Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate HSERO_RS01180 HSERO_RS01180 acetyl-CoA acetyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >FitnessBrowser__HerbieS:HSERO_RS01180 Length = 391 Score = 306 bits (784), Expect = 7e-88 Identities = 180/403 (44%), Positives = 253/403 (62%), Gaps = 16/403 (3%) Query: 1 MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQA 60 M+D I A RT IG++GGAL + A DLGA IKAL+ + G+ A+ +VI G A Sbjct: 1 MDDVVIVAAQRTAIGKFGGALSKIAAADLGAQVIKALLAKT-GIKPEAISEVILGQVLTA 59 Query: 61 GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120 G +N AR S + +GLP P + ++CGSG+ AV AA+AI+ G+AQ++IAGG E+M Sbjct: 60 GL-GQNPARQSVIKSGLPDMVPAFVVGKVCGSGLKAVQLAAQAIRCGDAQIVIAGGQENM 118 Query: 121 TRAPFVMGKAASAFTR-QAEIHDTTIG---WRFVNPLMKRQYGVDSMPETAENVAEQFGI 176 + +P V+ + F A++ DT I W N QY M TAENVA++F I Sbjct: 119 SASPHVLNNSRDGFRMGDAKLTDTMIVDGLWDVYN-----QY---HMGITAENVAKKFEI 170 Query: 177 SRADQDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLAR 236 SR +QDAFA ASQ KA AQ+ G EIV +EI KK + T + + ESLA Sbjct: 171 SREEQDAFAAASQNKAEAAQKAGKFKDEIVPIEIKGKKETVVFDTDEFVKHGVTAESLAT 230 Query: 237 LKGVVRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGI 296 L+ GTVTAGNASG+NDGA A+++ S + A + GL A++ ++AG++P IMG+ Sbjct: 231 LRPAFDKAGTVTAGNASGINDGAAAVVVTSAKLAAELGLPVLAKIKAYSSAGLDPSIMGM 290 Query: 297 GPAPATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGH 356 GP PA+Q L++ G T LD++E+NEAFA+Q +AV + +G D ++N NGGAIALGH Sbjct: 291 GPVPASQLTLKKAGWTPQDLDLMEINEAFAAQAIAVNKQMGW--DTSKINVNGGAIALGH 348 Query: 357 PLGASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIER 399 P+GASG R++ T LH++ R + + L ++CIG G G+AL +ER Sbjct: 349 PIGASGCRVLVTLLHEMVRRDAKKGLASLCIGGGMGVALAVER 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: 354 Number of extensions: 6 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