Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BPHYT_RS25360 BPHYT_RS25360 enoyl-CoA hydratase
Query= metacyc::MONOMER-15953 (257 letters) >FitnessBrowser__BFirm:BPHYT_RS25360 Length = 256 Score = 154 bits (389), Expect = 2e-42 Identities = 93/242 (38%), Positives = 130/242 (53%), Gaps = 2/242 (0%) Query: 17 ITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEMAERDLV 76 +TL RP A+N+LN ++ L A+L D R +V+TG+ +AF AGAD+ E AE Sbjct: 14 LTLDRPAAMNSLNREMATGLIAQLKAWRNDDAVRVLVVTGNGRAFCAGADLIEAAEATQP 73 Query: 77 GILE--DPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQPEINL 134 G E + V + + AF KP+IAAVNG L GG E+ + D+++A E AR G N Sbjct: 74 GRREFLELIVEFFDTLRAFPKPVIAAVNGLALAGGLEVVLACDVVLAAESARLGDAHSNF 133 Query: 135 GIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIERALAIAR 194 G+ PGAGG L R V ++A ++ +G A+ A + GLV+EV RA A+A Sbjct: 134 GVFPGAGGAAILPRKVPANVARYLLFTGDAMSAAELKGYGLVNEVLADAELRPRAQALAH 193 Query: 195 VIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAFQEKRRPEF 254 A+K+PL + K + D A LR E + D EG+RAF EKR P+F Sbjct: 194 KFAKKSPLVLARMKRVANETADKSAADALRHELLELRNHQRSYDVQEGLRAFAEKREPQF 253 Query: 255 TG 256 G Sbjct: 254 KG 255 Lambda K H 0.320 0.134 0.374 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: 158 Number of extensions: 6 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: 257 Length of database: 256 Length adjustment: 24 Effective length of query: 233 Effective length of database: 232 Effective search space: 54056 Effective search space used: 54056 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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