Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate BWI76_RS23445 BWI76_RS23445 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Koxy:BWI76_RS23445 Length = 391 Score = 242 bits (618), Expect = 1e-68 Identities = 143/398 (35%), Positives = 222/398 (55%), Gaps = 22/398 (5%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M + VIV RTPIG ++G L+ L ++ V+R+G+DP+ +++V++G + Sbjct: 1 MKDVVIVGALRTPIG-CFQGTLSRHSAVELGSVVVKALVERSGVDPQSIDEVILGQVLTA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G TG N AR++ +R GLP T + TI+ C SGL+A+ LA +++ ++ + GG E++ Sbjct: 60 G-TGQNPARQSAIRGGLPNTVSAITINDVCGSGLKALHLATQAIQCGEADVVIAGGQENM 118 Query: 121 SLVQN--------DKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEY 170 S + ++ +D + D + M TAE +A+ YGISRE QD + Sbjct: 119 SRAPHVLTDSRTGAQLGNSQLIDSLVHDGLWDAFNDYHMGVTAENLAREYGISRELQDAW 178 Query: 171 SLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230 +L SQ + A G+F DEI P+++++ + + + DE PR + +AE L Sbjct: 179 ALSSQHKARRAIDSGRFRDEIVPVTSELNGIPRL----------VDTDEQPRVDPSAEAL 228 Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290 A L + ++TAGNAS ++DGA+A ++MS+ A A GL L R S G +P M Sbjct: 229 ASLLPTFDQQGSVTAGNASSINDGAAAVMMMSETKAEALGLPILARIRAFASVGVDPALM 288 Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350 GI PV A R L+R G +D++ L E NEAFA Q + L D ++NVNGGAI++GH Sbjct: 289 GIAPVHATRRCLERAGWKLDEVDLIEANEAFAAQAISVGRVLEWDERRVNVNGGAIALGH 348 Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 P G SG R+ + E +R A+ + T+C+GGG G A Sbjct: 349 PIGASGCRILVSLVHEMIKRDARKGLATLCIGGGQGVA 386 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: 18 Number of successful extensions: 5 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: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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