GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-small in Amycolatopsis halophila YIM 93223

Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate WP_084037500.1 AMYHA_RS25265 methylmalonyl-CoA mutase

Query= BRENDA::O58013
         (147 letters)



>NCBI__GCF_000504245.1:WP_084037500.1
          Length = 746

 Score =  103 bits (258), Expect = 4e-27
 Identities = 51/123 (41%), Positives = 74/123 (60%), Gaps = 3/123 (2%)

Query: 6   ERSKVRVLVAKPGLDGHDRGAKVVARALRDAGYEVIYTGIRQTPEQIVEAVIEEDVDVLG 65
           E  + R+LVAK G DGHDRG KV+A A  D G++V    +  TP ++    +E DV V+G
Sbjct: 589 EGRRPRILVAKMGQDGHDRGQKVIATAFADIGFDVDVGPLFSTPAEVARQAVEADVHVIG 648

Query: 66  ISILSGAHMVLIPKILKLLEEKGIKVNEDVLVVAGGIIPPDDAEELKKMGVAEVFGPGTP 125
           +S L+  H+ L+P +   L E       D++VV GG+IPP D + L++ G A +F PGT 
Sbjct: 649 VSSLAAGHLTLVPALRAELAELD---RSDIMVVVGGVIPPQDFDALREAGAAAIFPPGTV 705

Query: 126 LRE 128
           + E
Sbjct: 706 IAE 708


Lambda     K      H
   0.318    0.140    0.383 

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: 225
Number of extensions: 10
Number of successful extensions: 2
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: 147
Length of database: 746
Length adjustment: 28
Effective length of query: 119
Effective length of database: 718
Effective search space:    85442
Effective search space used:    85442
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: 48 (23.1 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