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

GapMind for Amino acid biosynthesis

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

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate Pf6N2E2_3707 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases

Query= curated2:Q1J0C2
         (483 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3707
          Length = 457

 Score =  166 bits (419), Expect = 2e-45
 Identities = 150/478 (31%), Positives = 227/478 (47%), Gaps = 53/478 (11%)

Query: 7   ATDLARAVQARETTPQALLEAARRRAEAARDLNALISLND-RADEQAARVQVRLDAGETL 65
           A  LA A  +  T P  +LE A  +A  A   +  +SL + RA  +A     R  AG+ L
Sbjct: 13  AIALAEAFASGRTDPVQVLEQALEQASRAE--HVFVSLTEARARREAQASAARWRAGQPL 70

Query: 66  P-LAGVPIVVKDNLNVIGTRTTCGSRILANYVSPY-DATAVERLTGAGAVIIGKANMDEF 123
               GVP+  KD  +V G+ TT  + +  +      DA +V  L+ AG V +GK N+ EF
Sbjct: 71  SGFDGVPLAWKDLFDVAGSVTTAAAAVRRDAPPALLDAASVSLLSRAGMVCLGKTNLSEF 130

Query: 124 AMGSSTESSAWGPTLNPWD--RERVPGGSSGGSAVAVAANLTPVALGSDTGGSVRQPAAF 181
           A      +  +G  +NP+   + R+PGGSS GSAVAVAA + P+A+G+DT GS+R PAAF
Sbjct: 131 AYSGLGLNPHFGTPVNPFSDAQPRIPGGSSSGSAVAVAAGIVPIAMGTDTAGSIRVPAAF 190

Query: 182 TGIYGLKPTYGRVSRYGLVAYASSLDQIGPFARSAADLALLMNVLAGHDPRDATSLDAPP 241
             + G + +  R SR G+   A S+D IGP  RS  D  ++  +L G DPR      APP
Sbjct: 191 NALVGFRASSRRHSRDGVFPLAHSIDSIGPLTRSVRDAWMIDELLQGRDPR-----QAPP 245

Query: 242 AFRPGTPDDLQGLRVGVIREALEGNTPGVEAALNAT----LDALRGAGATVREVSVPSVQ 297
                    L G R  V +  LE     VEAA+ A     + ALR AGA V    +P+ Q
Sbjct: 246 V------RSLAGQRFWVEQAVLE--DASVEAAVRANVLAGVQALRTAGALVEIRPLPAFQ 297

Query: 298 HAIAAYYLIATPEASSNLARYDGMVYGERVSAPDAVSSMTLTREQGFGREVKRRIMLGTY 357
            ++A         A+   A ++ +     + + DA         +     V+RR+     
Sbjct: 298 ASLALIRDHGWLGAAEAFALHEAL-----LDSADA---------ERLDPRVRRRLEAARP 343

Query: 358 ALSSGYYDAYYSKAMKVRRLIAQ-DFARAFGNVDVLVTPTSPFPAFRRGEKTQDPLAMYA 416
             +S     Y +++   R+L+ + D A       VL+TPT    A        D      
Sbjct: 344 MTASQVLKLYDARSALQRQLVEELDGA-------VLITPTVAHVAPPLAPLEADDELFVR 396

Query: 417 ADVDTVAINLAG----LPALSVPAGFERVDGVRLPVGVQLIAPPLQDERLVALAGGLE 470
            ++ T+ + + G    +P++++P+G    D   LP G+ L  P  +D RL+ +A  +E
Sbjct: 397 TNLATLRLTMPGSLLDMPSVNLPSG---RDSQGLPTGLLLSVPQGEDARLLRVARSVE 451


Lambda     K      H
   0.316    0.132    0.375 

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: 518
Number of extensions: 27
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: 457
Length adjustment: 33
Effective length of query: 450
Effective length of database: 424
Effective search space:   190800
Effective search space used:   190800
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: 51 (24.3 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis