GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Dethiosulfovibrio salsuginis USBA 82

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_085544045.1 B9Y55_RS03840 hydroxyacid dehydrogenase

Query= reanno::BFirm:BPHYT_RS11290
         (321 letters)



>NCBI__GCF_900177735.1:WP_085544045.1
          Length = 316

 Score =  137 bits (346), Expect = 3e-37
 Identities = 97/274 (35%), Positives = 143/274 (52%), Gaps = 9/274 (3%)

Query: 36  VAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVL 95
           V  L  AD  I +++ +   ++    RLK +S    G+D  D+     + I ++N     
Sbjct: 43  VKRLAGADVAIIANMPLGGQVISSCDRLKMISVAFTGYDHVDMESCLSKRITVSNCAGYS 102

Query: 96  TESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGA 155
           T+S  +    L LA  R++V     V+AG  +      L G  + GKT+GIVG G IG  
Sbjct: 103 TDSVVELALGLSLAVVRKIVPCDGAVRAGKTKDG----LIGNQLAGKTVGIVGTGAIGVK 158

Query: 156 VARR-AALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLI 214
           VA    ALG N  V+  +RS   +   + G   + L +L+++ D + L +P   ET  LI
Sbjct: 159 VAAVFKALGCN--VVAYSRSQRDEVL-SMGIPYLSLKDLMSSCDLISLHLPCNGETAGLI 215

Query: 215 GAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETE-PLPSDSPLLKL 273
               + SMK+S+ LIN +RG  VD KAL +AL++G+I GAG+DVF+ E PL    PLL  
Sbjct: 216 DRDMISSMKRSSFLINTARGPIVDNKALADALKSGSIAGAGIDVFDMEPPLLEGYPLLDA 275

Query: 274 ANVVALPHIGSATHETRHAMARNAAENLVAALDG 307
            N V  PH+  AT E   + A  A +N+   +DG
Sbjct: 276 PNCVLTPHVAFATPEALQSRAVIAIDNVRLWMDG 309


Lambda     K      H
   0.317    0.131    0.366 

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: 192
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: 321
Length of database: 316
Length adjustment: 27
Effective length of query: 294
Effective length of database: 289
Effective search space:    84966
Effective search space used:    84966
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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