Alignments for a candidate for agx1 in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for agx1 in Pseudomonas fluorescens GW456-L13

Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate PfGW456L13_3745 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)

Query= SwissProt::Q94AL9
         (477 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3745
          Length = 426

 Score =  273 bits (698), Expect = 8e-78
 Identities = 164/427 (38%), Positives = 241/427 (56%), Gaps = 16/427 (3%)

Query: 59  DVILSKRKEFLSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDV 118
           D +L +R   L  +    Y KPL++V G+  +LFD  GRRYLD +  +  V  GHC+P V
Sbjct: 4   DTLLQRRHRVLGSASPLFYDKPLHLVRGEGVWLFDVDGRRYLDVYNNVPCV--GHCNPHV 61

Query: 119 VEPVINQIKRLQHPTVLYLNHAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKL 178
            E +  Q   L   T  YL+  +  ++E L +     L  V FT +G+EANELAL +A+ 
Sbjct: 62  TEAMHRQATTLNIHT-RYLDEQVVCYAERLTATFAAPLDTVMFTCTGSEANELALRLARF 120

Query: 179 YTGCQDIVAVRNGYHGNAAATMGATGQSMWKFNVVQNSVHHALNPDP--YRGVFGSD--- 233
            +G   I+     YHGN+A+    T       +    + H    P P  Y    G+    
Sbjct: 121 ASGGTGIIVSDYNYHGNSASLAEVTTALP---SPEPFAAHARAVPIPCLYHAPAGTTEAQ 177

Query: 234 -GEKYAKDLQDLIQYGTTGHI--AGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFI 290
             E+YA ++   I       I  A  + + +    G+  +   +++ A   ++ AGGLFI
Sbjct: 178 LAEQYAANIAAAIASMQAQGIRPAALLIDTLFANEGLPRVPASFVNKAAALIRAAGGLFI 237

Query: 291 ADEVQSGFARTGN-FWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRS-YF 348
           ADEVQSGF RTG+  WG +AH VVPDIVT+ K +GNG+PL  ++T   +     R + YF
Sbjct: 238 ADEVQSGFGRTGDHLWGHQAHGVVPDIVTLGKPMGNGYPLAGLITHKALVESFGRHAMYF 297

Query: 349 NTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLML 408
           NTFGG+ V+   G+AVL+VIE+++L +NA  VG+Y++++L  L  KH IIGDVRG+GL  
Sbjct: 298 NTFGGSPVAAAVGMAVLDVIEEQQLLQNAQNVGAYVQQRLQVLAGKHSIIGDVRGKGLFF 357

Query: 409 GVELVSDRKLKTPATAETLHIMDQMKELGVLIGKGGYFGNVFRITPPLCFTKDDADFLVE 468
            +ELV D   K PA  E   +++ M+E GVLI K G   N+ ++ PPL F++D AD  V+
Sbjct: 358 AMELVRDHASKEPAGLEARKVVNDMRENGVLISKIGAGDNILKLRPPLVFSRDHADLFVD 417

Query: 469 AMDYSMS 475
            +D ++S
Sbjct: 418 TLDSALS 424


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: 468
Number of extensions: 22
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: 426
Length adjustment: 33
Effective length of query: 444
Effective length of database: 393
Effective search space:   174492
Effective search space used:   174492
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis