Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_012113366.1 XAUT_RS06740 acyl-CoA/acyl-ACP dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >NCBI__GCF_000017645.1:WP_012113366.1 Length = 387 Score = 162 bits (410), Expect = 2e-44 Identities = 109/294 (37%), Positives = 160/294 (54%), Gaps = 15/294 (5%) Query: 13 RDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHWPKEYGGTGWSSV 72 RD VR D PA+ +K+ E R E+ V+ L K GW P+EYGG+G Sbjct: 13 RDAVRALCAD-FPAEYHRKVDEARAYP-EDFVD---ALTKAGWMAALIPEEYGGSGLGLT 67 Query: 73 QHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANVD-DWWCQGFSEP 131 + + EE+ A G + GSEEQ+KR+LP+IA + G +EP Sbjct: 68 EASVIMEEINRAGGNSGACHGQMYNMNTLVRHGSEEQRKRYLPKIAAGELRLQSMGVTEP 127 Query: 132 GSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDP---AAKKQEGISFI 188 +G+D +KT A KKGD+++INGQK W + QH+D + L RT P KK EG+S Sbjct: 128 TTGTDTTRIKTTAVKKGDRYVINGQKVWISRVQHSDLMILLARTTPLDQVKKKSEGLSIF 187 Query: 189 LVDMK---TKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFLLGNER 245 +VD+K +KG+TVRPI + HE NE+FFD++E+P ENL+G+E +G+ Y L ER Sbjct: 188 IVDIKEAMSKGMTVRPILNM-VNHETNELFFDNLEIPEENLIGEEGQGFKYILTGLNAER 246 Query: 246 TGIAR--VGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALEL 297 T IA +G I ++ A + G+P+ ++ + +A IE++A L Sbjct: 247 TLIAAECIGDGYWFIDKVTAYARERVVFGRPIGQNQGVQFPIAESFIEVEAANL 300 Lambda K H 0.317 0.135 0.411 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: 347 Number of extensions: 14 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: 396 Length of database: 387 Length adjustment: 31 Effective length of query: 365 Effective length of database: 356 Effective search space: 129940 Effective search space used: 129940 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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