Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_011428057.1 RHE_RS25075 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000092045.1:WP_011428057.1 Length = 401 Score = 238 bits (608), Expect = 2e-67 Identities = 156/414 (37%), Positives = 226/414 (54%), Gaps = 33/414 (7%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAG-IDPKEVEDVVMGAAMQ 59 MTEA I RTPIG+ + G+L+ L ++ ++R G +D V+DV+ G A Q Sbjct: 1 MTEAFICDYIRTPIGR-FAGSLSGVRADDLGAIPLKALMERNGAVDWDAVDDVIFGCANQ 59 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G N+AR ++L AGLPV GTTI+R C SG+ A+ AAR++ E+ + GG ES Sbjct: 60 AGEDNRNVARMSVLLAGLPVAVPGTTINRLCGSGMDAVITAARAIRAGEAELMIAGGVES 119 Query: 120 ISLVQ----------------NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGIS 163 +S +D + ++P ++ G +M +T E VA+ Y +S Sbjct: 120 MSRAPFVMPKAETAFSRTAEIHDTTIGWRFINPVMKKQYG--VDSMPETGENVAEDYHVS 177 Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223 RE QD +++ SQ + AAAQ G+ EI P++ D + + +DE PR Sbjct: 178 REDQDAFAVRSQAKAAAAQASGRLAKEITPVTIPQRKGDP---------VVVDRDEHPRA 228 Query: 224 ETTAEGLAGLKA-VRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVS 282 TT E LA L + EG T+TAGNAS ++DGA+A ++ S+ A GL P+ G S Sbjct: 229 -TTMEALAKLATPFKKEGGTVTAGNASGVNDGAAALIVASEAAARKYGLTPIARILGGAS 287 Query: 283 YGCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLN 340 P MG+GP+ A +L+ R G++ + + ELNEAFA Q L LGI D +++N Sbjct: 288 AAVPPRVMGVGPIPASRKLMARLGMNQEQFDVIELNEAFASQGLAVLRALGIADDDQRVN 347 Query: 341 VNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 NGGAI++GHP GMSGAR+ G A +E + KY++ TMC+G G G A E V Sbjct: 348 RNGGAIALGHPLGMSGARITGTAALELAEARGKYSLSTMCIGVGQGIAIALERV 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: 422 Number of extensions: 25 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 Apr 09 2024. 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