GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Pseudomonas simiae WCS417

Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate GFF179 PS417_00900 4-aminobutyrate aminotransferase

Query= SwissProt::Q940M2
         (476 letters)



>FitnessBrowser__WCS417:GFF179
          Length = 425

 Score =  194 bits (494), Expect = 4e-54
 Identities = 125/391 (31%), Positives = 188/391 (48%), Gaps = 8/391 (2%)

Query: 78  PLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHAT-TIYLH 136
           P+     K   + D  GR ++D   GI  ++ GH HP I+ A+TEQ   L H    +  +
Sbjct: 25  PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAY 84

Query: 137 HAIGDFAEALAAKMPGNL-KVVYFVNSGSEANELAMMMARLYTGSLEMISLRNAYHGGSS 195
               +  E + AK+PG+  K    V +GSEA E A+ +AR  TG   +I+   AYHG + 
Sbjct: 85  EPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAYHGRTM 144

Query: 196 NTIGLTAL---NTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDHIEYGTSGKVA 252
            T+GLT      +    L  G +   + P+   GV  SD    A              +A
Sbjct: 145 MTLGLTGKVVPYSAGMGLMPGGVFRALFPNELHGV--SDDDAIASIERIFKNDAEPRDIA 202

Query: 253 GFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGFQTQDVV 312
             I E +QG GG       ++K + E+    G + IADEVQTG GRTG+ ++  +   V 
Sbjct: 203 AIIIEPVQGEGGFYVAPKSFMKRLRELCDKHGILLIADEVQTGAGRTGT-FFAMEQMGVA 261

Query: 313 PDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAGGLAVLNVIDKEKR 372
            D+ T AK I  G PL  V    E    +A   L  T+ G+P+  A  LAV+ V ++E  
Sbjct: 262 ADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHL 321

Query: 373 QEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKAETSVLFEQL 432
            + C  VG  L+  LK +Q ++ +IG+VR  G M+ +EL  D     P  A  + +  + 
Sbjct: 322 LDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFDDGDTHKPNAAAVASVVAKA 381

Query: 433 RELGILVGKGGLHGNVFRIKPPMCFTKDDAD 463
           RE G+++   G +GNV R+  P+    +  D
Sbjct: 382 REKGLILLSCGTYGNVLRVLVPLTSPDEQLD 412


Lambda     K      H
   0.320    0.138    0.412 

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: 484
Number of extensions: 31
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: 476
Length of database: 425
Length adjustment: 33
Effective length of query: 443
Effective length of database: 392
Effective search space:   173656
Effective search space used:   173656
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