GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Echinicola vietnamensis KMM 6221, DSM 17526

Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate Echvi_1276 Echvi_1276 Dihydrodipicolinate synthase/N-acetylneuraminate lyase

Query= SwissProt::Q57695
         (289 letters)



>FitnessBrowser__Cola:Echvi_1276
          Length = 308

 Score =  152 bits (385), Expect = 7e-42
 Identities = 91/295 (30%), Positives = 165/295 (55%), Gaps = 11/295 (3%)

Query: 2   FKGVYPAIITPFKNK-EVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIE 60
           F+G+ P +ITP  ++ ++D  GLE  IN +I  GV G+  +GTTGES +LS++   ++++
Sbjct: 11  FRGIVPPMITPLADENQLDIPGLERLINHIIAGGVHGLFILGTTGESTSLSYDIRHELVK 70

Query: 61  KVVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFGK 120
           +   +VNGRV V+ G       E++ L+  A   GA AV++  PYY    Q  L +++  
Sbjct: 71  RTCAIVNGRVPVLVGITDTAATESLRLADTAAKEGAAAVVAAPPYYFSLGQPELIEYYEY 130

Query: 121 VAESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIHDAK-- 178
           + E ++LP+ LYN+PS T + +EP TVK L+ +Y NI  +K+++ N +  ++++   K  
Sbjct: 131 LVERLSLPLFLYNMPSHTKIVIEPDTVKTLS-QYDNIVGLKDSSANNAYFNKVMAKMKDR 189

Query: 179 --ITVLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFP 236
              ++  G +E+    + LG  G ++  AN+ P+ +V++   A  GD E  + +H  +  
Sbjct: 190 QDFSLFVGPEEIMAETVLLGAHGGVNGGANMFPELYVKLYAAAESGDLETVKRLHAIVMQ 249

Query: 237 LMKAM-----FIETNPIPVKTALNMMGRPAGELRLPLCEMSEEHKKILENVLKDL 286
           +   M     F  +    +K AL+++G  +  +  PL    E+ ++IL   LK++
Sbjct: 250 ISTKMYSLGQFGSSYLKGIKGALSLLGICSDYMASPLHRFREKEREILAEQLKEI 304


Lambda     K      H
   0.315    0.135    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: 199
Number of extensions: 5
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: 289
Length of database: 308
Length adjustment: 27
Effective length of query: 262
Effective length of database: 281
Effective search space:    73622
Effective search space used:    73622
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: 48 (23.1 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