GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolG in Sphingomonas koreensis DSMZ 15582

Align Inositol 2-dehydrogenase 3; EC 1.1.1.18; Myo-inositol 2-dehydrogenase 3; MI 2-dehydrogenase 3 (uncharacterized)
to candidate Ga0059261_3126 Ga0059261_3126 Predicted dehydrogenases and related proteins

Query= curated2:A4FIQ1
         (338 letters)



>FitnessBrowser__Korea:Ga0059261_3126
          Length = 707

 Score = 52.4 bits (124), Expect = 4e-11
 Identities = 56/183 (30%), Positives = 85/183 (46%), Gaps = 13/183 (7%)

Query: 6   GVIGTGMIGQDHIRRLTRVVTGAEIVAVTDIDADRAASVAGGVGARTMPSGADVIGSADV 65
           G   TGM+     +    + T A    VT + A R      G  A T  S + + G++D 
Sbjct: 401 GNYATGMLIPVFKKAGATLDTIASKEGVTGVHAGRKF----GFAATTTDSDSLLAGTSD- 455

Query: 66  DAVLVTSWGPTHAEHVLAAIEAGKAVFCEKPLATEVEDCLRIVEA-ESARGKRLVQVGFM 124
            AV++T+   +H   V AA++AGK+VF EKPL   + +   I  A  +A G   + VG+ 
Sbjct: 456 -AVVITTRHNSHGAMVAAALKAGKSVFVEKPLCLTLAEQAEIETAYAAAGGAARLMVGYN 514

Query: 125 RRYDAGYREMKELVDAGGIGTPLMAHCVHRN--PTVPETYHSAMAAQ---DTAVHEIDTL 179
           RR+    ++MK L+ AG  G       V+    P    T +S +        A H +D L
Sbjct: 515 RRFAPQVQKMKVLL-AGVTGPKAFVMTVNAGAIPAEHWTQNSEIGGGRIIGEACHFVDLL 573

Query: 180 RWL 182
           R+L
Sbjct: 574 RFL 576


Lambda     K      H
   0.319    0.134    0.401 

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: 552
Number of extensions: 16
Number of successful extensions: 1
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: 338
Length of database: 707
Length adjustment: 34
Effective length of query: 304
Effective length of database: 673
Effective search space:   204592
Effective search space used:   204592
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: 52 (24.6 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