Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate HSERO_RS19405 HSERO_RS19405 enoyl-CoA hydratase
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__HerbieS:HSERO_RS19405 Length = 258 Score = 141 bits (355), Expect = 2e-38 Identities = 88/250 (35%), Positives = 138/250 (55%), Gaps = 4/250 (1%) Query: 5 ERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQDLT 64 E + V ++ L+RP+ LNA++ L+ L AL + E+ +++TG+ +AF+AG D++ Sbjct: 9 ETHEKVGLIRLHRPKALNALSDGLMTELGEALLAFDAQEEIGCIIITGSEKAFAAGADIS 68 Query: 65 EFGDRKPDYEAHLRR--YNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVGA 122 DY + R E L + KP++ AV G A G G LA+ D +AA A Sbjct: 69 AMAGY--DYMDVFKGEFITRNWETLRRIRKPVIAAVAGYALGGGCELAMMCDFIIAADNA 126 Query: 123 SFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEKL 182 F +++G+VP +G + LPR V AKA +L L + AEEA GLV R+V A+KL Sbjct: 127 KFGQPEIKLGIVPGAGGTQRLPRAVSKAKAMDLALTGRMMDAEEAERAGLVSRIVAADKL 186 Query: 183 MEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGVRA 242 +EEA++ A +A+ P + + K + Y +L+E + E L T+D +EG++A Sbjct: 187 LEEAMAAAIIIAEMPRQVAMMVKDSVNRAYETTLSEGMKYERALFYSCFATEDQKEGMKA 246 Query: 243 FREKRPPRFQ 252 F EKR P F+ Sbjct: 247 FLEKRQPVFK 256 Lambda K H 0.318 0.135 0.371 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: 163 Number of extensions: 9 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: 254 Length of database: 258 Length adjustment: 24 Effective length of query: 230 Effective length of database: 234 Effective search space: 53820 Effective search space used: 53820 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