Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011840924.1 RSPH17029_RS06550 enoyl-CoA hydratase/isomerase family protein
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000015985.1:WP_011840924.1 Length = 258 Score = 135 bits (341), Expect = 6e-37 Identities = 90/262 (34%), Positives = 140/262 (53%), Gaps = 8/262 (3%) Query: 1 MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60 M Y I VE +G + VTL RP+ +NAL+ + +EL A+ E A A+V+TG + Sbjct: 1 MDYRTIRVEEQGGLCRVTLARPEVMNALSSRMREELLHAVTE--AGTRARALVLTGEGRG 58 Query: 61 FAAGADIGMMSTYTYMDVYKGDYITRNWETV-RSIRK---PIIAAVAGFALGGGCELAMM 116 F +G D+G D + + +E + R+I P +AAV G A G G LA+ Sbjct: 59 FCSGQDLGDARALGVPDFER--ILREEYEPLLRAIAHCPLPTLAAVNGVAAGAGANLALA 116 Query: 117 CDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGL 176 CD++ AA++A F Q ++G++P GGT LPR + A+AM L A + AA+A R G+ Sbjct: 117 CDVVIAAESAGFIQAFTRIGLIPDTGGTWTLPRQIGLARAMGATLFADRISAADAARWGM 176 Query: 177 VSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFA 236 + +P + A AA +AE P+ A +K+++ +++ + E + E RL A Sbjct: 177 IYEAVPDEAFEARWQARAAHLAEGPTEAYRGLKQALRASFDNSFEEQLALEARLQGQCGA 236 Query: 237 TEDQKEGMAAFVEKRKPVFKHR 258 + D EG+ AF+EKR F R Sbjct: 237 SADFLEGVTAFLEKRPATFSGR 258 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: 151 Number of extensions: 9 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: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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 10 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