GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_16090
          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:

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