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_077275113.1 BW732_RS01410 acetoin reductase

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



>NCBI__GCF_001998885.1:WP_077275113.1
          Length = 258

 Score =  137 bits (345), Expect = 2e-37
 Identities = 86/254 (33%), Positives = 130/254 (51%), Gaps = 12/254 (4%)

Query: 7   KTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKGDVA 66
           K  +VTG++ G+G+  A   A+ G  + ++  +S   A++ V E +  G   I V GDV+
Sbjct: 3   KVAVVTGSAGGLGKGIAERLARDGFSIVLHDINSQKLAET-VEEFKTNGFETIGVTGDVS 61

Query: 67  DPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMVQAA 126
                +  + +AVETFG++DV+V+NAG+      LD+    ++  F +N++G  F  QAA
Sbjct: 62  KKVDQESLITQAVETFGRLDVLVNNAGVDAVTPLLDITEKELQTIFNINVNGTVFGTQAA 121

Query: 127 AQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCNSVL 186
           A Q ++QG  G I+   SI+     +    Y  +K  V S   + A  L KH I  N+  
Sbjct: 122 ATQFIKQGEKGKIINACSIAGHESYDMLGTYCASKHAVRSFTHTAAKELAKHQITVNAYC 181

Query: 187 PGTILTEI-----------NKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMA 235
           PG   TE+           ++  L   E  E   A   L R   PED+A  + FLASD A
Sbjct: 182 PGIAKTEMWDRIDAAMVQHSQGRLKPGESFEQFTAGIALQRYQVPEDVANLVSFLASDEA 241

Query: 236 AYVTGAALLVDGGM 249
            Y+TG A+L DGG+
Sbjct: 242 DYITGQAILTDGGL 255


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: 121
Number of extensions: 6
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: 254
Length of database: 258
Length adjustment: 24
Effective length of query: 230
Effective length of database: 234
Effective search space:    53820
Effective search space used:    53820
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