GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Desulfovibrio vulgaris Hildenborough

Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate 207152 DVU1693 glutamyl-tRNA synthetase

Query= metacyc::MONOMER-13959
         (483 letters)



>MicrobesOnline__882:207152
          Length = 324

 Score =  179 bits (454), Expect = 1e-49
 Identities = 102/258 (39%), Positives = 147/258 (56%), Gaps = 4/258 (1%)

Query: 5   VRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLK 64
           +R R APSPTG++H+GNA   +  +L AR  GGK ++R+ED D  R      +  +  L+
Sbjct: 2   IRGRLAPSPTGNIHLGNAWAFMLAWLAARQAGGKVLLRMEDIDPDRARPEYAEGIMADLR 61

Query: 65  WLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIA 124
           WLG+DWDE  D+GG  GPY QS R   Y    + L   G  Y CYCT +EL         
Sbjct: 62  WLGLDWDEGPDIGGPCGPYVQSRRVQDYARVLDVLATLGAVYPCYCTRKELRTLAGAPHP 121

Query: 125 RGEMPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKG--EISFESDGI 182
                 Y G  R+LT EE  +   EGR+P++R R P+G V AF+D + G  +   ES G 
Sbjct: 122 GDLGAPYPGTCRNLTIEECSRKEKEGRRPAMRLRWPDG-VFAFDDGLFGPQQAGGESCG- 179

Query: 183 GDFVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHM 242
           GDF + + DG   Y  AV +DD  M +T V+RG D +S TP+Q+ +Y   G   P + H+
Sbjct: 180 GDFALRRSDGVFAYQLAVVVDDIAMGVTQVVRGADLLSCTPRQLALYSLLGAQPPAYLHV 239

Query: 243 TLIVNESRKKLSKRDESI 260
            L+++ + ++L+KR +S+
Sbjct: 240 PLLLDATGERLAKRHQSL 257


Lambda     K      H
   0.316    0.137    0.394 

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: 354
Number of extensions: 13
Number of successful extensions: 4
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: 483
Length of database: 324
Length adjustment: 31
Effective length of query: 452
Effective length of database: 293
Effective search space:   132436
Effective search space used:   132436
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: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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