Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011423740.1 RHE_RS01800 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000092045.1:WP_011423740.1 Length = 257 Score = 361 bits (926), Expect = e-105 Identities = 181/258 (70%), Positives = 212/258 (82%), Gaps = 1/258 (0%) Query: 1 MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60 MAYE ++VETRG VGLVTLNRP+ALNALN ++ EL AA F AD+AIGAIV+TGSE+A Sbjct: 1 MAYETLIVETRGNVGLVTLNRPQALNALNSTVLKELKAAYAAFHADEAIGAIVITGSERA 60 Query: 61 FAAGADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDII 120 FAAGADI M + + D+YK D+I+ W+ + RKP+IAAV+GFALGGGCELAMMCD I Sbjct: 61 FAAGADIKEMQSLQFADIYKSDFIS-GWDDIAKARKPVIAAVSGFALGGGCELAMMCDFI 119 Query: 121 FAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRV 180 A++TAKFGQPEI LG++PG GG+QRL RAV KAKAMDL LT R MDAAEAER+GLVSRV Sbjct: 120 IASETAKFGQPEITLGVIPGMGGSQRLTRAVGKAKAMDLVLTGRMMDAAEAERSGLVSRV 179 Query: 181 IPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQ 240 + L+DEA+AAA IA P+VMM KE+VNRA+ETTL EG+ FERRLFHSLFAT+DQ Sbjct: 180 VAPERLLDEALAAAEKIASLSQPSVMMAKEAVNRAFETTLEEGLRFERRLFHSLFATDDQ 239 Query: 241 KEGMAAFVEKRKPVFKHR 258 KEGMAAFVEKRKP FKHR Sbjct: 240 KEGMAAFVEKRKPAFKHR 257 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: 257 Number of extensions: 3 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: 257 Length adjustment: 24 Effective length of query: 234 Effective length of database: 233 Effective search space: 54522 Effective search space used: 54522 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