GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Pseudomonas simiae WCS417

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate GFF932 PS417_04730 bifunctional glyoxylate/hydroxypyruvate reductase B

Query= curated2:O27051
         (525 letters)



>FitnessBrowser__WCS417:GFF932
          Length = 324

 Score =  184 bits (468), Expect = 3e-51
 Identities = 104/268 (38%), Positives = 162/268 (60%), Gaps = 6/268 (2%)

Query: 54  KVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLAL 113
           K+ RE ++ A +L++++   VG DN DV    +RGIM+ N P+  + + A+ +  L+++ 
Sbjct: 55  KLGREQLQGASKLEVVSSVSVGYDNYDVAYFNERGIMLTNTPDVLTESTADLAFALLMSS 114

Query: 114 ARKIAIADRSVKEGKWEKN---RFMGIELNGKTLGIIGMGRIGSQVVVRTK-AFGMDIMV 169
           AR++A  D   K G+W+ +      G +++GKTLGI+GMG IG+ V  R +  F M I+ 
Sbjct: 115 ARRVAELDAWTKAGQWKASVGAPLFGCDVHGKTLGIVGMGNIGAAVARRGRLGFNMPIL- 173

Query: 170 YDPYISKEAAE-EMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIV 228
           Y     K A E E+G     L+ LL E+D V + VPL+ +TRHLIS  E  LMK +A ++
Sbjct: 174 YSGNSRKPALEQELGAQFRSLDELLAEADFVCLVVPLSDKTRHLISTRELGLMKSSAILI 233

Query: 229 NCARGGIIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQ 288
           N +RG ++DE AL  AL++  I GA LDV+E+EP   SPL +L N V  PHIG++T E +
Sbjct: 234 NISRGPVVDEPALIDALQNQTIRGAGLDVYEQEPLAESPLFQLSNAVTLPHIGSATHETR 293

Query: 289 RDAAIIVANEIKTVFQGGAPRNVLNMPV 316
              A    + +++   G  P++++N  V
Sbjct: 294 EAMANRALDNLRSALLGQRPQDLVNPQV 321


Lambda     K      H
   0.316    0.135    0.366 

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: 356
Number of extensions: 21
Number of successful extensions: 3
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: 525
Length of database: 324
Length adjustment: 31
Effective length of query: 494
Effective length of database: 293
Effective search space:   144742
Effective search space used:   144742
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 (21.6 bits)
S2: 50 (23.9 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