GapMind for Amino acid biosynthesis

 

Aligments for a candidate for pre-dehydr in Sphingomonas koreensis DSMZ 15582

Align Prephenate dehydrogenase (characterized, see rationale)
to candidate Ga0059261_2298 Ga0059261_2298 Prephenate dehydrogenase

Query= uniprot:A0A1L6J750
         (249 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_2298 Ga0059261_2298 Prephenate
           dehydrogenase
          Length = 249

 Score =  484 bits (1247), Expect = e-142
 Identities = 249/249 (100%), Positives = 249/249 (100%)

Query: 1   MKRFGIIGFGRFGQLAARHLRDHFSVVVTDTADVGEAAAAIGVKTGSLADAADCDVVMLA 60
           MKRFGIIGFGRFGQLAARHLRDHFSVVVTDTADVGEAAAAIGVKTGSLADAADCDVVMLA
Sbjct: 1   MKRFGIIGFGRFGQLAARHLRDHFSVVVTDTADVGEAAAAIGVKTGSLADAADCDVVMLA 60

Query: 61  VPVQAMAATIAAIAPLVRPGALVLDVASVKMLPARWMLEALPESVDIVATHPLFGPQSAR 120
           VPVQAMAATIAAIAPLVRPGALVLDVASVKMLPARWMLEALPESVDIVATHPLFGPQSAR
Sbjct: 61  VPVQAMAATIAAIAPLVRPGALVLDVASVKMLPARWMLEALPESVDIVATHPLFGPQSAR 120

Query: 121 GGLEGQPLVVCAVRGERHHKVAEFGRSLGLSVSITTAEEHDREMAYVQALTHLIGRALVN 180
           GGLEGQPLVVCAVRGERHHKVAEFGRSLGLSVSITTAEEHDREMAYVQALTHLIGRALVN
Sbjct: 121 GGLEGQPLVVCAVRGERHHKVAEFGRSLGLSVSITTAEEHDREMAYVQALTHLIGRALVN 180

Query: 181 IRIPDEELKTNSYQHLLELCGLIRDDSKELFFAIQNLNPYAEEITRQFIAEANGLLAESL 240
           IRIPDEELKTNSYQHLLELCGLIRDDSKELFFAIQNLNPYAEEITRQFIAEANGLLAESL
Sbjct: 181 IRIPDEELKTNSYQHLLELCGLIRDDSKELFFAIQNLNPYAEEITRQFIAEANGLLAESL 240

Query: 241 KAGNRSAAD 249
           KAGNRSAAD
Sbjct: 241 KAGNRSAAD 249


Lambda     K      H
   0.321    0.135    0.387 

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: 299
Number of extensions: 3
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: 249
Length of database: 249
Length adjustment: 24
Effective length of query: 225
Effective length of database: 225
Effective search space:    50625
Effective search space used:    50625
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 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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