Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_051302441.1 A3GO_RS0115400 2,3-dehydroadipyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_000428045.1:WP_051302441.1 Length = 259 Score = 221 bits (563), Expect = 1e-62 Identities = 125/255 (49%), Positives = 167/255 (65%), Gaps = 2/255 (0%) Query: 2 AYENILVETR-GRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60 AY +I V+T V L+ LNRP A NAL AL+ EL AL D + A+V+TGSEK Sbjct: 3 AYSDIQVDTPYNGVQLIRLNRPDAHNALRTALLGELATALAAAAEDKRVRAVVITGSEKV 62 Query: 61 FAAGADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDII 120 FAAGADI M+ + ++K D ++W+T+RS KP+IA+V G+ LGGG ELAM D+I Sbjct: 63 FAAGADIKEMAALDAVGLWK-DQRPQHWQTIRSFSKPLIASVNGYCLGGGMELAMHADMI 121 Query: 121 FAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRV 180 A + A+FGQPEI LGI+PGAGGTQRL R+V KA AM L L+ F++A EA AGLV+ V Sbjct: 122 IAGEDARFGQPEINLGIIPGAGGTQRLVRSVGKALAMKLVLSGEFINAREALAAGLVAEV 181 Query: 181 IPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQ 240 + A A A TIA A+ + KE++ +YET L++G+ ER+ F L T+D+ Sbjct: 182 TQPELTLKRATALAETIASKSPIALRLAKEAILASYETPLSQGLELERKAFLFLATTQDR 241 Query: 241 KEGMAAFVEKRKPVF 255 +EG+ AF+EKR P F Sbjct: 242 QEGIDAFLEKRPPQF 256 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: 162 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: 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