GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Escherichia coli BW25113

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate 17613 b3553 putative dehydrogenase (VIMSS)

Query= curated2:O27051
         (525 letters)



>FitnessBrowser__Keio:17613
          Length = 324

 Score =  184 bits (468), Expect = 3e-51
 Identities = 107/273 (39%), Positives = 153/273 (56%), Gaps = 5/273 (1%)

Query: 51  SRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLM 110
           S   V   ++E  P+L+  +   VG DN DV A T R I++++ P   + TVA+  + L+
Sbjct: 52  SNENVNAALLEKMPKLRATSTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALV 111

Query: 111 LALARKIAIADRSVKEGKWEKN---RFMGIELNGKTLGIIGMGRIGSQVVVRTK-AFGMD 166
           L+ AR++      VK G+W  +    + G +++ KTLGI+GMGRIG  +  R    F M 
Sbjct: 112 LSTARRVVEVAERVKAGEWTASIGPDWYGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMP 171

Query: 167 IMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAF 226
           I+       KEA E       DL+TLL+ESD V + +PLT ET HL   ++F  MK +A 
Sbjct: 172 ILYNARRHHKEAEERFNARYCDLDTLLQESDFVCLILPLTDETHHLFGAEQFAKMKSSAI 231

Query: 227 IVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEP-PEGSPLLELENVVLTPHIGASTS 285
            +N  RG ++DE+AL  AL+ GEI  A LDVFE+EP    SPLL + NVV  PHIG++T 
Sbjct: 232 FINAGRGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSMANVVAVPHIGSATH 291

Query: 286 EAQRDAAIIVANEIKTVFQGGAPRNVLNMPVMD 318
           E +   A    + +    QG   +N +N  V D
Sbjct: 292 ETRYGMAACAVDNLIDALQGKVEKNCVNPHVAD 324


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: 315
Number of extensions: 15
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: 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