GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Thiothrix lacustris DSM 21227

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_211248857.1 Q394_RS0118475 glucose 1-dehydrogenase

Query= BRENDA::Q8GR61
         (262 letters)



>NCBI__GCF_000621325.1:WP_211248857.1
          Length = 255

 Score =  103 bits (256), Expect = 5e-27
 Identities = 75/256 (29%), Positives = 114/256 (44%), Gaps = 15/256 (5%)

Query: 7   GKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCDVT 66
           GKV ++TGA   IG A A     EG  + L     E  E   A++R  G EA     DV 
Sbjct: 11  GKVVVITGASSGIGEAAAHAFGREGCKLVLGARRAEEGEAVAAAIRATGGEAVFVCTDVL 70

Query: 67  SEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVLKA 126
            E  +   V + +  FG +D LFNNAG +G  +   +  + ++   +  NV      ++ 
Sbjct: 71  QEADIARLVQTALDTFGGLDVLFNNAGTEGVSSAFTEQSTAEYDFTMNTNVRSVLWGMQH 130

Query: 127 VSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNAIS 186
             R M +   G I+N AS+    G  N A Y  SK A++ +T  AA++     IR+NA+ 
Sbjct: 131 AIRAMQSAG-GAIINNASIVAHVGFANTALYSASKAAVVGMTRVAAVEYFKQGIRINAVC 189

Query: 187 PGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFLLG 246
           PG              Q  +G +    D +      + + P  R G   EI   V FL  
Sbjct: 190 PGITYTPMS-------QRLLGGE----DEQ---NAFMATTPAGRTGQPEEIAAAVVFLAS 235

Query: 247 DDSSFMTGVNLPIAGG 262
            ++S+++G  L + GG
Sbjct: 236 GNASYISGQCLNVDGG 251


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: 143
Number of extensions: 9
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: 262
Length of database: 255
Length adjustment: 24
Effective length of query: 238
Effective length of database: 231
Effective search space:    54978
Effective search space used:    54978
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