GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_1374 Ga0059261_1374 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= curated2:C4L2D4
         (235 letters)



>FitnessBrowser__Korea:Ga0059261_1374
          Length = 272

 Score =  106 bits (264), Expect = 5e-28
 Identities = 73/166 (43%), Positives = 89/166 (53%), Gaps = 28/166 (16%)

Query: 95  PGSFIRDHVQIGNNAVVMMGAVVNIGAVIGDGSMVDMNAVIGARGTLGKNVHLGAGAVVA 154
           PGS +R    I  N VV+M + VNIGA +G+GSMVD  A +G+   +G+NVHL  G  + 
Sbjct: 107 PGSVVRHGAFISKN-VVLMPSFVNIGAYVGEGSMVDGWATVGSCAQIGRNVHLSGGVGIG 165

Query: 155 GVLEPPSKDPVIIEDGVMIGANAVILEGVRVGENAVV---------------AAGSVVTQ 199
           GVLEP   DPVII DG  IGA A + EGVRVGE AV+               A G V   
Sbjct: 166 GVLEPLQADPVIIGDGAFIGARAEVAEGVRVGEGAVLSMGVYLGASTKIVDRATGEVHRG 225

Query: 200 DVPP-GVVVAGT-----------PARIIKQKDEKTSEKTQLVDDLR 233
            VPP  VVV GT            A I+K  D +T  KT + + LR
Sbjct: 226 VVPPYSVVVPGTLPGKDGGPGLYCAVIVKTVDAQTRSKTGINELLR 271


Lambda     K      H
   0.315    0.133    0.360 

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: 134
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: 235
Length of database: 272
Length adjustment: 24
Effective length of query: 211
Effective length of database: 248
Effective search space:    52328
Effective search space used:    52328
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 Apr 09 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