Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate GFF3595 PGA1_c36500 enoyl-CoA hydratase/isomerase
Query= BRENDA::F4JML5 (301 letters) >FitnessBrowser__Phaeo:GFF3595 Length = 258 Score = 153 bits (387), Expect = 4e-42 Identities = 91/241 (37%), Positives = 132/241 (54%), Gaps = 2/241 (0%) Query: 55 IIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCAGADLKERRT 114 + ++ L+RP NA+N E+L L A E + R +++ F AGAD+KE Sbjct: 14 VCQIKLNRPEALNALNSELLSELCTALEEADASDKVRCIILTGSEKA-FAAGADIKEMSD 72 Query: 115 MSPSEVHTYVNSLRYMFSFIEALSIPTIAAIEGAALGGGLEMALACDLRICGENAVFGLP 174 S +EV + N + I A+ P IAA+ G ALGGG E+A+ CD I + A FG P Sbjct: 73 KSFTEVFS-TNLFAGVNDRISAIRKPIIAAVAGYALGGGCELAMLCDFIIAADTAKFGQP 131 Query: 175 ETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVNICVTAGEAHEKAI 234 E L +I G GGTQRL+R VG+S S ++ TGR + A EA GLV+ V A + ++A Sbjct: 132 EINLGVIAGIGGTQRLTRFVGKSKSMDMNLTGRFMTAEEAERAGLVSRVVPAKKLLDEAT 191 Query: 235 EMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQDRLEGLAAFAEKR 294 A +I EK L K+ ++ E ++ GL E + + T+D+ EG+AAF EKR Sbjct: 192 AAAHKIAEKSLLTAMAVKETVNRSYELPLSEGLLFERRVFHSMFATEDQKEGMAAFLEKR 251 Query: 295 K 295 + Sbjct: 252 E 252 Lambda K H 0.318 0.134 0.373 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: 155 Number of extensions: 10 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: 301 Length of database: 258 Length adjustment: 25 Effective length of query: 276 Effective length of database: 233 Effective search space: 64308 Effective search space used: 64308 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