GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Shewanella sp. ANA-3

Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 7025943 Shewana3_3091 4-aminobutyrate aminotransferase (RefSeq)

Query= BRENDA::Q9SR86
         (481 letters)



>FitnessBrowser__ANA3:7025943
          Length = 425

 Score =  194 bits (494), Expect = 4e-54
 Identities = 127/384 (33%), Positives = 191/384 (49%), Gaps = 13/384 (3%)

Query: 83  PLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVVNSVVKQLKLINHSTILYLNH 142
           P+    A+   V+D  GR ++D  GGIA ++ GH HP+V  +V  QL+  +H+  + L +
Sbjct: 25  PVFTARAENATVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFSHTCFMVLGY 84

Query: 143 -TISDFAEALVSTLPGDL--KVVFFTNSGTEANELAMMMARLYTGCNDIVSLRNSYHGNA 199
            +     E L   +PGD   K   FT SG+EA E A+ +AR YT    +++  + YHG  
Sbjct: 85  ESYIQVCEKLNQLVPGDFAKKTALFT-SGSEAVENAVKVARAYTKRAGVIAFTSGYHGRT 143

Query: 200 AATM---GATAQSNWKFNVVQSGVHHAINPDPYRGIFGSDGEKYASDVHDLIQFGTSGQV 256
            A +   G  A  +    ++ + V  A  P    G+  SD +  AS             +
Sbjct: 144 MAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGV--SDDDAMASIERIFKNDAEPSNI 201

Query: 257 AGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHFWGFQSHGV 316
           A  I E +QG GG    +P ++     +  + G + IADEVQ+G  RTGT F+  +  GV
Sbjct: 202 AAIILEPVQGEGGFYAASPEFMQRLRALCDREGIMLIADEVQTGAGRTGT-FFAMEQMGV 260

Query: 317 IPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSYFNTFGGNPMCTAAGHAVLRVLHEEK 376
             DI T AK I  G PL  +    E+   +       T+GGNP+  AA  AVL V  EEK
Sbjct: 261 SADITTFAKSIAGGFPLSGITGKAEVMDAIGPGGLGGTYGGNPLACAAALAVLEVFEEEK 320

Query: 377 LQENANLVGSHLKRRLTLLKNKYELIGDVRGRGLMLGVEFVKDRDLKTPAKAETLHLMDQ 436
           L E AN +G  +K  L  ++ ++  I DVRG G M+ +E +++     PA      ++ +
Sbjct: 321 LLERANAIGERIKSALNTMQVEHPQIADVRGLGAMIAIELMEE---GKPAPQYCAQILAE 377

Query: 437 MKEMGVLVGKGGFYGNVFRITPPL 460
            +  G+++   G YGNV RI  PL
Sbjct: 378 ARNRGLILLSCGTYGNVLRILVPL 401


Lambda     K      H
   0.320    0.136    0.406 

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: 464
Number of extensions: 23
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: 481
Length of database: 425
Length adjustment: 33
Effective length of query: 448
Effective length of database: 392
Effective search space:   175616
Effective search space used:   175616
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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