GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Lactobacillus shenzhenensis LY-73

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_022530640.1 L248_RS12645 SDR family oxidoreductase

Query= BRENDA::Q1J2J0
         (255 letters)



>NCBI__GCF_000469325.1:WP_022530640.1
          Length = 246

 Score =  165 bits (418), Expect = 7e-46
 Identities = 106/246 (43%), Positives = 149/246 (60%), Gaps = 12/246 (4%)

Query: 15  RLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDG-TFERLNVTD 73
           RL+ +HA+VTGGAQGIG  I +  A  GA+V IAD+N D G   A ++ G  F  L+VT 
Sbjct: 4   RLESKHAIVTGGAQGIGLAITKRFAAEGAQVIIADVNADEGAKVAADIPGAAFHVLDVTS 63

Query: 74  ADA----VADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFG 129
            ++     AD  ++L  +D+LVNNAGI R A  E T   DW+AV++VNL G F    ++G
Sbjct: 64  EESWQALFADAEKQLGRIDILVNNAGIARMADIEHTTLADWQAVIAVNLTGNF-LGNKYG 122

Query: 130 RTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASR--GVRVNA 187
              +    GAIV+ +S++GL+ +     AAY ASK  V  LT+S+A   A +   +RVN+
Sbjct: 123 VIHMKDHGGAIVNMSSIAGLVGD--PNSAAYTASKGGVRLLTKSVASYCAEQHYNIRVNS 180

Query: 188 VAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLV 247
           V PG  ATP+   G+      +    + P+GR+A+P EIA  VL++ASD AS+ TG   +
Sbjct: 181 VHPGVVATPMV-AGIPKAIVAKV-AAQNPMGRIAQPEEIANMVLFVASDEASYSTGSEFI 238

Query: 248 VDGGYT 253
           VDGG T
Sbjct: 239 VDGGTT 244


Lambda     K      H
   0.319    0.134    0.408 

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: 196
Number of extensions: 11
Number of successful extensions: 5
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: 246
Length adjustment: 24
Effective length of query: 231
Effective length of database: 222
Effective search space:    51282
Effective search space used:    51282
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 (21.8 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