Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_097068496.1 CRO22_RS02395 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_900217815.1:WP_097068496.1 Length = 391 Score = 251 bits (640), Expect = 3e-71 Identities = 155/401 (38%), Positives = 218/401 (54%), Gaps = 21/401 (5%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 MT VIVS ART +G ++ GA T L IE V RAGID EV + ++G + Sbjct: 1 MTNVVIVSAARTAVG-SFNGAFANTPAHDLGAAVIEAVVARAGIDKAEVSETILGQVLSA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G G N AR+A ++AGLP+ +A I++ C SGL+ +AL A+ + +I V GG ES+ Sbjct: 60 GQ-GQNPARQAHIKAGLPIESAAWGINQVCGSGLRTVALGAQHIQLGDADIVVAGGQESM 118 Query: 121 SLVQN-------DKMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYS 171 SL + KM +D ++ D + M TAE VA ++ ISRE QD + Sbjct: 119 SLSPHVAHLRAGTKMGDMKMIDSMIKDGLWDAFNGYHMGQTAENVAAQWQISREMQDALA 178 Query: 172 LESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLA 231 L SQ + AAQ+ GKF DEI P + K DI + DE R T E + Sbjct: 179 LASQNKAEAAQKAGKFTDEIVPFTVK----------TRKGDIVVDADEYIRHGATLESMQ 228 Query: 232 GLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMG 291 LK + T+TAGNAS ++DGA+ ++M+++ AA +GL P+ + G +P MG Sbjct: 229 KLKPAFIKDGTVTAGNASGINDGAAVVLLMTEEEAAKRGLTPMARIASWATAGLDPSIMG 288 Query: 292 IGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHP 351 GP+ A + L++ G + D+ L E NEAFA Q +G D K+NVNGGAI++GHP Sbjct: 289 CGPIPASRKALEKAGWTAADLDLIEANEAFAAQACAVNKDMGWDTAKVNVNGGAIAIGHP 348 Query: 352 YGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 G SG R+ + E +R AK + T+C+GGGMG A E Sbjct: 349 IGASGCRILNTLVFEMKRSGAKKGLATLCIGGGMGVAMCLE 389 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: 387 Number of extensions: 17 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: 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