Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate Ac3H11_3921 3-oxoadipate CoA-transferase subunit B (EC 2.8.3.6)
Query= reanno::psRCH2:GFF1044 (209 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3921 Length = 201 Score = 207 bits (526), Expect = 1e-58 Identities = 109/198 (55%), Positives = 137/198 (69%), Gaps = 3/198 (1%) Query: 13 AQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEIDPDLINAGKQ 72 AQ++ DG YVNLGIG PTLVAN+IPEG +V LQSENG+LG+GP P D DLINAGKQ Sbjct: 2 AQDIHDGAYVNLGIGQPTLVANHIPEGREVILQSENGILGMGPAPAAGLEDYDLINAGKQ 61 Query: 73 TVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMI--PGKMVKGMGGAM 130 VT LPG ++F +A SFAM+RGGH+++ +LGA QVS GDLANW PG + +GGAM Sbjct: 62 PVTLLPGGAYFHHADSFAMMRGGHLDICVLGAYQVSATGDLANWSTGEPG-AIPAVGGAM 120 Query: 131 DLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVTEQGLKLVEL 190 DL G K+ V+M+ K GA KI+ C PLTG+ V RI TDL L T GL+L++ Sbjct: 121 DLAIGAKQTWVMMDLLTKQGASKIVTQCTYPLTGVACVKRIYTDLCTLACTPTGLQLIDT 180 Query: 191 AEGVSFDELQEATGSPIQ 208 G+S EL++ G PI+ Sbjct: 181 VPGLSQTELEQLVGLPIR 198 Lambda K H 0.318 0.138 0.404 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: 188 Number of extensions: 6 Number of successful extensions: 2 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: 209 Length of database: 201 Length adjustment: 21 Effective length of query: 188 Effective length of database: 180 Effective search space: 33840 Effective search space used: 33840 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 (21.7 bits) S2: 45 (21.9 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