Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_068168283.1 HTA01S_RS06660 acetyl-CoA C-acetyltransferase
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_001592305.1:WP_068168283.1 Length = 392 Score = 282 bits (722), Expect = 1e-80 Identities = 170/399 (42%), Positives = 239/399 (59%), Gaps = 10/399 (2%) Query: 2 EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61 + +I A RT G++GG+L A +L + I+ L+ R G+ V +++ G AG Sbjct: 3 DIVIVSAARTAVGKFGGSLAKTPATELGSIVIKELLART-GLPVDAVGEVIMGQVLAAG- 60 Query: 62 DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121 +N AR A + AG+ P T+N +CGS L AV +AA+A+ G+ +++IAGG E+M+ Sbjct: 61 CGQNPARQAMMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSEIVIAGGQENMSA 120 Query: 122 APFVM-GKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180 +P V+ G + + DT I V+ L Y M TAENVA I R Q Sbjct: 121 SPHVLNGSRDGQRMGDWKMTDTMI----VDGLWDV-YNQYHMGITAENVAKAQGITREMQ 175 Query: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240 DA A SQQ+ AAAQAAG F EI ++IPQ+KGDP++ +DE TT LA L+ Sbjct: 176 DALAAGSQQKAAAAQAAGKFKDEIVGVSIPQRKGDPVLFNSDEFINAKTTAEVLAGLRPA 235 Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300 G+VTAGNASG+NDGA A+++ + K A L P AR+ T+G+ P +MG GP P Sbjct: 236 FDKSGSVTAGNASGINDGAAAVMVMTAKKAAALGLTPLARIAAFGTSGLDPALMGMGPVP 295 Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360 A +K LA+ G + +DV ELNEAFAAQ AV ++ L D A VN NGGAIAIGHP+GA Sbjct: 296 ASQKALARAGWKASDVDVFELNEAFAAQACAV--NMALDIDPAKVNVNGGAIAIGHPIGA 353 Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIER 399 SG R++ T +++++R G + L +CIG G G++L +ER Sbjct: 354 SGCRILVTLLHEMQRRGAKKGLAALCIGGGMGVSLAVER 392 Lambda K H 0.320 0.135 0.394 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: 403 Number of extensions: 13 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: 401 Length of database: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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