Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_029134162.1 A3GO_RS0115395 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000428045.1:WP_029134162.1 Length = 263 Score = 152 bits (384), Expect = 7e-42 Identities = 92/267 (34%), Positives = 149/267 (55%), Gaps = 17/267 (6%) Query: 1 MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60 M+Y IL + + V +TLNRP++LN+ N + E+ AL++ D I +++TG+ + Sbjct: 1 MSYNAILFQVQDGVATLTLNRPESLNSFNTEMHGEIRDALKQVKQDRTIRCLLLTGAGRG 60 Query: 61 FAAGADIGMMSTYTYMDVYKGDY-------ITRNWE----TVRSIRKPIIAAVAGFALGG 109 F AG D+ + V G+ I RN+ T+ ++ KP+I AV G A G Sbjct: 61 FCAGQDLNDRA------VAPGEAMPDLSLSIKRNYNPLVRTLTTLDKPVICAVNGVAAGA 114 Query: 110 GCELAMMCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAA 169 G LA+ CDI+ AA +A F Q K+G++P +GGT LPR V +A+AM + + + + A Sbjct: 115 GANLALACDIVLAARSANFIQGFSKIGLIPDSGGTWTLPRLVGRARAMGMAMLSGKLSAE 174 Query: 170 EAERAGLVSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERR 229 +A + GL+ +V+ L+ EA A+ +A P+ + + K ++N A +L + + E Sbjct: 175 QAAQWGLIWQVVDDDQLMSEANTLASHLASQPTKGLALTKRAINAAGGNSLEQQLELECD 234 Query: 230 LFHSLFATEDQKEGMAAFVEKRKPVFK 256 L + + D +EG+AAFV KRKP FK Sbjct: 235 LQYIAGCSHDYREGVAAFVGKRKPEFK 261 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: 144 Number of extensions: 7 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: 263 Length adjustment: 25 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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