Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_041314714.1 HM1_RS04890 acetyl-CoA C-acyltransferase
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_000019165.1:WP_041314714.1 Length = 392 Score = 283 bits (723), Expect = 8e-81 Identities = 168/401 (41%), Positives = 239/401 (59%), Gaps = 19/401 (4%) Query: 2 EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61 E + A+RTPFG++GGA+ +++A DL AA I+ + R GV+ VE + G Q G Sbjct: 3 EVVFVSAVRTPFGKFGGAMASLKAVDLGAAAIQGAL-RQGGVEPEMVEYVTMGQVLQGGA 61 Query: 62 DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121 + +R A LAG+P P TVN++C S + AV +AAR I +GE++ +AGG+ESM++ Sbjct: 62 -GQIPSRQAARLAGIPWETPSLTVNKVCASGMIAVALAARMIAAGEIEAAVAGGMESMSQ 120 Query: 122 APFVM-----GKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQIN 176 AP+ + G+ F + + F N M A +G D +A ++ ++ Sbjct: 121 APYFLPAARWGQRMFNFEAVDLMVHDGLWCPFYNRHM-ALHGAD--------MAREYGVS 171 Query: 177 RADQDAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAK 236 R +QD +ALRSQ+R AAA A G+ A EI P+T+PQKKG P VV+ DE PRP TT LAK Sbjct: 172 REEQDEWALRSQERAAAAIAGGYMAEEIVPVTVPQKKGAPTVVSQDEQPRP-TTREGLAK 230 Query: 237 LKGVVRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGF 296 L + P GT+TAGNA VNDGA ALLL S + A+ ++P A ++G + R + Sbjct: 231 LAPIFDPQGTITAGNAPSVNDGAGALLLMSREKAESLGIRPLATLIGHTEVALEARELAA 290 Query: 297 GPAPAVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGH 356 P A+ ++LA+ G L Q+D+ E+NEAFAA L + G D VN NGGA+A GH Sbjct: 291 APGHAINRLLAKTGKRLDQVDLFEVNEAFAAVVLVSQKVAGF--DLEKVNINGGAVAFGH 348 Query: 357 PLGASGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVI 397 P+GASGAR++ T I+ L R GG + +C G QG AL++ Sbjct: 349 PIGASGARIIATLIHSLRRKGGGIGMAAICSGAAQGDALMV 389 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: 432 Number of extensions: 23 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: 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 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