Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011386482.1 AMB_RS20905 enoyl-CoA hydratase/carnithine racemase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000009985.1:WP_011386482.1 Length = 254 Score = 126 bits (317), Expect = 4e-34 Identities = 79/252 (31%), Positives = 124/252 (49%), Gaps = 4/252 (1%) Query: 4 ENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAA 63 E +L G V +V +NRP NAL + L A + +ADD + ++ GS+ F+A Sbjct: 3 ELVLSHVEGGVQVVRMNRPDKKNALIGEMYAALAEAFAKGEADDDVNVFLILGSQTDFSA 62 Query: 64 GADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAA 123 G D+ T+ + G R V RKP++AAV G A+G G L CD+++AA Sbjct: 63 GNDLPDFLTW---EALSGSVADRFIRAVAGARKPVVAAVRGAAIGIGSTLLPHCDLVYAA 119 Query: 124 DTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPA 183 +F P I LGI+P AG +Q +P +A ++ + AE GL++ V+P Sbjct: 120 PGTRFHMPFINLGIVPEAGSSQTMPALAGHRRAAEMLMLGEPFGVDTAEAVGLINGVVPG 179 Query: 184 ASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEG 243 L + A+AAA +A P ++ +K + E + + + E +F + E E Sbjct: 180 EDLEETAMAAARKLAAKPRSILVQIKALMKTPAE-PIMDRLTREAAVFDTCLKGEALNEA 238 Query: 244 MAAFVEKRKPVF 255 ++AF EKR P F Sbjct: 239 VSAFKEKRAPDF 250 Lambda K H 0.321 0.134 0.380 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: 155 Number of extensions: 11 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: 258 Length of database: 254 Length adjustment: 24 Effective length of query: 234 Effective length of database: 230 Effective search space: 53820 Effective search space used: 53820 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 (21.9 bits) S2: 47 (22.7 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