GapMind for catabolism of small carbon sources

 

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

Align 2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-phosphogluconate aldolase; 2-dehydro-3-deoxy-galactonate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase; EC 4.1.2.14; EC 4.1.2.51; EC 4.1.2.-; EC 4.1.2.21 (characterized)
to candidate 350423 BT0895 dihydrodipicolinate synthase (NCBI ptt file)

Query= SwissProt::Q6KZI8
         (266 letters)



>FitnessBrowser__Btheta:350423
          Length = 297

 Score =  114 bits (285), Expect = 2e-30
 Identities = 64/194 (32%), Positives = 106/194 (54%), Gaps = 3/194 (1%)

Query: 1   MITPLDAHGNIDYNATNILIKYLEGINVDYLFPMGSTGVFPYFTLKERKDFLKFV--REN 58
           +ITP     ++DY+A   L+ YL   N D+L  +G+T   P  T +E+K   K V  R N
Sbjct: 13  LITPFKEDESVDYDALMRLVDYLLQNNADFLCVLGTTAETPTLTEEEKKTIKKMVIDRVN 72

Query: 59  SKKPIMAGVGSSSINEVNELMKFSMDIGIEAAVLMPPYYIKLNQEAIYHYYKEILSSNDM 118
            + PI+ GVG ++   + E +K     G++A + + PYY K +QE IY +YK I  + ++
Sbjct: 73  GRIPILLGVGGNNTRAIVETLKNDDFTGVDAILSVVPYYNKPSQEGIYQHYKAISEATEL 132

Query: 119 DLLIYNIPQFTN-KIDPETVKNLKSEFSSVKGVKDSSADIRGFMEMLSLSDDDFAVFQGQ 177
            +++YN+P  T   +  ET   +   FS+V  +K++S +I    +++    D+F V  G 
Sbjct: 133 PIVLYNVPGRTGVNMTAETTLRIARNFSNVIAIKEASGNITQMDDIIKNKPDNFNVISGD 192

Query: 178 DDLLFTSLELGASG 191
           D + F  + LGA G
Sbjct: 193 DGITFPLITLGAVG 206


Lambda     K      H
   0.319    0.139    0.400 

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: 226
Number of extensions: 11
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: 266
Length of database: 297
Length adjustment: 26
Effective length of query: 240
Effective length of database: 271
Effective search space:    65040
Effective search space used:    65040
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: 47 (22.7 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