Align 3-oxoadipate CoA-transferase (EC 2.8.3.6) (characterized)
to candidate WP_090446767.1 BLS63_RS16775 CoA transferase subunit A
Query= reanno::WCS417:GFF1318 (285 letters) >NCBI__GCF_900100495.1:WP_090446767.1 Length = 283 Score = 525 bits (1352), Expect = e-154 Identities = 249/283 (87%), Positives = 272/283 (96%) Query: 1 MAEILALRDAVKQFVNDGDTVALEGFTHLIPTAAGHEIIRQGKKDLTLVRMTPDLIYDQL 60 MAE+++L +A+++FVNDGDTVALEGFTHLIPTAA HEIIRQ K++LTLVRMTPDL+YD L Sbjct: 1 MAELISLGEAIQRFVNDGDTVALEGFTHLIPTAASHEIIRQNKRELTLVRMTPDLVYDLL 60 Query: 61 IGAGCARKLIFSWGGNPGVGSLHRLRDAVEKQWPQPLEIEEHSHADLANAYVAGASGLPF 120 IGAGCA+KL+FSWGGNPGVGSLHRLRDAVEK WP+PLEIEEHSHAD+ANAYVAGASGLPF Sbjct: 61 IGAGCAKKLVFSWGGNPGVGSLHRLRDAVEKGWPRPLEIEEHSHADMANAYVAGASGLPF 120 Query: 121 AVLRAYAGSDLPKVNPLIKTVTCPFTGEVLAAVPSVRPDVTVIHAQKADRKGNVLLWGIL 180 AVLRAYAGSDLPKVNPL+KTVTCPFTGEVLAAVPSVRPDVTVIHAQKADRKGNVLLWGIL Sbjct: 121 AVLRAYAGSDLPKVNPLLKTVTCPFTGEVLAAVPSVRPDVTVIHAQKADRKGNVLLWGIL 180 Query: 181 GVQKEAALAAKRCIVTVEEIVDDLNAPMNSCVLPTWALTAVCHVPGGAHPSYAHGYNERD 240 GVQKEAALAAKRCIVTVEEIVD+LNAPMN+CVLP+WALTAVCHVPGGAHPSYAHGY+ERD Sbjct: 181 GVQKEAALAAKRCIVTVEEIVDELNAPMNACVLPSWALTAVCHVPGGAHPSYAHGYSERD 240 Query: 241 NRFYQAWDPIARDRGTFTAWINEYIHGTADFTEFQAKLATAQE 283 NRFYQAWDPIARDR TFTAWI+ YI GTADF +QAKLA A++ Sbjct: 241 NRFYQAWDPIARDRETFTAWIDTYIRGTADFAAYQAKLAEAKQ 283 Lambda K H 0.320 0.136 0.421 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: 374 Number of extensions: 7 Number of successful extensions: 1 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: 285 Length of database: 283 Length adjustment: 26 Effective length of query: 259 Effective length of database: 257 Effective search space: 66563 Effective search space used: 66563 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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