GapMind for Amino acid biosynthesis

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011386083.1
          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:

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