GapMind for Amino acid biosynthesis

 

Aligments for a candidate for agx1 in Pedobacter sp. GW460-11-11-14-LB5

Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein

Query= SwissProt::Q94AL9
         (477 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS15205 CA265_RS15205 aspartate
           aminotransferase family protein
          Length = 378

 Score =  197 bits (502), Expect = 4e-55
 Identities = 134/387 (34%), Positives = 190/387 (49%), Gaps = 34/387 (8%)

Query: 81  LNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVL--YLN 138
           L  V  K  Y++D   ++++D  AGI V N GHCHP VV+ +  Q +   H  V   Y+ 
Sbjct: 2   LEFVRAKGIYIYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQAETYMHLMVYGEYVQ 61

Query: 139 HAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAA 198
               +F++ALA  LP  L   +F NSGTEA E A+ +AK YTG +  +A +N YHG+   
Sbjct: 62  TPQVNFAKALADILPESLSCTYFLNSGTEAVEGAMKLAKRYTGRKGFIACKNAYHGS--- 118

Query: 199 TMGATGQSMWKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTGHIAGFIC 258
           T GA          +  S  ++    P+             DL+ +     T  IA    
Sbjct: 119 TQGAES--------LMESDFYSSGYGPFLPHVSFIEHNNLADLEKI-----TNEIAAVFI 165

Query: 259 EAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVPDIVT 318
           E IQG  GI      Y+ A      + G L I DE+QSGF R+G  + FE +NVVPD++ 
Sbjct: 166 EPIQGEAGIRVSDLSYMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDVLL 225

Query: 319 MAKGIGNGFPLGAVVTTPEIAGVLTRR---SYFNTFGGNSVSTTAGLAVLNVIEKEKLQE 375
           +AKGIG G P+GA +++ EI  VL+      +  TFGG+ V   AGLA L  +  + + +
Sbjct: 226 LAKGIGGGMPIGAFISSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHIVD 285

Query: 376 NAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKE 435
                G   K+ L     +H  I ++RG+GLML VE  +    K         I+D    
Sbjct: 286 EVEEKGQLFKQLL-----QHPAIKEIRGKGLMLAVEFENFEINK--------KIIDACIL 332

Query: 436 LGVLIGKGGYFGNVFRITPPLCFTKDD 462
            GVL     +  N  RI PPL  TK++
Sbjct: 333 DGVLSDWFLHCSNSMRIAPPLIITKEE 359


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: 418
Number of extensions: 24
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: 378
Length adjustment: 32
Effective length of query: 445
Effective length of database: 346
Effective search space:   153970
Effective search space used:   153970
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 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