Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_011765903.1 AZO_RS10980 acetyl-CoA C-acyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_000061505.1:WP_011765903.1 Length = 393 Score = 298 bits (763), Expect = 2e-85 Identities = 169/398 (42%), Positives = 245/398 (61%), Gaps = 9/398 (2%) Query: 3 DAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGE 62 + + A+R+ +G +GG+LKD+ +LG V +K I R GVD + V G Sbjct: 5 EVVVLSAVRSAVGGFGGSLKDMEPAELGGVVVKEAISR-AGVDPKQVTFATVGNCIPTES 63 Query: 63 DNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTR 122 VAR++ + G+ ++ +NRLCGS A+ +A+AI G+A + GGVE M+R Sbjct: 64 RYPYVARVATIQGGMSMESVAFAVNRLCGSAQQAIVNSAQAILLGDADYAVGGGVEVMSR 123 Query: 123 APFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQD 182 ++M A A + DT V ++ +GV M TAEN+A ++GISR +QD Sbjct: 124 GAYLM----PALRNGARMGDTKAIDAMV-AVLTDPFGVGHMGITAENLAAKWGISREEQD 178 Query: 183 AFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVR 242 AFAL SQ++AA A DG +IV + +KG + T DEHPR T++E+LA++K + Sbjct: 179 AFALESQRRAAEAIADGRFKGQIVPITFETRKGPVVFDT-DEHPRATTMEALAKMKPAFK 237 Query: 243 PDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPAT 302 DG+VTAGNASG+ND A L++A A G + AR+V A AGV +MG GP P++ Sbjct: 238 KDGSVTAGNASGINDAAAFLVLADAAKASAAGHKPMARLVSYAIAGVPNDLMGEGPIPSS 297 Query: 303 QKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASG 362 + L++ G+TLD++D+IE NEAFA+Q L V + GL D + NPNGGAIALGHP+GA+G Sbjct: 298 KLALQRAGLTLDKIDLIESNEAFAAQSLTVAK--GLELDPAKTNPNGGAIALGHPVGATG 355 Query: 363 ARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 A ++T LH+L+R+ GR+ + TMCIG GQGI + ER+ Sbjct: 356 AVIITKLLHELQRTGGRYGMATMCIGGGQGITTIWERI 393 Lambda K H 0.319 0.134 0.386 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: 406 Number of extensions: 18 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: 400 Length of database: 393 Length adjustment: 31 Effective length of query: 369 Effective length of database: 362 Effective search space: 133578 Effective search space used: 133578 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