Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_011383120.1 AMB_RS03480 isovaleryl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >NCBI__GCF_000009985.1:WP_011383120.1 Length = 389 Score = 108 bits (270), Expect = 3e-28 Identities = 85/261 (32%), Positives = 126/261 (48%), Gaps = 23/261 (8%) Query: 3 LNFSKEEIA--FRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 LNF E A RD V F + + + I+ + E+ W R L G Sbjct: 8 LNFDLGETADMMRDSVAAFAATEIAPRAAE--IDRSNEFPNEL--WPR-LGAMGLLGITV 62 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGV--SMVGPVIYTFGSEEQKKRFLPRIA 118 ++YGG G ++H + EE+ A A L++G ++ I G+E QK ++LP++ Sbjct: 63 DEKYGGAGMGYLEHVVAMEEISRASASVGLSYGAHSNLCVNQIKRNGTEAQKMKYLPKLI 122 Query: 119 NVDDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPA 178 + + SEP +GSD+ S+K KAEKKGD++++NG K W T AD I +TD Sbjct: 123 SGEYIGALAMSEPNAGSDVVSMKLKAEKKGDRYVLNGTKMWITNGPDADVIVVYAKTDVT 182 Query: 179 AKKQEGISFILVDMKTKGITVRPIQTID----GGHEVNEVFFDDVEVPLENLVGQENK-- 232 A + GI+ LV+ KG +V Q +D G E+ F D EVP EN++G K Sbjct: 183 AGPR-GITAFLVEKTFKGFSV--AQKLDKLGMRGSNTGELVFQDCEVPEENVLGAVGKGV 239 Query: 233 -----GWDYAKFLLGNERTGI 248 G DY + +L GI Sbjct: 240 NVLMSGLDYERVVLTGGPLGI 260 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: 317 Number of extensions: 18 Number of successful extensions: 3 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: 389 Length adjustment: 31 Effective length of query: 365 Effective length of database: 358 Effective search space: 130670 Effective search space used: 130670 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 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