GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Shew_2732 in Saccharomonospora marina XMU15

Align small component of L-lactate and L-malate uptake system (characterized)
to candidate WP_009154192.1 SACMADRAFT_RS12545 DUF4212 domain-containing protein

Query= reanno::PV4:5209924
         (88 letters)



>NCBI__GCF_000244955.1:WP_009154192.1
          Length = 103

 Score = 90.9 bits (224), Expect = 3e-24
 Identities = 41/76 (53%), Positives = 53/76 (69%)

Query: 12 YWRENLRLVLGLLAIWAAVSFGCGILLVDVLNEIHFMGFKLGFWFAQQGAMYVFVALIFV 71
          YWR NLRL L LL+IW  V FG GIL V+ LN++ F G+ LGFW AQQG++Y F+ LI +
Sbjct: 20 YWRRNLRLKLILLSIWFVVPFGGGILFVEQLNQVSFGGYPLGFWIAQQGSIYTFLVLILI 79

Query: 72 YVAKANALDKKYNVHE 87
          Y  + + LD K+ V E
Sbjct: 80 YAVRMDRLDDKFGVSE 95


Lambda     K      H
   0.329    0.143    0.455 

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: 51
Number of extensions: 1
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: 88
Length of database: 103
Length adjustment: 10
Effective length of query: 78
Effective length of database: 93
Effective search space:     7254
Effective search space used:     7254
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.3 bits)
S2: 39 (19.6 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