Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate BWI76_RS13135 BWI76_RS13135 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Koxy:BWI76_RS13135 Length = 401 Score = 258 bits (659), Expect = 2e-73 Identities = 171/413 (41%), Positives = 233/413 (56%), Gaps = 31/413 (7%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59 M +A I RTPIG+ Y GAL + L + + R DP ++DV++G A Q Sbjct: 1 MRDAFICDGIRTPIGR-YGGALASMRADDLAAIPLRELLSRNPKFDPASIDDVILGCANQ 59 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G N+A A L AG P T GTT++R C SGL AI AAR++ ++ + GG ES Sbjct: 60 AGEDNRNVAHMATLLAGYPHTVPGTTVNRLCGSGLDAIGFAARAIKAGEADLMIAGGVES 119 Query: 120 ISLV-------------QNDKMNT---FHAVDPALEAIKGDVYMAMLDTAETVAKRYGIS 163 +S Q + +T + V+P ++ G +M +TAE VA+ IS Sbjct: 120 MSRAPFVMGKASAAYQRQAELFDTTIGWRFVNPLMQQRFGTD--SMPETAENVAELLNIS 177 Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223 R QD ++ SQ+R+A AQ+ G EI P+ G GAVS T+ +DE PR Sbjct: 178 RADQDAFAYRSQQRSARAQRDGILAQEIVPVPIIGG-----KGAVS----TVYEDEHPRA 228 Query: 224 ETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSY 283 ETT E L+ LK +G +TAGNAS ++DGA+A +I S + A A+GL P M + Sbjct: 229 ETTLEQLSRLKTPFRKGGVVTAGNASGVNDGAAALIIASSQQAIAQGLTPRARIVAMATA 288 Query: 284 GCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNV 341 G EP MG+GPV AV ++L+R GLS+ D+ L ELNEAFA Q L +LG+ D +N Sbjct: 289 GVEPKLMGLGPVPAVRKVLERAGLSIKDMDLIELNEAFAAQALGVLRQLGLADDAPHVNP 348 Query: 342 NGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 NGGAI++GHP GMSGARLA A +E +RR +YA+ TMC+G G G A + E V Sbjct: 349 NGGAIALGHPLGMSGARLALSASLELQRRSGRYALCTMCIGVGQGIAMILERV 401 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: 405 Number of extensions: 27 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: 401 Length adjustment: 31 Effective length of query: 364 Effective length of database: 370 Effective search space: 134680 Effective search space used: 134680 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