GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Vagococcus penaei CD276

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_077276827.1 BW732_RS11280 3-oxoacyl-[acyl-carrier-protein] reductase

Query= metacyc::MONOMER-16230
         (256 letters)



>NCBI__GCF_001998885.1:WP_077276827.1
          Length = 244

 Score =  158 bits (400), Expect = 9e-44
 Identities = 97/254 (38%), Positives = 150/254 (59%), Gaps = 12/254 (4%)

Query: 2   LLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAG-ALSLAEEIAAFGGTA 60
           +L +KTV++TG+SRGIG+  AR  A+QGA +V+       GR   +  L EEI +FG   
Sbjct: 1   MLKNKTVVITGSSRGIGQELARSFAKQGANIVLN------GRKPISKELIEEIESFGVKT 54

Query: 61  IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120
             V  D       E+L+  A E FGSVD+L+NNAGI      + M  + +   +  NL G
Sbjct: 55  HCVIGDIQYFAQAEQLILEAKEVFGSVDILINNAGITRDTLLMRMTEDDFNSVLQVNLTG 114

Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180
            + T++ A++ M +Q R G II ++S+  L G A Q +Y  +KAG++ L +S A  L   
Sbjct: 115 TFNTIKHASKIMLKQ-RSGIIINMASVVGLTGNAGQANYAASKAGVVGLTKSVARELASR 173

Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYV 240
           GI CNA+ PG I+TD+   D+ + + +E++  ++PL R+G   D+A   +FLA+  + Y+
Sbjct: 174 GITCNAIAPGYISTDMT--DVLNEKVKEQVVQQIPLRRIGSVTDVAQTAIFLAT--SPYI 229

Query: 241 TGASLLVDGGLFVN 254
           TG  + VDGG+ +N
Sbjct: 230 TGQVINVDGGMVMN 243


Lambda     K      H
   0.319    0.136    0.383 

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: 7
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: 256
Length of database: 244
Length adjustment: 24
Effective length of query: 232
Effective length of database: 220
Effective search space:    51040
Effective search space used:    51040
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