GapMind for Amino acid biosynthesis

 

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

Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate 7025943 Shewana3_3091 4-aminobutyrate aminotransferase (RefSeq)

Query= SwissProt::Q94AL9
         (477 letters)



>FitnessBrowser__ANA3:7025943
          Length = 425

 Score =  195 bits (496), Expect = 2e-54
 Identities = 127/372 (34%), Positives = 184/372 (49%), Gaps = 12/372 (3%)

Query: 91  LFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNH-AIADFSEALA 149
           ++D  GR ++D   GIAV+N GH HP V   V  Q++   H   + L + +     E L 
Sbjct: 36  VWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFSHTCFMVLGYESYIQVCEKLN 95

Query: 150 SKLPGDL--KVVFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATGQSM 207
             +PGD   K   FT SG+EA E A+ +A+ YT    ++A  +GYHG   A +  TG+  
Sbjct: 96  QLVPGDFAKKTALFT-SGSEAVENAVKVARAYTKRAGVIAFTSGYHGRTMAALALTGKVA 154

Query: 208 ---WKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTGHIAGFICEAIQGV 264
                  ++  +V  A  P    GV  SD +  A   +         +IA  I E +QG 
Sbjct: 155 PYSKGMGLMSANVFRAEFPCALHGV--SDDDAMASIERIFKNDAEPSNIAAIILEPVQGE 212

Query: 265 GGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVPDIVTMAKGIG 324
           GG    +P ++        + G + IADEVQ+G  RTG F+  E   V  DI T AK I 
Sbjct: 213 GGFYAASPEFMQRLRALCDREGIMLIADEVQTGAGRTGTFFAMEQMGVSADITTFAKSIA 272

Query: 325 NGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGSYL 384
            GFPL  +    E+   +       T+GGN ++  A LAVL V E+EKL E A  +G  +
Sbjct: 273 GGFPLSGITGKAEVMDAIGPGGLGGTYGGNPLACAAALAVLEVFEEEKLLERANAIGERI 332

Query: 385 KEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKELGVLIGKGG 444
           K  L  ++ +H  I DVRG G M+ +EL+ + K   PA      I+ + +  G+++   G
Sbjct: 333 KSALNTMQVEHPQIADVRGLGAMIAIELMEEGK---PAPQYCAQILAEARNRGLILLSCG 389

Query: 445 YFGNVFRITPPL 456
            +GNV RI  PL
Sbjct: 390 TYGNVLRILVPL 401


Lambda     K      H
   0.320    0.136    0.403 

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: 490
Number of extensions: 26
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: 477
Length of database: 425
Length adjustment: 33
Effective length of query: 444
Effective length of database: 392
Effective search space:   174048
Effective search space used:   174048
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 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