Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate WP_011444227.1 SARO_RS02825 CoA transferase subunit B
Query= BRENDA::P0A102 (213 letters) >NCBI__GCF_000013325.1:WP_011444227.1 Length = 219 Score = 178 bits (451), Expect = 8e-50 Identities = 94/200 (47%), Positives = 130/200 (65%), Gaps = 4/200 (2%) Query: 8 SRTEMAQRVAADIQEGAYVNLGIGAPTLVANYLGD-KEVFLHSENGLLGMGPSPAPGEED 66 SR +MA R A ++++G YVNLGIG PTLVAN++ + V L SENG+LG+GP P E D Sbjct: 12 SRDQMAARAAKELRDGYYVNLGIGIPTLVANHVPEGMTVTLQSENGMLGIGPFPYDDEVD 71 Query: 67 DDLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANWHTGAEGS 126 DLINAGKQ ++ L A+F A SF+M+RGG +D+ VLGA +V+ GD+ANW + Sbjct: 72 PDLINAGKQTISELPQSAYFDSATSFAMIRGGKIDLTVLGAMEVAENGDIANWMVPGK-M 130 Query: 127 IPAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDLAVLEVTP 186 I +GGAMDL G +++ V+M+H+ K G K +P CT PLTG V I TDLAV + Sbjct: 131 IKGMGGAMDLVAGVKKIIVVMEHVAKDGSPKFIPTCTLPLTGRNVVDMIVTDLAVFQRPD 190 Query: 187 EG--LKVVEICADIDFDELQ 204 ++VE+ + DE++ Sbjct: 191 HNSPFRLVELAPGVTADEVR 210 Lambda K H 0.318 0.137 0.399 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: 165 Number of extensions: 8 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: 213 Length of database: 219 Length adjustment: 22 Effective length of query: 191 Effective length of database: 197 Effective search space: 37627 Effective search space used: 37627 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 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