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

GapMind for Amino acid biosynthesis

Aligments 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_878 Amidase clustered with urea ABC transporter and nitrile hydratase functions

Query= curated2:Q8THJ1
         (476 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_878
          Length = 504

 Score =  263 bits (673), Expect = 8e-75
 Identities = 158/426 (37%), Positives = 236/426 (55%), Gaps = 24/426 (5%)

Query: 60  GPLAGVPIAIKDNISVVGLPNSCGSKILEGYVPPFNAHVIEKLLDAGAVILGKTNLDEFA 119
           G L+G  +A+KDNIS+ G+P   G+  LEG+VP F+A V+ +LLDAGA ILGK   + + 
Sbjct: 86  GKLSGKTVALKDNISLAGVPMMNGAAPLEGFVPSFDATVVTRLLDAGATILGKATCEHYC 145

Query: 120 MGSSTETSYYGPTANPWDLERVPGGSSGGSAAVVAAGEAPFALGSDTGGSVRCPAAFCGV 179
           +   + TS   P  NP+      GGSS GSAA+VA G    A+G D GGS+R PAA+CG+
Sbjct: 146 LSGGSHTSDPAPVHNPFRHGYTTGGSSSGSAALVATGAVDLAIGGDQGGSIRIPAAWCGI 205

Query: 180 VGLKPTYGAVSRYGVVAYANSLEQVGPLANNVEDIAILMDVIAGYDRRDSTSIDSKTE-Y 238
            G+KPT+G V   GV+A  ++ + VGP+ +NV D A++++V+AG D  D      K + Y
Sbjct: 206 YGMKPTWGLVPYTGVMAIESTFDHVGPMTSNVRDNALMLEVMAGADGLDPRQAAPKVDAY 265

Query: 239 QKALVDDVKGLKIGVPKEFFG-EGIHPGVEKAVWNAIHKFESLGATRQEVSMPNINYALA 297
              L   V GL+IGV +E F      P + + V +AI + E+LGA  +EVS+P  N A +
Sbjct: 266 CDYLERGVTGLRIGVLQEGFQLANQDPRIAEKVRSAIARLEALGARVEEVSVPEHNLAGS 325

Query: 298 SYYIIAMSEASSNLARFDGTRYGFRANGENWHAMVS----------KTRAEGFGTEVKRR 347
            +  I     +  +   +G        G NW  +            + +A      +K  
Sbjct: 326 LWSPIGCEGLTMQMMHGNGA-------GFNWKGLYDVGLLDKQAGWRDQANALSPSLKLC 378

Query: 348 ILLGTYALSAGYHDKYYLKALKVRTLVKQDFDKALSTVDLLMAPTMP---NPAFRIGEKI 404
           + +G + L   Y+ +YY KA  +    +  +DKAL T DLL+ PT+P    P    G  I
Sbjct: 379 MFVGQFGLER-YNGRYYAKAQNIARFARAAYDKALDTYDLLVMPTVPITAQPLPEPGSSI 437

Query: 405 EDPLTLYLSDV-NTCPINLAGVPSVSVPCGFTDGLPVGLQIMGKPFDEPTVLRAAYTFEK 463
            + +T  L  + NT   ++ G P++S+PCG  DGLPVGL ++G+ + E T+ +AA  FE 
Sbjct: 438 TETVTRALEMLGNTAAQDITGHPAMSIPCGLVDGLPVGLMLVGRHYAEGTLYQAAAAFEA 497

Query: 464 NTDYHT 469
           + D+ T
Sbjct: 498 SVDWRT 503


Lambda     K      H
   0.315    0.134    0.391 

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: 635
Number of extensions: 40
Number of successful extensions: 4
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: 476
Length of database: 504
Length adjustment: 34
Effective length of query: 442
Effective length of database: 470
Effective search space:   207740
Effective search space used:   207740
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 (21.5 bits)
S2: 52 (24.6 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:

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, 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

GapMind for Amino acid biosynthesis