GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Pseudomonas fluorescens FW300-N2E2

Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate Pf6N2E2_5159 glutamyl-Q-tRNA synthetase

Query= SwissProt::Q8DLI5
         (485 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5159
          Length = 293

 Score =  138 bits (348), Expect = 2e-37
 Identities = 91/246 (36%), Positives = 124/246 (50%), Gaps = 23/246 (9%)

Query: 6   RLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEGLQWLG 65
           R AP+P+G+LH G+   A+ ++L AR  GG+++LR+ED D  R  P     IL+ L+  G
Sbjct: 7   RFAPTPSGHLHFGSLVAALASYLDARAMGGRWLLRMEDLDPPREEPGAQAAILKALESYG 66

Query: 66  LTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPRYDNRH 125
             WD     QS+R D Y Q I  L  +GLAY C C+ ++LEA       +G  P      
Sbjct: 67  FEWDGEMVRQSERHDAYDQVINRLFSQGLAYACTCSRKQLEAY------QGIYPGLCRNA 120

Query: 126 RHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIARAAPRG 185
            H T  E AA     R P + +   D  Q E++  +   V        GD VI R     
Sbjct: 121 GHGT--EDAAIRL--RVPELEYHFTDRVQGEFRQHLGREV--------GDFVIRR----- 163

Query: 186 EIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPLILNST 245
             G   Y L VV+DD   G+TD++RG D + +TP+Q+ L E LG   P + H PLI    
Sbjct: 164 RDGLYAYQLAVVLDDAWQGVTDIVRGADLLDSTPRQLYLQELLGLPQPRYLHVPLITQPD 223

Query: 246 GQKLSK 251
           G KL K
Sbjct: 224 GHKLGK 229


Lambda     K      H
   0.320    0.136    0.418 

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: 424
Number of extensions: 30
Number of successful extensions: 2
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: 485
Length of database: 293
Length adjustment: 30
Effective length of query: 455
Effective length of database: 263
Effective search space:   119665
Effective search space used:   119665
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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