Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_084055719.1 B9A12_RS01220 acetyl-CoA C-acyltransferase
Query= SwissProt::P14611 (393 letters) >NCBI__GCF_900176285.1:WP_084055719.1 Length = 418 Score = 265 bits (677), Expect = 2e-75 Identities = 168/420 (40%), Positives = 231/420 (55%), Gaps = 38/420 (9%) Query: 1 MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60 M DVV+VS RT VG++ G+L ++ A +L A V+ A+ RAG++P QV EV++GQ G Sbjct: 1 MRDVVLVSGVRTPVGRYLGALREVEAYDLAARVLDEAVRRAGIEPAQVDEVVLGQAYQNG 60 Query: 61 SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120 N AR A +KAG P +P +T+++ C +GL V A I +G A +VVAGG E+MS Sbjct: 61 EYVNIARMALLKAGWPESIPGITLDRRCCTGLDVVRYGALLIRSGAARVVVAGGVESMSN 120 Query: 121 APHVLP-------GSRDGFRMGDAKLVDTMIVDGLWDV-------------YNQYHMGIT 160 A LP G R+G G L +W + Q G+ Sbjct: 121 AEFYLPGHIKWGVGGREGMPRGHGDL-------SIWGLPFYDRIQRARVMSQPQERYGVL 173 Query: 161 ------AENVAKEYGITREAQDEFAVGSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAF 214 AE A++ GI+R D +AV S KA AA G+F E+VPV + KG PV Sbjct: 174 PSMMSWAEVAARQEGISRNDCDAWAVESHRKACAAWAEGRFRAELVPVEVRAPKGPPVVV 233 Query: 215 KTDEFVRQGATLDSMSGLKPAFDKAGTVTAANASGLNDGAAAVVVMSAAKAKELGLTPLA 274 DE R+ T++ ++ LKP G TA N+S NDGAAAVV+M + A E GL P+A Sbjct: 234 DRDETPREDTTVEKLARLKPVL--GGVCTAGNSSSENDGAAAVVLMDSRTALEWGLRPMA 291 Query: 275 TIKSYANAGVDPKVMGMGPVPASKRALSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWD 334 + + A A DP+ A RAL + + +DL+E+ EAFAAQ LA +QMG Sbjct: 292 RVLACAVAACDPRRTYEAVPTAVNRALDQVGLHLEAMDLIEVQEAFAAQVLADLKQMGIG 351 Query: 335 T---SKVNVNGGAIAIGHPIGASGCRILVTLLHEMKRRDAKKGLASLCIGGGMGVALAVE 391 +VNVNG I++GHPI +G R+LVTL HEM+RR + GL ++C GGG+G+A E Sbjct: 352 PERYDRVNVNGSGISLGHPIACTGVRVLVTLCHEMRRRGVRYGLEAICGGGGLGIAAVFE 411 Lambda K H 0.315 0.131 0.369 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: 371 Number of extensions: 13 Number of successful extensions: 4 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: 393 Length of database: 418 Length adjustment: 31 Effective length of query: 362 Effective length of database: 387 Effective search space: 140094 Effective search space used: 140094 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 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