Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_057508008.1 ABB28_RS07330 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_001431535.1:WP_057508008.1 Length = 391 Score = 212 bits (540), Expect = 1e-59 Identities = 141/404 (34%), Positives = 216/404 (53%), Gaps = 23/404 (5%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M+ VI + RT IG ++ G N TL AI A++ +G+ +V +V+MG + Sbjct: 1 MSNIVIAAAKRTAIG-SFLGQFNGVPTPTLGATAIAAALEASGVPASDVTEVIMGCVLPA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G AR+A + GLP++T TT+++ C SG++AI L + I V GG ES+ Sbjct: 60 NL-GQAPARQAAIAGGLPLSTGATTLNKVCGSGMKAIMLGHDLIKAGSASIVVAGGMESM 118 Query: 121 S----LVQN----DKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEY 170 S L+ N ++ F AVD + Y AM + AE +Y SRE QD Y Sbjct: 119 SNAPHLLPNSRTGNRFGNFQAVDHMAHDGLVNAYDGKAMGEFAECAVDKYQFSREEQDAY 178 Query: 171 SLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230 ++ES +R AAQ G F DEI + A ++ +S DE P A+ Sbjct: 179 AIESVKRAQAAQASGAFADEIVAVKV----------ASRKGEVEISIDEQPTRADIAKIP 228 Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290 A + +G ++TA ++S +SDGA+A V++S++ A A+GL+PL ++ EP+ Sbjct: 229 TLRPAFKKDG-SVTAASSSSISDGAAAVVLLSEEDAQARGLQPLARIVAHATHSQEPEWF 287 Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350 P+ A+ +LL + G ++ D+ L+E+NEAFAV + +LGI +KLNVNGGA ++GH Sbjct: 288 TTAPIGAIHKLLDKAGWTLADVDLFEVNEAFAVVAMAPMRELGIAHDKLNVNGGACALGH 347 Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 P G SGARL + R R K + T+C+GGG +A E++ Sbjct: 348 PIGASGARLVVTLVHALRSRGGKRGIATLCIGGGEATAIAIELI 391 Lambda K H 0.316 0.134 0.378 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: 392 Number of extensions: 21 Number of successful extensions: 3 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: 395 Length of database: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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