GapMind for Amino acid biosynthesis

 

Aligments for a candidate for PPYAT in Magnetospirillum magneticum AMB-1

Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_011386083.1 AMB_RS18860 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::Q9RAT0
         (391 letters)



>lcl|NCBI__GCF_000009985.1:WP_011386083.1 AMB_RS18860 pyridoxal
           phosphate-dependent aminotransferase
          Length = 410

 Score =  176 bits (446), Expect = 1e-48
 Identities = 112/360 (31%), Positives = 186/360 (51%), Gaps = 6/360 (1%)

Query: 31  DIIKLTLGEPDFYTPEHVKQAGIAAIENNQSH-YTGMAGLLELRQAASEFLLKKYGLSYA 89
           DII   +G PD  TP H+    + A  N ++H Y+   G+  LR+A S +  +++ +   
Sbjct: 34  DIIDFGMGNPDQPTPAHIVDKLVEAARNPRAHRYSMSRGIPGLRKALSGYYQRRFAVDID 93

Query: 90  AEDEILVTVGVTEAISSVLLSILVAGDEVLIPAPAYPGYEPLITLAGGSLVEIDTRANDF 149
            E E +VT+G  E ++++  +I   GD VL+P P+YP +     +AGGS   +    +  
Sbjct: 94  PETECIVTLGSKEGLANLANAITSPGDIVLVPNPSYPIHPYGFIIAGGSCRFVPVTPDAE 153

Query: 150 VLTPEMLDQAIIEREGKVKAVILNYPANPTGVTYNREQIKDLAEVLKKHEVFVIADEVYS 209
            L  + LD+A+     K  A++LNYP+NPT +  + +    + E  + H +++++D  YS
Sbjct: 154 FL--KALDRAVRHSVPKPIALVLNYPSNPTALLADLDFYGQVVEFCRHHGIWILSDLAYS 211

Query: 210 ELNYTDQPHVSIAEY--APEQTIVLNGLSKSHAMTGWRIGLIFAARELVAQIIKTHQYLV 267
           E+ +   P  SI +   A E  +    +SK++ M GWRIG     + L+A + +   YL 
Sbjct: 212 EIYFDVAPPPSILQIPGAKEIAVEFTSMSKTYNMPGWRIGFAAGNKTLIAALGRIKSYLD 271

Query: 268 TSASTQSQFAAIEALKNGADDALPMKKEYLKRRDYIIEKMSALGFKIIEPDGAFYIFAKI 327
             A T  Q AA  AL    D    ++  Y  RRD +IE +SA G++I  P    + +A I
Sbjct: 272 YGAFTPIQVAATAALNGPQDCVDDIRALYKGRRDALIEGLSAAGWEIPSPPATMFAWAPI 331

Query: 328 P-ADLEQDSFKFAVDFAKENAVAIIPGIAFGQYGEGFVRLSYAASMDVIEQAMARLTDYV 386
           P A     S +F+    +E  VA+ PGI FG+YG+  VR+    ++    QA+  +  ++
Sbjct: 332 PKAFAHLGSLEFSKLLMREAQVAVAPGIGFGEYGDSHVRIGLVENVQRTRQAVRNIKTFL 391


Lambda     K      H
   0.318    0.135    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: 378
Number of extensions: 22
Number of successful extensions: 5
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: 391
Length of database: 410
Length adjustment: 31
Effective length of query: 360
Effective length of database: 379
Effective search space:   136440
Effective search space used:   136440
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 (21.7 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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