GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Shewanella loihica PV-4

Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate 5208066 Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

Query= SwissProt::Q94AL9
         (477 letters)



>FitnessBrowser__PV4:5208066
          Length = 405

 Score =  163 bits (413), Expect = 9e-45
 Identities = 109/339 (32%), Positives = 168/339 (49%), Gaps = 31/339 (9%)

Query: 84  VDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNHAIAD 143
           V G+   ++D+ G  ++D   GIAV   GHCHP +V  +  Q +++ H   +  N     
Sbjct: 28  VRGEGSRVWDQEGNEFVDFAGGIAVNCLGHCHPALVGALKEQGEKIWHLANVMTNEPAL- 86

Query: 144 FSEALASKLPGDL--KVVFFTNSGTEANELALMMAKLYT----GCQ--DIVAVRNGYHGN 195
              ALA+KL      + V+F NSG EANE AL +A+ Y     G +   I+A    +HG 
Sbjct: 87  ---ALATKLVEATFAEKVYFANSGAEANEAALKLARRYALDKFGAEKDQIIAFDKAFHGR 143

Query: 196 AAATMGATGQSMWK--FNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTGHI 253
              T+   GQ+ +   F     S+ H     P+  +   + E   K              
Sbjct: 144 TFFTVSVGGQAAYSDGFGPKPQSITHL----PFNDIAALEAEVSDKT------------- 186

Query: 254 AGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVV 313
              + E +QG GGI++  P +L A      K   L I DEVQ+G  R G  + +    V 
Sbjct: 187 CAIMLEPLQGEGGIIDADPEFLRAVRALADKHNALVIFDEVQTGVGRLGELYAYMRTEVT 246

Query: 314 PDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKL 373
           PDI+T AK +G GFP+ A++TT EIA  L   ++ +T+GGN ++   G AVL+V+   ++
Sbjct: 247 PDILTTAKALGGGFPIAAMLTTTEIASHLKIGTHGSTYGGNPLACAIGNAVLDVVNTPEV 306

Query: 374 QENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVEL 412
            +        L++ L Q+ EK+ +  +VRG+GL+LG  L
Sbjct: 307 LDGVKRREQLLRDGLNQINEKYHVFTEVRGQGLLLGAVL 345


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: 459
Number of extensions: 18
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: 405
Length adjustment: 32
Effective length of query: 445
Effective length of database: 373
Effective search space:   165985
Effective search space used:   165985
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