GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Pseudomonas fluorescens FW300-N1B4

Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate Pf1N1B4_2861 glutamyl-Q-tRNA synthetase

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2861
          Length = 298

 Score =  132 bits (333), Expect = 1e-35
 Identities = 89/281 (31%), Positives = 136/281 (48%), Gaps = 35/281 (12%)

Query: 8   RYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLKWLG 67
           R+AP+P+GHLH G+   AL +YL AR+ GG++++R+ED D  R   G + + L  L+  G
Sbjct: 12  RFAPTPSGHLHFGSLVAALASYLDARSVGGRWLVRMEDLDPPREEPGAQAAILKALESYG 71

Query: 68  IDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIARGE 127
            +WD  +         RQSER+  Y      L  +GLAY C C+ ++LE         G 
Sbjct: 72  FEWDGDM--------VRQSERHAAYDEVINRLFNQGLAYACTCSRKQLEP------YHGI 117

Query: 128 MPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEI-SFESDGIGDFV 186
            P +       T+             +IR RVPE +   F D V+GE        +GDFV
Sbjct: 118 YPGFCRNAGHGTE-----------NAAIRLRVPELE-YHFIDRVQGEFRQHLGREVGDFV 165

Query: 187 IVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTLIV 246
           I ++DG   Y  AV +DD    +T ++RG D + +TP+Q+ + +  G   P++ H+ LI 
Sbjct: 166 IRRRDGLYAYQLAVVLDDAWQGITDIVRGADLLDSTPRQLYLQELLGLPQPRYLHIPLIT 225

Query: 247 NESRKKLSK--------RDESIIQFIEQYKELGYLPEALFN 279
                KL K         D++    +   + LG+ P    N
Sbjct: 226 QPDGHKLGKSYRSPPLTEDQATPLLLRALRALGHKPATELN 266


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: 378
Number of extensions: 17
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: 298
Length adjustment: 30
Effective length of query: 453
Effective length of database: 268
Effective search space:   121404
Effective search space used:   121404
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