GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Shewanella amazonensis SB2B

Align glucose transporter, ATPase component (characterized)
to candidate 6938852 Sama_2955 ABC transporter, ATP-binding protein (RefSeq)

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



>FitnessBrowser__SB2B:6938852
          Length = 250

 Score = 98.2 bits (243), Expect = 1e-25
 Identities = 74/230 (32%), Positives = 117/230 (50%), Gaps = 17/230 (7%)

Query: 13  TPLVEMKDISISF--GGIK--AVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMD 68
           TP+V M++IS SF  GG +   +D++++D++PGE V L G +G+GKSTL+ +++G  Q D
Sbjct: 2   TPIVAMQEISKSFQDGGERHRVLDNLTLDIHPGETVALTGPSGSGKSTLLNLIAGFDQPD 61

Query: 69  AGEIRVNGDKVEITNPRD---ARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVD 125
            G IR+ G   +  +  D    R   +  ++Q   L + L+  +N+        P  L +
Sbjct: 62  DGHIRLLGRPSKHFSASDWDRFRRSELGMVFQQFNLLEPLNVQANIHF------PLAL-N 114

Query: 126 DSAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALG 185
               +  C  + +RL    +  S PV +LSGGQ+Q VAIARA+     +L+ DEPT  L 
Sbjct: 115 GKPWDDWCHTLTSRLGLT-ELLSRPVDSLSGGQQQRVAIARALSQRPPLLLADEPTGNLD 173

Query: 186 PHETQMVAELIQQL-KAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGT 234
            H    V  L+  L +     I ++ H          R   + NGQ+  T
Sbjct: 174 EHSGDEVMALLTSLARESNTAILMVTHSERCA-AFMQRRWHLCNGQIAET 222


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: 129
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: 250
Length adjustment: 24
Effective length of query: 236
Effective length of database: 226
Effective search space:    53336
Effective search space used:    53336
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