Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate 16332 b2224 acetyl-CoA acetyltransferase (NCBI)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Keio:16332 Length = 394 Score = 261 bits (668), Expect = 2e-74 Identities = 168/403 (41%), Positives = 230/403 (57%), Gaps = 23/403 (5%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M VIVS RT IG ++ G+L +T L I+ A++RA ID + V++V+MG +Q Sbjct: 1 MKNCVIVSAVRTAIG-SFNGSLASTSAIDLGATVIKAAIERAKIDSQHVDEVIMGNVLQA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G G N AR+ALL++GL T G T+++ C SGL+++ALAA+++ + V GG E++ Sbjct: 60 GL-GQNPARQALLKSGLAETVCGFTVNKVCGSGLKSVALAAQAIQAGQAQSIVAGGMENM 118 Query: 121 SLVQ---NDKMNTFHAVDPA--LEAIKGDVYMA------MLDTAETVAKRYGISRERQDE 169 SL + K + + + + I D M M TAE VAK YGI+RE QDE Sbjct: 119 SLAPYLLDAKARSGYRLGDGQVYDVILRDGLMCATHGYHMGITAENVAKEYGITREMQDE 178 Query: 170 YSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEG 229 +L SQR+ AAA + G F EI P++ VV + K SQDE P+ +TAE Sbjct: 179 LALHSQRKAAAAIESGAFTAEIVPVN----VVTRK------KTFVFSQDEFPKANSTAEA 228 Query: 230 LAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDE 289 L L+ + T+TAGNAS ++DGA+A VIM + A A GL PL + S G P Sbjct: 229 LGALRPAFDKAGTVTAGNASGINDGAAALVIMEESAALAAGLTPLARIKSYASGGVPPAL 288 Query: 290 MGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVG 349 MG+GPV A + L+ GL + DI L E NEAFA Q L LG D EK+NVNGGAI++G Sbjct: 289 MGMGPVPATQKALQLAGLQLADIDLIEANEAFAAQFLAVGKNLGFDSEKVNVNGGAIALG 348 Query: 350 HPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 HP G SGAR+ L + R + T+C+GGG G A + E Sbjct: 349 HPIGASGARILVTLLHAMQARDKTLGLATLCIGGGQGIAMVIE 391 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: 417 Number of extensions: 23 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