GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-small in Sphingomonas koreensis DSMZ 15582

Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate Ga0059261_3988 Ga0059261_3988 Methylmalonyl-CoA mutase, N-terminal domain/subunit

Query= BRENDA::A4YIE3
         (155 letters)



>FitnessBrowser__Korea:Ga0059261_3988
          Length = 712

 Score =  106 bits (264), Expect = 9e-28
 Identities = 57/139 (41%), Positives = 85/139 (61%), Gaps = 4/139 (2%)

Query: 10  LRDMILLMDKRI----KVVVAKLGLDGHDRGAKVIARALKDAGMEVVYTGLRQTPEQIVR 65
           L+D +   ++R+    +++VAK+G DGHDRGA +++ A  D G EVV   L QTP++   
Sbjct: 561 LKDGVAATERRLGRKPRMLVAKMGQDGHDRGANLVSSAFGDLGFEVVPGPLFQTPQEAAE 620

Query: 66  TAIQEDADVIGISILSGAHLELMPKIVEALKKAGLDDVGLVLGGVIPPEDIPKLKAMGVD 125
            AI E+ DV+G S L+  H  L+P+++  LK AG  D+ ++ GGVIP +D   L+  GV 
Sbjct: 621 LAIAENVDVVGASSLAAGHKTLIPQMIGHLKDAGRGDIKVIAGGVIPAQDYQFLRDAGVQ 680

Query: 126 DVFLPGTSLKEIAQRVSKL 144
            +F PGT+L   A  V  L
Sbjct: 681 AIFGPGTNLVNAAADVLTL 699


Lambda     K      H
   0.319    0.140    0.382 

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: 248
Number of extensions: 11
Number of successful extensions: 1
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: 155
Length of database: 712
Length adjustment: 28
Effective length of query: 127
Effective length of database: 684
Effective search space:    86868
Effective search space used:    86868
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 (21.7 bits)
S2: 48 (23.1 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