GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Rhizobium etli CFN 42

Align BadH (characterized)
to candidate WP_004671535.1 RHE_RS29990 SDR family oxidoreductase

Query= metacyc::MONOMER-893
         (255 letters)



>NCBI__GCF_000092045.1:WP_004671535.1
          Length = 255

 Score =  156 bits (394), Expect = 4e-43
 Identities = 85/247 (34%), Positives = 128/247 (51%), Gaps = 3/247 (1%)

Query: 4   LQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCD 63
           L  +  ++TGGG GIG AT   FA+ GA + V D+N DAA +VA  I   G  A  VR D
Sbjct: 3   LNQRVCIVTGGGSGIGRATAELFAKNGAYVVVADVNEDAAVRVANEI---GSKAFGVRVD 59

Query: 64  IADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHH 123
           ++     ++ +  TT   G VD+LVNNAG+             W+R++++N+ G      
Sbjct: 60  VSSAKDAESMVEKTTAKWGRVDVLVNNAGFGTTGNVVTIPEETWDRIMSVNVKGIFLCSK 119

Query: 124 AVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVV 183
            V+P M     G I+N  S  A    +    Y A KG + + ++ +A +HA+ GI VN V
Sbjct: 120 YVIPVMRRNGGGSIINTTSYTATSAIADRTAYVASKGAISSLTRAMAMDHAKEGIRVNAV 179

Query: 184 CPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQ 243
            PG  D+     + + A +P KL   F     + R+G  +++A A+ F  SD + F TG 
Sbjct: 180 APGTIDSPYFTKIFAEAKDPAKLRSDFNARAVMDRMGTAEEIAEAMLFLASDRSRFATGS 239

Query: 244 VLSVSGG 250
           +L+V GG
Sbjct: 240 ILTVDGG 246


Lambda     K      H
   0.318    0.135    0.398 

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: 159
Number of extensions: 9
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: 255
Length of database: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
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 Apr 09 2024. 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