Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate AO353_01065 AO353_01065 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__pseudo3_N2E3:AO353_01065 Length = 392 Score = 248 bits (633), Expect = 2e-70 Identities = 153/398 (38%), Positives = 227/398 (57%), Gaps = 25/398 (6%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M E VIV+ RT IG +++GAL+A L I +++ GID ++++V++G + Sbjct: 1 MNEVVIVAATRTAIG-SFQGALSAIPATELGAAVIRRLLEQTGIDAAQIDEVILGQVLTA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 GA G N AR+ ++AGLP TT T+++ C SGL+A+ LA +++ E+ + GG E++ Sbjct: 60 GA-GQNPARQTAIKAGLPHTTPALTLNKVCGSGLKAVHLAVQAIRCGDAELVIAGGQENM 118 Query: 121 SLVQ------NDKMNTFHA------VDPALEAIKGDVYMAMLDTAETVAKRYGISRERQD 168 SL + HA + L D +M + TAE +A++Y ISRE QD Sbjct: 119 SLAPYVLPKARTGLRMGHAQLQDSMIQDGLWDAFNDYHMGI--TAENLAQKYEISREAQD 176 Query: 169 EYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAE 228 ++ SQ++ AAA +GG+F EI PI ++ + G + + DE PR ++TA+ Sbjct: 177 TFAAASQQKAAAAIEGGRFQSEITPI-----LIPQRKG----EPLVFDTDEQPRIDSTAQ 227 Query: 229 GLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPD 288 LA LK + ++TAGNAS L+DGA+ ++ S A A GL L + S G +P Sbjct: 228 ALAKLKPAFQKDGSVTAGNASTLNDGAAVLLLASAAKAQALGLPVLARIKAYASAGVDPS 287 Query: 289 EMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISV 348 MGIGPV A L++ G +V+D+ L E NEAFA Q L +LG D K+NVNGGAI++ Sbjct: 288 IMGIGPVPATRLTLQKAGWNVEDLDLIEANEAFAAQALAVGKELGWDTSKVNVNGGAIAL 347 Query: 349 GHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMG 386 GHP G SGAR+ + E RR K + T+C+GGG G Sbjct: 348 GHPIGASGARILVSLVHELIRRDGKKGLATLCIGGGQG 385 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: 393 Number of extensions: 17 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: 392 Length adjustment: 31 Effective length of query: 364 Effective length of database: 361 Effective search space: 131404 Effective search space used: 131404 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