GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-alpha in Shewanella amazonensis SB2B

Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate 6939345 Sama_3438 isoquinoline 1-oxidoreductase, alpha subunit, putative (RefSeq)

Query= metacyc::MONOMER-20832
         (151 letters)



>FitnessBrowser__SB2B:6939345
          Length = 151

 Score =  154 bits (389), Expect = 6e-43
 Identities = 71/143 (49%), Positives = 99/143 (69%), Gaps = 5/143 (3%)

Query: 3   LRINQKAYQVDADADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLVDGNVVRSCVTPVA 62
           L+IN + + +DAD   PLLW +RD +GLTGTKYGCG   CGAC+V VDG  +R+C+T + 
Sbjct: 4   LKINGRLFTLDADPKMPLLWALRDLMGLTGTKYGCGAGLCGACTVHVDGEPMRACLTSIK 63

Query: 63  GVVGREITTIEAIETDEVGKRVVATWVEHQVAQCGYCQSGQVMAATALLKHTPAPSKAQI 122
            + G+ +TTIE +  +++      +W  H+V QCG+CQ+GQ+M+A AL+   P PS +QI
Sbjct: 64  SLEGKSVTTIEGLADEQLKD----SWRRHKVPQCGFCQAGQLMSAAALVSKHPRPSDSQI 119

Query: 123 DAAMI-NLCRCGTYNAIHAAVDD 144
           D AM  N+CRCGTY  I AA+ D
Sbjct: 120 DEAMAGNICRCGTYTRIRAAIKD 142


Lambda     K      H
   0.320    0.134    0.410 

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: 104
Number of extensions: 5
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: 151
Length of database: 151
Length adjustment: 16
Effective length of query: 135
Effective length of database: 135
Effective search space:    18225
Effective search space used:    18225
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 (21.8 bits)
S2: 43 (21.2 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