GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Burkholderia phytofirmans PsJN

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate BPHYT_RS04770 BPHYT_RS04770 short-chain dehydrogenase

Query= BRENDA::Q8GR61
         (262 letters)



>FitnessBrowser__BFirm:BPHYT_RS04770
          Length = 246

 Score =  160 bits (404), Expect = 3e-44
 Identities = 95/259 (36%), Positives = 138/259 (53%), Gaps = 17/259 (6%)

Query: 4   KFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVC 63
           + NGKV +VTGAG  IG ATAL+ A+EG  +A+ D+N +A+ +  A+    G +A  +  
Sbjct: 2   RLNGKVTIVTGAGQGIGAATALKFAKEGARVAVCDVNHDAVSRVVAACHAAGAQALGFTL 61

Query: 64  DVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHV 123
           DVT+  AV G V  V   F +ID L NNAG     A +Q      F  V+ +N+ G FH 
Sbjct: 62  DVTNRAAVDGMVADVRERFRQIDVLVNNAGIT-RDARLQKMTLQQFDDVIDVNLRGVFHA 120

Query: 124 LKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVN 183
            +AV   MI Q  G I+N +S+ G+ G      Y  +K  +I  T+T + +L P  IRVN
Sbjct: 121 AQAVVDTMIAQGSGVILNASSVVGLYGNYGQTNYAAAKFGVIGFTKTWSRELGPKGIRVN 180

Query: 184 AISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAF 243
           AI+PG+                + +   ST P+ V  +M   VP+RR G   EI  + AF
Sbjct: 181 AIAPGF----------------IDTPILSTVPQEVLAKMREQVPLRRLGTPEEIANIYAF 224

Query: 244 LLGDDSSFMTGVNLPIAGG 262
           L  D++S++ G  +  +GG
Sbjct: 225 LASDEASYINGAVIEASGG 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: 172
Number of extensions: 6
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: 246
Length adjustment: 24
Effective length of query: 238
Effective length of database: 222
Effective search space:    52836
Effective search space used:    52836
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