GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntEIIA in Megamonas funiformis YIT 11815

Align PTS system, IIA component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex (characterized)
to candidate WP_008538999.1 HMPREF9454_RS07880 PTS sugar transporter subunit IIA

Query= TCDB::Q82ZC8
         (150 letters)



>NCBI__GCF_000245775.1:WP_008538999.1
          Length = 147

 Score = 77.8 bits (190), Expect = 7e-20
 Identities = 46/151 (30%), Positives = 77/151 (50%), Gaps = 8/151 (5%)

Query: 1   MLGIVIATHGALSDGAKDAATVIMGATENIETVNLNSGDDVQALGGQIKTAIENVQQGDG 60
           MLGI++ THG L++   +   +I G  +N+ TV L  G+  + L  +   A+E +   +G
Sbjct: 1   MLGIIVGTHGHLAEELVNTCAMICGQPDNLTTVTLVPGEGPEDLMAKYNKAMEEMDTTNG 60

Query: 61  VLVMVDLLSASPYNQAVLVINELEPALQKKIFVVSGTNLPMVLEAINHQLL---GTPIAE 117
           V+++ DL   SPYN A  V  E       K  +V+G +LPM++E IN++L       + +
Sbjct: 61  VIILNDLFGGSPYNAACRVAME-----NDKCGIVTGVSLPMLVEVINYRLCNGENANVQD 115

Query: 118 AAQAIVAQGKESVQAWDISMTSFEDEEDEDD 148
           A +  V       Q +  S    E +++ DD
Sbjct: 116 AMEKAVEASVAGAQKFHKSQVESETDDEGDD 146


Lambda     K      H
   0.312    0.130    0.350 

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: 56
Number of extensions: 2
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: 150
Length of database: 147
Length adjustment: 16
Effective length of query: 134
Effective length of database: 131
Effective search space:    17554
Effective search space used:    17554
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 42 (20.8 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