Align Butyrate--acetoacetate CoA-transferase subunit B; Short=Coat B; EC 2.8.3.9 (characterized, see rationale)
to candidate Ac3H11_3921 3-oxoadipate CoA-transferase subunit B (EC 2.8.3.6)
Query= uniprot:P23673 (221 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3921 Length = 201 Score = 147 bits (372), Expect = 1e-40 Identities = 86/210 (40%), Positives = 126/210 (60%), Gaps = 14/210 (6%) Query: 16 VARELKNGQLVNLGVGLPTMVADYIPKNFKITFQSENGIVGMGASPKINEADKDVVNAGG 75 VA+++ +G VNLG+G PT+VA++IP+ ++ QSENGI+GMG +P D D++NAG Sbjct: 1 VAQDIHDGAYVNLGIGQPTLVANHIPEGREVILQSENGILGMGPAPAAGLEDYDLINAGK 60 Query: 76 DYTTVLPDGTFFDSSVSFSLIRGGHVDVTVLGALQVDEKGNIANWIV--PGKMLSGMGGA 133 T+LP G +F + SF+++RGGH+D+ VLGA QV G++ANW PG + +GGA Sbjct: 61 QPVTLLPGGAYFHHADSFAMMRGGHLDICVLGAYQVSATGDLANWSTGEPG-AIPAVGGA 119 Query: 134 MDLVNGAKKVIIAM-RHTNKGQPKILKKCTLPLTAKSQANLIVTELGVIEVINDGLLLTE 192 MDL GAK+ + M T +G KI+ +CT PLT + I T+L + GL L Sbjct: 120 MDLAIGAKQTWVMMDLLTKQGASKIVTQCTYPLTGVACVKRIYTDLCTLACTPTGLQL-- 177 Query: 193 INKNTTIDEIRSLTAADL--LISNELRPMA 220 ID + L+ +L L+ +RP A Sbjct: 178 ------IDTVPGLSQTELEQLVGLPIRPAA 201 Lambda K H 0.316 0.136 0.376 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: 145 Number of extensions: 5 Number of successful extensions: 3 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: 221 Length of database: 201 Length adjustment: 21 Effective length of query: 200 Effective length of database: 180 Effective search space: 36000 Effective search space used: 36000 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: 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