GapMind for Amino acid biosynthesis

 

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

Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized)
to candidate Echvi_3850 Echvi_3850 acetylglutamate kinase

Query= curated2:A8AA51
         (264 letters)



>FitnessBrowser__Cola:Echvi_3850
          Length = 266

 Score =  110 bits (274), Expect = 4e-29
 Identities = 75/225 (33%), Positives = 123/225 (54%), Gaps = 28/225 (12%)

Query: 3   VVKAGGRTLLN--NMDEIVKSISRLE-KAVFVHGGGDLVDEWERKMGMEPQFKVSASGIK 59
           +VK GG  + +   + E +   +RLE K + VHGGG +  ++ +++G+EP+         
Sbjct: 5   IVKIGGNVIDDPAKLQEFLMLFARLEGKKILVHGGGVMASKFGQQLGIEPKMVDGR---- 60

Query: 60  FRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKVIVQEKV 119
            R TDE  L+V   V  G++NKKIVA      + A+G TGADG ++I   K+ V      
Sbjct: 61  -RITDEATLDVVTMVYAGMINKKIVAKLQQLEQNAMGFTGADG-NLIRSAKRPV------ 112

Query: 120 GERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGDQMAAEL 179
                 + I  G+ G +KEV T+L++ L+E+ +VPV + I    +G LLN N D +A+E+
Sbjct: 113 ------KDIDYGFVGDVKEVDTELMEVLLEKDVVPVFSAITHDRKGNLLNTNADTIASEI 166

Query: 180 AKALSAEYLVLL---TDVPGVLM----DGKVVPEIKSSEAEEVAK 217
           A A++ ++ V L    +  GVL+    D  +VP+I     +E+ +
Sbjct: 167 ATAMAVKHTVRLYFCFNKAGVLIDEHNDDSLVPKINEDIYDELKR 211


Lambda     K      H
   0.316    0.136    0.379 

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: 180
Number of extensions: 9
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: 264
Length of database: 266
Length adjustment: 25
Effective length of query: 239
Effective length of database: 241
Effective search space:    57599
Effective search space used:    57599
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: 47 (22.7 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