GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Escherichia coli BW25113

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate 15502 b1380 D-lactate dehydrogenase (NCBI)

Query= BRENDA::O58256
         (333 letters)



>FitnessBrowser__Keio:15502
          Length = 329

 Score =  133 bits (334), Expect = 7e-36
 Identities = 91/280 (32%), Positives = 148/280 (52%), Gaps = 24/280 (8%)

Query: 55  TREVLENAER--LKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINL 112
           +R VLE  ++  +K I+   AG++N+DL+ A + G+ V +V     EAVAE  +G+++ L
Sbjct: 57  SRPVLEELKKHGVKYIALRCAGFNNVDLDAAKELGLKVVRVPAYDPEAVAEHAIGMMMTL 116

Query: 113 MRKIHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKL 172
            R+IH A +  R   +       TGF    ++YGK  G++G G IG A+ R L  FG++L
Sbjct: 117 NRRIHRAYQRTRDANFSLEG--LTGF----TMYGKTAGVIGTGKIGVAMLRILKGFGMRL 170

Query: 173 YYWSRHRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERVKKLE-GKYL 231
             +  +       EL   Y+D+  L  +SD++ L  PLT + YH++NE   ++++ G  +
Sbjct: 171 LAFDPYPSA-AALELGVEYVDLPTLFSESDVISLHCPLTPENYHLLNEAAFEQMKNGVMI 229

Query: 232 VNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKE----------PVREHELFKYE---WE 278
           VN  RGAL+D +A  EA+K  K+     DV+E E           V + ++F+       
Sbjct: 230 VNTSRGALIDSQAAIEALKNQKIGSLGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHN 289

Query: 279 TVLTPHYAGLALEAQEDVGFRAVENLLKVLRGEV-PEDLV 317
            + T H A L  EA   +    ++NL  + +GE  P +LV
Sbjct: 290 VLFTGHQAFLTAEALTSISQTTLQNLSNLEKGETCPNELV 329


Lambda     K      H
   0.319    0.139    0.393 

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: 245
Number of extensions: 15
Number of successful extensions: 5
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: 333
Length of database: 329
Length adjustment: 28
Effective length of query: 305
Effective length of database: 301
Effective search space:    91805
Effective search space used:    91805
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 (21.7 bits)
S2: 49 (23.5 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