GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA6 in Bacteroides thetaiotaomicron VPI-5482

Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate 353409 BT3883 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (NCBI ptt file)

Query= reanno::Smeli:SM_b21112
         (281 letters)



>FitnessBrowser__Btheta:353409
          Length = 204

 Score = 93.2 bits (230), Expect = 4e-24
 Identities = 61/181 (33%), Positives = 91/181 (50%), Gaps = 5/181 (2%)

Query: 72  KFICIGLNYSDHAAETGAT-VPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIV 130
           K I +G+NY+ H  E G T V  EP+IFMK  SAI+       +P  S +  +E EL + 
Sbjct: 2   KIIAVGMNYALHNQELGHTSVNKEPVIFMKPDSAILKDGKPFFIPDFSNEVHYETELVVR 61

Query: 131 IGKTAKYVSEAEALDYVAGYCTVHDVSERAFQT---ERHGQWTKGKSCDTFGPTGPWLVT 187
           I +  K +S   A  Y        D + R  Q    E    W   K  D+    G + V 
Sbjct: 62  INRLGKNISPRFASRYYDALTVGIDFTARDLQRKFREAGNPWELCKGFDSSAAIGTF-VP 120

Query: 188 KDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGV 247
            D   D Q L   L ++G+ +Q G T  M++    +++Y+S+F++L+ GD++ TGTP GV
Sbjct: 121 VDRYKDIQSLNFNLMIDGKEVQRGCTADMLFKVDDIIAYVSKFVTLKIGDLLFTGTPAGV 180

Query: 248 G 248
           G
Sbjct: 181 G 181


Lambda     K      H
   0.315    0.136    0.408 

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: 144
Number of extensions: 7
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: 281
Length of database: 204
Length adjustment: 23
Effective length of query: 258
Effective length of database: 181
Effective search space:    46698
Effective search space used:    46698
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: 42 (22.0 bits)
S2: 46 (22.3 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