GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Magnetospirillum magneticum AMB-1

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_011386083.1 AMB_RS18860 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>NCBI__GCF_000009985.1:WP_011386083.1
          Length = 410

 Score =  153 bits (387), Expect = 8e-42
 Identities = 123/398 (30%), Positives = 183/398 (45%), Gaps = 27/398 (6%)

Query: 8   LSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGET-KYTP 66
           + R+ P     V+      +A G D+I  G G PD  TP +I    ++A       +Y+ 
Sbjct: 10  IKRLPPYVFAEVNAMKARARAAGEDIIDFGMGNPDQPTPAHIVDKLVEAARNPRAHRYSM 69

Query: 67  VSGIPELREAIAKKFKRENNLDYTA-AQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYW 125
             GIP LR+A++  ++R   +D     + IV  G K+ L N   A  +PGD V++P P +
Sbjct: 70  SRGIPGLRKALSGYYQRRFAVDIDPETECIVTLGSKEGLANLANAITSPGDIVLVPNPSY 129

Query: 126 VSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAI---TPKTKWFVFNSPSNPSGAAYS 182
             +P    + GG+  FVP   +  F LKA  LDRA+    PK    V N PSNP+ A  +
Sbjct: 130 PIHPYGFIIAGGSCRFVPVTPDAEF-LKA--LDRAVRHSVPKPIALVLNYPSNPT-ALLA 185

Query: 183 HEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYA 242
             +         +H  +W+L+D  Y  + Y D      +   PG  E  +    +SK Y 
Sbjct: 186 DLDFYGQVVEFCRHHGIWILSDLAYSEI-YFDVAPPPSILQIPGAKEIAVEFTSMSKTYN 244

Query: 243 MTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRR 302
           M GWRIG+AAG   LI A+  I+     GA +  Q AA  ALNGPQD +   + +++GRR
Sbjct: 245 MPGWRIGFAAGNKTLIAALGRIKSYLDYGAFTPIQVAATAALNGPQDCVDDIRALYKGRR 304

Query: 303 DLVVSMLNQAKGISCPTPEGAFYVY---PSCAGLIGKTAPSGKVIETDEDFVSELLETEG 359
           D ++  L+ A G   P+P    + +   P     +G             +F   L+    
Sbjct: 305 DALIEGLS-AAGWEIPSPPATMFAWAPIPKAFAHLGSL-----------EFSKLLMREAQ 352

Query: 360 VAVVHGSAFGL--GPNFRISYATSEALLEEACRRIQRF 395
           VAV  G  FG     + RI    +     +A R I+ F
Sbjct: 353 VAVAPGIGFGEYGDSHVRIGLVENVQRTRQAVRNIKTF 390


Lambda     K      H
   0.318    0.134    0.402 

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: 410
Number of extensions: 22
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: 400
Length of database: 410
Length adjustment: 31
Effective length of query: 369
Effective length of database: 379
Effective search space:   139851
Effective search space used:   139851
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:

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