Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_004299880.1 C665_RS03170 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000310185.1:WP_004299880.1 Length = 401 Score = 258 bits (658), Expect = 3e-73 Identities = 167/411 (40%), Positives = 225/411 (54%), Gaps = 27/411 (6%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59 MT+A I RTPIG+ Y G L + L ++ + R +D VED++ G A Q Sbjct: 1 MTQAFICDAIRTPIGR-YGGTLASVRADDLGAVPLKALMTRNPQVDWTAVEDIIYGCANQ 59 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G N+AR + L AGLP+ GTT++R C SG+ AI LAARS+ E+ + GG ES Sbjct: 60 AGEDNRNVARMSGLLAGLPIEVPGTTVNRLCGSGMDAIGLAARSIKSGETELMIAGGVES 119 Query: 120 IS---LVQNDKMNTFHAVDPALEAIKGDVYM-----------AMLDTAETVAKRYGISRE 165 +S V + F + G ++ +M TA+ VA + ISR Sbjct: 120 MSRAPFVMGKAESAFSRSAAIYDTTIGWRFINPLMKKLYETHSMPQTADNVAADFDISRA 179 Query: 166 RQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPET 225 QD ++L SQ+R AAA G+F DE+ P+ V+ + G I DE PRPET Sbjct: 180 DQDAFALRSQQRWAAAHAAGRFKDELVPV-----VIPRKKG----DPIVFDTDEHPRPET 230 Query: 226 TAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGC 285 T E LA LK V G ++TAGNAS ++DGA A ++ SD AA GL P M + G Sbjct: 231 TLEMLAKLKGVNGPELSVTAGNASGVNDGACALLLASDAAAAKHGLTPRARVVAMATAGV 290 Query: 286 EPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNVNG 343 P MG GP AV ++L + GL++D + + ELNEAFA Q L LG+ D E++N NG Sbjct: 291 APRIMGFGPAPAVRKVLAKAGLTLDQMDVIELNEAFAAQGLAVLRDLGLADDEERVNPNG 350 Query: 344 GAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 GAI++GHP GMSGARL A E +RR +YA+ TMC+G G G A + E V Sbjct: 351 GAIALGHPLGMSGARLVTTAAYELQRRNGRYALCTMCIGVGQGIAMIIERV 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: 382 Number of extensions: 19 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: 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 24 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