GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glyXS in Desulforamulus ruminis DSM 2154

Align UPF0237 protein MMP0657 (characterized, see rationale)
to candidate WP_013842373.1 DESRU_RS12000 ACT domain-containing protein

Query= uniprot:Q6LZH1
         (90 letters)



>NCBI__GCF_000215085.1:WP_013842373.1
          Length = 100

 Score =  102 bits (253), Expect = 1e-27
 Identities = 46/87 (52%), Positives = 68/87 (78%)

Query: 4   VVITVVGVDKPGIVAEVTKVLAQNSANIVDIRQTIMEDLFTMIMLVDISKISSDFSELNV 63
           V+ITV+G D+ GI+A V+ VLA+N  NI+DI QTI++  F+M+++ DI K +S+ S+L  
Sbjct: 14  VIITVIGQDRVGIIAGVSGVLAENKVNILDISQTILQGFFSMVLVADIEKSTSELSKLKE 73

Query: 64  ALEKLGSEIGVKINVQHENIFKYMHRI 90
            L +LG E+GVKI+ QHE++F+YMHRI
Sbjct: 74  KLNQLGQELGVKIDAQHEDVFRYMHRI 100


Lambda     K      H
   0.320    0.136    0.355 

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: 50
Number of extensions: 4
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: 90
Length of database: 100
Length adjustment: 10
Effective length of query: 80
Effective length of database: 90
Effective search space:     7200
Effective search space used:     7200
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: 39 (20.9 bits)
S2: 39 (19.6 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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