Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_086511176.1 BZY95_RS17490 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >NCBI__GCF_002151265.1:WP_086511176.1 Length = 257 Score = 195 bits (496), Expect = 7e-55 Identities = 118/253 (46%), Positives = 153/253 (60%), Gaps = 4/253 (1%) Query: 7 LVETRGRVGLV--TLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EKAFAA 63 L+E G+V T+NRPKALNALN A++ EL A L E + + A+++TG+ EKAF A Sbjct: 5 LIEMVDNAGVVRLTINRPKALNALNSAVLTELEALLTELEKRSDLRALLITGAGEKAFVA 64 Query: 64 GADIGMMSTYTYMDVYK-GDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFA 122 GADI M T T + R + + ++ P++A V GF LGGGCELA+ CD A Sbjct: 65 GADITEMRTKTPEEARAFASQALRTIKRLETLPVPVVALVNGFCLGGGCELALACDWAVA 124 Query: 123 ADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIP 182 +D A FGQPE+ LG++PG GGTQRLPR V A A+DL T R +DA EA R GLV+RV+P Sbjct: 125 SDNAIFGQPEVLLGVIPGFGGTQRLPRRVGPAMALDLVTTGRKIDAQEALRIGLVNRVMP 184 Query: 183 AASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKE 242 A L A +A AV K++V+ + L + E LF FA +QKE Sbjct: 185 QAELEAYAEELTKQLAGNGPLAVRSAKQAVHDGMDQDLDSALALETSLFALGFAGSEQKE 244 Query: 243 GMAAFVEKRKPVF 255 GM+AFVEKRKP F Sbjct: 245 GMSAFVEKRKPNF 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: 165 Number of extensions: 8 Number of successful extensions: 3 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 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