GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Paraburkholderia bryophila 376MFSha3.1

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate H281DRAFT_05213 H281DRAFT_05213 gluconate 2-dehydrogenase

Query= curated2:B1L765
         (332 letters)



>FitnessBrowser__Burk376:H281DRAFT_05213
          Length = 321

 Score =  268 bits (685), Expect = 1e-76
 Identities = 146/323 (45%), Positives = 206/323 (63%), Gaps = 6/323 (1%)

Query: 4   RVFVTREIPERGLSKIEEHFELDLWKDEAPPSKKVIIERVKDCDALVSLLTDPIDAEVFE 63
           ++   + +PE  L+ +++H E+       P      +  ++D D  +      I   + E
Sbjct: 3   KIVAWKSLPEDVLAYLQQHVEV---VQVDPAQHDAFVAALRDADGGIGASVK-ITPAMLE 58

Query: 64  AAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARRVVEAD 123
            A +L+ ++  +VG+D  DV + T+RGI + +TP VLTE+TAD  F+L++A+ARRVVE  
Sbjct: 59  GATRLKALSTISVGFDQFDVADLTRRGIVLAHTPDVLTESTADTVFSLILASARRVVELA 118

Query: 124 RYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARRAK-GFGMRILYYDSIRRE 182
            +V+ G+W+ +  P    G DV G+TLGIVG+GRIG AVARRA  GF M++LY +     
Sbjct: 119 AWVKAGQWQQSIGPAQF-GVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANR 177

Query: 183 DFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNTSRGKVV 242
           + E+  G   V L +LL  +DFV L VPLT +T HMIG ++L  MK++AIL+N SRG  V
Sbjct: 178 EAEEAYGARRVELPELLANADFVCLQVPLTPQTRHMIGAKELSSMKKSAILINASRGATV 237

Query: 243 DQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKLENVVLAPHAASASHETRSRMAEMV 302
           D+KAL +AL+ G I GAGLDVFE EP+P D PLLKL NVV  PH  SA+ ETR  MA   
Sbjct: 238 DEKALIEALQNGTIHGAGLDVFETEPLPADSPLLKLANVVALPHIGSATRETRHAMARNA 297

Query: 303 AENLIAFKRGEIPPNLVNQEVVK 325
           AENL+A   G +  N+VN+EV++
Sbjct: 298 AENLVAALNGTLTTNIVNREVLQ 320


Lambda     K      H
   0.319    0.137    0.398 

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: 245
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: 332
Length of database: 321
Length adjustment: 28
Effective length of query: 304
Effective length of database: 293
Effective search space:    89072
Effective search space used:    89072
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: 48 (23.1 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