Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Ac3H11_178 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_178 Length = 394 Score = 228 bits (582), Expect = 2e-64 Identities = 144/400 (36%), Positives = 209/400 (52%), Gaps = 21/400 (5%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGA 62 E V+VS RT IG + G+L L ++ ++ RA ++ K+V VV G + Sbjct: 4 EVVVVSAVRTAIG-TFGGSLKDIAPTDLGALVVKESLARASVEGKDVGHVVFGHVVNTEP 62 Query: 63 TGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGE---- 118 ++R A + G T ++R C SGLQAI AA+++ ++ +G G E Sbjct: 63 KDMYLSRVAAINGGCAEGTPAFNVNRLCGSGLQAIVSAAQAIQLGDADVTIGAGAEVMSR 122 Query: 119 ----SISLVQNDKMNTFHAVDPALEAIKGDVYMAMLD-TAETVAKRYGISRERQDEYSLE 173 S+++ +M VD + A+ + + TAE +A ++GISRE QD+ ++E Sbjct: 123 APFASLNMRWGARMGDTKMVDMMIGALHDPFHTIHMGVTAENIAAKWGISREDQDKLAVE 182 Query: 174 SQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGL 233 S R A G F D+I P++ K D+ + DE RP T + A L Sbjct: 183 SHNRAERATAAGYFKDQIVPVTLKS----------KKGDVQYATDEHFRPGATLDDFAKL 232 Query: 234 KAVR-GEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGI 292 K V E T+TAGNAS ++D A+A V+M A A+G KPL G +P MGI Sbjct: 233 KPVFVKENGTVTAGNASGINDAAAAVVLMDAAAAKARGAKPLARLVAYAHAGVDPKYMGI 292 Query: 293 GPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPY 352 GPV A LK+ GL+V D+ + E NEAFA Q LG+DP K+N NG IS+GHP Sbjct: 293 GPVPATQLALKKAGLTVADLDVIEANEAFAAQACAVTKDLGLDPAKVNPNGSGISLGHPI 352 Query: 353 GMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 G +GA + A+ E +R + +YA+VTMC+GGG G A +FE Sbjct: 353 GATGALITVKAIHELQRVQGRYALVTMCIGGGQGIAAIFE 392 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: 425 Number of extensions: 19 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 395 Length of database: 394 Length adjustment: 31 Effective length of query: 364 Effective length of database: 363 Effective search space: 132132 Effective search space used: 132132 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