GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Halopiger salifodinae KCY07-B2

Align glucose transporter, ATPase component (characterized)
to candidate WP_049988549.1 LT39_RS00685 ATP-binding cassette domain-containing protein

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



>NCBI__GCF_000784335.1:WP_049988549.1
          Length = 369

 Score = 97.8 bits (242), Expect = 3e-25
 Identities = 65/218 (29%), Positives = 109/218 (50%), Gaps = 8/218 (3%)

Query: 16  VEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVN 75
           + +  ++  F G+ AVD +S  +  GE+ GLLG NGAGKSTLI +L       +G   VN
Sbjct: 4   IHVDGLTKEFDGVTAVDDLSFTVERGELFGLLGPNGAGKSTLINMLVALLPPSSGTASVN 63

Query: 76  GDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECRK 135
           G   ++ + + A   ++  ++Q  AL + L  A NL     L   +G       +    +
Sbjct: 64  GH--DVRSEKGAVRSSLGIVFQEPALDEELTGAENLAFHSRL---YGQARSDRAD-RIDE 117

Query: 136 IMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAEL 195
           ++  +  +  +  +PV   SGG ++ + IAR +     +L +DEPT  L     +   E 
Sbjct: 118 VLGLVGLSAVR-DDPVGTYSGGMKRRLEIARGLLHEPAVLFLDEPTVGLDARTRRDTWEY 176

Query: 196 IQQL-KAQGIGIFLIDHDVNAVMELCDRASVMKNGQLV 232
           I+QL +A G+ I L  H +     LCDR +++ +G +V
Sbjct: 177 IEQLNEAAGVSIVLTTHYIEEADRLCDRVAIVDDGDIV 214


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: 219
Number of extensions: 9
Number of successful extensions: 3
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: 369
Length adjustment: 27
Effective length of query: 233
Effective length of database: 342
Effective search space:    79686
Effective search space used:    79686
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: 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