Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate 3610436 Dshi_3817 beta-ketoadipyl CoA thiolase (RefSeq)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Dino:3610436 Length = 400 Score = 261 bits (667), Expect = 2e-74 Identities = 172/411 (41%), Positives = 226/411 (54%), Gaps = 31/411 (7%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQQG 61 +AVI RTPIG+ Y GAL++ L I + R G+D V++V+ GAA Q G Sbjct: 2 DAVICDGVRTPIGR-YGGALSSVRADDLAALPIAALMARNPGVDWARVDEVIYGAANQAG 60 Query: 62 ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121 N+AR A L AGLP G T++R CASG+ A+ AAR + ++A+ GG ES+S Sbjct: 61 EDNRNVARMAALLAGLPEEVPGLTVNRLCASGMDAVGAAARGIKAGEYDLAIAGGIESMS 120 Query: 122 LVQ----------------NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRE 165 +D + V+P + A+ G M TA+TVA Y ISR Sbjct: 121 RAPFVMPKAESAFTRAATVHDTTIGWRFVNPKIAAMHG--IDTMPQTADTVAAAYEISRA 178 Query: 166 RQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPET 225 QD ++ SQ R AAA G F DEI P+ I + +DE PRP T Sbjct: 179 DQDAFAARSQARWAAADAAGLFADEIVPVPVPQR---------GSAPILVDRDEHPRPGT 229 Query: 226 TAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGC 285 A LAGLK + G G ++TAGNAS ++DGA+A +I S A A GL P+ GM S G Sbjct: 230 DAARLAGLKGINGPGLSVTAGNASGVNDGAAALLIASAAAARAHGLTPMARVVGMASAGV 289 Query: 286 EPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNVNG 343 P MGIGPV A +LL R GL++D + + ELNEAFA Q L +LG+ D ++N NG Sbjct: 290 APRVMGIGPVPASRKLLDRAGLTLDQMDVIELNEAFASQSLATLRQLGLADDDVRVNPNG 349 Query: 344 GAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 GAI++GHP GMSGARL A + RR +YA+ TMCVG G G+A + E V Sbjct: 350 GAIAMGHPLGMSGARLVLTAAHQLRRTGGRYALCTMCVGVGQGTALILERV 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: 438 Number of extensions: 32 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: 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