GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Desulfovibrio vulgaris Hildenborough

Align glucose transporter, ATPase component (characterized)
to candidate 209324 DVU0388 amino acid ABC transporter, ATP-binding protein

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



>MicrobesOnline__882:209324
          Length = 255

 Score =  104 bits (260), Expect = 2e-27
 Identities = 69/223 (30%), Positives = 121/223 (54%), Gaps = 6/223 (2%)

Query: 12  ATPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGE 71
           ATP++ ++ +S++ GG   +  VS+D+  G++  L+G +GAGKSTL++ ++     DAG 
Sbjct: 5   ATPILRVEHLSVALGGRPILRDVSLDVDRGQLKVLIGPSGAGKSTLLQCINHLILPDAGT 64

Query: 72  IRVNGDKVEITNPRD--ARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAM 129
           + + G  V+     D  A    +  I+Q   L D+LDA SN+ +    V   G+   +A 
Sbjct: 65  VSLEGRAVDAHRKADLYAFRQQVGMIFQEFNLFDHLDALSNVSIALRKVR--GMSRAAAR 122

Query: 130 EAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHET 189
           E    ++  R+  + +    P   LSGGQ+Q VAIARA+  + K++++DEPT+AL P   
Sbjct: 123 ERAMAEL-ERVGLSSRHALYPAQ-LSGGQKQRVAIARALAMDPKVMLLDEPTSALDPELV 180

Query: 190 QMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLV 232
             V  +I+ L   G+ + +  H ++    L +    M+ G ++
Sbjct: 181 GEVLAVIRDLAKGGMTMVMATHQMDFARALANEIVFMERGAII 223


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: 150
Number of extensions: 4
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: 255
Length adjustment: 24
Effective length of query: 236
Effective length of database: 231
Effective search space:    54516
Effective search space used:    54516
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