GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Pseudomonas stutzeri RCH2

Align Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase; PhPPA-AT; EC 2.6.1.1; EC 2.6.1.78; EC 2.6.1.79 (characterized)
to candidate GFF973 Psest_1004 Aspartate/tyrosine/aromatic aminotransferase

Query= SwissProt::E9L7A5
         (479 letters)



>FitnessBrowser__psRCH2:GFF973
          Length = 390

 Score =  197 bits (500), Expect = 7e-55
 Identities = 131/399 (32%), Positives = 200/399 (50%), Gaps = 20/399 (5%)

Query: 75  SLSPRVNSVKPSKTVAITDQATALVQAGVPVIRLAAGEPDFDTPAPIVEAGINAIREGHT 134
           S S R  +++P   +A+ ++A  L   G  VI L  GEPDF T APIV AG  A+  GHT
Sbjct: 4   SYSARSRAIEPFHVMALLERANQLQVQGHDVIHLEIGEPDFTTAAPIVAAGQAALAAGHT 63

Query: 135 RYTPNAGTMELRSAISHKLKEENGLSYTPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPA 194
           RYTP  G  +LR AI+    +  GLS  P +IL++ G   +++ A   +  PG   L+  
Sbjct: 64  RYTPARGLPQLREAIAAFYAQRYGLSIDPGRILITPGGSGALLLAASLLVDPGKHWLLAD 123

Query: 195 PYWVSYPEMARLADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVYP 254
           P +       RL +    ++P      + L P+L+E      S   ++ SP+NPTG++  
Sbjct: 124 PGYPCNRHFLRLVEGAAQLVPVGPDVRYQLTPELVERYWDRDSVGALVASPANPTGTLLE 183

Query: 255 RKLLEQIAEIVARHPRLLVISDEIYEHIIYAPATHTSFASLPGMWDRTLTVNGFSKAFAM 314
           R  L +++  +      LV+ DEIY  + Y        AS+  + D    +N FSK F M
Sbjct: 184 RDELARLSAALKERGGHLVV-DEIYHGLTYG----VDAASVLEVDDDAFVLNSFSKYFGM 238

Query: 315 TGWRLGYIAGPKHFIAACNKIQSQFTSGASSISQKAAVAALGLGYAGGELVATMVKSFRE 374
           TGWRLG++  P   +    K+       A S++Q AA+A      A  E++      F  
Sbjct: 239 TGWRLGWLVAPPTAVPELEKLAQNLYISAPSMAQHAALAC--FEPATLEILEARRAEFAR 296

Query: 375 RRDYLVKSFGEIEGVKISEPRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKAQV 434
           RRD+L+ +  E+      EP+GAFYL+ D+S++ G          ++ + C+++L+   V
Sbjct: 297 RRDFLLPALRELGFGIAVEPQGAFYLYADISAFGG----------DAYAFCQHMLETEFV 346

Query: 435 ALVPGDAFGDDTC---IRISYAASLSTLQAAVERIKKAL 470
           A+ PG  FG       +R +Y   L  LQ AVERI + L
Sbjct: 347 AITPGLDFGRFQAGHHVRFAYTQDLPRLQQAVERIARGL 385


Lambda     K      H
   0.317    0.132    0.375 

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: 440
Number of extensions: 19
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: 479
Length of database: 390
Length adjustment: 32
Effective length of query: 447
Effective length of database: 358
Effective search space:   160026
Effective search space used:   160026
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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