Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_040660251.1 ON16_RS05715 thiolase family protein
Query= BRENDA::P45359 (392 letters) >NCBI__GCF_000307265.1:WP_040660251.1 Length = 395 Score = 390 bits (1003), Expect = e-113 Identities = 213/397 (53%), Positives = 272/397 (68%), Gaps = 9/397 (2%) Query: 1 MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60 M+ + I AVRTAIG YG SLK VPA +GA I+EA+ +AG+ V+EVILG V Q+ Sbjct: 1 MENIYIMGAVRTAIGKYGGSLKSVPAHQMGALVIREALTRAGVDGGTVDEVILGEVRQST 60 Query: 61 LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120 N AR A+ +AGLP +P T+N++C S ++ Q I G+ADVI+AGG ENMSR Sbjct: 61 ESSNIARCAALEAGLPETVPGYTVNRLCASAMQAAFCGCQEIWCGEADVIVAGGTENMSR 120 Query: 121 APYLANNARWGYRMGNAK-FVDEMITDGLWDA-FNDYHMGI----TAENIAERWNISREE 174 AP NARWG GN VD I G A + Y G+ TAEN+AER+ ISREE Sbjct: 121 APVYVRNARWG---GNKMAMVDSNIEAGSTAAPASVYGSGLSMTKTAENVAERFGISREE 177 Query: 175 QDEFALASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPA 234 QD FA SQ++A AI++G FK EIVPV I +K + DTDE PR G+T+E LA LK Sbjct: 178 QDAFAAESQRRALAAIEAGYFKKEIVPVEITEKKRSFIFDTDEFPRPGTTMEVLAGLKSI 237 Query: 235 FKKDGTVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFY 294 K GTVTAGN+ GLND AA LV+MS K KE G+KPLA+IV ++ +DP IMGYGP + Sbjct: 238 VKPGGTVTAGNSCGLNDGAAALVLMSERKVKETGLKPLARIVGMTASALDPTIMGYGPVF 297 Query: 295 ATKAAIEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASG 354 AT+ +E+ G +++LDLIE NEAFA+QS+A +DL D KVN+NGGAIALGHP+G +G Sbjct: 298 ATRKLLERTGMQIEQLDLIELNEAFASQSVACVRDLGLDPAKVNINGGAIALGHPLGCTG 357 Query: 355 ARILVTLVHAMQKRDAKKGLATLCIGGGQGTAILLEK 391 AR++VTL+H +Q+ + GLATLCIGGGQG A ++EK Sbjct: 358 ARLIVTLLHNLQRTGGRFGLATLCIGGGQGMATIIEK 394 Lambda K H 0.315 0.132 0.375 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: 483 Number of extensions: 19 Number of successful extensions: 2 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: 392 Length of database: 395 Length adjustment: 31 Effective length of query: 361 Effective length of database: 364 Effective search space: 131404 Effective search space used: 131404 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