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_013451244.1 CALNI_RS05615 gamma carbonic anhydrase family protein

Query= curated2:B1L0V4
         (236 letters)



>NCBI__GCF_000183405.1:WP_013451244.1
          Length = 178

 Score = 57.0 bits (136), Expect = 2e-13
 Identities = 40/133 (30%), Positives = 69/133 (51%), Gaps = 27/133 (20%)

Query: 103 DKVIIGENSVIMMGAVINIGAEIGEGTMVDMNAVVGARGKLGKNVHLGAGAVVAGVLEPP 162
           ++V IGE S +  G VI++          D    +     +GKNV +G  A + G     
Sbjct: 49  ERVEIGECSNVQDGTVIHVTK--------DKYPTI-----IGKNVTIGHNATLHG----- 90

Query: 163 SSDPCTIEDNVLIGANAVILEGIKIGKGSVVAAGSIVTTD--VPENVVVAGAPAKIIKEV 220
               C I+DNVL+G  A+IL+   I + +++AAG++V  +   P N ++ G+P K++K +
Sbjct: 91  ----CKIKDNVLVGIGAIILDNTVISENTIIAAGTLVPPNKTFPPNSLIMGSPGKVVKTL 146

Query: 221 DVKTKDKTKLLDD 233
              T ++ K + D
Sbjct: 147 ---TGEEIKSITD 156



 Score = 29.6 bits (65), Expect = 4e-05
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 7/57 (12%)

Query: 98  GAIIRDKVIIGENSVIMMGAVINIGAEIGEGTMVDMN-------AVVGARGKLGKNV 147
           G  I+D V++G  ++I+   VI+    I  GT+V  N        ++G+ GK+ K +
Sbjct: 90  GCKIKDNVLVGIGAIILDNTVISENTIIAAGTLVPPNKTFPPNSLIMGSPGKVVKTL 146


Lambda     K      H
   0.315    0.137    0.374 

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: 9
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 236
Length of database: 178
Length adjustment: 21
Effective length of query: 215
Effective length of database: 157
Effective search space:    33755
Effective search space used:    33755
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 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