Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_012275149.1 SHAL_RS00075 acetyl-CoA C-acyltransferase FadA
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000019185.1:WP_012275149.1 Length = 387 Score = 296 bits (757), Expect = 9e-85 Identities = 173/404 (42%), Positives = 241/404 (59%), Gaps = 23/404 (5%) Query: 1 MRDVFICDAIRTPIGRF-GGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQ 59 M++ I D IRTP+GR G VRA+ L+A +K+L+E NP + + +++V +GC Q Sbjct: 1 MKNAVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKSLLERNPKLDPNTIEDVMWGCVQQ 60 Query: 60 AGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVES 119 E N+AR A LLAG+P+ + VT+NRLC S MDA+ A RAI +G+ + I GGVE Sbjct: 61 TLEQGFNIARNAALLAGIPKQVGAVTVNRLCGSSMDALHQAARAIMTGQGDTFIVGGVEH 120 Query: 120 MSRAPFVMG-KAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSR 178 M P G G + N+ +G TA+ + + ++R Sbjct: 121 MGHVPMNHGVDFHPGLANNVAKGSAMMGL------------------TAEMLGKMHGITR 162 Query: 179 ADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETI-VERDEHLRPETTLEALTKL 237 QDAFA+RS Q+A AA G FA EIV + G I V+ DE +RPET++E+L+ L Sbjct: 163 EQQDAFAVRSHQRAHAATVEGRFANEIVAIEGHDADGALIRVDHDEVIRPETSMESLSGL 222 Query: 238 KPVNGP-DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGI 296 +P P + TVTAG +S ++DGA+A+++ E K GL RAR+ MA G +MG Sbjct: 223 RPAFDPANGTVTAGTSSALSDGASAMLVMEEEKAKALGLPIRARIRSMAIAGCDAAIMGY 282 Query: 297 GPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQ-VNPNGGAIALG 355 GPVPA +K +R G+ V D DVIELNEAFA+Q L +++LG+ D + VN NGGAIALG Sbjct: 283 GPVPATQKALKRAGLTVDDLDVIELNEAFAAQSLPCVKDLGLMDVVDEKVNLNGGAIALG 342 Query: 356 HPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399 HPLG SG R+ T ++ +E + GLATMC+G+GQG+A ER Sbjct: 343 HPLGCSGTRISTTLINLMEAKDAKYGLATMCIGLGQGIATIFER 386 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: 398 Number of extensions: 27 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: 387 Length adjustment: 31 Effective length of query: 369 Effective length of database: 356 Effective search space: 131364 Effective search space used: 131364 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