Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate YP_001313806.1 Smed_5096 acetyl-CoA acetyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_000017145.1:YP_001313806.1 Length = 395 Score = 254 bits (650), Expect = 2e-72 Identities = 153/388 (39%), Positives = 222/388 (57%), Gaps = 9/388 (2%) Query: 11 RTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNRNVARM 70 RTP+G + G LKD A DLG I ++R G+ AVD+V++GC AG+ + AR Sbjct: 14 RTPLGSFQGELKDFSAPDLGGAAIADALKR-AGIAPDAVDEVVFGCVLTAGQ-GQAPARQ 71 Query: 71 SALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPFVMGKA 130 +AL AGLP T+N++CGSGM A A IKA A +++AGG+ESMT AP+++ +A Sbjct: 72 AALSAGLPLGVGATTVNKMCGSGMKAAMLAHDLIKAESASIVVAGGMESMTNAPYLLDRA 131 Query: 131 ASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFALASQQ 190 + H + F++ L M AE+ AE + +R QD +A+ S + Sbjct: 132 RQGYRIG---HQRALDHMFLDGLEDAYDKGRLMGTFAEDCAEAYQFTRGAQDDYAIGSLE 188 Query: 191 KAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDGTVTAG 250 KA +A DG+ A EIV + KG V+LDE P++ E + LK R GTVTA Sbjct: 189 KAKKAGADGSFANEIVPLSTGSGKGGT--VSLDEQPQKARAEKIPLLKPAFREGGTVTAA 246 Query: 251 NASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKLLRQLG 310 NAS ++DGA AL++ + AAE G+ A V G AT P++ P A L +++G Sbjct: 247 NASSISDGAAALVLMRRSAAETQGVTPLAIVRGHATHADAPKLFPTAPIGAITALCQRIG 306 Query: 311 MTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARLVTTAL 370 + +D+ E+NEAFA +A +R LGL + +VN NGGA ALGHP+GASGAR++ T + Sbjct: 307 WDIGGVDLFEINEAFAVVPMAAIRDLGLAAE--KVNVNGGACALGHPIGASGARVIVTLV 364 Query: 371 HQLERSNGRFALCTMCIGVGQGIALVIE 398 + L R R + ++CIG G+ A+ +E Sbjct: 365 NALRRRGLRRGIASVCIGGGEATAVAVE 392 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: 419 Number of extensions: 29 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