GapMind for catabolism of small carbon sources

 

Alignments for a candidate for epi in Desulfatiglans anilini DSM 4660

Align Methylmalonyl-CoA epimerase; DL-methylmalonyl-CoA racemase; EC 5.1.99.1 (characterized)
to candidate WP_028321972.1 H567_RS0114620 methylmalonyl-CoA epimerase

Query= SwissProt::O58010
         (136 letters)



>NCBI__GCF_000422285.1:WP_028321972.1
          Length = 144

 Score = 88.6 bits (218), Expect = 3e-23
 Identities = 50/134 (37%), Positives = 81/134 (60%), Gaps = 5/134 (3%)

Query: 7   RIDHVGIAVKNLEEAIKIWEGLGFKVEEIEEVPDQ--KVKVAVIKVGENRIELLEATTED 64
           ++DH+ IAV++L+ A K+WE +  K    +   D+  K++VA   VGE   EL+E+TT D
Sbjct: 5   KLDHICIAVRDLDAAKKVWEPVLGKSGPDDAYVDEPEKIRVARYWVGEVGFELMESTTPD 64

Query: 65  SPIAKFIEKRGEGIHHLAIRVENIESKLEELKQKGYKLI---DEKPRVGAGGAKIAFIHP 121
            P+AK+I+K GEG+  +++ V++    +EEL+ K Y  I   D +        + AF+HP
Sbjct: 65  GPVAKWIDKHGEGVMLVSLNVDDTRKAVEELQSKDYPFIPTPDGEVARPFRDCEFAFVHP 124

Query: 122 KSVTGVLLELCERK 135
           K +  VLLE+ + K
Sbjct: 125 KKMNNVLLEVIDYK 138


Lambda     K      H
   0.317    0.138    0.389 

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: 73
Number of extensions: 6
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: 136
Length of database: 144
Length adjustment: 15
Effective length of query: 121
Effective length of database: 129
Effective search space:    15609
Effective search space used:    15609
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: 42 (20.8 bits)

This GapMind analysis is from Sep 24 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