Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate Ga0059261_2803 Ga0059261_2803 Enoyl-CoA hydratase/carnithine racemase
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__Korea:Ga0059261_2803 Length = 266 Score = 128 bits (322), Expect = 1e-34 Identities = 82/253 (32%), Positives = 125/253 (49%), Gaps = 10/253 (3%) Query: 17 LVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNL------- 69 L+LT+ +P RNAL P++ A + A D S+ V++TGA + FCAGGN+ Sbjct: 15 LILTIDDPATRNALSPELTRALVAACAEANADMSVSCVILTGAGDVFCAGGNIKDMYARA 74 Query: 70 NRLLENRAKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAA 129 N N A+ + +A + L + P IAAV+GAA GAG A C + +A+ Sbjct: 75 NHFAGNAAEIRRTYQAGVQTIARALYDLEV---PSIAAVNGAAMGAGMDFATMCTMRIAS 131 Query: 130 DDAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKP 189 + AKF S+ ++GLT GG+WFL +A+ A E+ + G I AAR E+G+V+ + Sbjct: 132 ERAKFAESFIKLGLTSAAGGAWFLNRAIGASAAAELALTGDTIDAARALEIGLVSGVVPH 191 Query: 190 GTARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEG 249 D A A A + + +S+ L+ + LS L + E Sbjct: 192 AALLDEARALAKRIARHPAHSIRLNTRLLRESARLDLSAALEIASAMQAVVQQTDDQYEA 251 Query: 250 ISAFLEKRAPVYK 262 ++A +EKR P YK Sbjct: 252 VAAAVEKRPPAYK 264 Lambda K H 0.317 0.132 0.377 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: 138 Number of extensions: 5 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: 262 Length of database: 266 Length adjustment: 25 Effective length of query: 237 Effective length of database: 241 Effective search space: 57117 Effective search space used: 57117 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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