GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-dehydr in Desulfarculus baarsii DSM 2075

Align Prephenate dehydrogenase (characterized, see rationale)
to candidate WP_013257307.1 DEBA_RS02390 prephenate dehydrogenase/arogenate dehydrogenase family protein

Query= uniprot:A0A1L6J750
         (249 letters)



>NCBI__GCF_000143965.1:WP_013257307.1
          Length = 259

 Score = 86.3 bits (212), Expect = 6e-22
 Identities = 61/179 (34%), Positives = 92/179 (51%), Gaps = 12/179 (6%)

Query: 51  AADCDVVMLAVPVQAMAATIAAIAPLVRPGALVLDVASVKMLPARWMLEALPESVDIVAT 110
           A +C V++LAVPV  M   +A + PL RP  LV+D+ S+K  P + ML      V  V  
Sbjct: 50  AQNCHVLVLAVPVGQMTTVMAELGPLTRPDGLVVDLCSLKETPLQAMLAHARGQV--VGC 107

Query: 111 HPLFGPQSARGGLEGQPLVVCAVRGERH-HKVAEFGRSLGLSVSITTAEEHDREMAYVQA 169
           HPLFGP +   GL+GQ + +C  RG+    ++  F  +   +V   TA EHD+ MA VQ+
Sbjct: 108 HPLFGPTA--NGLDGQTVFLCPGRGQSWLERLQNFLHTQNANVVSLTATEHDKLMAIVQS 165

Query: 170 LTHL----IGRALVNIRIPDEELKTNS---YQHLLELCGLIRDDSKELFFAIQNLNPYA 221
           L H+    +G+ L N  I  + +   +   + HL +L          L+  +   NP+A
Sbjct: 166 LRHILVAALGQTLANSDINLKAILPMAGPWFNHLAQLLQNQAAQPASLYAHLATQNPHA 224


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: 136
Number of extensions: 10
Number of successful extensions: 4
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: 259
Length adjustment: 24
Effective length of query: 225
Effective length of database: 235
Effective search space:    52875
Effective search space used:    52875
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: 47 (22.7 bits)

This GapMind analysis is from Jul 25 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