Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_043827862.1 RSPH17029_RS00115 acetyl-CoA C-acyltransferase family protein
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_000015985.1:WP_043827862.1 Length = 389 Score = 330 bits (847), Expect = 3e-95 Identities = 187/400 (46%), Positives = 256/400 (64%), Gaps = 11/400 (2%) Query: 1 MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQA 60 M+D + A+RT IG +GGAL V DL +A ++R GV+ V V++G Sbjct: 1 MSDILVLSAVRTAIGGFGGALAAVPPGDLATTVTRAALER-AGVEPGRVGHVVFGHVINT 59 Query: 61 GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120 + ++R++A+ AG+P++ P +NRLCGSG+ A+ +A +A+ G+A++ +AGG ESM Sbjct: 60 EPRDMYLSRVAAMQAGIPSEVPAMNVNRLCGSGVQAIVSAMQALMLGDAEVALAGGAESM 119 Query: 121 TRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRAD 180 +RAP+ + A R + T + + +G M TAE VAE+ GISR D Sbjct: 120 SRAPYALTTA-----RWGQKMGDTRALDMMTGALNCPFGTGHMGITAEIVAERHGISRED 174 Query: 181 QDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGV 240 QDAFAL SQ + ARAQ +G +IV VEIA +KG + + DEHP+ T+LE+LA L+ Sbjct: 175 QDAFALESQTRTARAQEEGRFDGQIVPVEIASRKGP-VSFSRDEHPKATTLEALAGLRPA 233 Query: 241 VRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAP 300 + GTVTAGNASG+NDGA AL++A + A G R R++G A AGV+P +MG+GP P Sbjct: 234 FQKGGTVTAGNASGINDGAGALILAREGAVP--GARPLGRLIGYAHAGVDPEVMGLGPIP 291 Query: 301 ATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGA 360 A Q L + G+++ DVIE NEAFA+Q LAV R L D RVNPNGGAIALGHP+GA Sbjct: 292 AVQALCARTGLSVADFDVIESNEAFAAQALAVARALDF--DPARVNPNGGAIALGHPVGA 349 Query: 361 SGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 +GA + ALH+L R+ GR AL TMCIG GQGIAL +ER+ Sbjct: 350 TGAIITVKALHELHRTGGRRALVTMCIGGGQGIALALERV 389 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: 422 Number of extensions: 23 Number of successful extensions: 6 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: 389 Length adjustment: 31 Effective length of query: 369 Effective length of database: 358 Effective search space: 132102 Effective search space used: 132102 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 10 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