Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate RR42_RS25210 RR42_RS25210 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Cup4G11:RR42_RS25210 Length = 394 Score = 487 bits (1253), Expect = e-142 Identities = 246/394 (62%), Positives = 300/394 (76%), Gaps = 2/394 (0%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M EAVIVSTART IG+AY+G+LN T+ TL+GH I HAV+RAGI +E+EDVV+G +M Sbjct: 1 MREAVIVSTARTGIGRAYKGSLNHTKSPTLMGHVISHAVQRAGIAAEEIEDVVIGTSMPG 60 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G G NI R + L GLPV AG +IDRQCASGL A+A AA+ ++ D +++ V GG ESI Sbjct: 61 GTAGMNIGRLSALAGGLPVNVAGQSIDRQCASGLMAMATAAKQIIVDEMDVVVAGGQESI 120 Query: 121 SLVQNDKMNTF-HAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179 SLVQ+ + A D L YM ML TAE VA+RYGISRE QD Y+ ESQRRTA Sbjct: 121 SLVQDRFVEWMTSAADSELIERVPHAYMPMLQTAELVARRYGISREAQDTYAAESQRRTA 180 Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239 AQ+ G+F EI P T M + D+ TG +SF+D+ L +DEG RP+TT EGLA L+ V + Sbjct: 181 LAQEEGRFAAEIVPFQTSMAIQDRETGEISFRDVLLDRDEGNRPDTTVEGLAKLRTVI-D 239 Query: 240 GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVP 299 G +T GNASQLSDGASA+V+M + A +GL+PLGI+RG+ GC P+EMGIGPVFA+P Sbjct: 240 GGVVTGGNASQLSDGASASVLMDRRLAERRGLQPLGIYRGIAVAGCAPEEMGIGPVFAIP 299 Query: 300 RLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARL 359 +LL+RHGL V DIGLWELNEAFA QVLYCRD+LGIDP++LNVNGG IS+GHPYGM+GARL Sbjct: 300 KLLERHGLKVSDIGLWELNEAFACQVLYCRDRLGIDPDRLNVNGGGISIGHPYGMTGARL 359 Query: 360 AGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEI 393 GHALIEG+RR KY VVTMCVGGGMG+AGLFE+ Sbjct: 360 VGHALIEGKRRGEKYVVVTMCVGGGMGAAGLFEV 393 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: 517 Number of extensions: 16 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: 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