GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Escherichia coli BW25113

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 14480 b0342 galactoside O-acetyltransferase (NCBI)

Query= curated2:B1IMX1
         (236 letters)



>FitnessBrowser__Keio:14480
          Length = 203

 Score = 68.6 bits (166), Expect = 9e-17
 Identities = 53/161 (32%), Positives = 79/161 (49%), Gaps = 23/161 (14%)

Query: 75  EQDRRKSAIP-LLDMLKVNARIEPGAIIR--DKVLIGEN--AVIMMGAVINIGAEIGEGT 129
           E ++R+S I  +   +  NA +EP         + IG N  A   +  V +    IG+  
Sbjct: 43  EVEKRESLIKEMFATVGENAWVEPPVYFSYGSNIHIGRNFYANFNLTIVDDYTVTIGDNV 102

Query: 130 MVDMNAVVGARG-----KLGKNVHLGAGAVVAGVLEPPSSDPCTIEDNVLIGANAVILEG 184
           ++  N  +   G     +L KN  +              S P TI +NV IG++ VI  G
Sbjct: 103 LIAPNVTLSVTGHPVHHELRKNGEM-------------YSFPITIGNNVWIGSHVVINPG 149

Query: 185 VKIGKGSVVAAGSIVTTDVPENVVVAGAPAKIIKEVDVKTK 225
           V IG  SV+ AGSIVT D+P NVV AG P ++I+E++ + K
Sbjct: 150 VTIGDNSVIGAGSIVTKDIPPNVVAAGVPCRVIREINDRDK 190


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: 133
Number of extensions: 13
Number of successful extensions: 3
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: 236
Length of database: 203
Length adjustment: 22
Effective length of query: 214
Effective length of database: 181
Effective search space:    38734
Effective search space used:    38734
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: 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:

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