Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate Echvi_4069 Echvi_4069 Enoyl-CoA hydratase/carnithine racemase
Query= BRENDA::F4JML5 (301 letters) >FitnessBrowser__Cola:Echvi_4069 Length = 261 Score = 174 bits (440), Expect = 3e-48 Identities = 100/256 (39%), Positives = 149/256 (58%), Gaps = 2/256 (0%) Query: 46 NRLSGSDSGIIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCA 105 N LS + GI+ + ++R NAIN + L+ L+N F + + S R V++ F A Sbjct: 6 NILSENKDGILYLTINRESKLNAINFDTLEELKNIFNEVSDNKSIRGVVLTGSGEKAFVA 65 Query: 106 GADLKERRTMSPSEVHTYVNSLRYMFSFIEALSIPTIAAIEGAALGGGLEMALACDLRIC 165 GAD+ E ++ + + + +FS IE+ P IA + G ALGGG E+++AC +RI Sbjct: 66 GADISEIAELNELNARKFSENGQEVFSLIESCHKPVIAVVNGFALGGGCELSMACHMRIA 125 Query: 166 GENAVFGLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVN-ICV 224 NA FG PE L IIPG GGTQRL+ L+GR+ + EL+ TG +DA EA GLVN + Sbjct: 126 TSNAKFGQPEVNLGIIPGYGGTQRLTFLIGRTKANELLMTGDMVDAAEAKALGLVNYVTQ 185 Query: 225 TAGEAHEKAIEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQDRL 284 T EA +KA E+ Q+I K PL+I M ++ + +N +G +E + + + ++D Sbjct: 186 TKAEAIQKAEEILQKIMTKAPLSIGMIIDCVN-AVYSNDENGYLIEANSFARCVKSEDYS 244 Query: 285 EGLAAFAEKRKPLYTG 300 EG +AF EKRKP + G Sbjct: 245 EGTSAFLEKRKPNFKG 260 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: 169 Number of extensions: 7 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: 261 Length adjustment: 26 Effective length of query: 275 Effective length of database: 235 Effective search space: 64625 Effective search space used: 64625 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