Align 3-oxoadipate CoA-transferase (EC 2.8.3.6) (characterized)
to candidate WP_050654881.1 C1M55_RS10595 CoA transferase subunit A
Query= reanno::WCS417:GFF1318 (285 letters) >NCBI__GCF_002893965.1:WP_050654881.1 Length = 322 Score = 285 bits (730), Expect = 7e-82 Identities = 142/276 (51%), Positives = 192/276 (69%), Gaps = 2/276 (0%) Query: 5 LALRDAVKQFVNDGDTVALEGFTHLIPTAAGHEIIRQGKKDLTLVRMTPDLIYDQLIGAG 64 L++++AV ++V DG TVALEGF+HLIP AA HEIIRQG+KDLTL RMTPD++ DQL+ AG Sbjct: 23 LSMKEAVGRYVEDGMTVALEGFSHLIPFAAAHEIIRQGRKDLTLCRMTPDIVSDQLVAAG 82 Query: 65 CARKLIFSWGGNPGVGSLHRLRDAVEKQWPQPLEIEEHSHADLANAYVAGASGLPFAVLR 124 C RKL+ S+ + GSL+ LR +E Q P PLE+EE+SH + Y AGA+ LPF LR Sbjct: 83 CVRKLVASFFASGSAGSLYELRRRIENQDPLPLEVEEYSHYGMVCRYQAGAARLPFFPLR 142 Query: 125 AYAGSDLPKVNPLIKTVTCPFTGEVLAAVPSVRPDVTVIHAQKADRKGNVLLWGILGVQK 184 +YAGSDLP +NP ++ V P+ G + VP + PDVT+I AQ+AD GN +WGI GVQ+ Sbjct: 143 SYAGSDLPALNPQLRLVEDPYGGGSVYVVPPLNPDVTIIGAQRADTSGNAQIWGIAGVQQ 202 Query: 185 EAALAAKRCIVTVEEIVDD--LNAPMNSCVLPTWALTAVCHVPGGAHPSYAHGYNERDNR 242 EA AAK+ IV VEE+VDD + + + ++P+ A+ AV P GAHPSYA GY +RD Sbjct: 203 EAVYAAKKAIVVVEELVDDEVIRSDPSRTLIPSHAVDAVVVCPRGAHPSYAQGYYDRDCG 262 Query: 243 FYQAWDPIARDRGTFTAWINEYIHGTADFTEFQAKL 278 FY+ W I++D W++E+++ D E+ AKL Sbjct: 263 FYRRWTEISKDPSLLRNWLDEWVYTLGDHDEYLAKL 298 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: 268 Number of extensions: 9 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: 285 Length of database: 322 Length adjustment: 27 Effective length of query: 258 Effective length of database: 295 Effective search space: 76110 Effective search space used: 76110 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 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