Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_013451474.1 CALNI_RS06825 acetyl-CoA C-acyltransferase
Query= BRENDA::P45359 (392 letters) >NCBI__GCF_000183405.1:WP_013451474.1 Length = 392 Score = 372 bits (955), Expect = e-107 Identities = 190/391 (48%), Positives = 260/391 (66%), Gaps = 1/391 (0%) Query: 1 MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60 MK V + +RT GS+G +L D+PA +L + IKE +K + + NEVI+G V+Q G Sbjct: 1 MKNVYLIDGIRTPFGSFGGALSDIPAPELASILIKELQQKYNLPSDAANEVIIGQVIQGG 60 Query: 61 LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120 Q PARQA AGL + AMT+NKVCGSGL++V LA Q I GD+ ++ AGGMENMS Sbjct: 61 SRQAPARQAMRLAGLSDSVHAMTVNKVCGSGLKSVMLATQSILLGDSSLVYAGGMENMSM 120 Query: 121 APYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFAL 180 AP+ + AR+GYRMG++ F D MI D L D ++ HMG E ++ I+REEQD +A+ Sbjct: 121 APFAMDKARFGYRMGHSTFFDLMIYDALQDPYSGKHMGEITEESIKKNGITREEQDNYAI 180 Query: 181 ASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKDGT 240 S A+ AI++G + EI+PV+ K +KGE ++D DE P F I L LKP F KDG+ Sbjct: 181 RSYTLAQSAIENGTIRSEILPVIKKTKKGEQIIDKDEDP-FKGDIAKLESLKPVFAKDGS 239 Query: 241 VTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAAI 300 +TAGNAS +ND AA+ +I + K+ G +P +IV+Y + + P+ G P A + + Sbjct: 240 ITAGNASKINDGAAITLIADDDAVKKYGFQPKIRIVAYSTNSIHPSDFGEAPIGAIEKVV 299 Query: 301 EKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILVT 360 EKA +D++DL E NEAFAA L K LK D+NKVNVNGGA+A GHP+GASGAR+L+T Sbjct: 300 EKAQLNLDQIDLFEINEAFAAVPLMAIKKLKLDINKVNVNGGAVAFGHPVGASGARLLIT 359 Query: 361 LVHAMQKRDAKKGLATLCIGGGQGTAILLEK 391 L M +++ K G+ATLCIGGG+ A+L+EK Sbjct: 360 LAREMIQKNKKYGIATLCIGGGEAVAVLIEK 390 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: 432 Number of extensions: 14 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: 392 Length adjustment: 31 Effective length of query: 361 Effective length of database: 361 Effective search space: 130321 Effective search space used: 130321 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