GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_2 in Marivita geojedonensis DPG-138

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate WP_085635951.1 MGEO_RS06670 glycosyl transferase family protein

Query= curated2:B1I3Z8
         (346 letters)



>NCBI__GCF_002115805.1:WP_085635951.1
          Length = 316

 Score = 76.3 bits (186), Expect = 1e-18
 Identities = 66/208 (31%), Positives = 92/208 (44%), Gaps = 5/208 (2%)

Query: 15  LEQHEAEAVMAEIMDGEATSAQIGALLAGLRLKKETAAEIRGFARAMRARAEQVPTRHEL 74
           L + EA   M  ++   A  A IGALL  LR+K ETA EI GFA+A +     +P   ++
Sbjct: 20  LTRDEARDAMRSMLSEGAEPAAIGALLMLLRMKGETAEEIAGFAQAAQEWGPDLP---QV 76

Query: 75  VADTCGTGGDGAQTFNISTTAAFVVAGAGVPVAKHGNTAVSSRCGSADVLRHLGVNLDLT 134
             D         +       +A +VA AG  V  HG     +   +   L   G+ +  T
Sbjct: 77  DLDWPSYAAGRTRGHPWFLLSAKLVAEAGHTVLLHGFNGPDAAVRNG--LTDAGIGIADT 134

Query: 135 PAQMGACLDEVGIAFLFAPRLHRAMQHAAGPRKELGIRTVFNILGPLTNPVRPRVQVLGV 194
           PA +   L +  IA+L   + H  +      R  LG+R+  N +  + NP R R  V GV
Sbjct: 135 PATLSRLLAQDRIAYLPLEQWHPRLFDLLRLRDVLGLRSCINTICRMLNPARARASVQGV 194

Query: 195 FDAAVAELVADALAGLEVERAFVIHGAG 222
           F  +   L ADA   L  E   VI G G
Sbjct: 195 FHPSYRLLQADAATQLGWESLSVIKGGG 222


Lambda     K      H
   0.319    0.135    0.384 

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: 249
Number of extensions: 16
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: 346
Length of database: 316
Length adjustment: 28
Effective length of query: 318
Effective length of database: 288
Effective search space:    91584
Effective search space used:    91584
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: 49 (23.5 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