GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Allochromatium vinosum DSM 180

Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_043795594.1 ALVIN_RS09555 aspartate aminotransferase family protein

Query= SwissProt::Q94AL9
         (477 letters)



>NCBI__GCF_000025485.1:WP_043795594.1
          Length = 392

 Score =  192 bits (487), Expect = 2e-53
 Identities = 142/411 (34%), Positives = 209/411 (50%), Gaps = 44/411 (10%)

Query: 71  PSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQ 130
           P M    R P+    G+  +L+D +G+RYLDA +GIAV   GH HP V + +  Q  RL 
Sbjct: 4   PLMATYNRLPVTFDRGEGVWLWDTNGKRYLDALSGIAVCGLGHAHPAVRDALCEQAGRLI 63

Query: 131 HPTVLYLNHAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKLYT---GCQD--I 185
           H + +Y   A  +   AL ++  G +  VFF NSG EANE A+ +A+L+    G ++  I
Sbjct: 64  HTSNIY-GVAEQERLGALLTEQAG-MDRVFFANSGAEANEAAIKLARLHAHRRGIENPAI 121

Query: 186 VAVRNGYHGNAAATMGATGQSMWKFN---VVQNSVHHALNPDPYRGVFGSDGEKYAKDLQ 242
           +   + +HG   AT+ ATG    +     +VQ  V       PY             D  
Sbjct: 122 LVAEHSFHGRTLATLSATGNRKVQAGFEPLVQGFVRV-----PY-------------DDL 163

Query: 243 DLIQYGTTG--HIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFAR 300
           D I+   T   +I   + E IQG GGI   +  YL    +   ++G L + DE+Q+G  R
Sbjct: 164 DAIETAATNRPNIVAILIEPIQGEGGIRLPSDDYLVRLREICDRSGWLLMLDEIQTGMGR 223

Query: 301 TGNFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTA 360
           TG  + F+   + PD+VT+AKG+GNG P+GA +     A V +  S+ +TFGGN ++   
Sbjct: 224 TGRLFAFQHAGIQPDVVTLAKGLGNGMPIGACLARGAAAEVFSPGSHGSTFGGNPLACRV 283

Query: 361 GLAVLNVIEKEKLQENAAMVGSYLKEKL-TQLKEKHEIIGDVRGRGLMLGVELVSDRKLK 419
           G AVL  +  E L ENAA  G+YL + L   L E H ++ ++RGRGLM+G+EL  DR   
Sbjct: 284 GRAVLETLIDENLTENAAAQGAYLLDSLRAALGETHGLV-EIRGRGLMVGIEL--DRPCG 340

Query: 420 TPATAETLHIMDQMKELGVLIGKGGYFGNVFRITPPLCFTKDDADFLVEAM 470
                    ++ +  + G+LI        V R+ PPL   +   D LV  +
Sbjct: 341 --------ELVGRALDAGLLINVTA--ERVIRLLPPLIIDRAQIDELVATL 381


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: 429
Number of extensions: 23
Number of successful extensions: 4
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: 392
Length adjustment: 32
Effective length of query: 445
Effective length of database: 360
Effective search space:   160200
Effective search space used:   160200
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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