GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Gracilibacillus halophilus YIM-C55.5

Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate WP_003466622.1 J416_RS05700 SDR family oxidoreductase

Query= CharProtDB::CH_091826
         (259 letters)



>NCBI__GCF_000359605.1:WP_003466622.1
          Length = 232

 Score = 84.3 bits (207), Expect = 2e-21
 Identities = 46/126 (36%), Positives = 73/126 (57%), Gaps = 1/126 (0%)

Query: 60  VDATDEASVEALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLC 119
           VD TDE SVE       + + + D+L+ SAG+     + +    DFD  + VNL G +L 
Sbjct: 55  VDVTDEQSVEMFLSKTRDHYSQIDVLINSAGIGMFDSLLESNTADFDRMIAVNLRGTYLA 114

Query: 120 SREFSKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITV 179
            + F K+M +D  KG+II + S +G++    N GY+A+KFG +GL++ L  +L   G+ V
Sbjct: 115 CKHFGKVM-KDQQKGQIINLVSIAGQIALPSNGGYTASKFGVMGLSKVLQAELRSEGVQV 173

Query: 180 HSLMLG 185
            S++ G
Sbjct: 174 TSVLPG 179


Lambda     K      H
   0.319    0.136    0.387 

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: 131
Number of extensions: 7
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: 259
Length of database: 232
Length adjustment: 24
Effective length of query: 235
Effective length of database: 208
Effective search space:    48880
Effective search space used:    48880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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