Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_011766784.1 AZO_RS15365 3-oxoadipyl-CoA thiolase
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_000061505.1:WP_011766784.1 Length = 402 Score = 627 bits (1618), Expect = 0.0 Identities = 312/396 (78%), Positives = 348/396 (87%) Query: 5 ICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGEDNR 64 +CDAIRTPFGRYGG L +VRADDLAA PIR+L+ RNPGVDW+ V+D++YGCANQAGEDNR Sbjct: 7 LCDAIRTPFGRYGGLLSSVRADDLAALPIRALIARNPGVDWNLVDDVIYGCANQAGEDNR 66 Query: 65 NVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRAPF 124 NVARMA LLAGLP+ VPGSTVNRLCGSSLDA+G AARAI +GE +LMIAGGVESM+RAPF Sbjct: 67 NVARMAALLAGLPVEVPGSTVNRLCGSSLDAIGSAARAIAAGEAELMIAGGVESMSRAPF 126 Query: 125 VMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDAFA 184 V+GKA+SAF+RSA I DTTIGWRFVNPLMKAQYG+DSMPETAENVATDF ++RADQDA A Sbjct: 127 VLGKADSAFSRSAKIEDTTIGWRFVNPLMKAQYGVDSMPETAENVATDFNVSRADQDALA 186 Query: 185 LRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVVRPD 244 LRSQQRWA+A GFFA EI P+ IP+KKGDP+ +TTDEHPRPDTTL LAKLKGVVRPD Sbjct: 187 LRSQQRWASANERGFFAREIVPVDIPRKKGDPVRMTTDEHPRPDTTLDMLAKLKGVVRPD 246 Query: 245 GTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPAVRK 304 GTVTAGNASGVNDGA A+LLAS A + L PRAR+LG A AGVAPRIMG GPAPA K Sbjct: 247 GTVTAGNASGVNDGAAAVLLASEAAVKRHGLTPRARILGSAAAGVAPRIMGIGPAPASEK 306 Query: 305 VLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGASGAR 364 +LA++G+ +A+ DVIELNEAFAAQ LAV R LGL DD A VNPNGGAI+IGHPLGASGAR Sbjct: 307 LLARLGMGIARFDVIELNEAFAAQALAVTRRLGLADDDARVNPNGGAISIGHPLGASGAR 366 Query: 365 LVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400 LVTTA+NQLE SGGRY L TMCIGVGQGIAL IER+ Sbjct: 367 LVTTALNQLETSGGRYGLATMCIGVGQGIALAIERI 402 Lambda K H 0.320 0.135 0.394 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: 580 Number of extensions: 19 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: 401 Length of database: 402 Length adjustment: 31 Effective length of query: 370 Effective length of database: 371 Effective search space: 137270 Effective search space used: 137270 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: 50 (23.9 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