GapMind for Amino acid biosynthesis

 

Aligments for a candidate for agx1 in Magnetospirillum magneticum AMB-1

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_011386083.1 AMB_RS18860 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::D2Z0I0
         (402 letters)



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

 Score =  417 bits (1073), Expect = e-121
 Identities = 204/395 (51%), Positives = 271/395 (68%), Gaps = 5/395 (1%)

Query: 1   MSEEWMFPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVAN 60
           MS +  F ++K+LP YVFA VN +K + R  GEDI+D GMGNPD P   HI+DKL E A 
Sbjct: 1   MSSQHDFHRIKRLPPYVFAEVNAMKARARAAGEDIIDFGMGNPDQPTPAHIVDKLVEAAR 60

Query: 61  RPNVHGYSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGD 120
            P  H YS S+GIP LRKA+  +Y+RR+ V++DPE   I+T+G+KEG ++L  A+  PGD
Sbjct: 61  NPRAHRYSMSRGIPGLRKALSGYYQRRFAVDIDPETECIVTLGSKEGLANLANAITSPGD 120

Query: 121 TVIVPNPTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSF 180
            V+VPNP+YPIH Y  II GG    VP+ P+ +F    L+ L   ++ S  KP A+VL++
Sbjct: 121 IVLVPNPSYPIHPYGFIIAGGSCRFVPVTPDAEF----LKALDRAVRHSVPKPIALVLNY 176

Query: 181 PHNPTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVEL 240
           P NPT L  DL+F+ +VV+  +  GIWI+ D AY+++ FD   PPSILQ+ GA ++AVE 
Sbjct: 177 PSNPTALLADLDFYGQVVEFCRHHGIWILSDLAYSEIYFDVAPPPSILQIPGAKEIAVEF 236

Query: 241 YSMSKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKN 300
            SMSK ++M GWR+ F  GN+ LI  L  +KSYLDYG FTPIQVA+  AL  P + V+  
Sbjct: 237 TSMSKTYNMPGWRIGFAAGNKTLIAALGRIKSYLDYGAFTPIQVAATAALNGPQDCVDDI 296

Query: 301 REIYRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVG-MNSLDFSLFLLREAKVAVS 359
           R +Y+ RRD L+EGL+  GWE+  P  +MF WA +P+    + SL+FS  L+REA+VAV+
Sbjct: 297 RALYKGRRDALIEGLSAAGWEIPSPPATMFAWAPIPKAFAHLGSLEFSKLLMREAQVAVA 356

Query: 360 PGIGFGEYGEGYVRFALVENEHRIRQAVRGIKKAL 394
           PGIGFGEYG+ +VR  LVEN  R RQAVR IK  L
Sbjct: 357 PGIGFGEYGDSHVRIGLVENVQRTRQAVRNIKTFL 391


Lambda     K      H
   0.322    0.141    0.425 

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: 513
Number of extensions: 25
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: 402
Length of database: 410
Length adjustment: 31
Effective length of query: 371
Effective length of database: 379
Effective search space:   140609
Effective search space used:   140609
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 (21.9 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 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