GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Shewanella amazonensis SB2B

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 6937211 Sama_1381 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)

Query= BRENDA::Q8GR61
         (262 letters)



>FitnessBrowser__SB2B:6937211
          Length = 252

 Score =  106 bits (265), Expect = 4e-28
 Identities = 77/263 (29%), Positives = 120/263 (45%), Gaps = 27/263 (10%)

Query: 8   KVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCDVTS 67
           KV ++TG  G +GLA A  LA  G  +AL+D+++E LE+A A + +   E + Y  D+T 
Sbjct: 6   KVIVITGGAGGLGLAMAKDLAAHGAKLALIDVDQERLERACADIGD-ATEVQGYALDITD 64

Query: 68  EEAVIGTVDSVVRDFGKIDFLFNNAGY--QGAFAPVQD------YPSDDFARVLTINVTG 119
           EE V+     ++ DFG I  L NNAG    G     +D         D F  V+ +N+TG
Sbjct: 65  EEDVVAGFRYILEDFGVIHGLVNNAGILRDGLLIKAKDGVVTDRMSLDQFQSVINVNLTG 124

Query: 120 AFHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYN 179
            F   +  +  MI    G ++   S     G      Y  SK  +  +    A +LA +N
Sbjct: 125 TFLCGREAAAAMIESGQGGVIVNISSLARAGNMGQTNYAASKAGVATMAVGWAKELARFN 184

Query: 180 IRVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPG 239
           IR  A++PG +          E+ A +  +          +++   VP+ R G   EI  
Sbjct: 185 IRAAAVAPGVIA--------TEMTAAMKPE--------ALERLEKMVPVGRLGQAEEIAS 228

Query: 240 VVAFLLGDDSSFMTGVNLPIAGG 262
            V F++ +D  ++ G    I GG
Sbjct: 229 TVRFIMEND--YVNGRVFEIDGG 249


Lambda     K      H
   0.318    0.135    0.384 

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: 144
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: 262
Length of database: 252
Length adjustment: 24
Effective length of query: 238
Effective length of database: 228
Effective search space:    54264
Effective search space used:    54264
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