Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_034990820.1 DL88_RS01280 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000745425.1:WP_034990820.1 Length = 400 Score = 503 bits (1296), Expect = e-147 Identities = 256/400 (64%), Positives = 314/400 (78%), Gaps = 2/400 (0%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M FICD IRTPIGR+GG LA VR DDLAA+PL AL+ NP + V+E++ GCANQA Sbjct: 1 MTQAFICDYIRTPIGRYGGVLAPVRTDDLAALPLAALLARNPGLDPGAVEEIWMGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARMALLLAG P ++PGVT+NRLC SG++A+ A RAI +G+++LAIAGGVESM Sbjct: 61 GEDNRNVARMALLLAGFPANVPGVTVNRLCGSGLEAVAAAARAIRTGDIDLAIAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 +RAPFV+ K S +SR ++ DTTIGWRF+NP + + YG DSMPETA N+ADDY VSR D Sbjct: 121 TRAPFVIPKGASAWSRASEIYDTTIGWRFVNPRIAAAYGTDSMPETAQNLADDYAVSRED 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETI-VERDEHLRPETTLEALTKLKP 239 QDAFALRSQ++AAAAQA+G FA EI+PV + +G+++ V +DEH R TTL L +LKP Sbjct: 181 QDAFALRSQERAAAAQASGRFAAEILPVEVPLGRGKSLDVLKDEHPR-ATTLADLARLKP 239 Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299 + PD ++TAGNASGVNDGAAALI+AS A ++ GLTP ARV+ +S GVAPR+MG GPV Sbjct: 240 ITRPDGSITAGNASGVNDGAAALIIASEAAARRFGLTPLARVVAASSAGVAPRIMGYGPV 299 Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359 PAV+ L R G+++ IELNEAFA+Q L VLR+LG+ADD P+VN NGGAIALGHPLG Sbjct: 300 PAVKTLCARTGISLDTIATIELNEAFAAQALVVLRQLGIADDDPRVNSNGGAIALGHPLG 359 Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399 MSGAR+ TA +L + GGR LATMCVGVGQG AL +ER Sbjct: 360 MSGARITGTAALELVRGGGRYALATMCVGVGQGAALLLER 399 Lambda K H 0.318 0.134 0.383 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: 474 Number of extensions: 16 Number of successful extensions: 1 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: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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