GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Pseudomonas fluorescens GW456-L13

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate PfGW456L13_3652 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)

Query= curated2:C0QKZ5
         (490 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3652
          Length = 482

 Score =  250 bits (638), Expect = 9e-71
 Identities = 179/491 (36%), Positives = 251/491 (51%), Gaps = 51/491 (10%)

Query: 5   ELTLEGARALLLSGEISSKDLTTCLLDRIKTHDADLGAFITVDAAGALEAATAADERIAR 64
           EL +  A A +  G+ISS+  T  LL R  T  +DLGAFIT+D A  L AA A D   A 
Sbjct: 16  ELGVAAAAAAIRRGDISSESYTAALLRRAHTF-SDLGAFITIDEAAVLAAARACDTARAT 74

Query: 65  GEDAPLLGIPLALKDLLCTSGVRTTCASKILENFVPTYDATAVTLLKQAGAVIVGKTNLD 124
           G  APLLG+P+A+KD   T G+RTT   + LENFVP  DA  V  +K AG ++ GK NL 
Sbjct: 75  GSTAPLLGVPVAVKDSYLTQGLRTTLGIRSLENFVPARDAEVVRAIKDAGGIVFGKNNLV 134

Query: 125 EFGMGSSTENSAFHLTRNPWNLDHVPGGSSGGSAAAVAARMCTAALGTDTGGSIRQPASH 184
           E   G +  NS F   +NP N +HV GGSS G+ A+V A++  AALG DT GSIR PAS 
Sbjct: 135 EMSYGLTGHNSHFGQAKNPHNPEHVTGGSSSGAGASVGAQIVPAALGGDTVGSIRVPASF 194

Query: 185 CGVVGLKPSYGRVSRFGMVAYASSLDQIGPITRTVKDAALMMNVISGHDPKDSTSAAIDK 244
           CGVVG KPS GR S  G+   + +LD  G   RTV+D AL+  V++              
Sbjct: 195 CGVVGFKPSPGRWSGDGIAPISHTLDTAGVFARTVEDCALIDQVVTK------------- 241

Query: 245 PDFTQAFAGFDAKGLAGMK-AGIPREYIGMKGLDPEVERSFKNACKVLEDLGVEVIDVSL 303
              T +    D  GL G++ A  PR++  ++ ++ EVE  FK   + L D G EV++V L
Sbjct: 242 ---TTSTVHGDWTGLRGIRLAYAPRQH--LERINHEVEEHFKETIRRLCDAGAEVVEVDL 296

Query: 304 PHTNFAVA-----AYYVLAPSEASANLSRYDGVKYGFRQTGCDDLMDMYKQTRSSGFGPE 358
               FA+      + +     E+ A   R + +   F     +D+ +  K      +G  
Sbjct: 297 GEDFFAMTERSTWSIFFHETMESVAGFLRKNRIPSSF-----EDIYNELKPGLKDAWGHL 351

Query: 359 VKRRIIMGTYALSAGYYDEYYGRASRVRTLIMADFSKAFDQ--CDIILSPVAPTPAFKI- 415
           V   +  G   +S   ++ Y       R  I   F+ AF       ++ P  P PA  I 
Sbjct: 352 V---LPSGAGFIS---HETYQTALDHDRPEIQRRFNMAFSSSGAQALIMPTTPCPAPTIE 405

Query: 416 --------GENVDDPLTMYLGDIFTLSANMAGIPGLSVPCAMSTTGLPIGLQILGRRFDE 467
                   G+ VDD          T++ ++AG+PG+S+P  MS+ GLPIGL+I G+  D+
Sbjct: 406 QQTKFTIAGQEVDDLALAR----HTVAGSIAGLPGISIPMGMSSNGLPIGLEIDGKNGDD 461

Query: 468 MSVLKAGYGLE 478
             +L+    +E
Sbjct: 462 RKLLELARRVE 472


Lambda     K      H
   0.319    0.136    0.397 

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: 568
Number of extensions: 20
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: 490
Length of database: 482
Length adjustment: 34
Effective length of query: 456
Effective length of database: 448
Effective search space:   204288
Effective search space used:   204288
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 (21.7 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