GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Calditerrivibrio nitroreducens DSM 19672

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; EC 2.3.1.89; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase (uncharacterized)
to candidate WP_013452079.1 CALNI_RS10005 colanic acid biosynthesis acetyltransferase WcaF

Query= curated2:A7HJ58
         (249 letters)



>NCBI__GCF_000183405.1:WP_013452079.1
          Length = 183

 Score = 57.0 bits (136), Expect = 3e-13
 Identities = 50/157 (31%), Positives = 72/157 (45%), Gaps = 17/157 (10%)

Query: 88  IAHNSAIPLSDISKFNARIEPGAIIREYVEIGNNAVIMMGAVINLGAIIGEGTMIDMNTV 147
           I + S I +  +  F A+I    +I+  V I     + +G  +     IGE   ID  T 
Sbjct: 35  IPYPSKIKVLLLRIFGAKIGKNVVIKPCVNIKYPWFLKIGDNV----WIGENVWIDNLTT 90

Query: 148 IGARARIGKYCHIGAGSVIAGVVEPPSAQ-------PVIIEDNVVIGANAVILEGVRVGE 200
           +     IG    I  G+ I         Q       PVIIED V IGA A++  GVR   
Sbjct: 91  V----EIGNNVCISQGAYIFTGNHNYKTQSFDLIIKPVIIEDGVWIGAKAIVCPGVRCKS 146

Query: 201 HSVVAAGAVVVEDVPPYTVVAGVPAKVIKK--VDEKT 235
           HS+++ G+V  +D+  YTV  G PA   +K  +D+ T
Sbjct: 147 HSILSVGSVATKDLEEYTVYQGNPAVPKRKRIIDDGT 183


Lambda     K      H
   0.318    0.137    0.375 

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: 7
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: 249
Length of database: 183
Length adjustment: 22
Effective length of query: 227
Effective length of database: 161
Effective search space:    36547
Effective search space used:    36547
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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