GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Magnetovibrio blakemorei MV-1

Align glucose transporter, ATPase component (characterized)
to candidate WP_069957998.1 BEN30_RS08935 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF3641
         (260 letters)



>NCBI__GCF_001746755.1:WP_069957998.1
          Length = 233

 Score =  100 bits (250), Expect = 2e-26
 Identities = 71/230 (30%), Positives = 129/230 (56%), Gaps = 16/230 (6%)

Query: 13  TPLVEMKDISISFGG----IKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMD 68
           +PL+E+K IS  +G     + A+  VS+++YPG+V+GLLG +G+GK+TL+ ++    +  
Sbjct: 7   SPLIELKHISKHYGEGETRVDALRDVSLEVYPGQVIGLLGPSGSGKTTLLNIIGCIVEAS 66

Query: 69  AGEIRVNGDKVEI-----TNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGL 123
           +G  +++GD +       ++ R  R   +  I+Q   L   L++  N+ +  +L    G+
Sbjct: 67  SGWAKLDGDVIYDNAWMKSDLRRLRLDKVGFIFQFHNLLPFLNSMENVSVVLDLA---GV 123

Query: 124 VDDSAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAA 183
             D A +   ++++  L    ++ + P   LSGG+ Q VAIARA+  N +I++ DEPTAA
Sbjct: 124 PADRAKQ-RAQELLEYLEVGHRRDAYPAH-LSGGEAQRVAIARALANNPRIILADEPTAA 181

Query: 184 LGPHETQMVAELIQQLKA-QGIGIFLIDHDVNAVMELCDRASVMKNGQLV 232
           L      +V +L+++L   Q   +  + HD   + +  DR   +++GQLV
Sbjct: 182 LDSERALIVMKLLRKLAVEQDAAVLAVTHD-EKIYDQFDRIFHVRDGQLV 230


Lambda     K      H
   0.317    0.135    0.373 

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: 134
Number of extensions: 10
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: 260
Length of database: 233
Length adjustment: 24
Effective length of query: 236
Effective length of database: 209
Effective search space:    49324
Effective search space used:    49324
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 (21.7 bits)
S2: 46 (22.3 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