GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Pseudomonas fluorescens FW300-N2C3

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate AO356_27355 AO356_27355 amidase

Query= curated2:Q8THJ1
         (476 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27355
          Length = 504

 Score =  263 bits (673), Expect = 8e-75
 Identities = 158/426 (37%), Positives = 235/426 (55%), Gaps = 24/426 (5%)

Query: 60  GPLAGVPIAIKDNISVVGLPNSCGSKILEGYVPPFNAHVIEKLLDAGAVILGKTNLDEFA 119
           G LAG  +A+KDNIS+ G+P   G+  LEG+VP  +A V+ +LLDAGA ILGK   + + 
Sbjct: 86  GKLAGKTVALKDNISLAGVPMMNGAAPLEGFVPSLDATVVTRLLDAGATILGKATCEHYC 145

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

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

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

Query: 298 SYYIIAMSEASSNLARFDGTRYGFRANGENWHAMVS----------KTRAEGFGTEVKRR 347
            +  I     +  +   +G        G NW  +            + +A      +K  
Sbjct: 326 LWSPIGCEGLTMQMMHGNGA-------GFNWKGLYDVGLLDKQVGWRDQANALSPSLKLC 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: 616
Number of extensions: 39
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:

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