GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Klebsiella michiganensis M5al

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95; 2-oxoglutarate reductase; EC 1.1.1.399 (uncharacterized)
to candidate BWI76_RS26960 BWI76_RS26960 bifunctional glyoxylate/hydroxypyruvate reductase B

Query= curated2:P35136
         (525 letters)



>FitnessBrowser__Koxy:BWI76_RS26960
          Length = 323

 Score =  158 bits (400), Expect = 2e-43
 Identities = 101/307 (32%), Positives = 157/307 (51%), Gaps = 9/307 (2%)

Query: 13  DGLQPLIESDFIEIVQKNVADAEDELHTF---DAL-LVRSATKVTEDLFNKMTSLKIVGR 68
           D LQ  +E  F     KN+       H     +A+ L+ S+ KV   L  KM  L+    
Sbjct: 13  DDLQQRLEQHFTVTQVKNLRPETVSQHAAAFAEAVGLLGSSEKVDTALLEKMPKLRATST 72

Query: 69  AGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQANISVKSREWNR 128
             VG DN D+D      V++++ P   T + A+   A++ S  R + +    VK+ EW +
Sbjct: 73  ISVGYDNFDVDALNARKVLLMHTPTVLTETVADTVMALVLSTARRVVEVANRVKAGEWTK 132

Query: 129 TA---YVGSELYGKTLGIVGLGRIGSEIAQRARA-FGMTVHVFDPFLTEERAKKIGVNSR 184
           +    + G++++ KTLGIVG+GRIG  +AQRA A FGM +         +  ++      
Sbjct: 133 SIGPDWFGNDVHHKTLGIVGMGRIGMALAQRAHAGFGMPILYNARRQHPQAEERFNARYC 192

Query: 185 TFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAALLEALEN 244
             + +L+ AD + +  PLT+ET  L  K   AK K     IN  RG ++DE AL+ AL+ 
Sbjct: 193 DLDTLLQEADFVCLILPLTEETHHLFGKAQFAKMKSSAIFINAGRGPVVDEKALIAALQE 252

Query: 245 GHVAGAALDVFEVEP-PVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQFAKGL 303
           G +  A LDVFE EP   D+ L+  P V+A PH+G++T E + N+AA   + ++    G 
Sbjct: 253 GEIYAAGLDVFEQEPLAKDSPLLSMPNVVALPHIGSATHETRYNMAACAVDNLIDALNGS 312

Query: 304 PVMSAIN 310
              + +N
Sbjct: 313 VEKNCVN 319


Lambda     K      H
   0.317    0.134    0.373 

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: 347
Number of extensions: 18
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: 525
Length of database: 323
Length adjustment: 31
Effective length of query: 494
Effective length of database: 292
Effective search space:   144248
Effective search space used:   144248
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