Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate CA265_RS06590 CA265_RS06590 acetyl-CoA acetyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >FitnessBrowser__Pedo557:CA265_RS06590 Length = 391 Score = 245 bits (625), Expect = 2e-69 Identities = 151/401 (37%), Positives = 223/401 (55%), Gaps = 11/401 (2%) Query: 1 MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQA 60 M + I A+RTPIG +GG+L A LG IKA I++ G+ + +V G A Sbjct: 1 MKEVVIVSAVRTPIGSFGGSLAQFSATQLGGFAIKAAIEK-AGLKPEQIQEVYMGNVLSA 59 Query: 61 GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120 + A +A AGLP D P TIN++C SG A+ AA++I G+ ++++AGG+ESM Sbjct: 60 NL-GQAPATQAAKFAGLP-DLPATTINKVCASGTKAIMLAAQSIANGDNEIIVAGGMESM 117 Query: 121 TRAPFVMGKAASAFTR-QAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRA 179 + P+ + KA + + +I D V + Y M AE A + I+R Sbjct: 118 SNVPYYLDKARNGYRLGHGQITDG-----LVKDGLWDVYNDYHMGSAAELCATECNINRE 172 Query: 180 DQDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKG 239 QD FA++S ++A AQ G A EIV +E+ +KGD V D+ P + + LK Sbjct: 173 AQDNFAISSYKRAQAAQTSGKFANEIVAIEVKDRKGDITLVDTDDEPTAVKFDKIPSLKP 232 Query: 240 VVRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPA 299 V + DGTVTA NAS +NDGA AL++ S A++ GL A+++G A A P P+ Sbjct: 233 VFKKDGTVTAANASTLNDGAAALVLMSADKAKELGLTPLAKILGYADAQQAPEWFTTAPS 292 Query: 300 PATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLG 359 A L + + ++ +D E+NEAFA +A ++L L D+ +VN NGGA++LGHPLG Sbjct: 293 KAIPLALHKANVNINDVDFFEINEAFAVVSIANNQLLALNDN--QVNVNGGAVSLGHPLG 350 Query: 360 ASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 ASGAR+V T L L +++G+ + +C G G ALVI +L Sbjct: 351 ASGARIVVTLLSVLAQNDGKIGVAGICNGGGGASALVIGKL 391 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: 361 Number of extensions: 14 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: 400 Length of database: 391 Length adjustment: 31 Effective length of query: 369 Effective length of database: 360 Effective search space: 132840 Effective search space used: 132840 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 17 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