +A L+ + L + Sbjct: 142 GAALAGAQLKRYPHNDVDGAARQLASRAEAGA---LLATDGIFSMDGDLAPLRELARLCE 198 Query: 201 KYDALVMVDDSHAVGFVGENGRGSHEYCDVMGR-VDIITGTLGKALGGASGGYTAARKEV 259 + DA +MVDD+H +G +G+NG G+ D+ R V ++ TLGKAL G G + A + Sbjct: 199 QEDATLMVDDAHGLGVLGDNGAGTLSMLDLGQRDVPVLMATLGKAL-GCHGAFVAGSANL 257 Query: 260 VEWLRQRSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRDRLWSNARLFREKMTAAGFIL 319 VE L Q +R Y+++ ++ PA+ AA++ + + A S R++L + R FR+ G L Sbjct: 258 VEGLLQSARTYVYTTAMPPAVAAAALAAVRIARAESWRREKLAALIRRFRDGAQQLGLPL 317 Query: 320 AGADHAIIPVMLGEATVAQEFARELQKEGIYVTGFFYPVVPKGQARIRTQMSAAHTPEQI 379 +D AI P++LGEAT A A L+ G V P VP G+AR+R +SAAH E + Sbjct: 318 MPSDTAIQPLLLGEATTAMAAAGALEAVGFLVGAIRPPTVPAGKARLRITLSAAHEEEHV 377 Query: 380 ERAVEAFT 387 ++ +EA + Sbjct: 378 DQLLEALS 385 Lambda K H 0.321 0.136 0.390 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: 409 Number of extensions: 16 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: 397 Length of database: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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 (21.8 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