GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagB in Sinorhizobium meliloti 1021

Align Glutamine--fructose-6-phosphate aminotransferase [isomerizing]; EC 2.6.1.16 (characterized, see rationale)
to candidate SM_b21218 SM_b21218 sugar-processing protein

Query= uniprot:Q92VI1
         (339 letters)



>lcl|FitnessBrowser__Smeli:SM_b21218 SM_b21218 sugar-processing
           protein
          Length = 339

 Score =  637 bits (1643), Expect = 0.0
 Identities = 339/339 (100%), Positives = 339/339 (100%)

Query: 1   MSISKDRPAGLIAIDREMARQHADAIASYEGATATAQRIAASLKSTGRLLLLGMGGSHAV 60
           MSISKDRPAGLIAIDREMARQHADAIASYEGATATAQRIAASLKSTGRLLLLGMGGSHAV
Sbjct: 1   MSISKDRPAGLIAIDREMARQHADAIASYEGATATAQRIAASLKSTGRLLLLGMGGSHAV 60

Query: 61  GRAVEPLYRALGIEAVAVPLSEQLGEPLSIEGKTILVTSQSGESAEVLRWFRETDGGTSE 120
           GRAVEPLYRALGIEAVAVPLSEQLGEPLSIEGKTILVTSQSGESAEVLRWFRETDGGTSE
Sbjct: 61  GRAVEPLYRALGIEAVAVPLSEQLGEPLSIEGKTILVTSQSGESAEVLRWFRETDGGTSE 120

Query: 121 TFGLTLEEDAFLAKAVPSLVGSGGTERAFAATRSLTVTFALHLAVLAALGADPADALRAL 180
           TFGLTLEEDAFLAKAVPSLVGSGGTERAFAATRSLTVTFALHLAVLAALGADPADALRAL
Sbjct: 121 TFGLTLEEDAFLAKAVPSLVGSGGTERAFAATRSLTVTFALHLAVLAALGADPADALRAL 180

Query: 181 RDPEAPVIDGALAALADVGAIVTSGRKLQGLAEAIALGLTELSRLPCFSLEGGQLRHGPM 240
           RDPEAPVIDGALAALADVGAIVTSGRKLQGLAEAIALGLTELSRLPCFSLEGGQLRHGPM
Sbjct: 181 RDPEAPVIDGALAALADVGAIVTSGRKLQGLAEAIALGLTELSRLPCFSLEGGQLRHGPM 240

Query: 241 EMLGASVGVVLFRAADPTAKLVGAMATSAAEAGSPVIVFDASDESPAAGATTIRFKPAAG 300
           EMLGASVGVVLFRAADPTAKLVGAMATSAAEAGSPVIVFDASDESPAAGATTIRFKPAAG
Sbjct: 241 EMLGASVGVVLFRAADPTAKLVGAMATSAAEAGSPVIVFDASDESPAAGATTIRFKPAAG 300

Query: 301 LAAILAMLPVAQSLMIAFADARVENAGTPVRSTKVTRSE 339
           LAAILAMLPVAQSLMIAFADARVENAGTPVRSTKVTRSE
Sbjct: 301 LAAILAMLPVAQSLMIAFADARVENAGTPVRSTKVTRSE 339


Lambda     K      H
   0.316    0.131    0.356 

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: 494
Number of extensions: 12
Number of successful extensions: 1
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: 339
Length of database: 339
Length adjustment: 28
Effective length of query: 311
Effective length of database: 311
Effective search space:    96721
Effective search space used:    96721
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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