GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Oscillibacter ruminantium GH1

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_040659684.1 ON16_RS04320 SDR family oxidoreductase

Query= metacyc::MONOMER-16231
         (254 letters)



>NCBI__GCF_000307265.1:WP_040659684.1
          Length = 264

 Score =  132 bits (332), Expect = 7e-36
 Identities = 90/256 (35%), Positives = 130/256 (50%), Gaps = 15/256 (5%)

Query: 4   LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63
           L GK  ++TG  +GIG   A   + +GA VAI        A+    E+   G++A   K 
Sbjct: 10  LTGKVAVITGGGSGIGLGVAQLLSAYGAAVAI--VDVSDKAEEKAQEMRDAGRQAAFFKC 67

Query: 64  DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMV 123
           DV   ++    VA  VE FG++D++ +NAG+    A  D+     +    V L G + M 
Sbjct: 68  DVTSEESVTATVAAIVEKFGRIDILHNNAGVTVRKAMADLSEKEWDFVLDVGLKGLFLMS 127

Query: 124 QAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCN 183
           +    +M + G GGSIV   S   L GG+    Y   K G+ ++ ++ AI  GK+ IR N
Sbjct: 128 KHVIPEMQKVG-GGSIVNTGSGWGLKGGDLAAAYCAVKGGIVNVTRAMAIDYGKYNIRVN 186

Query: 184 SVLPGTILT-----------EINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLAS 232
           SV PG  +T           EI  D   D   +     R PL R+G PED+A  ++FL S
Sbjct: 187 SVNPGDTVTAMMVSEGRQTGEIKSDADIDAFLKSCGSGR-PLARIGQPEDIANGVLFLCS 245

Query: 233 DMAAYVTGAALLVDGG 248
            +A++VTGAAL+VDGG
Sbjct: 246 GLASWVTGAALVVDGG 261


Lambda     K      H
   0.318    0.133    0.379 

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: 138
Number of extensions: 6
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: 254
Length of database: 264
Length adjustment: 24
Effective length of query: 230
Effective length of database: 240
Effective search space:    55200
Effective search space used:    55200
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