Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_085772689.1 B1812_RS17255 enoyl-CoA hydratase-related protein
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_002117405.1:WP_085772689.1 Length = 249 Score = 107 bits (267), Expect = 2e-28 Identities = 74/245 (30%), Positives = 118/245 (48%), Gaps = 3/245 (1%) Query: 6 ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGA 65 ++V G V + L+RP NAL + AAL E D+++ A++ G F AG Sbjct: 5 LIVSREGGVLRIVLDRPAKKNALTRDMYLRALAALEEASGDESLRAVLFCGEGGTFTAGN 64 Query: 66 DIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAADT 125 D+ +++ + R + V S KP++AAVAG A+G G + CD+++A+ + Sbjct: 65 DLADFLSFSGEPM--AFPALRFIKAVASFEKPLVAAVAGDAVGIGATMLFHCDLVYASPS 122 Query: 126 AKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAAS 185 A+F I LG+ P G + P +AKA +L + DA E R GLV+ ++P Sbjct: 123 ARFKAAFIDLGLPPEGGVSLLAPMRFGEAKAAELLMLGEAFDAKEGHRVGLVNAILPEEE 182 Query: 186 LVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEGMA 245 L A AA +A P A+ + + R L E + E RLF + + + A Sbjct: 183 LQARAFEAATRLAAKPLTALRDTRRLL-RGDRGRLLERIDEEARLFAQALRSPEVQARFA 241 Query: 246 AFVEK 250 AF++K Sbjct: 242 AFLKK 246 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: 146 Number of extensions: 4 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: 249 Length adjustment: 24 Effective length of query: 234 Effective length of database: 225 Effective search space: 52650 Effective search space used: 52650 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 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