GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Megamonas funiformis YIT 11815

Align Glyoxylate reductase 1; EC 1.1.1.26 (characterized)
to candidate WP_008537918.1 HMPREF9454_RS03270 2-hydroxyacid dehydrogenase

Query= SwissProt::P53839
         (350 letters)



>NCBI__GCF_000245775.1:WP_008537918.1
          Length = 315

 Score =  118 bits (295), Expect = 2e-31
 Identities = 77/234 (32%), Positives = 116/234 (49%), Gaps = 18/234 (7%)

Query: 92  GYDQIDVEPFKKRHIQVANVPDLVSNATADTHVFLLLGALRNF---GIGNRRLIEGNWPE 148
           G D +D++   + +I V+N     + A ++  + + +   R     G+  +     N   
Sbjct: 82  GVDHVDMDYCHEHNILVSNCSGYANEAVSELVIGMCISLYRKLAECGMATKNHETSNGLR 141

Query: 149 AGPACGSPFGYDPEGKTVGILGLGRIGRCILERLKPFGFENFIYHNRHQLPSEEEHGCEY 208
               C   FG         I+G G IG  + +  K FG E + Y  R  +P   E   E+
Sbjct: 142 GLELCRKKFG---------IIGAGAIGLKVAKLAKAFGCEVYCY--RRHIPENSEF--EF 188

Query: 209 VGFEEFLKRSDIVSVNVPLNHNTHHLINAETIEKMKDGVVIVNTARGAVIDEQAMTDALR 268
           V  +  LK  DI+S+++PL   T  +INAE I  MK   +++NTARG VID QA+ DAL 
Sbjct: 189 VDMDTILKECDIISLHMPLTKETTSMINAEKIALMKKNAILINTARGKVIDTQALADALN 248

Query: 269 SGKIRSAGLDVFEYEPKISKE--LLSMSQVLGLPHMGTHSVETRKKMEELVVEN 320
            GKI  A +DVF+ EP I  E  LL+   V+  PH+G  + E  +K   + +EN
Sbjct: 249 KGKIAGASVDVFDTEPPIGAENPLLTAKNVVLSPHIGFDTQEAMQKRAIIALEN 302


Lambda     K      H
   0.317    0.136    0.396 

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: 268
Number of extensions: 15
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: 350
Length of database: 315
Length adjustment: 28
Effective length of query: 322
Effective length of database: 287
Effective search space:    92414
Effective search space used:    92414
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 (21.6 bits)
S2: 49 (23.5 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