Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AO356_30295 AO356_30295 fatty-acid oxidation protein subunit alpha
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30295 Length = 703 Score = 122 bits (307), Expect = 2e-32 Identities = 78/202 (38%), Positives = 112/202 (55%), Gaps = 16/202 (7%) Query: 4 ENILV--ETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAF 61 E+++V E G V ++T+N P +NAL + + A+ +AD A+ AIV+ G + F Sbjct: 3 ESLMVSYEVEGVVAVITVNNPP-VNALTPEMRGSIIDAVTHANADPAVAAIVLMGGGQNF 61 Query: 62 AAGADIGMMSTYTYMDVYKGDYITRNWETVR--SIRKPIIAAVAGFALGGGCELAMMCDI 119 AGADI K IT + + KP +AA+ G+ALGGG E A+ C Sbjct: 62 IAGADIRQFG--------KARTITTSMSAAALDASAKPTVAAIHGYALGGGLEHALACHY 113 Query: 120 IFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSR 179 A TAK G PE+ LG++PG GGTQRLPR V A A DL +++R + A EA + GL+S+ Sbjct: 114 RIALPTAKLGLPEVALGLIPGGGGTQRLPRLVGAAVATDLLVSSRHIHAPEALQIGLISQ 173 Query: 180 VIPAA---SLVDEAIAAAATIA 198 ++P L D A+ A +A Sbjct: 174 IVPGTQNQELRDAAVRYAKAVA 195 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: 379 Number of extensions: 15 Number of successful extensions: 2 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: 703 Length adjustment: 32 Effective length of query: 226 Effective length of database: 671 Effective search space: 151646 Effective search space used: 151646 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: 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