GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Sphingomonas indica Dd16

Align Phosphoglycerate mutase (characterized, see rationale)
to candidate WP_085218187.1 B9N75_RS07190 2,3-diphosphoglycerate-dependent phosphoglycerate mutase

Query= uniprot:A0A0H2XA29
         (214 letters)



>NCBI__GCF_900177405.1:WP_085218187.1
          Length = 228

 Score = 49.7 bits (117), Expect = 4e-11
 Identities = 36/126 (28%), Positives = 56/126 (44%), Gaps = 8/126 (6%)

Query: 3   ILLARHGETPWNAEGRYQGQIDIPLSPVGEGQGAALGARLQALQITRAVASPLSRAQATA 62
           ++L RHG++ WN E R+ G  D+ L+P GE +  A G  L    +   +     + +A  
Sbjct: 4   LVLIRHGQSAWNLENRFTGWWDVNLTPQGEAEAKAAGELLAERGLDFDICFTSLQTRAIK 63

Query: 63  TLALGSARAGLLQTDAD----LQEIAHGEWEGLLASEINDKDPA-RLRAWREE---PDTV 114
           TL +     G L    +    L E  +G   GL  +E   K  A ++  WR     P   
Sbjct: 64  TLNIALEAMGRLWLPVEKHWRLNERHYGGLTGLDKAETAAKHSAEQVHIWRRSFDIPPPA 123

Query: 115 LMPGGE 120
           + PGG+
Sbjct: 124 MEPGGD 129


Lambda     K      H
   0.319    0.135    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: 136
Number of extensions: 9
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: 214
Length of database: 228
Length adjustment: 22
Effective length of query: 192
Effective length of database: 206
Effective search space:    39552
Effective search space used:    39552
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 (21.8 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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