Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_011385133.1 AMB_RS13850 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000009985.1:WP_011385133.1 Length = 400 Score = 270 bits (690), Expect = 5e-77 Identities = 173/413 (41%), Positives = 237/413 (57%), Gaps = 32/413 (7%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59 MTEA+I RTPIG+ Y G+L L H I+ + R AG+D V++V G A Q Sbjct: 1 MTEALICDYTRTPIGR-YAGSLAGVRTDDLAAHPIKALMARHAGLDWSRVDEVAYGCANQ 59 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G N+AR ALL AGLP + GTT++R C SG+ A+ AAR+V+ E+ + GG ES Sbjct: 60 AGEDNRNVARMALLLAGLPHSIGGTTLNRLCGSGMDAVGYAARAVMTGEAELMIAGGVES 119 Query: 120 IS---LVQNDKMNTFHA-------------VDPALEAIKGDVYMAMLDTAETVAKRYGIS 163 +S V N + F V+ +E G +M +TAE VA+++ IS Sbjct: 120 MSRAPFVMNKADSAFSRDARLYDTTIGWRFVNALMEKAYGTD--SMPETAENVAEQFNIS 177 Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223 RE QD ++ SQ + +AAQ+ G+F EI+P++ D + +S DE PR Sbjct: 178 REDQDAFAARSQAKASAAQKNGRFAQEISPVTLPARKGDP---------VVVSHDEHPR- 227 Query: 224 ETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSY 283 ETT E LA LKA G +ITAGNAS ++DGA+A +I S A A GL P+ GM + Sbjct: 228 ETTVEALAKLKAPFRAGGSITAGNASGVNDGAAALLIASPAAAKAHGLTPIARILGMATA 287 Query: 284 GCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNV 341 G EP MGIGPV A +LL R GL++ D+ + E NEAFA Q L C +LG+ D +++N Sbjct: 288 GVEPRIMGIGPVPATQKLLARLGLTMADLDVMEFNEAFAAQALACTRQLGLADDDQRVNP 347 Query: 342 NGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 NGGAI++GHP GMSGAR+ G A ++ + + A+ TMC+G G G A E V Sbjct: 348 NGGAIALGHPLGMSGARIVGTAALQLAQTGGRRALSTMCIGVGQGIAMAIERV 400 Lambda K H 0.316 0.134 0.378 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: 440 Number of extensions: 28 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: 395 Length of database: 400 Length adjustment: 31 Effective length of query: 364 Effective length of database: 369 Effective search space: 134316 Effective search space used: 134316 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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