GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Phyllobacterium leguminum ORS 1419

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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