Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_036261146.1 DL86_RS10295 acetyl-CoA C-acyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_000746085.1:WP_036261146.1 Length = 395 Score = 242 bits (618), Expect = 1e-68 Identities = 154/393 (39%), Positives = 221/393 (56%), Gaps = 8/393 (2%) Query: 6 ICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNR 65 I A RTPIG + G K + A DLGA IKA + R+ G+ +D+VI GC AG+ + Sbjct: 9 IVAAARTPIGGFQGDFKGLAATDLGAAAIKAAVARS-GLRPEDIDEVILGCVLSAGQ-GQ 66 Query: 66 NVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPF 125 AR +AL AGLP A TIN++CGSGM A+ ++A A +++AGG+ESMT AP+ Sbjct: 67 APARQAALKAGLPEAAGCVTINKMCGSGMKAIMFGHDLLRADSAAIVLAGGMESMTNAPY 126 Query: 126 VMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFA 185 ++ +A + + H I F++ L M AE+ AE F +RA QDAFA Sbjct: 127 LLDRARAGYRMG---HGRIIDHMFLDGLEDAYGQRLPMGAFAEDCAEAFQFTRAAQDAFA 183 Query: 186 LASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDG 245 L S ++A +A DG+ EI V K D + + DE P + ++ ++ LK R G Sbjct: 184 LCSLERAQKAIADGSFEAEIAQVSAPAGKIDRM-IAEDEQPLKARIDKISTLKPAFRDGG 242 Query: 246 TVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKL 305 TVTA N+S ++DGA AL++ + AE+ G A + AT P P A +KL Sbjct: 243 TVTAANSSSISDGAAALVLMRRSDAERRGASALAIIRAHATHAQAPDQFATAPIGALRKL 302 Query: 306 LRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARL 365 + + G +L +D+ E+NEAFA +A +R L L + +VN +GGA ALGHP+GASGAR+ Sbjct: 303 MDKTGWSLPDVDLFEINEAFAVVTMAAMRELALPHE--KVNVHGGACALGHPIGASGARI 360 Query: 366 VTTALHQLERSNGRFALCTMCIGVGQGIALVIE 398 V T L L++ + +CIG G+ AL IE Sbjct: 361 VATLLAALKKYGLKRGAAALCIGGGEATALAIE 393 Lambda K H 0.319 0.134 0.386 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: 413 Number of extensions: 23 Number of successful extensions: 6 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: 400 Length of database: 395 Length adjustment: 31 Effective length of query: 369 Effective length of database: 364 Effective search space: 134316 Effective search space used: 134316 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 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