GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Desulfovibrio vulgaris Miyazaki F

Align glucose transporter, ATPase component (characterized)
to candidate 8500828 DvMF_1569 ABC transporter related (RefSeq)

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



>FitnessBrowser__Miya:8500828
          Length = 261

 Score =  104 bits (260), Expect = 2e-27
 Identities = 71/234 (30%), Positives = 126/234 (53%), Gaps = 7/234 (2%)

Query: 1   MSTAKELRAAGATPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKV 60
           M+T + +  +G TP++ +++I  + GG + +  +S+D+  GE+  L+G +GAGKSTL++ 
Sbjct: 1   MATPESVTTSG-TPILRLENIGKTLGGKRILSDISMDVDKGELKVLIGPSGAGKSTLLQC 59

Query: 61  LSGAYQMDAGEIRVNGDKVEITNPRD--ARSHNIETIYQTLALADNLDAASNLFLGRELV 118
           ++     D G IR+ G  V+     +  A    +  I+Q   L D+LDA SN+ +    V
Sbjct: 60  INYLIPPDEGHIRLEGRVVDAACKSELYAFRQQVGMIFQDFNLFDHLDALSNVSIALRKV 119

Query: 119 TPFGLVDDSAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMD 178
              G+   +A E    ++  R+    +    P   LSGGQ+Q VAIARA+  + K++++D
Sbjct: 120 R--GMSRKAAAERAMAEL-ERVGLANRATLYPAQ-LSGGQKQRVAIARALAMDPKVMLLD 175

Query: 179 EPTAALGPHETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLV 232
           EPT+AL P     V  +I+ L   G+ + +  H ++    L      M+ G+++
Sbjct: 176 EPTSALDPELVGEVLAVIRDLARGGMTMVMASHQMDFTRALAHEILFMERGRII 229


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: 156
Number of extensions: 6
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: 261
Length adjustment: 25
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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