Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_041661616.1 AFER_RS01500 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000023265.1:WP_041661616.1 Length = 259 Score = 124 bits (310), Expect = 3e-33 Identities = 79/223 (35%), Positives = 119/223 (53%), Gaps = 3/223 (1%) Query: 6 ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGA 65 + +E G V V ++RP NA++ + L A R FDADD V++G+ +F AGA Sbjct: 7 VRIERAGAVWTVLIDRPAVRNAVDRPTAEALADAFRAFDADDEAAVAVLSGTGGSFCAGA 66 Query: 66 DIGMMSTYTYMDVYK-GDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAAD 124 D+G T + GD V S KP+IAA+ G+A+ GG ELA+ CD+ AA+ Sbjct: 67 DLGAFGTERENRLDPTGDGPMGPTRMVLS--KPVIAAIEGWAVAGGLELALWCDLRVAAE 124 Query: 125 TAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAA 184 A G + G+ GGT RLPR + +++A+DL LT R +DA EA GLV+RV+ Sbjct: 125 DAVLGVFSRRFGVPLIDGGTVRLPRLIGRSRALDLILTGRAVDATEALAMGLVNRVVGRG 184 Query: 185 SLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFE 227 + +D A A +A FP + + ++ A + A+ + E Sbjct: 185 AALDAATELARQLAGFPQACLRSDRAALYAAEGQSEADALRTE 227 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: 171 Number of extensions: 5 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: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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