Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate SMc00966 SMc00966 acetyl-COA acyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Smeli:SMc00966 Length = 397 Score = 226 bits (576), Expect = 9e-64 Identities = 158/399 (39%), Positives = 217/399 (54%), Gaps = 34/399 (8%) Query: 5 VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATG 64 V+++ RTP+G+ G+L A E A L IE + GID E++DV++G A + Sbjct: 12 VVIAALRTPVGRV-NGSLAAVEPARLAALLIERIIADTGIDRAEIDDVLVGNAAN---SA 67 Query: 65 GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS--- 121 GN+AR A L AGLPV G T+DRQC SGL+AI LAAR + + GG ES S Sbjct: 68 GNLARLAALEAGLPVAIPGVTVDRQCGSGLEAIVLAARQIQAGAGRFYLAGGTESASRAH 127 Query: 122 ------LVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQ 175 L + ++ A ++I GD M + AE VA GISRERQD ++LES Sbjct: 128 IRLRPPLTRGEEPQPVKRARMAPDSI-GDPDMGV--AAENVATACGISRERQDRFALESH 184 Query: 176 RRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKA 235 RR AA+ G+F+ EI P+ T G +++DE PR +AE L+ L+ Sbjct: 185 RRAVAAEAEGRFSREIVPVPTPEG--------------PIARDECPRANASAETLSRLRP 230 Query: 236 VRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGI-FRGMVSYGCEPDEMGIGP 294 V G T+TAGNA ++DGA A V+M++ A K G+ F + G EP +G+GP Sbjct: 231 VFVAGGTVTAGNACPVNDGA-AMVLMTNLAEARKLGTRFGLAFTDAATAGVEPKLLGLGP 289 Query: 295 VFAVPRLLKRH-GLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYG 353 V A+ +L R+ L V + E NEAFA QVL D+L I PE++N +GGAI++GHPYG Sbjct: 290 VPAMAKLRARNPALDVARVDFIEFNEAFASQVLGSLDQLDIAPERVNRDGGAIALGHPYG 349 Query: 354 MSGARLAGHALIEGRRRKA-KYAVVTMCVGGGMGSAGLF 391 SGA L + + + M +GGGMG A F Sbjct: 350 ASGAILVVRLFSQMLAASSPAEGLAMMGIGGGMGIAAHF 388 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: 433 Number of extensions: 23 Number of successful extensions: 5 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: 397 Length adjustment: 31 Effective length of query: 364 Effective length of database: 366 Effective search space: 133224 Effective search space used: 133224 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 17 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