Align BadH (characterized)
to candidate WP_110751435.1 C7477_RS09440 L-iditol 2-dehydrogenase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_003217235.1:WP_110751435.1 Length = 258 Score = 155 bits (391), Expect = 1e-42 Identities = 93/258 (36%), Positives = 139/258 (53%), Gaps = 9/258 (3%) Query: 3 RLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRC 62 RL+ K+A ITG GIG A FA+EGA +A+ D++LD A++ A I G A AV+ Sbjct: 4 RLEGKSAFITGAARGIGFAFAEAFAREGATVALADIDLDRAQESAAKI---GERAYAVQI 60 Query: 63 DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMH 122 D+ D S++ A+A G +DILVNNA P + +ERL A+N+ G L Sbjct: 61 DVTDIASIERAVAEAVAKTGGIDILVNNAALFDMAPMVEITRESFERLYAVNVHGVLFTM 120 Query: 123 HAVLPGMVER-RHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVN 181 AV M+ R R G+I+N+AS A R G + AVY + K +++ +++ + RHGI VN Sbjct: 121 QAVARAMIARGRGGKIINMASQAGRRGEALVAVYCSTKAAVISLTQSAGLDLIRHGINVN 180 Query: 182 VVCPGPTDTALLADVTSGAANPE-----KLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDD 236 + PG D A V + A E + +A+P GR+G+P+DL G F + Sbjct: 181 AIAPGVVDGEHWAGVDALFAKHENRPLGEKKRLVGEAVPFGRMGRPEDLTGMAIFLAGPE 240 Query: 237 AGFITGQVLSVSGGLTMN 254 + ++ Q +V GG M+ Sbjct: 241 SDYVVAQTYNVDGGNWMS 258 Lambda K H 0.318 0.135 0.398 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: 197 Number of extensions: 17 Number of successful extensions: 4 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: 255 Length of database: 258 Length adjustment: 24 Effective length of query: 231 Effective length of database: 234 Effective search space: 54054 Effective search space used: 54054 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 24 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