Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate H281DRAFT_03491 H281DRAFT_03491 short chain enoyl-CoA hydratase (EC 4.2.1.17)/Enoyl-CoA hydratase (EC 4.2.1.17)
Query= metacyc::MONOMER-15953 (257 letters) >FitnessBrowser__Burk376:H281DRAFT_03491 Length = 266 Score = 141 bits (356), Expect = 1e-38 Identities = 101/256 (39%), Positives = 134/256 (52%), Gaps = 14/256 (5%) Query: 13 GVRLITLQRPEALNALNT-QLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEMA 71 GV ITL RPE NAL +++D L L A+ D RA+VLTG+ AF++G +IK M Sbjct: 12 GVATITLNRPETRNALTEMEVVDALVESLERAQADLNVRAIVLTGAGPAFSSGGNIKHM- 70 Query: 72 ERDLVG--------ILEDPRVAHWQRIAAFSK---PLIAAVNGFCLGGGCELAMHADILI 120 RD VG I E+ R + AF + P IAAVNG G GC+LA+ DI I Sbjct: 71 -RDEVGTFGGNSAQIRENYRRGIQRIPRAFHELDLPCIAAVNGPAHGAGCDLALMCDIRI 129 Query: 121 AGEDARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVT 180 A A F + +GI+PG GG L RAVG S A +M+ +G IDA+ A GLVS V Sbjct: 130 AAHSALFAESFAKIGIIPGDGGAWLLPRAVGLSRAAEMIFTGTPIDAQCALDWGLVSRVV 189 Query: 181 LPELTIERALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRA 240 + A +A IA P +R++K + + + DL S L ++ TAD Sbjct: 190 PDAELLSTARELAARIASNPPNVLRMSKRLIREGQRMDLPSLLELSAAFQGIVHRTADHR 249 Query: 241 EGIRAFQEKRRPEFTG 256 E + A EKR P +TG Sbjct: 250 EALAATFEKRTPNYTG 265 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: 175 Number of extensions: 12 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: 266 Length adjustment: 25 Effective length of query: 232 Effective length of database: 241 Effective search space: 55912 Effective search space used: 55912 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