Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Koxy:BWI76_RS16135 Length = 400 Score = 245 bits (626), Expect = 1e-69 Identities = 160/413 (38%), Positives = 230/413 (55%), Gaps = 32/413 (7%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59 M +A I RTP G+ + G L L ++ ++R G+DP ++DV+ G A Q Sbjct: 1 MNQAFICDAVRTPFGR-FGGTLATLRADDLAALPLKALLERNPGLDPARIDDVIYGCANQ 59 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G N+AR ALL AGLP + G+T++R C S L AI +AAR++ ++ + GG ES Sbjct: 60 AGEDNRNVARMALLLAGLPESVPGSTVNRLCGSSLDAIGIAARAIKSGETQLMIAGGVES 119 Query: 120 IS----------------LVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGIS 163 +S + D + ++P ++A+ G +M +TAE VA + IS Sbjct: 120 MSRAPFVMGKAESAFSRTMRMEDTTIGWRFINPQMKALYG--VDSMPETAENVADDFAIS 177 Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223 R QD ++L SQ RTAAAQ+ G+F DE+ +S V + G + + S+DE PR Sbjct: 178 RADQDAFALRSQLRTAAAQEAGRFADELIAVS-----VPQRKG----EPLLFSRDEHPRT 228 Query: 224 ETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSY 283 TTAE LA L+ V T+TAGNAS ++DGA A ++ S++ AA L+PL G+ + Sbjct: 229 -TTAEALARLRGVVRPDGTVTAGNASGVNDGACALLLASEQALAANDLQPLARVVGVATA 287 Query: 284 GCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNV 341 G P MG GP AV ++L + GL++ + + ELNEAFA Q L LG+ D +N Sbjct: 288 GVAPRIMGFGPAPAVRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDDAAYVNP 347 Query: 342 NGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 NGGAI++GHP G SG RLA A + RR +YA+ TMC+G G G A + E V Sbjct: 348 NGGAIALGHPLGASGGRLAMTAAYQLRRTGGRYALCTMCIGVGQGIALIIERV 400 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: 400 Number of extensions: 21 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: 400 Length adjustment: 31 Effective length of query: 364 Effective length of database: 369 Effective search space: 134316 Effective search space used: 134316 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