Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_043745132.1 AMB_RS18210 acetyl-CoA C-acyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_000009985.1:WP_043745132.1 Length = 394 Score = 260 bits (665), Expect = 4e-74 Identities = 156/396 (39%), Positives = 227/396 (57%), Gaps = 10/396 (2%) Query: 5 VYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGED 64 + I A RTP+G F G A++ A L A ++A VER+ Q+DEV++GC AG Sbjct: 6 IVIVGAARTPMGGFQGDFASLAAPQLGAAAIRAAVERSGLAP-DQVDEVFMGCVLPAGV- 63 Query: 65 NRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRA 124 + AR A L AGLP S T++++C SGM A A + +G A++++AGG+ESMS A Sbjct: 64 GQAPARQASLGAGLPRSAGCTTISKVCGSGMKAAMLAHDLLVAGTAKVMVAGGMESMSNA 123 Query: 125 PYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQDA 184 PY++ KA + G + F++ L A M A+ A YK +R QD Sbjct: 124 PYLLDKARGGYRLGH---GKVLDHMFLDGLEDAYDRGRLMGTFAEECAGSYKFTREAQDG 180 Query: 185 FALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTL-EALAKLKPVNG 243 FAL S A +A A G FA EI PV + G+KGET++ DE +P L + + LKP Sbjct: 181 FALASLSRAKKAIADGLFAAEITPVAVAGRKGETLITIDE--QPGKALPDKIPTLKPAFA 238 Query: 244 PDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPAV 303 D TVTA N+S ++DG+ AL++ +K GLK A VLG + P + PV A+ Sbjct: 239 KDGTVTAANSSSISDGAAALVMMRRSEAEKRGLKPLATVLGHTNFAQEPALFTTAPVGAI 298 Query: 304 RKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGASG 363 + LL+++ D D+ E+NEAFA +A +L + + RVN +GGA ALGHP+GASG Sbjct: 299 KTLLDKVGCKAGDIDLWEINEAFAVVTMAAMHDLKL--EHERVNVHGGACALGHPIGASG 356 Query: 364 ARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVE 399 AR+++T + L+ G +RG+ ++C+G G+ AL VE Sbjct: 357 ARIIVTLLSALKTYGMKRGVASLCIGGGEATALMVE 392 Lambda K H 0.317 0.134 0.379 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: 408 Number of extensions: 22 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: 401 Length of database: 394 Length adjustment: 31 Effective length of query: 370 Effective length of database: 363 Effective search space: 134310 Effective search space used: 134310 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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