GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_4374 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase (EC 2.3.1.89)

Query= curated2:Q8TY70
         (245 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4374
          Length = 221

 Score = 81.6 bits (200), Expect = 1e-20
 Identities = 46/124 (37%), Positives = 65/124 (52%), Gaps = 9/124 (7%)

Query: 103 IEPGAIIREKVKLGKGVVVMMGAVINIGAKIGDGTMVDMNAVVGSRAEVGKNVHIGAGAV 162
           I PG I    + +G G  +  G ++     +GD T +   +VVG   ++G +V +  G  
Sbjct: 94  IHPG-IDLTMITMGVGTYLQEGVIMQAQVSLGDNTSISAGSVVGHEGQIGHSVFMAPGVC 152

Query: 163 IAGVLEPPSAKPVVIEDDVVIGANAVILEGVRVGKGAVVAAGAVVTEDVPPSKVVAGVPA 222
           IAG +E        I D   IG NA IL  +R+G+   + AGAVVT+DVP   VV G PA
Sbjct: 153 IAGCVE--------IGDGTFIGTNATILPRLRIGRWVTIGAGAVVTKDVPDYAVVVGSPA 204

Query: 223 RVVK 226
           R +K
Sbjct: 205 RTIK 208


Lambda     K      H
   0.315    0.136    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: 120
Number of extensions: 12
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 245
Length of database: 221
Length adjustment: 23
Effective length of query: 222
Effective length of database: 198
Effective search space:    43956
Effective search space used:    43956
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: 42 (22.0 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 (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