GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapH in Pseudomonas putida KT2440

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 PP_3392 PP_3392 conserved protein of unknown function

Query= curated2:Q9CIS5
         (256 letters)



>lcl|FitnessBrowser__Putida:PP_3392 PP_3392 conserved protein of
           unknown function
          Length = 174

 Score = 62.8 bits (151), Expect = 5e-15
 Identities = 43/134 (32%), Positives = 70/134 (52%), Gaps = 19/134 (14%)

Query: 115 EPGAIIRDQVTIGDSAVIMMGAII---NIGAEIGEGTMIDMGAIL----GGRATVGKNSH 167
           E  ++I D VT+     +   A++   N    IG+ + +  GA+L    G   TVG+   
Sbjct: 21  EDASVIGD-VTLEQGVSVWPQAVLRGDNEAIRIGQHSNVQEGAVLHADPGFALTVGQGVT 79

Query: 168 IGAGAVLAGVIEPASAEPVRVGDNVLVGANAVVIEGVQVGSGSVVAAGAIVTQD--VPEN 225
           IG  A+L G           +GD  L+G  AVV+ G  +G+  +V AGAIVT+    P+N
Sbjct: 80  IGHQAMLHGCT---------IGDGALIGIQAVVLNGAVIGNNCLVGAGAIVTEGKVFPDN 130

Query: 226 VVVAGVPARIIKEI 239
            ++ G PA++++E+
Sbjct: 131 SLILGAPAKVVREL 144


Lambda     K      H
   0.316    0.135    0.368 

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: 128
Number of extensions: 10
Number of successful extensions: 5
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: 256
Length of database: 174
Length adjustment: 21
Effective length of query: 235
Effective length of database: 153
Effective search space:    35955
Effective search space used:    35955
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 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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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