GapMind for Amino acid biosynthesis

 

Aligments for a candidate for gltX in Pseudomonas fluorescens FW300-N2C3

Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate AO356_16090 AO356_16090 glutamyl-Q tRNA(Asp) ligase

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



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16090 AO356_16090
           glutamyl-Q tRNA(Asp) ligase
          Length = 293

 Score =  130 bits (327), Expect = 6e-35
 Identities = 83/249 (33%), Positives = 124/249 (49%), Gaps = 27/249 (10%)

Query: 8   RYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLKWLG 67
           R+AP+P+GHLH G+   AL +YL AR   G++++R+ED D  R   G + + L  L+  G
Sbjct: 7   RFAPTPSGHLHFGSLVAALASYLDARAVDGRWLLRMEDLDPPREEPGAQAAILKALESYG 66

Query: 68  IDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIARGE 127
            +WD  +         RQSER+D Y      L  +GLAY C C+ ++LE           
Sbjct: 67  FEWDGEM--------VRQSERHDAYDQVINRLFSQGLAYACTCSRKQLE----------- 107

Query: 128 MPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEI-SFESDGIGDFV 186
              Y G +  L +             +IR RVPE +   F D V+GE        +GDFV
Sbjct: 108 --AYQGIYPGLCRNAGH----GTEDAAIRLRVPELE-YHFTDRVQGEFRQHLGREVGDFV 160

Query: 187 IVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTLIV 246
           I ++DG   Y   V +DD    +T ++RG D + +TP+Q+ + +  G   P++ H+ LI 
Sbjct: 161 IRRRDGLYAYQLGVVLDDAWQGVTDIVRGADLLDSTPRQLYLQELLGLPQPRYLHVPLIT 220

Query: 247 NESRKKLSK 255
                KL K
Sbjct: 221 QPDGHKLGK 229


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: 359
Number of extensions: 19
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: 483
Length of database: 293
Length adjustment: 30
Effective length of query: 453
Effective length of database: 263
Effective search space:   119139
Effective search space used:   119139
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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