GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-small in Rhodobacter ovatus JA234

Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate WP_097028688.1 CRO07_RS00240 methylmalonyl-CoA mutase

Query= BRENDA::A4YIE3
         (155 letters)



>NCBI__GCF_900207575.1:WP_097028688.1
          Length = 709

 Score =  110 bits (276), Expect = 4e-29
 Identities = 58/131 (44%), Positives = 80/131 (61%)

Query: 19  KRIKVVVAKLGLDGHDRGAKVIARALKDAGMEVVYTGLRQTPEQIVRTAIQEDADVIGIS 78
           +R +++V K+G DGHDRGAKVIA A  D G +V    L QTPE+  + AI  D  V+GIS
Sbjct: 578 RRPRMLVVKMGQDGHDRGAKVIATAFADIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGIS 637

Query: 79  ILSGAHLELMPKIVEALKKAGLDDVGLVLGGVIPPEDIPKLKAMGVDDVFLPGTSLKEIA 138
            L+  H  L PK++EALK  G  D+ ++ GGVIP +D   L   GV  +F PGT++   A
Sbjct: 638 SLAAGHKTLAPKLIEALKAQGAGDILVICGGVIPQQDYDFLYNSGVKAIFGPGTNIPSAA 697

Query: 139 QRVSKLASTKR 149
           +++  L    R
Sbjct: 698 KQILDLIRQAR 708


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: 221
Number of extensions: 9
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: 709
Length adjustment: 28
Effective length of query: 127
Effective length of database: 681
Effective search space:    86487
Effective search space used:    86487
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 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