GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Erythrobacter gangjinensis K7-2

Align glucose transporter, ATPase component (characterized)
to candidate WP_047006407.1 AAW01_RS06625 ABC transporter ATP-binding protein

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



>NCBI__GCF_001010925.1:WP_047006407.1
          Length = 239

 Score = 97.4 bits (241), Expect = 2e-25
 Identities = 71/224 (31%), Positives = 110/224 (49%), Gaps = 12/224 (5%)

Query: 13  TPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEI 72
           T  +E + +S+   G   +D+VS  +  GE+  LLG NGAGKS+ +    G  Q  AGE+
Sbjct: 2   TAPLEARSLSLVRDGNAVLDNVSFSVAQGEIFALLGGNGAGKSSTLLTFLGFLQPSAGEV 61

Query: 73  RVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNL--FLGRELVTPFGLVDDSAME 130
            V G  V    P  ARS  I  + +  +L  ++ A  NL  FL         L   SA  
Sbjct: 62  LVRGRSVHSDIPA-ARSA-IAYLPEAASLYGHMSAYENLEYFLD--------LAGRSASR 111

Query: 131 AECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQ 190
            +      R+    +  S  + + S G RQ  AIA A+     IL++DEPT+ L P    
Sbjct: 112 GDLDAAFERVALADEARSRRLQSYSKGMRQKAAIALALLRETPILLLDEPTSGLDPVAID 171

Query: 191 MVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGT 234
              +L+++L + G  I ++ HDV    ++ DR  +++ G+LVG+
Sbjct: 172 EFHDLVKKLASSGQTILMVTHDVYGACQVADRVGLLRRGKLVGS 215


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: 119
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: 239
Length adjustment: 24
Effective length of query: 236
Effective length of database: 215
Effective search space:    50740
Effective search space used:    50740
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