GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Echinicola vietnamensis KMM 6221, DSM 17526

Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate Echvi_3848 Echvi_3848 Ornithine/acetylornithine aminotransferase

Query= SwissProt::Q94AL9
         (477 letters)



>FitnessBrowser__Cola:Echvi_3848
          Length = 381

 Score =  176 bits (445), Expect = 2e-48
 Identities = 125/372 (33%), Positives = 183/372 (49%), Gaps = 42/372 (11%)

Query: 91  LFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNHAIADFSEALAS 150
           ++D+ G  YLD + G AV++ GH HP   + +  Q+  +      Y N       + LA+
Sbjct: 22  IWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNI----AFYSNSVQIPIQKELAT 77

Query: 151 KLPGDLKV-----VFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATGQ 205
           KL G L       +F  NSG EANE AL +A   TG +  +A   G+HG  +  +  T  
Sbjct: 78  KL-GQLSGYPDYDLFLCNSGAEANENALKLASFETGKKGFIAFTKGFHGRTSGAVALTDN 136

Query: 206 SMWKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTGHIAGFICEAIQGVG 265
                 +   + H  ++  P+             DL+ + +   TG IAG I E IQGVG
Sbjct: 137 PKI---IAPFNAHEGVHILPFN------------DLEAVEKQLATGTIAGVIVEGIQGVG 181

Query: 266 GIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFE-AHNVVPDIVTMAKGIG 324
           GI    P +L       K+ G   I DEVQSG+AR+G F+  +    + PD++T+AKG+G
Sbjct: 182 GIQVPDPAFLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVEGLKPDLITVAKGMG 241

Query: 325 NGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGSYL 384
           NGFP+G V+ +PE     +      TFGGN ++  A LAVL VI++E L   AA  G  +
Sbjct: 242 NGFPIGGVLISPEFKA--SHGLLGTTFGGNHLACAAALAVLEVIDEENLITAAAENGKAI 299

Query: 385 KEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKELGVLIGKGG 444
              L    EK   + +VRG+GLM+G +L ++     P  A  +H      E  +  G  G
Sbjct: 300 MAAL----EKVAGVTEVRGKGLMIGFDLATE---AGPVRAALIH------EHKIFTGSAG 346

Query: 445 YFGNVFRITPPL 456
              +  R+ PPL
Sbjct: 347 -GKHTIRLLPPL 357


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: 469
Number of extensions: 29
Number of successful extensions: 6
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: 381
Length adjustment: 32
Effective length of query: 445
Effective length of database: 349
Effective search space:   155305
Effective search space used:   155305
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