GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-small in Chryseobacterium arthrosphaerae CC-VM-7

Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate WP_065401015.1 BBI00_RS21385 methylmalonyl-CoA mutase

Query= BRENDA::O58013
         (147 letters)



>NCBI__GCF_001684965.1:WP_065401015.1
          Length = 707

 Score =  109 bits (273), Expect = 7e-29
 Identities = 55/136 (40%), Positives = 86/136 (63%), Gaps = 4/136 (2%)

Query: 6   ERSKVRVLVAKPGLDGHDRGAKVVARALRDAGYEVIYTGIRQTPEQIVEAVIEEDVDVLG 65
           E  + R++VAK G DGHDRGAKVVA A  D G++V    + QTPE++ +  IE D+ +LG
Sbjct: 575 EGRRPRIMVAKMGQDGHDRGAKVVATAFADMGFDVDVAPLFQTPEEVAKQAIENDIHILG 634

Query: 66  ISILSGAHMVLIPKILKLLEEKGIKVNEDVLVVAGGIIPPDDAEELKKMGVAEVFGPGTP 125
           +S L+  H  L+P++++ L + G    +D+ +V GG+IP  D E L   G   +FGPGT 
Sbjct: 635 VSSLAAGHKTLVPQVVEELSKLGA---DDITIVVGGVIPQQDYEFLYANGADFIFGPGTN 691

Query: 126 LRE-IIEFIDKNVGKL 140
           L +  +E +++ + K+
Sbjct: 692 LPKCAVEILERLLAKI 707


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: 190
Number of extensions: 9
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: 707
Length adjustment: 27
Effective length of query: 120
Effective length of database: 680
Effective search space:    81600
Effective search space used:    81600
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