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_040658761.1 ON16_RS01385 glucose 1-dehydrogenase

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



>NCBI__GCF_000307265.1:WP_040658761.1
          Length = 245

 Score =  151 bits (382), Expect = 1e-41
 Identities = 99/246 (40%), Positives = 131/246 (53%), Gaps = 10/246 (4%)

Query: 7   KTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKGDVA 66
           K  LVTG   GIGRA A   A+ G DVA+NY  S   A+  V E+   G RA A + DVA
Sbjct: 3   KVALVTGGGRGIGRAIARKLAEQGYDVAVNYQQSRAVAEELVNELRQAGCRAGAFQADVA 62

Query: 67  DPQTAQDFVAKAVETFGKVDVMVSNAGIC-PFHAFLDMPVDVVERTFKVNLHGAYFMVQA 125
           +P   +  +       G V+ +V+NAGI  P   F D+  +   R F VN+ G   +++A
Sbjct: 63  EPNAVKAMLHAVETELGPVETLVNNAGIALPGGLFQDVDDETWNRAFAVNVGGMRNVIRA 122

Query: 126 AAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCNSV 185
               M+ +   GSIV +SSI  L G   +  Y  TKA V  L +S A+ L    IR N+V
Sbjct: 123 VLPHMLHEKR-GSIVNLSSIWGLRGASCEVTYACTKAAVVGLTRSLALELAPSHIRVNAV 181

Query: 186 LPGTILTEINKDDLADQEKREYMEA---RTPLGRLGAPEDLAGPIVFLASDMAAYVTGAA 242
            PG I T     D+     RE M+A    TPLGRLG PED+A  + FLA + A+++TG  
Sbjct: 182 APGCIDT-----DMVSSLGRETMDALAQDTPLGRLGTPEDIAAAVAFLAGEDASFITGQV 236

Query: 243 LLVDGG 248
           L  DGG
Sbjct: 237 LTADGG 242


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: 141
Number of extensions: 6
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: 254
Length of database: 245
Length adjustment: 24
Effective length of query: 230
Effective length of database: 221
Effective search space:    50830
Effective search space used:    50830
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: 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