GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Enterococcus termitis LMG 8895

Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate WP_069665046.1 BCR25_RS18255 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

Query= BRENDA::A0A0H2UNY1
         (205 letters)



>NCBI__GCF_001730305.1:WP_069665046.1
          Length = 233

 Score = 55.8 bits (133), Expect = 6e-13
 Identities = 39/120 (32%), Positives = 59/120 (49%), Gaps = 2/120 (1%)

Query: 67  IHPGAQIDSGVFIDHGSGLVIGETAIVEKGVLLYHGVTLGGTGKDCGKRHPTVRKGALIS 126
           I+ GA I  G  ID G+  ++G  A V K   +  G  L G  +    +   +    LI 
Sbjct: 115 INIGAVIGEGTMIDMGA--ILGGRATVGKQCHIGAGTVLAGVVEPPSAQPVIIEDNVLIG 172

Query: 127 AHAQVIGPVEIGENAKVGAAAVVVADVPSDVTVVGIPAKIVRLHGKKDEPVIHEVEEKRE 186
           A+A V+  V +GE A V A A+VV DV     V G+PA+ ++   +K +     +EE R+
Sbjct: 173 ANAVVLEGVRVGEGAVVAAGAIVVDDVAPYTVVAGVPARKIKDIDEKTKSKTTMLEELRK 232


Lambda     K      H
   0.319    0.137    0.418 

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: 101
Number of extensions: 9
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: 205
Length of database: 233
Length adjustment: 22
Effective length of query: 183
Effective length of database: 211
Effective search space:    38613
Effective search space used:    38613
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: 45 (21.9 bits)

This GapMind analysis is from Jul 26 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