Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_110806646.1 C8J30_RS14960 acetyl-CoA C-acyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_003217355.1:WP_110806646.1 Length = 395 Score = 264 bits (675), Expect = 3e-75 Identities = 162/390 (41%), Positives = 225/390 (57%), Gaps = 9/390 (2%) Query: 11 RTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNRNVARM 70 RTP+G + GA D+ A DLGAV ++A + R G+ AVD+VI GC AG+ + AR Sbjct: 13 RTPMGGFQGAFADLAAADLGAVALRAALSR-AGLPAEAVDEVILGCVLPAGQ-GQAPARQ 70 Query: 71 SALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPFVMGKA 130 +AL AGLP A TIN++CGSGM A + AG AQ+++AGG+ESMT AP+++ KA Sbjct: 71 AALKAGLPLAAGATTINKMCGSGMKAAMFGHDLLLAGSAQVVLAGGMESMTNAPYLLPKA 130 Query: 131 ASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFALASQQ 190 H + F++ L M AE+ AE+FG +RA QD +A+ S Sbjct: 131 RGGLRLG---HGQVMDHMFLDGLEDAYDRGRLMGTFAEDCAEEFGFTRAAQDGYAITSLT 187 Query: 191 KAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDGTVTAG 250 +A A G A EI V I+ K + V DE P + ++ +A LK RP GTVTA Sbjct: 188 RAQAAIASGAFAAEIAPVVISGKT--EVTVNTDEQPGKARMDKIATLKPAFRPGGTVTAA 245 Query: 251 NASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKLLRQLG 310 N+S ++DGA AL++ AE GL ARV+G AT +P + P A KL +L Sbjct: 246 NSSSISDGAAALVLMRASEAEARGLTPLARVLGHATHADKPNLFPTAPIGALSKLSEKLD 305 Query: 311 MTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARLVTTAL 370 + L +D+ E+NEAFA +A + +L L + RVN +GGA ALGHP+GASGAR++ T L Sbjct: 306 LDLRAVDLFEVNEAFAVVAMAAMTVLNLPHE--RVNVHGGACALGHPIGASGARVLVTLL 363 Query: 371 HQLERSNGRFALCTMCIGVGQGIALVIERL 400 L+R R + T+CIG G+ A+ IER+ Sbjct: 364 AALQRHGLRTGVATLCIGGGEATAMAIERI 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: 375 Number of extensions: 18 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 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