GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Marivita geojedonensis DPG-138

Align Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized, see rationale)
to candidate WP_085641330.1 MGEO_RS19085 gamma-glutamyl-gamma-aminobutyrate hydrolase family protein

Query= uniprot:Q72EV2_DESVH
         (209 letters)



>NCBI__GCF_002115805.1:WP_085641330.1
          Length = 237

 Score = 46.6 bits (109), Expect = 4e-10
 Identities = 40/117 (34%), Positives = 55/117 (47%), Gaps = 20/117 (17%)

Query: 70  LPRTVPVLGVCLGHQVLGLYAGATVEVGPRIMHGK--------------TSDITHDGAGL 115
           L R +PVLG+C G Q+L +  G T++      +G+                D TH    L
Sbjct: 89  LERNIPVLGICRGSQMLNVALGGTLDQDAWGTYGRERMIKTVLPKREIHVEDRTH--LSL 146

Query: 116 FAGLPQPMTVGRYHSLIVRAEEKPDLLEVTARTPEGEVMAM-RYRDRPWVGVQFHPE 171
            +G   PM V   H+  V  +   D L V+AR   G V A+ R RD   +GVQ+HPE
Sbjct: 147 ISG-NDPMKVNALHTQAV--DRLGDGLRVSARDTGGMVQAVERVRDPFALGVQWHPE 200


Lambda     K      H
   0.323    0.141    0.444 

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: 129
Number of extensions: 6
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: 209
Length of database: 237
Length adjustment: 22
Effective length of query: 187
Effective length of database: 215
Effective search space:    40205
Effective search space used:    40205
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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