Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_067646635.1 I596_RS08905 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_001632775.1:WP_067646635.1 Length = 264 Score = 111 bits (277), Expect = 2e-29 Identities = 83/260 (31%), Positives = 123/260 (47%), Gaps = 8/260 (3%) Query: 6 ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGA 65 I ++ RG + L+RP NA + AL+ EL AAL+ DAD A+ A+VVTG+ F+AGA Sbjct: 5 IQIDRRGSAAYLVLDRPGVHNAFDAALIAELTAALKSLDADPAVRAVVVTGAGATFSAGA 64 Query: 66 DIGMMSTYTYMDVYKGD----YITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIF 121 D+ M + D + + + T+ + KP IA V G A GGG L CDI Sbjct: 65 DLNWMRSMAAADEAENRADSLRLAQLMRTLNFLSKPTIARVNGSAYGGGVGLVACCDIAV 124 Query: 122 AADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVI 181 ++AKF E KLG++P A + + A+ +A +A DAAEA R GL+ + Sbjct: 125 GVESAKFSLSEAKLGLVP-AVISPYVSAAIGVRQARRYFASAEVFDAAEAARIGLLHECV 183 Query: 182 PAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERR---LFHSLFATE 238 A +L + + A K R T +R L L + Sbjct: 184 AAEALDATVERLLHMLGKCGPIAQDEAKRLALRVAGITRDGAEQADRENAALIARLRVSA 243 Query: 239 DQKEGMAAFVEKRKPVFKHR 258 + +EG+ AF++KR P + R Sbjct: 244 EGQEGLTAFLDKRAPAWAGR 263 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: 154 Number of extensions: 7 Number of successful extensions: 4 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: 264 Length adjustment: 25 Effective length of query: 233 Effective length of database: 239 Effective search space: 55687 Effective search space used: 55687 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 24 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