GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Moritella dasanensis ArB 0140

Align glucose transporter, ATPase component (characterized)
to candidate WP_026006295.1 A923_RS0116615 arginine ABC transporter ATP-binding protein ArtP

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



>NCBI__GCF_000276805.1:WP_026006295.1
          Length = 246

 Score =  102 bits (254), Expect = 8e-27
 Identities = 67/228 (29%), Positives = 119/228 (52%), Gaps = 17/228 (7%)

Query: 16  VEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVN 75
           +E+K+I  S+G +  + ++ +    GE + LLG +GAGKS+L++VL+     D G I + 
Sbjct: 3   IELKNICKSWGQLDVLQNIDLKCAKGETLVLLGPSGAGKSSLLRVLNLLDTPDNGSISIA 62

Query: 76  GDKVEITNPRDARS---------HNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDD 126
           G+  + +     +            +  ++Q   L  ++    NL     +  P  ++  
Sbjct: 63  GETFDFSTKLSDKKLIKRSQMLRQKVGMVFQQYNLWPHMSVMDNL-----IEAPVKILKQ 117

Query: 127 SAMEA--ECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAAL 184
           +   A  E  KI+ +L    +    P+ ALSGGQ+Q VAIARA+    ++L+ DEPTAAL
Sbjct: 118 TKQHAREEAMKILEQLQLTDKADVFPL-ALSGGQQQRVAIARALMMKPEVLLFDEPTAAL 176

Query: 185 GPHETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLV 232
            P  T  VAE+I+ L   GI   ++ H+V+   ++  +   +++G++V
Sbjct: 177 DPEVTNQVAEIIKSLAITGITQVVVTHEVDFARKVASQVCYLESGEIV 224


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: 139
Number of extensions: 3
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: 246
Length adjustment: 24
Effective length of query: 236
Effective length of database: 222
Effective search space:    52392
Effective search space used:    52392
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