GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacD in Azospirillum brasilense Sp245

Align D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized)
to candidate AZOBR_RS26635 AZOBR_RS26635 mandelate racemase

Query= metacyc::MONOMER-18070
         (393 letters)



>FitnessBrowser__azobra:AZOBR_RS26635
          Length = 393

 Score =  126 bits (317), Expect = 9e-34
 Identities = 109/362 (30%), Positives = 163/362 (45%), Gaps = 20/362 (5%)

Query: 26  VLVRVTTNDGRVGWGETVSALRAEAVAN-FVKKINTVLKGNDVFNVEKNRLEWYKHDFNM 84
           +LVR+TT+DG VGWGE      AE   +  +  +   L G       +   + Y    + 
Sbjct: 33  LLVRITTDDGLVGWGEGGQYGPAEPPESCIIDVLAPRLIGRRADQPVRVFEDLYSFCRDF 92

Query: 85  TISLESTTAYSAVDIASWDIIGKELGAPLYKLLGGKTRDKVLVYANGWYQNCVKPEDFAE 144
                   A SA+DIA WD+ GK L  P++ L+GG  RDKV  Y  G    C  P+ F +
Sbjct: 93  GQKGTYIEALSAIDIALWDLWGKSLNRPVHALMGGAFRDKVAAYGTG----CYYPDYFRD 148

Query: 145 KAKEIVKMGYKALKFDPFGPYFNDISKKGLDIAE--ERVKAVREAVGDNVDILIEHHGRF 202
             + +  +  +A ++   G     I    L IA+  ERV  VR+ +G +  I+++ +  +
Sbjct: 149 TPRMMAALAEEAQRYREAGLPAIKIKIGLLPIAQDIERVALVRDVLGPDTLIMVDANHAY 208

Query: 203 NANSAIMIAKRLEKYNPLFMEEPIHPEDVEGLRKYRNNTSLRIALGERIINKQQALYFMK 262
           N   AI I + LE+++  + EEP+ PED +G R+ R++  + IA GE    +      + 
Sbjct: 209 NTAGAIRIGRALERFDVRWFEEPVPPEDRQGYRRVRDSIDVPIAGGECEYTRYGFRELLA 268

Query: 263 EGLVDFLQADLYRIGGVTETKKVVGIAETFDVQMAFHNAQGPILNAVTLQFDAFIP---- 318
            G +D  Q DL   GG TE +K++ +     V    H     I  A  LQ  A  P    
Sbjct: 269 GGCIDIAQPDLCCAGGFTEWQKILALTTAHGVMTVPHIWGSGIALAAALQALATAPLVPY 328

Query: 319 --------NFLIQESFYDWFPSWKRELIYNGTPIDNGYAIIPERPGLGVEVNEKMLDSLK 370
                   N  + E      P     LI N T +D G   +P   GLGVEV+   L    
Sbjct: 329 TALGVPLQNEPMVEFDRTHNPLRDDLLIDNFTLVD-GCLALPGGAGLGVEVDPDQLARYT 387

Query: 371 VK 372
           V+
Sbjct: 388 VR 389


Lambda     K      H
   0.319    0.137    0.409 

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: 371
Number of extensions: 18
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 393
Length of database: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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 (21.7 bits)
S2: 50 (23.9 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