Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_043745132.1 AMB_RS18210 acetyl-CoA C-acyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_000009985.1:WP_043745132.1 Length = 394 Score = 239 bits (611), Expect = 8e-68 Identities = 149/393 (37%), Positives = 221/393 (56%), Gaps = 8/393 (2%) Query: 6 ICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNR 65 I A RTP+G + G + A LGA I+A ++R+ G+ VD+V GC AG + Sbjct: 8 IVGAARTPMGGFQGDFASLAAPQLGAAAIRAAVERS-GLAPDQVDEVFMGCVLPAGV-GQ 65 Query: 66 NVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPF 125 AR ++L AGLP A TI+++CGSGM A A + AG A++M+AGG+ESM+ AP+ Sbjct: 66 APARQASLGAGLPRSAGCTTISKVCGSGMKAAMLAHDLLVAGTAKVMVAGGMESMSNAPY 125 Query: 126 VMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFA 185 ++ KA + H + F++ L M AE A + +R QD FA Sbjct: 126 LLDKARGGYRLG---HGKVLDHMFLDGLEDAYDRGRLMGTFAEECAGSYKFTREAQDGFA 182 Query: 186 LASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDG 245 LAS +A +A DG A EI V +A +KG+ + +T+DE P + + + LK DG Sbjct: 183 LASLSRAKKAIADGLFAAEITPVAVAGRKGETL-ITIDEQPGKALPDKIPTLKPAFAKDG 241 Query: 246 TVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKL 305 TVTA N+S ++DGA AL++ + AE+ GL+ A V+G EP + P A + L Sbjct: 242 TVTAANSSSISDGAAALVMMRRSEAEKRGLKPLATVLGHTNFAQEPALFTTAPVGAIKTL 301 Query: 306 LRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARL 365 L ++G +D+ E+NEAFA +A + L L + RVN +GGA ALGHP+GASGAR+ Sbjct: 302 LDKVGCKAGDIDLWEINEAFAVVTMAAMHDLKLEHE--RVNVHGGACALGHPIGASGARI 359 Query: 366 VTTALHQLERSNGRFALCTMCIGVGQGIALVIE 398 + T L L+ + + ++CIG G+ AL++E Sbjct: 360 IVTLLSALKTYGMKRGVASLCIGGGEATALMVE 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: 388 Number of extensions: 19 Number of successful extensions: 5 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: 394 Length adjustment: 31 Effective length of query: 369 Effective length of database: 363 Effective search space: 133947 Effective search space used: 133947 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 17 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