Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_012112924.1 XAUT_RS04530 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000017645.1:WP_012112924.1 Length = 402 Score = 261 bits (668), Expect = 2e-74 Identities = 177/414 (42%), Positives = 230/414 (55%), Gaps = 32/414 (7%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59 M A I ARTPIG+ Y GAL L H I +R G+D + V+DV++G A Q Sbjct: 1 MAHAFICDFARTPIGR-YAGALKDVRADDLAAHPIRVLKERNPGVDWEAVDDVILGCANQ 59 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G ++AR A L AGLPV+ GTT++R C SGL A+ + AR+++ ++ V GG ES Sbjct: 60 AGEDNRDVARMAALLAGLPVSAPGTTVNRLCGSGLDAVGIGARAIMTGDADLIVAGGVES 119 Query: 120 IS---LVQNDKMNTFHA-------------VDPALEAIKGDVYMAMLDTAETVAKRYGIS 163 ++ VQ F V+P ++A G +M +T E VA+ + +S Sbjct: 120 MTRAPFVQGKAQEAFSRQAEIYDTTIGWRFVNPLMKAQYG--VDSMPETGENVAEDFQVS 177 Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223 R QD ++ SQ+R AAQ G F EIAPI K GAV I + DE PR Sbjct: 178 RADQDLFAYRSQQRVKAAQDAGFFAREIAPIEVK-----GKKGAV----IRVEADEHPRA 228 Query: 224 ETTAEGLAGLKA-VRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVS 282 ETT E LAGLKA R G T+TAGNAS ++DGA A ++ S+ A GL P +V Sbjct: 229 ETTLEQLAGLKAPFRKAGGTVTAGNASGVNDGAGALILASEAAAKKYGLTPRARVVSVVQ 288 Query: 283 YGCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLN 340 G P MGIGP A +LL+++GL++ DI L ELNEAFA Q L +LG+ D E +N Sbjct: 289 AGVPPRIMGIGPAPATRKLLEKNGLALADIDLIELNEAFAAQALAVLRQLGLPDDAEHVN 348 Query: 341 VNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 NGGAI++GHP GMSGARLA A+ R AV TMC+G G G A L E V Sbjct: 349 PNGGAIALGHPLGMSGARLAMTAVSALEVRGGTRAVATMCIGVGQGIAALIERV 402 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: 427 Number of extensions: 30 Number of successful extensions: 6 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: 402 Length adjustment: 31 Effective length of query: 364 Effective length of database: 371 Effective search space: 135044 Effective search space used: 135044 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 Apr 09 2024. 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