Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_011766784.1 AZO_RS15365 3-oxoadipyl-CoA thiolase
Query= SwissProt::P45363 (394 letters) >NCBI__GCF_000061505.1:WP_011766784.1 Length = 402 Score = 326 bits (835), Expect = 8e-94 Identities = 185/403 (45%), Positives = 259/403 (64%), Gaps = 10/403 (2%) Query: 1 MSDTIVIVDAGRTAIGTFGGALSALQATDIGTTVLKALIERT-GIAPEQVSEVILGQVLT 59 M+ T+ + DA RT G +GG LS+++A D+ ++ALI R G+ V +VI G Sbjct: 1 MTHTVYLCDAIRTPFGRYGGLLSSVRADDLAALPIRALIARNPGVDWNLVDDVIYGCANQ 60 Query: 60 AG-CGQNPARQTTLMAGLPHTVPAMTINKVCGSGLKAVHLAMQAVACGDAEIVIAGGQES 118 AG +N AR L+AGLP VP T+N++CGS L A+ A +A+A G+AE++IAGG ES Sbjct: 61 AGEDNRNVARMAALLAGLPVEVPGSTVNRLCGSSLDAIGSAARAIAAGEAELMIAGGVES 120 Query: 119 MSQSSHVLPRSREGQRMGDWPMKDTMIVDGLWDAFNQCHMGV-----TAENIAKKYAFTR 173 MS++ VL ++ + ++DT I + + GV TAEN+A + +R Sbjct: 121 MSRAPFVLGKA-DSAFSRSAKIEDTTIGWRFVNPLMKAQYGVDSMPETAENVATDFNVSR 179 Query: 174 EAQDAFAAASQQKAEAAIQSGRFADEIIPVSIPQRKGDPLVFDTDEFPRPGTTAETLGRL 233 QDA A SQQ+ +A + G FA EI+PV IP++KGDP+ TDE PRP TT + L +L Sbjct: 180 ADQDALALRSQQRWASANERGFFAREIVPVDIPRKKGDPVRMTTDEHPRPDTTLDMLAKL 239 Query: 234 RPAFDKQGTVTAGNASGINDGAAMVVVMKESKAKELGLTPMARLVAFSSAGVDPAIMGTG 293 + GTVTAGNASG+NDGAA V++ E+ K GLTP AR++ ++AGV P IMG G Sbjct: 240 KGVVRPDGTVTAGNASGVNDGAAAVLLASEAAVKRHGLTPRARILGSAAAGVAPRIMGIG 299 Query: 294 PIPASTDCLKKAGWAPADLDLVEANEAFAAQAMSVNQEMGW--DLSKVNVNGGAIAIGHP 351 P PAS L + G A D++E NEAFAAQA++V + +G D ++VN NGGAI+IGHP Sbjct: 300 PAPASEKLLARLGMGIARFDVIELNEAFAAQALAVTRRLGLADDDARVNPNGGAISIGHP 359 Query: 352 IGASGARVLVTLLYEMQKRDAKKGLATLCIGGGQGVALAVERL 394 +GASGAR++ T L +++ + GLAT+CIG GQG+ALA+ER+ Sbjct: 360 LGASGARLVTTALNQLETSGGRYGLATMCIGVGQGIALAIERI 402 Lambda K H 0.317 0.131 0.380 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: 363 Number of extensions: 10 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: 394 Length of database: 402 Length adjustment: 31 Effective length of query: 363 Effective length of database: 371 Effective search space: 134673 Effective search space used: 134673 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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