Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_035235994.1 Q366_RS02505 acetyl-CoA C-acetyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_000745975.1:WP_035235994.1 Length = 428 Score = 310 bits (793), Expect = 7e-89 Identities = 180/437 (41%), Positives = 258/437 (59%), Gaps = 47/437 (10%) Query: 1 MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQR-------------------- 40 M +A I +RT +G +GG+LK V +LG +K +++R Sbjct: 1 MQEAVIVSGVRTSVGTFGGSLKSVPVVELGTYVMKDVLKRAGLKPAQDPGNDEFSPATLK 60 Query: 41 --------NPGVDWRA------VDDVIYGCANQAGEDNRNVARMSALLAGLPADAPGATI 86 N G D+ VD+VI G QAG+ +N AR + + AG+ P T+ Sbjct: 61 DQGMIDIENSGYDYGDDLTDIYVDEVIMGNVLQAGQ-GQNTARQAMIGAGISRTTPAMTV 119 Query: 87 NRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPFVMGKAA----SAFTRQAEIHD 142 N++CGSG+ A+ A+AI AG+AQ+++AGG ESM+ AP + KA T Q +HD Sbjct: 120 NKICGSGLKAIALGAQAILAGQAQVVLAGGQESMSNAPMALLKARWGHRMELTGQGPVHD 179 Query: 143 TTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFALASQQKAARAQRDGTLA 202 + + L + YG M +TAEN+ E++GI+R +QD AL S +A A DGT Sbjct: 180 LMV----YDGLYEIFYGYH-MGQTAENIVEKYGITRQEQDELALLSHTRALGAVHDGTFD 234 Query: 203 QEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDGTVTAGNASGVNDGACAL 262 QEIV V I +KGD + V DE P ETS+E LA+L+ R DG+VTAGNASG+NDGA A+ Sbjct: 235 QEIVPVVIKNRKGDIV-VNKDERPMETSMEKLAKLRPAFRKDGSVTAGNASGINDGAAAV 293 Query: 263 LIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKLLRQLGMTLDQLDVIELN 322 L+ + Q A++ GL A V G A+ G++P MG+GP PA +++L+Q GM L +D+IELN Sbjct: 294 LMMTAQRAKELGLEVLATVKGFASGGLDPAYMGLGPVPAVKRVLKQTGMALSDIDMIELN 353 Query: 323 EAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARLVTTALHQLERSNGRFAL 382 EAFA+Q + +R L + D R N G I+LGHP+G +GAR + TA+HQ++R L Sbjct: 354 EAFAAQAIGCMRELDI--DVERPNELGSGISLGHPIGCTGARQMVTAIHQMQRKGYNTGL 411 Query: 383 CTMCIGVGQGIALVIER 399 +MCIG G G+A+++ER Sbjct: 412 ISMCIGGGMGMAMIVER 428 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: 447 Number of extensions: 14 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 400 Length of database: 428 Length adjustment: 31 Effective length of query: 369 Effective length of database: 397 Effective search space: 146493 Effective search space used: 146493 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