GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgA in Bacteroides thetaiotaomicron VPI-5482

Align 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16; EC 4.1.2.55) (characterized)
to candidate 350017 BT0489 putative gluconate aldolase (NCBI ptt file)

Query= metacyc::MONOMER-4906
         (205 letters)



>FitnessBrowser__Btheta:350017
          Length = 223

 Score = 97.8 bits (242), Expect = 1e-25
 Identities = 60/175 (34%), Positives = 88/175 (50%), Gaps = 5/175 (2%)

Query: 12  IVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFLKEKGA---IIGAG 68
           +V V      E AK+   A ++GGV   E T     A  V  E+     K      IG G
Sbjct: 18  MVPVFYHKDAEVAKKVVKACYDGGVRAFEFTNRGDFAQEVFAEIVKYAAKECPEMAIGIG 77

Query: 69  TVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTIL 128
           ++         ++ GA F+V P  + EI++ C  + V Y PG  + +E+  A ++G  + 
Sbjct: 78  SIVDPATAAMYLQLGANFVVGPLFNPEIAKICNRRLVAYTPGCGSVSEVGFAQEVGCDLC 137

Query: 129 KLFPGEVVGPQFVKAMKGPFPNVKFVPTGGV--NLDNVCEWFKAGVLAVGVGSAL 181
           K+FPG+V G  FVK +  P P  K + TGGV  + +N+  W KAGV  VG+GS L
Sbjct: 138 KVFPGDVYGTNFVKGLMAPMPWSKLMVTGGVEPSKENLTAWIKAGVFCVGMGSKL 192


Lambda     K      H
   0.318    0.136    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: 128
Number of extensions: 6
Number of successful extensions: 1
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: 205
Length of database: 223
Length adjustment: 22
Effective length of query: 183
Effective length of database: 201
Effective search space:    36783
Effective search space used:    36783
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: 45 (21.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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