GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Sphingomonas koreensis DSMZ 15582

Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate Ga0059261_2906 Ga0059261_2906 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= metacyc::MONOMER-11802
         (255 letters)



>FitnessBrowser__Korea:Ga0059261_2906
          Length = 257

 Score =  117 bits (293), Expect = 2e-31
 Identities = 84/259 (32%), Positives = 130/259 (50%), Gaps = 11/259 (4%)

Query: 1   MHIANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAV--A 58
           M +  +  I++GAA G+G ATA +L E GA V L+D N + + ++A    D  R  V   
Sbjct: 5   MSLDGRSVIITGAAQGIGLATAHLLYELGAHVTLLDRNEERL-SEAASAFDAQRILVQCG 63

Query: 59  DISDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGS 118
            I+D      A+ A ++ FG++ GLVN AGI     +        L  +  VI+VNL G 
Sbjct: 64  SITDRSFVGRAMAAHIARFGAVDGLVNNAGITRTAMIEKMT----LEDWQAVIDVNLTGV 119

Query: 119 FNLLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARE 178
           FN+L+     M   A +     G I+N +S A   G IGQ  Y A+K  +  +T+ AARE
Sbjct: 120 FNMLQAVGTTMIARAKEGEANPGAIVNISSDAGRKGTIGQINYGAAKSGVLGITMSAARE 179

Query: 179 LARFGIRVMTIAPGIFETPMM-AGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIE-- 235
             R GIRV ++A G+ ET M     S++ R    + +P   R   P E A     ++   
Sbjct: 180 WGRHGIRVNSVAYGVVETEMTEIARSEKFRDRYLSNIPL-GRFLSPDEAAYSIAFLLSPA 238

Query: 236 NSMLNGEVIRLDGALRMAA 254
           ++ + G+ + ++G   + A
Sbjct: 239 SAFITGQHLSVNGGGHITA 257


Lambda     K      H
   0.318    0.131    0.358 

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: 134
Number of extensions: 4
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: 255
Length of database: 257
Length adjustment: 24
Effective length of query: 231
Effective length of database: 233
Effective search space:    53823
Effective search space used:    53823
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 17 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