Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate RR42_RS31890 RR42_RS31890 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Cup4G11:RR42_RS31890 Length = 400 Score = 456 bits (1172), Expect = e-133 Identities = 232/400 (58%), Positives = 290/400 (72%), Gaps = 6/400 (1%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M EAVIV+ ARTPIGKA+RGA N TE L H + V+RAGIDP EV+DV++GAA QQ Sbjct: 1 MREAVIVAVARTPIGKAFRGAFNDTEAPALGAHVVRAVVERAGIDPAEVDDVLIGAAAQQ 60 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G G N+ R + AGLP + G T+DR C+SGL IA AA+S++ +I V GG ESI Sbjct: 61 GTQGYNLGRLCAVAAGLPDSVPGMTMDRMCSSGLMTIATAAKSIICGEADIVVAGGAESI 120 Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAA 180 SL QN N + A A+ A + D YMAM++TAE VA+RYGI+R QDEY+L SQ+RTA Sbjct: 121 SLTQNKHKNAYRAQSEAVLARQPDAYMAMIETAEVVAQRYGIARAAQDEYALRSQQRTAE 180 Query: 181 AQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRG-- 238 AQ+ G F+DEI P+ T+ + DKA ++ + L+ DE RP+T+A+ LA LK V Sbjct: 181 AQRQGLFDDEIVPLETRRALFDKAGALTGYETVRLALDECNRPDTSADSLAALKPVWSGG 240 Query: 239 ----EGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGP 294 +G ITAGNASQLSDGA+A ++MS + A +GL+PLG +RGM GC DEMGIGP Sbjct: 241 RTVPQGLHITAGNASQLSDGAAAVLLMSGEQAERRGLRPLGRYRGMAVAGCAADEMGIGP 300 Query: 295 VFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGM 354 VFAVPRLL RHGL+V D+GLWELNEAFA QVLYCRD LGI +LNVNGGAI++GHP+GM Sbjct: 301 VFAVPRLLARHGLTVKDVGLWELNEAFACQVLYCRDTLGIPDARLNVNGGAIAIGHPFGM 360 Query: 355 SGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 SGAR+ HAL+E RRR A +AVVTMCVGGGMG+A LF+++ Sbjct: 361 SGARMTAHALLEARRRGAAHAVVTMCVGGGMGAAALFDVL 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: 481 Number of extensions: 21 Number of successful extensions: 2 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