Align 3-oxoadipate CoA-transferase subunit A; 3-oxoadipate:succinyl-CoA transferase subunit A; Beta-ketoadipate:succinyl-CoA transferase subunit A; EC 2.8.3.6 (characterized)
to candidate WP_036258219.1 DL86_RS03250 CoA-transferase
Query= SwissProt::Q8VPF3 (282 letters) >NCBI__GCF_000746085.1:WP_036258219.1 Length = 320 Score = 126 bits (317), Expect = 5e-34 Identities = 87/273 (31%), Positives = 136/273 (49%), Gaps = 8/273 (2%) Query: 15 VNDGDTVALEG-FTHLIPTAASHEIIRQGKKDLHLVRMTPDLVYDLLIGAGCARKLTFSW 73 V DG VA+ G + P A I+R+G K L +V + DLL G G + + S+ Sbjct: 26 VKDGSVVAVGGGLSSREPMALLRAILRRGVKGLTVVGSAHGIDIDLLSGGGAISRSSESY 85 Query: 74 GG-NPGVGSLHRLRDAVEKGWPNALEIDEHSHADLANSYVAGASGLPFAVLRAYAGSDLP 132 G G R A+E G A+ +D+ L A GLPF +R+ G+ P Sbjct: 86 VGFEQDFGMAPNYRRALESG---AVSVDDSCCYTLVQQLRAAIQGLPFLPIRSVRGTSFP 142 Query: 133 KVNPNIKFINCPFTGEQLAAVPSVRPDVTVIHAQKADRKGNVLLWGILGVQKEAALAAKR 192 ++P K + CPFTGE+L VP++ P+V +IHAQ D +GN+L+ G A A++ Sbjct: 143 SLHPEYKRMICPFTGEELLLVPAIEPEVALIHAQYGDAQGNLLIQGPPVADILFAKASRE 202 Query: 193 CIVTVEEIVDDLN-APMNSCVLPTWALSAVCHVPGGSHPSYAHGYYERDNRFYQAWDPIA 251 + TVEEIV + +P + ++AV VP G+HP+ + +Y D R + A Sbjct: 203 VLATVEEIVSTARLKELGGVSIPYFYVTAVSEVPMGAHPTACYPFYAYDRRHTVLYYEAA 262 Query: 252 R-DRETFTA-WIDEYIRGTKDFSEFQAKIAEGK 282 R + F A ++ ++ G D +++ A+I K Sbjct: 263 RKGADAFLAEYLSVFVHGAPDHADYLAQIGGEK 295 Lambda K H 0.320 0.136 0.424 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: 235 Number of extensions: 13 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: 282 Length of database: 320 Length adjustment: 27 Effective length of query: 255 Effective length of database: 293 Effective search space: 74715 Effective search space used: 74715 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: 48 (23.1 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