GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xdhA in Magnetospirillum magneticum AMB-1

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_011384971.1 AMB_RS13035 NAD(P)-dependent oxidoreductase

Query= BRENDA::Q8GR61
         (262 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384971.1 AMB_RS13035
           NAD(P)-dependent oxidoreductase
          Length = 248

 Score =  135 bits (339), Expect = 1e-36
 Identities = 83/259 (32%), Positives = 129/259 (49%), Gaps = 17/259 (6%)

Query: 4   KFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVC 63
           KF  KV L+TG    IG  T   +AE G  + + D+N EA EKA A +  KG +A     
Sbjct: 2   KFEDKVALITGGASGIGYCTVKSMAELGADVLIADINVEAGEKAAAELTAKGFKAEFVRL 61

Query: 64  DVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHV 123
           DVT +  +    + VV   G++D L N AG+ G   P  D      A+V+++N+TG   +
Sbjct: 62  DVTDKANIARVKEHVVATRGRLDILCNVAGW-GHIQPFVDNDDAFIAKVMSLNLTGPIEL 120

Query: 124 LKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVN 183
           ++A    MI +  G+IVN AS AG  G    + Y  +KG +IA ++  A + A +NI VN
Sbjct: 121 IRAFFPLMIEKKTGKIVNVASDAGRVGSLGESVYSAAKGGLIAFSKALAREGARFNINVN 180

Query: 184 AISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAF 243
           AI PG                   +    ++P+   +  +  +PMRR+G   E+   + F
Sbjct: 181 AICPG----------------PTDTPLLKSEPEKFLEAFLKVIPMRRFGQPQEVADSIVF 224

Query: 244 LLGDDSSFMTGVNLPIAGG 262
           +  + + ++TG  L + GG
Sbjct: 225 MASNRADYITGQVLSVNGG 243


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: 248
Length adjustment: 24
Effective length of query: 238
Effective length of database: 224
Effective search space:    53312
Effective search space used:    53312
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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